Combining and Aggregating Environmental Data for Status and Trend Assessments: Challenges and Approaches

Increasingly, natural resource management agencies and nongovernmental organizations are sharing monitoring data across geographic and jurisdictional boundaries. Doing so improves their abilities to assess local-, regional-, and landscape-level environmental conditions, particularly status and trends, and to improve their ability to make short-and long-term management decisions. Status monitoring assesses the current condition of a population or environmental condition across an area. Monitoring for trends aims at monitoring changes in populations or environmental condition through time. We wrote this paper to inform agency and nongovernmental organization managers, analysts, and consultants regarding the kinds of environmental data that can be combined with suitable techniques and statistically aggregated for new assessments. By doing so, they can increase the (1) use of available data and (2) the validity and reliability of the assessments. Increased awareness of the difficulties inherent in combining and aggregating data for local-and regional-level analyses can increase the likelihood that future monitoring efforts will be modified and/or planned to accommodate data from multiple sources

Urban and Rural-residential Land Uses: Their Role in Watershed Health and the Rehabilitation of Oregon’s Wild Salmonids

This technical report by the Independent Multidisciplinary Science Team (IMST) is a comprehensive review of how human activities in urban and rural-residential areas can alter aquatic ecosystems and resulting implications for salmonid recovery, with a geographic focus on the state of Oregon. The following topics are considered in the form of science questions, and comprise the major components of this report: The effects of urban and rural-residential development on Oregon’s watersheds and native wild salmonids. Actions that can be used to avoid or mitigate undesirable changes to aquatic ecosystems near developing urban and rural-residential areas. The benefits and pitfalls of salmonid habitat rehabilitation within established urban or rural-residential areas. Suggested research and monitoring focus areas that will facilitate the recovery of salmonid populations affected by development. The fundamental concepts presented in this report should be applicable to most native salmonid populations across the state. IMST encourages managers and policy-makers with interest in a specific species or geographic region to carefully research local ecological conditions, as well as specific life history characteristics of salmonids in the region. Conserving watershed condition and salmonids in the face of increasing development requires consideration of two distinct sets of processes. First are the human social and economic processes that drive patterns in land use change. Second are the ecological processes, altered by land use, that underlie salmonid habitat changes. This report focuses on the latter and summarizes the effects of rural-residential and urban development on native, wild salmonid populations and the watersheds upon which they depend

A METHOD OF MODELING SOURCE AREA RESPONSE TO CLIMATE VARIABILITY

ABSTRACT: A modeling framework for understanding spatially-explicit relationships between soil moisture dynamics and streamflow generation in upland humid forested watersheds is described. The framework consists of a dynamic canopy interception module and a 2D finite element hillslope hydrology model (IHDM4) having hillslope planes objectively delineated using contour-based terrain analysis (TAPES-C). This approach is fine-scaled both in space and time allowing for the inclusion of topographic and soil heterogeneities necessary for mapping oscillations in the variable source areas of streamflow generation. The modeling framework is implemented for a small control watershed (WS2) at the Coweeta Hydrologic Laboratory. Simulation results to be presented at the conference include the climate-scale response of variable source areas for hillslope cross-sections to hourly climate data spanning years in which total precipitation was: (a) >20% above average, (b) near average, (c) >20% below average

Combining and aggregating environmental data for status and trend assessments: challenges and approaches

Increasingly, natural resource management agencies and nongovernmental organizations are sharing monitoring data across geographic and jurisdictional boundaries. Doing so improves their abilities to assess local-, regional-, and landscape-level environmental conditions, particularly status and trends, and to improve their ability to make short-and long-term management decisions. Status monitoring assesses the current condition of a population or environmental condition across an area. Monitoring for trends aims at monitoring changes in populations or environmental condition through time. We wrote this paper to inform agency and nongovernmental organization managers, analysts, and consultants regarding the kinds of environmental data that can be combined with suitable techniques and statistically aggregated for new assessments. By doing so, they can increase the (1) use of available data and (2) the validity and reliability of the assessments. Increased awareness of the difficulties inherent in combining and aggregating data for local-and regional-level analyses can increase the likelihood that future monitoring efforts will be modified and/or planned to accommodate data from multiple sources.Keywords: Lurking variable, Change of support problem, Simpson's paradox, Modifiable areal unit problem, Data aggregation, Environmental monitorin

Matrix and Tensor Factorization Methods for Toxicogenomic Modeling and Prediction

