The role of de-excitation in the final-state interactions of protons in neutrino-nucleus interactions

Present and next generation of long-baseline accelerator experiments are bringing the measurement of neutrino oscillations into the precision era with ever-increasing statistics. One of the most challenging aspects of achieving such measurements is developing relevant systematic uncertainties in the modeling of nuclear effects in neutrino-nucleus interactions. To address this problem, state-of-the-art detectors are being developed to extract detailed information about all particles produced in neutrino interactions. To fully profit from these experimental advancements, it is essential to have reliable models of propagation of the outgoing hadrons through nuclear matter able to predict how the energy is distributed between all the final-state observed particles. In this article, we investigate the role of nuclear de-excitation in neutrino-nucleus scattering using two Monte Carlo cascade models: NuWro and INCL coupled with the de-excitation code ABLA. The ablation model ABLA is used here for the first time to model de-excitation in neutrino interactions. As input to ABLA, we develop a consistent simulation of nuclear excitation energy tuned to electron-scattering data. The paper includes the characterization of the leading proton kinematics and of the nuclear cluster production during cascade and de-excitation. The observability of nuclear clusters as vertex activity and their role in a precise neutrino energy reconstruction is quantified.Comment: 14 pages, 13 figure

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Do Perennial Habitat Fragments Support Greater Parasitoid Diversity and Pest Regulation in Ephemeral Crops?

Background/Question/Methods To examine the role of native perennial vegetation in agricultural landscapes in providing critical habitat for supporting ecosystem services and sustainable agriculture, we sampled mobile arthropods in short-cycle, organically-managed crops in California. These agroecosystems are notoriously challenging for achieving conservation biological control because frequent disturbance precludes the establishment of resident communities of natural enemies of pests. Tachinidae, a diverse and ubiquitous family of parasitoid flies, were sampled for three seasons in 35 organic farm fields situated within a mosaic of agricultural and preserved lands in coastal California. Using a GIS, we characterized land-use and vegetative cover within 500m and 1500m, including grasslands, chaparral, oak woodlands, and coniferous forests. Results/Conclusions The abundance and species richness of tachinid flies captured in field crops in spring and summer were positively associated with the cover of semi-wild perennial vegetation, and the species richness of parasitoids emerging from sentinel lepidopteran pests exposed on potted plants in these organic vegetable fields was negatively associated with annual cropland cover. We discuss the importance of maintaining semi-wild, perennial habitat fragments as refugia to support parasitoids that provide ecosystem services in annual and short-cycle crop fields, and distinctions between fragments dominated by native versus introduced plants

Do Perennial Habitat Fragments Support Greater Parasitoid Diversity and Pest Regulation in Ephemeral Crops?

Background/Question/Methods To examine the role of native perennial vegetation in agricultural landscapes in providing critical habitat for supporting ecosystem services and sustainable agriculture, we sampled mobile arthropods in short-cycle, organically-managed crops in California. These agroecosystems are notoriously challenging for achieving conservation biological control because frequent disturbance precludes the establishment of resident communities of natural enemies of pests. Tachinidae, a diverse and ubiquitous family of parasitoid flies, were sampled for three seasons in 35 organic farm fields situated within a mosaic of agricultural and preserved lands in coastal California. Using a GIS, we characterized land-use and vegetative cover within 500m and 1500m, including grasslands, chaparral, oak woodlands, and coniferous forests. Results/Conclusions The abundance and species richness of tachinid flies captured in field crops in spring and summer were positively associated with the cover of semi-wild perennial vegetation, and the species richness of parasitoids emerging from sentinel lepidopteran pests exposed on potted plants in these organic vegetable fields was negatively associated with annual cropland cover. We discuss the importance of maintaining semi-wild, perennial habitat fragments as refugia to support parasitoids that provide ecosystem services in annual and short-cycle crop fields, and distinctions between fragments dominated by native versus introduced plants

Perennial Habitat Fragments, Parasitoid Diversity and Parasitism in Ephemeral Crops

Agricultural intensification has led to the removal of semi-wild, perennial vegetation in agricultural landscapes. However, in short-cycle crops, frequent disturbance from insecticides, harvesting and tillage disrupts the establishment of resident communities of natural enemies of pests. Semi-wild perennial vegetation may provide critical habitat for mobile arthropods supporting ecosystem services and sustainable agriculture. We sampled tachinid parasitoids, an important taxon for biological control of vegetable pests, in 35 organic farm fields situated within a mosaic of agricultural, residential and preserved lands in coastal California. Using a GIS, we characterized land-use and vegetative cover within 500 and 1500 m, including grasslands, chaparral, oak woodlands and coniferous forests. The abundance and species richness of tachinid flies captured in Malaise traps in spring and summer were positively associated with the cover of semi-wild perennial vegetation, especially in mesic habitats. The effective number of tachinid species (eH) was correlated positively with semi-wild perennial vegetation cover and negatively with annual crop cover in the landscape in September and May. The richness of parasitoids emerging from sentinel lepidopteran pests exposed on potted plants within farm fields was negatively associated with annual cropland cover. Parasitism rates dropped precipitously as percentage annual crop cover exceeded species-specific thresholds. Synthesis and applications. Maintaining semi-wild, perennial habitat fragments as refugia to support parasitoids can increase biodiversity and provide ecosystem services in annual and short-cycle crop fields. Our results indicated that crop pests escaped parasitism by two important tachinid species in landscapes with greater than 38% and 51% cover of annual cropland, respectively. Landscape-level research is critical for integrating science and policy to conserve biodiversity, promote sustainable agroecosystems and evaluate new anti-wildlife vegetation removal campaigns that may harm biological control agents while targeting microbial food contamination

