User's manual for biosphere and dose simulation program (Biodose)

This user's manual describes the BIOsphere Transport and DOSE program (BIODOSE) prepared for, and delivered to, Lawrence Livermore Laboratory (LLL) by the Analytic Sciences Corporation (TASC). BIODOSE simulates the transport of radionuclides in surface water systems and the resulting concentration of nuclides in the food chain. It includes the prediction of human dosage risks for individuals and for populations resulting from release of radionuclides into surface water or well water. The BIODOSE program was designed for easy use, including standard defaults and a flexible input scheme

Influence of next-nearest-neighbor electron hopping on the static and dynamical properties of the 2D Hubbard model

Comparing experimental data for high temperature cuprate superconductors with numerical results for electronic models, it is becoming apparent that a hopping along the plaquette diagonals has to be included to obtain a quantitative agreement. According to recent estimations the value of the diagonal hopping $t'$ appears to be material dependent. However, the values for $t'$ discussed in the literature were obtained comparing theoretical results in the weak coupling limit with experimental photoemission data and band structure calculations. The goal of this paper is to study how $t'$ gets renormalized as the interaction between electrons, $U$, increases. For this purpose, the effect of adding a bare diagonal hopping $t'$ to the fully interacting two dimensional Hubbard model Hamiltonian is investigated using numerical techniques. Positive and negative values of $t'$ are analyzed. Spin-spin correlations, $n(\bf{k})$, $\langle n\rangle$ vs $\mu$, and local magnetic moments are studied for values of $U/t$ ranging from 0 to 6, and as a function of the electronic density. The influence of the diagonal hopping in the spectral function $A(\bf{k},\omega)$ is also discussed, and the changes in the gap present in the density of states at half-filling are studied. We introduce a new criterion to determine probable locations of Fermi surfaces at zero temperature from $n(\bf{k})$ data obtained at finite temperature. It appears that hole pockets at ${\bf{k}}=(\pi/2,\pi/2)$ may be induced for negative $t'$ while a positive $t'$ produces similar features at ${\bf{k}}=(\pi,0)$ and $(0,\pi)$. Comparisons with the standard 2D Hubbard ($t'=0$) model indicate that a negative $t'$ hopping amplitude appears to be dynamically generated. In general, we conclude that it is very dangerous to extract a bare parameter of the Hamiltonian $(t')$ from PES data whereComment: 9 pages (RevTex 3.0), 12 figures (postscript), files packed with uufile

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

Joint effects of patch edges and habitat degradation on faunal predation risk in a widespread marine foundation species

Human activities degrade and fragment coastal marine habitats, reducing their structural complexity and making habitat edges a prevalent seascape feature. Though habitat edges frequently are implicated in reduced faunal survival and biodiversity, results of experiments on edge effects have been inconsistent, calling for a mechanistic approach to the study of edges that explicitly includes indirect and interactive effects of habitat alteration at multiple scales across biogeographic gradients. We used an experimental network spanning 17 eelgrass (Zostera marina) sites across the Atlantic and Pacific oceans and the Mediterranean Sea to determine (1) if eelgrass edges consistently increase faunal predation risk, (2) whether edge effects on predation risk are altered by habitat degradation (shoot thinning), and (3) whether variation in the strength of edge effects among sites can be explained by biogeographical variability in covarying eelgrass habitat features. Contrary to expectations, at most sites, predation risk for tethered crustaceans (crabs or shrimps) was lower along patch edges than in patch interiors, regardless of the extent of habitat degradation. However, the extent to which edges reduced predation risk, compared to the patch interior, was correlated with the extent to which edges supported higher eelgrass structural complexity and prey biomass compared to patch interiors. This suggests an indirect component to edge effects in which the impact of edge proximity on predation risk is mediated by the effect of edges on other key biotic factors. Our results suggest that studies on edge effects should consider structural characteristics of patch edges, which may vary geographically, and multiple ways that humans degrade habitats

Diving into the vertical dimension of elasmobranch movement ecology

Knowledge of the three-dimensional movement patterns of elasmobranchs is vital to understand their ecological roles and exposure to anthropogenic pressures. To date, comparative studies among species at global scales have mostly focused on horizontal movements. Our study addresses the knowledge gap of vertical movements by compiling the first global synthesis of vertical habitat use by elasmobranchs from data obtained by deployment of 989 biotelemetry tags on 38 elasmobranch species. Elasmobranchs displayed high intra- and interspecific variability in vertical movement patterns. Substantial vertical overlap was observed for many epipelagic elasmobranchs, indicating an increased likelihood to display spatial overlap, biologically interact, and share similar risk to anthropogenic threats that vary on a vertical gradient. We highlight the critical next steps toward incorporating vertical movement into global management and monitoring strategies for elasmobranchs, emphasizing the need to address geographic and taxonomic biases in deployments and to concurrently consider both horizontal and vertical movements

Towards an integrated set of surface meteorological observations for climate science and applications

Observations are the foundation for understanding the climate system. Yet, currently available land meteorological data are highly fractured into various global, regional and national holdings for different variables and timescales, from a variety of sources, and in a mixture of formats. Added to this, many data are still inaccessible for analysis and usage. To meet modern scientific and societal demands as well as emerging needs such as the provision of climate services, it is essential that we improve the management and curation of available land-based meteorological holdings. We need a comprehensive global set of data holdings, of known provenance, that is truly integrated both across Essential Climate Variables (ECVs) and across timescales to meet the broad range of stakeholder needs. These holdings must be easily discoverable, made available in accessible formats, and backed up by multi-tiered user support. The present paper provides a high level overview, based upon broad community input, of the steps that are required to bring about this integration. The significant challenge is to find a sustained means to realize this vision. This requires a long-term international program. The database that results will transform our collective ability to provide societally relevant research, analysis and predictions in many weather and climate related application areas across much of the globe

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