Peer reviewe

A Review of Urban Water Body Challenges and Approaches: (1) Rehabilitation and Remediation

We review how urbanization alters aquatic ecosystems, as well as actions that managers can take to remediate urban waters. Urbanization affects streams by fundamentally altering longitudinal and lateral processes that in turn alter hydrology, habitat, and water chemistry; these effects create physical and chemical stressors that in turn affect the biota. Urban streams often suffer from multiple stressor effects that have collectively been termed an “urban stream syndrome,” in which no single factor dominates degraded conditions. Resource managers have multiple ways of combating the urban stream syndrome. These approaches range from whole-watershed protection to reach-scale habitat rehabilitation, but the prescription must be matched to the scale of the factors that are causing the problem, and results will likely not be immediate because of lengthy recovery times. Although pristine or reference conditions are far from attainable, urban stream rehabilitation is a worthy goal because appropriate actions can provide ecosystem improvements as well as increased ecosystem service benefits for human society

Negative Regulation of Active Zone Assembly by a Newly Identified SR Protein Kinase

A neuronal serine-arginine protein kinase that localizes to the presynaptic active zone is required for kinase-dependent repression of active zone assembly

A Global View of Cancer-Specific Transcript Variants by Subtractive Transcriptome-Wide Analysis

BACKGROUND: Alternative pre-mRNA splicing (AS) plays a central role in generating complex proteomes and influences development and disease. However, the regulation and etiology of AS in human tumorigenesis is not well understood. METHODOLOGY/PRINCIPAL FINDINGS: A Basic Local Alignment Search Tool database was constructed for the expressed sequence tags (ESTs) from all available databases of human cancer and normal tissues. An insertion or deletion in the alignment of EST/EST was used to identify alternatively spliced transcripts. Alignment of the ESTs with the genomic sequence was further used to confirm AS. Alternatively spliced transcripts in each tissue were then subtractively cross-screened to obtain tissue-specific variants. We systematically identified and characterized cancer/tissue-specific and alternatively spliced variants in the human genome based on a global view. We identified 15,093 cancer-specific variants of 9,989 genes from 27 types of human cancers and 14,376 normal tissue-specific variants of 7,240 genes from 35 normal tissues, which cover the main types of human tumors and normal tissues. Approximately 70% of these transcripts are novel. These data were integrated into a database HCSAS (http://202.114.72.39/database/human.html, pass:68756253). Moreover, we observed that the cancer-specific AS of both oncogenes and tumor suppressor genes are associated with specific cancer types. Cancer shows a preference in the selection of alternative splice-sites and utilization of alternative splicing types. CONCLUSIONS/SIGNIFICANCE: These features of human cancer, together with the discovery of huge numbers of novel splice forms for cancer-associated genes, suggest an important and global role of cancer-specific AS during human tumorigenesis. We advise the use of cancer-specific alternative splicing as a potential source of new diagnostic, prognostic, predictive, and therapeutic tools for human cancer. The global view of cancer-specific AS is not only useful for exploring the complexity of the cancer transcriptome but also widens the eyeshot of clinical research

Genome-Wide Analysis of Histone H3 Lysine9 Modifications in Human Mesenchymal Stem Cell Osteogenic Differentiation

Mesenchymal stem cells (MSCs) possess self-renewal and multi-lineage differentiation potentials. It has been established that epigenetic mechanisms such as histone modifications could be critical for determining the fate of stem cells. In this study, full human genome promoter microarrays and expression microarrays were used to explore the roles of histone modifications (H3K9Ac and H3K9Me2) upon the induction of MSC osteogenic differentiation. Our results revealed that the enrichment of H3K9Ac was decreased globally at the gene promoters, whereas the number of promoters enriched with H3K9Me2 was increased evidently upon osteogenic induction. By a combined analysis of data from both ChIP-on-chip and expression microarrays, a number of differentially expressed genes regulated by H3K9Ac and/or H3K9Me2 were identified, implicating their roles in several biological events, such as cell cycle withdraw and cytoskeleton reconstruction that were essential to differentiation process. In addition, our results showed that the vitamin D receptor played a trans-repression role via alternations of H3K9Ac and H3K9Me2 upon MSC osteogenic differentiation. Data from this study suggested that gene activation and silencing controlled by changes of H3K9Ac and H3K9Me2, respectively, were crucial to MSC osteogenic differentiation