Perennial habitat fragments, parasitoid diversity and parasitism in ephemeral crops. Applied Ecology 49(6

Summary 1. Agricultural intensification has led to the removal of semi-wild, perennial vegetation in agricultural landscapes. However, in short-cycle crops, frequent disturbance from insecticides, harvesting and tillage disrupts the establishment of resident communities of natural enemies of pests. Semi-wild perennial vegetation may provide critical habitat for mobile arthropods supporting ecosystem services and sustainable agriculture. 2. We sampled tachinid parasitoids, an important taxon for biological control of vegetable pests, in 35 organic farm fields situated within a mosaic of agricultural, residential and preserved lands in coastal California. Using a GIS, we characterized land-use and vegetative cover within 500 and 1500 m, including grasslands, chaparral, oak woodlands and coniferous forests. 3. The abundance and species richness of tachinid flies captured in Malaise traps in spring and summer were positively associated with the cover of semi-wild perennial vegetation, especially in mesic habitats. The effective number of tachinid species (e H ) was correlated positively with semi-wild perennial vegetation cover and negatively with annual crop cover in the landscape in September and May. 4. The richness of parasitoids emerging from sentinel lepidopteran pests exposed on potted plants within farm fields was negatively associated with annual cropland cover. Parasitism rates dropped precipitously as percentage annual crop cover exceeded species-specific thresholds. 5. Synthesis and applications. Maintaining semi-wild, perennial habitat fragments as refugia to support parasitoids can increase biodiversity and provide ecosystem services in annual and short-cycle crop fields. Our results indicated that crop pests escaped parasitism by two important tachinid species in landscapes with greater than 38% and 51% cover of annual cropland, respectively. Landscape-level research is critical for integrating science and policy to conserve biodiversity, promote sustainable agroecosystems and evaluate new anti-wildlife vegetation removal campaigns that may harm biological control agents while targeting microbial food contamination

Perennial Habitat Fragments, Parasitoid Diversity and Parasitism in Ephemeral Crops

Agricultural intensification has led to the removal of semi-wild, perennial vegetation in agricultural landscapes. However, in short-cycle crops, frequent disturbance from insecticides, harvesting and tillage disrupts the establishment of resident communities of natural enemies of pests. Semi-wild perennial vegetation may provide critical habitat for mobile arthropods supporting ecosystem services and sustainable agriculture. We sampled tachinid parasitoids, an important taxon for biological control of vegetable pests, in 35 organic farm fields situated within a mosaic of agricultural, residential and preserved lands in coastal California. Using a GIS, we characterized land-use and vegetative cover within 500 and 1500 m, including grasslands, chaparral, oak woodlands and coniferous forests. The abundance and species richness of tachinid flies captured in Malaise traps in spring and summer were positively associated with the cover of semi-wild perennial vegetation, especially in mesic habitats. The effective number of tachinid species (eH) was correlated positively with semi-wild perennial vegetation cover and negatively with annual crop cover in the landscape in September and May. The richness of parasitoids emerging from sentinel lepidopteran pests exposed on potted plants within farm fields was negatively associated with annual cropland cover. Parasitism rates dropped precipitously as percentage annual crop cover exceeded species-specific thresholds. Synthesis and applications. Maintaining semi-wild, perennial habitat fragments as refugia to support parasitoids can increase biodiversity and provide ecosystem services in annual and short-cycle crop fields. Our results indicated that crop pests escaped parasitism by two important tachinid species in landscapes with greater than 38% and 51% cover of annual cropland, respectively. Landscape-level research is critical for integrating science and policy to conserve biodiversity, promote sustainable agroecosystems and evaluate new anti-wildlife vegetation removal campaigns that may harm biological control agents while targeting microbial food contamination

Disturbance, Resources, and Exotic Plant Invasion: Gap Size Effects in a Redwood Forest

Volume: 57Start Page: 11End Page: 1

Green/ing Jobs: Definitions, Dilemmas and Strategies: W3 Conference 2011

This brochure outlines the agenda and brief versions of conference papers from a conference held at York University, Toronto on January 20th 2011. Speakers Clare Demerse, Pembina Institute, Sara Letourneau, Bluegreen Alliance (US), and Carla Lipsig-Mummé, York University addressed the issue of defining “green jobs”. In a second panel, John Cartwright, Toronto And York Region Labour Council Tony Clarke, Polaris Institute Of Canada and Marjorie Griffin Cohen, Simon Fraser University addressed Green/Ing Economies: Strategies And Dilemmas – particularly related to Canada’s oil and gas industry.Work in a Warming World (W3