Choice or rank data in stated preference surveys?

Should researchers collect choice or rank data in stated preference (SP) surveys? Answer to this question can have significant implications on survey costs and modeling outputs available for policy analysis. In particular, the exploded rank multinomial logit model (MNL) is compared with the ordinary choice-based MNL model. Using the empirical SP rank data collected among the public light bus operators in Hong Kong, the selected modeling approaches are compared in terms of model assumptions, model fit, modeling outputs and policy implications. Besides, the reliability of the exploded rank data is tested. The mixed results suggest that extra care must be exercised in the design of SP ranking tasks.published_or_final_versio

Solving the subset-sum problem with a light-based device

We propose a special computational device which uses light rays for solving the subset-sum problem. The device has a graph-like representation and the light is traversing it by following the routes given by the connections between nodes. The nodes are connected by arcs in a special way which lets us to generate all possible subsets of the given set. To each arc we assign either a number from the given set or a predefined constant. When the light is passing through an arc it is delayed by the amount of time indicated by the number placed in that arc. At the destination node we will check if there is a ray whose total delay is equal to the target value of the subset sum problem (plus some constants).Comment: 14 pages, 6 figures, Natural Computing, 200

Ecosystem service provision by marine habitats in Southeast Asia

Southeast Asia is an area of rich marine biodiversity providing a host of ecosystem services that contribute to the well-being of coastal communities and beyond. Sustainable management of ecosystems and the services they provide requires a good understanding of their underlying ecological functions and processes. This understanding can be gained through the rigorous assessment of studies identifying and quantifying ecological functions and ecosystem services. The aims of this study were to review the ecosystem services provided by marine and coastal habitats in Southeast Asia. The ecosystem service potential was scored for each habitat. The review was focused on nine key marine and coastal habitats, identified across four case study sites in Southeast Asia, contributing 18 marine relevant ecosystem services. The approach comprised a literature review supplemented with observations from experts from the case study areas. The four case study sites consist of three Man and Biosphere Reserves in Southeast Asia: Palawan in the Philippines, Cu Lao Cham- Hoi An in Viet Nam, Take-Bonerate Kepulauan Selayar in Indonesia, and a recently gazetted marine protected area, the Tun Mustapha Marine Park in Malaysia (Figure 1). The nine key habitats (eight benthic and one pelagic) covered in this review, identified as highly relevant for most case study sites, were mangrove forests, coral reefs, seagrass meadows, sand, mud, rock, coarse substratum, pelagic and modified habitats. Further division of these habitats into sub-habitats on the basis of biological type and substrate type was used to capture data on differential provision of ecosystem services within the broad habitat types. To ensure relevance in the four case study sites, firstly an ecosystem services typology was created tailored to these sites. After exploring several ecosystem service typologies, our final classification was adapted from the Common International Classification of Ecosystem services (CICES) V4.3 because it was considered to be most relevant to the objectives of this task. Provisioning, regulation and maintenance, and cultural services were assessed. Provisioning services focused on food for consumption by humans from plants, pelagic animals, demersal fish and invertebrates; energy from harvested plants; other materials from plants and animals, such as fibres, building and housing materials, medicines, decoration, handicrafts and souvenirs; and genetic material from plants and animals (including seeds, spat, spores, whole plants or animals, individual genes), for example seed or brood-stock collection for aquaculture and mangrove replanting and new plantations. Regulation and maintenance services assessed were treatment and assimilation of wastes or toxic substances; coastal erosion control; water flow regulation contributing to dampening the intensity of storm, floods, tsunamis, and hurricanes and the maintenance of localized water flows such as coastal current structures; maintenance of nursery,reproduction and feeding habitats; maintenance of critical habitats for charismatic species such as turtles, dugongs, cetaceans, sharks, seahorses, bats, fireflies, birds, monkeys, orchids and other epiphytes; and climate regulation through impacts on the hydrological cycle, temperature regulation, and the contribution to regulation of climate-influencing gases in the atmosphere, for example through carbon sequestration and long-term, decadal storage. Cultural services examined included uses of habitats as places for active and passive recreation; ceremonial activities; creative activities; and knowledge-based activities, such as educational activities, and citizen science or community environmental activities. The comprehensive literature review included peer-reviewed scientific research literature as well as grey literature such as government and other reports. To ensure a wide breadth of coverage, the research focused on studies from Southeast Asia. When no evidence was found in the literature, evidence was sought from experts, and where useful, was accompanied by observations from the authors in their respective case study sites. The evidence gathered was used to assess the potential of each habitat to provide an ecosystem service, rather than to assess the actual provision of ecosystem services from each case study site. This important distinction allows the differentiation between services provided by the ecosystem (i.e. the potential supply of ecosystem services that a habitat could deliver) and (achieved or used) benefits (i.e. the demand for ecosystem services). The knowledge gained from the literature, local and regional reports, together with observations from the study team and experts, was critically assessed using a robust methodology that captured different types of information together with a confidence score for the supporting evidence. The contribution of each habitat to each ecosystem service was then scored relative to other habitats. Our objective was to provide baseline information to enable better understanding of the ecosystem services arising from marine and coastal habitats in SE Asia. This provides a foundation for future assessments of natural capital and ecosystem services which may be used to inform sustainable management. The report will serve as a useful reference to many different readers. Regulators, managers of marine sites and policy makers might use this report to inform their management choices. This should enable more sustainable use of the marine environment and maximise the ecosystem service provision of all types of services addressed in this study. Stakeholders of the marine environment such as fisherfolk or residents might use this report to help them engage in management processes, to gain deeper understanding of the marine environment or confirm their observations of the marine environment. Academics can use it as a reference source or a base for further studies, in particular for valuation studies or when considering the trade-offs between ecosystem services in marine and coastal habitats. Finally, it is hoped that this report may bring a new appreciation and understanding of the marine environment and the life support it provides to society and inspire readers to improve management of the marine environment. This report is one of the outputs of the UK Research and Innovation’s Global Challenges Research Fund (UKRI GCRF) Blue Communities Programme (GCRF Blue Communities Global Challenges Research Fund via the United Kingdom Research and Innovation (UKRI) under grant agreement reference NE/P021107/1, www.blue-communities.org), which aims to “build capacity for sustainable interactions with marine ecosystems for the benefit of the health, well-being, food security and livelihoods of coastal communities in SE Asia”. GCRF Blue Communities is developing interdisciplinary research capability and lasting collaborations that can facilitate innovative application of integrated planning in the marine environment and respond to the UN Sustainable Development Goals of ‘no poverty’, ‘zero hunger’, ‘good health and well-being’ for coastal communities as well as ‘conserve and sustainably use the oceans, seas and marine resources for sustainable development’ through the sustainable use of marine resources

