The ecological module of BOATS-1.0 : a bioenergetically constrained model of marine upper trophic levels suitable for studies of fisheries and ocean biogeochemistry

Unidad de excelencia María de Maeztu MdM-2015-0552Environmental change and the exploitation of marine resources have had profound impacts on marine communities, with potential implications for ocean biogeochemistry and food security. In order to study such global-scale problems, it is helpful to have computationally efficient numerical models that predict the first-order features of fish biomass production as a function of the environment, based on empirical and mechanistic understandings of marine ecosystems. Here we describe the ecological module of the BiOeconomic mArine Trophic Size-spectrum (BOATS) model, which takes an Earth-system approach to modelling fish biomass at the global scale. The ecological model is designed to be used on an Earth-system model grid, and determines size spectra of fish biomass by explicitly resolving life history as a function of local temperature and net primary production. Biomass production is limited by the availability of photosynthetic energy to upper trophic levels, following empirical trophic efficiency scalings, and by well-established empirical temperature-dependent growth rates. Natural mortality is calculated using an empirical size-based relationship, while reproduction and recruitment depend on both the food availability to larvae from net primary production and the production of eggs by mature adult fish. We describe predicted biomass spectra and compare them to observations, and conduct a sensitivity study to determine how they change as a function of net primary production and temperature. The model relies on a limited number of parameters compared to similar modelling efforts, while retaining reasonably realistic representations of biological and ecological processes, and is computationally efficient, allowing extensive parameter-space analyses even when implemented globally. As such, it enables the exploration of the linkages between ocean biogeochemistry, climate, and upper trophic levels at the global scale, as well as a representation of fish biomass for idealized studies of fisheries

A coupled human-Earth model perspective on long-term trends in the global marine fishery

Unidad de excelencia María de Maeztu MdM-2015-0552The global wild marine fish harvest increased fourfold between 1950 and a peak value near the end of the 20th century, reflecting interactions between anthropogenic and ecological forces. Here, we examine these interactions in a bio-energetically constrained, spatially and temporally resolved model of global fisheries. We conduct historical hindcasts with the model, which suggest that technological progress can explain most of the 20th century increase of fish harvest. In contrast, projections extending this rate of technological progress into the future under open access suggest a long-term decrease in harvest due to over-fishing. Climate change is predicted to gradually decrease the global fish production capacity, though our model suggests that this is of secondary importance to social and economic factors. Our study represents a novel way to integrate human-ecological interactions within a single model framework for long-term simulations

The First VERITAS Telescope

The first atmospheric Cherenkov telescope of VERITAS (the Very Energetic Radiation Imaging Telescope Array System) has been in operation since February 2005. We present here a technical description of the instrument and a summary of its performance. The calibration methods are described, along with the results of Monte Carlo simulations of the telescope and comparisons between real and simulated data. The analysis of TeV $\gamma$-ray observations of the Crab Nebula, including the reconstructed energy spectrum, is shown to give results consistent with earlier measurements. The telescope is operating as expected and has met or exceeded all design specifications.Comment: Accepted by Astroparticle Physic

Very-high energy gamma-ray astronomy: A 23-year success story in high-energy astroparticle physics

Very-high energy (VHE) gamma quanta contribute only a minuscule fraction - below one per million - to the flux of cosmic rays. Nevertheless, being neutral particles they are currently the best "messengers" of processes from the relativistic/ultra-relativistic Universe because they can be extrapolated back to their origin. The window of VHE gamma rays was opened only in 1989 by the Whipple collaboration, reporting the observation of TeV gamma rays from the Crab nebula. After a slow start, this new field of research is now rapidly expanding with the discovery of more than 150 VHE gamma-ray emitting sources. Progress is intimately related with the steady improvement of detectors and rapidly increasing computing power. We give an overview of the early attempts before and around 1989 and the progress after the pioneering work of the Whipple collaboration. The main focus of this article is on the development of experimental techniques for Earth-bound gamma-ray detectors; consequently, more emphasis is given to those experiments that made an initial breakthrough rather than to the successors which often had and have a similar (sometimes even higher) scientific output as the pioneering experiments. The considered energy threshold is about 30 GeV. At lower energies, observations can presently only be performed with balloon or satellite-borne detectors. Irrespective of the stormy experimental progress, the success story could not have been called a success story without a broad scientific output. Therefore we conclude this article with a summary of the scientific rationales and main results achieved over the last two decades.Comment: 45 pages, 38 figures, review prepared for EPJ-H special issue "Cosmic rays, gamma rays and neutrinos: A survey of 100 years of research

Tomato: a crop species amenable to improvement by cellular and molecular methods

Tomato is a crop plant with a relatively small DNA content per haploid genome and a well developed genetics. Plant regeneration from explants and protoplasts is feasable which led to the development of efficient transformation procedures. In view of the current data, the isolation of useful mutants at the cellular level probably will be of limited value in the genetic improvement of tomato. Protoplast fusion may lead to novel combinations of organelle and nuclear DNA (cybrids), whereas this technique also provides a means of introducing genetic information from alien species into tomato. Important developments have come from molecular approaches. Following the construction of an RFLP map, these RFLP markers can be used in tomato to tag quantitative traits bred in from related species. Both RFLP's and transposons are in the process of being used to clone desired genes for which no gene products are known. Cloned genes can be introduced and potentially improve specific properties of tomato especially those controlled by single genes. Recent results suggest that, in principle, phenotypic mutants can be created for cloned and characterized genes and will prove their value in further improving the cultivated tomato.

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Why is management research irrelevant?

At least since 1980, there has been a practically continuous, but somewhat fragmented discussion on the relevance of management research. This discussion has addressed practically all fields of management; here, besides general management, operations management, project management and construction management are examined in more detail. Although many different proposals have been made to rectify the situation, no definitive resolution has been found. In this paper, it is argued that prior analyses have not reached the root causes of the irrelevance problem. By an analysis of the recent history of management research, the following novel findings are reached. First, the root cause of the irrelevance is argued to lie in the 1959 reports on American business education, written by Pierson and Gordon & Howell. Second, while the proposed direction in the 1959 reports was deficient in several ways, the rejection of production as an integral part of organizations and management has been perhaps the most damaging feature of those reports. Third, current research on management suffers from a variety of immediate causes for irrelevance, insufficiently recognized by the scholarly community. It is suggested that reaching the root causes for irrelevance will facilitate finding suitable cures

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers.

Gene fusions represent an important class of somatic alterations in cancer. We systematically investigated fusions in 9,624 tumors across 33 cancer types using multiple fusion calling tools. We identified a total of 25,664 fusions, with a 63% validation rate. Integration of gene expression, copy number, and fusion annotation data revealed that fusions involving oncogenes tend to exhibit increased expression, whereas fusions involving tumor suppressors have the opposite effect. For fusions involving kinases, we found 1,275 with an intact kinase domain, the proportion of which varied significantly across cancer types. Our study suggests that fusions drive the development of 16.5% of cancer cases and function as the sole driver in more than 1% of them. Finally, we identified druggable fusions involving genes such as TMPRSS2, RET, FGFR3, ALK, and ESR1 in 6.0% of cases, and we predicted immunogenic peptides, suggesting that fusions may provide leads for targeted drug and immune therapy