Tradable credit scheme for rush hour travel choice with heterogeneous commuters

This article proposes a tradable credit scheme for managing commuters travel choices. The scheme considers bottleneck congestion and modal split in a competitive highway-transit network with heterogeneous commuters who are distinguished by their valuation of travel time. The scheme charges all auto travelers who pass the bottleneck during a peak-time window in the form of mobility credits. Those who avoid the peak-time window, by either traveling outside the peak-time window or switching to the transit mode, may be rewarded credits. An artificial market is created so that the travelers may trade these credits with each other. We formulate the credit price and the rewarded and charged credits under tradable credit scheme. Our analyses indicate that the optimal tradable credit scheme can achieve nearly 40% efficiency gains depending on the level of commuters heterogeneity. In addition, this scheme distributes the benefits among all the commuters directly through the credit trading. Our results suggest that in assessing the efficiency of tradable credit scheme, it is important to take into account the commuters heterogeneity. Numerical experiments are conducted to examine the sensitivity of tradable credit scheme designs to various system parameters

Tumor-educated Tregs drive organ-specific metastasis in breast cancer by impairing NK cells in the lymph node niche

Breast cancer is accompanied by systemic immunosuppression, which facilitates metastasis formation, but how this shapes organotropism of metastasis is poorly understood. Here, we investigate the impact of mammary tumorigenesis on regulatory T cells (Tregs) in distant organs and how this affects multi-organ metastatic disease. Using a preclinical mouse mammary tumor model that recapitulates human metastatic breast cancer, we observe systemic accumulation of activated, highly immunosuppressive Tregs during primary tumor growth. Tumor-educated Tregs show tissue-specific transcriptional rewiring in response to mammary tumorigenesis. This has functional consequences for organotropism of metastasis, as Treg depletion reduces metastasis to tumor-draining lymph nodes, but not to lungs. Mechanistically, we find that Tregs control natural killer (NK) cell activation in lymph nodes, thereby facilitating lymph node metastasis. In line, an increased Treg/NK cell ratio is observed in sentinel lymph nodes of breast cancer patients compared with healthy controls. This study highlights that immune regulation of metastatic disease is highly organ dependent

A software pipeline for processing and identification of fungal ITS sequences

<p>Abstract</p> <p>Background</p> <p>Fungi from environmental samples are typically identified to species level through DNA sequencing of the nuclear ribosomal internal transcribed spacer (<it>ITS</it>) region for use in BLAST-based similarity searches in the International Nucleotide Sequence Databases. These searches are time-consuming and regularly require a significant amount of manual intervention and complementary analyses. We here present software – in the form of an identification pipeline for large sets of fungal <it>ITS </it>sequences – developed to automate the BLAST process and several additional analysis steps. The performance of the pipeline was evaluated on a dataset of 350 <it>ITS </it>sequences from fungi growing as epiphytes on building material.</p> <p>Results</p> <p>The pipeline was written in Perl and uses a local installation of NCBI-BLAST for the similarity searches of the query sequences. The variable subregion <it>ITS2 </it>of the <it>ITS </it>region is extracted from the sequences and used for additional searches of higher sensitivity. Multiple alignments of each query sequence and its closest matches are computed, and query sequences sharing at least 50% of their best matches are clustered to facilitate the evaluation of hypothetically conspecific groups. The pipeline proved to speed up the processing, as well as enhance the resolution, of the evaluation dataset considerably, and the fungi were found to belong chiefly to the <it>Ascomycota</it>, with <it>Penicillium </it>and <it>Aspergillus </it>as the two most common genera. The <it>ITS2 </it>was found to indicate a different taxonomic affiliation than did the complete <it>ITS </it>region for 10% of the query sequences, though this figure is likely to vary with the taxonomic scope of the query sequences.</p> <p>Conclusion</p> <p>The present software readily assigns large sets of fungal query sequences to their respective best matches in the international sequence databases and places them in a larger biological context. The output is highly structured to be easy to process, although it still needs to be inspected and possibly corrected for the impact of the incomplete and sometimes erroneously annotated fungal entries in these databases. The open source pipeline is available for UNIX-type platforms, and updated releases of the target database are made available biweekly. The pipeline is easily modified to operate on other molecular regions and organism groups.</p

Revisiting consistency with random utility maximisation: theory and implications for practical work

While the paradigm of utility maximisation has formed the basis of the majority of applications in discrete choice modelling for over 40 years, its core assumptions have been questioned by work in both behavioural economics and mathematical psychology as well as more recently by developments in the RUM-oriented choice modelling community. This paper reviews the basic properties with a view to explaining the historical pre-eminence of utility maximisation and addresses the question of what departures from the paradigm may be necessary or wise in order to accommodate richer behavioural patterns. We find that many, though not all, of the behavioural traits discussed in the literature can be approximated sufficiently closely by a random utility framework, allowing analysts to retain the many advantages that such an approach possesses

Historical Reconstruction Reveals Recovery in Hawaiian Coral Reefs

Coral reef ecosystems are declining worldwide, yet regional differences in the trajectories, timing and extent of degradation highlight the need for in-depth regional case studies to understand the factors that contribute to either ecosystem sustainability or decline. We reconstructed social-ecological interactions in Hawaiian coral reef environments over 700 years using detailed datasets on ecological conditions, proximate anthropogenic stressor regimes and social change. Here we report previously undetected recovery periods in Hawaiian coral reefs, including a historical recovery in the MHI (∼AD 1400–1820) and an ongoing recovery in the NWHI (∼AD 1950–2009+). These recovery periods appear to be attributed to a complex set of changes in underlying social systems, which served to release reefs from direct anthropogenic stressor regimes. Recovery at the ecosystem level is associated with reductions in stressors over long time periods (decades+) and large spatial scales (>103 km2). Our results challenge conventional assumptions and reported findings that human impacts to ecosystems are cumulative and lead only to long-term trajectories of environmental decline. In contrast, recovery periods reveal that human societies have interacted sustainably with coral reef environments over long time periods, and that degraded ecosystems may still retain the adaptive capacity and resilience to recover from human impacts

Evolution of sex-specific pace-of-life syndromes: genetic architecture and physiological mechanisms

Sex differences in life history, physiology, and behavior are nearly ubiquitous across taxa, owing to sex-specific selection that arises from different reproductive strategies of the sexes. The pace-of-life syndrome (POLS) hypothesis predicts that most variation in such traits among individuals, populations, and species falls along a slow-fast pace-of-life continuum. As a result of their different reproductive roles and environment, the sexes also commonly differ in pace-of-life, with important consequences for the evolution of POLS. Here, we outline mechanisms for how males and females can evolve differences in POLS traits and in how such traits can covary differently despite constraints resulting from a shared genome. We review the current knowledge of the genetic basis of POLS traits and suggest candidate genes and pathways for future studies. Pleiotropic effects may govern many of the genetic correlations, but little is still known about the mechanisms involved in trade-offs between current and future reproduction and their integration with behavioral variation. We highlight the importance of metabolic and hormonal pathways in mediating sex differences in POLS traits; however, there is still a shortage of studies that test for sex specificity in molecular effects and their evolutionary causes. Considering whether and how sexual dimorphism evolves in POLS traits provides a more holistic framework to understand how behavioral variation is integrated with life histories and physiology, and we call for studies that focus on examining the sex-specific genetic architecture of this integration