2007 biennial report to Congress on the progress and findings of studies of striped bass populations

The 1997 reauthorization of the Atlantic Striped Bass Conservation Act (Striped Bass Act) mandated biennial reports to Congress and to the Atlantic States Marine Fisheries Commission (Commission) from the secretaries of the Department of Commerce and the Department of the Interior concerning the progress and findings of studies of Atlantic striped bass (Morone saxatilis). The Striped Bass Act specifically requests updates on studies that include, but are not limited to: annual stock assessments, investigations on the causes of fluctuations in Atlantic striped bass populations, the effects of environmental factors on the recruitment, spawning potential, mortality, and abundance of Atlantic striped bass populations, and investigations of interactions between Atlantic striped bass and other fish. This document is the fifth such report to Congress and includes data available through 2007 with emphasis on the 2005 and 2006 calendar years.

Accelerating loss of seagrasses across the globe threatens coastal ecosystems

Coastal ecosystems and the services they provide are adversely affected by a wide variety of human activities. In particular, seagrass meadows are negatively affected by impacts accruing from the billion or more people who live within 50 km of them. Seagrass meadows provide important ecosystem services, including an estimated $1.9 trillion per year in the form of nutrient cycling; an order of magnitude enhancement of coral reef fish productivity; a habitat for thousands of fish, bird, and invertebrate species; and a major food source for endangered dugong, manatee, and green turtle. Although individual impacts from coastal development, degraded water quality, and climate change have been documented, there has been no quantitative global assessment of seagrass loss until now. Our comprehensive global assessment of 215 studies found that seagrasses have been disappearing at a rate of 110 square kilometers per year since 1980 and that 29% of the known areal extent has disappeared since seagrass areas were initially recorded in 1879. Furthermore, rates of decline have accelerated from a median of 0.9% per year before 1940 to 7% per year since 1990. Seagrass loss rates are comparable to those reported for mangroves, coral reefs, and tropical rainforests and place seagrass meadows among the most threatened ecosystems on earth.

Age, growth, mortality, and distribution of pinfish (Lagodon rhomboides) in Tampa Bay and adjacent Gulf of Mexico waters

Life-history dynamics of pinfish (Lagodon rhomboides) were examined from data derived from random station surveys conducted in Tampa Bay and adjacent Gulf of Mexico waters during 1993–97. In addition, patterns in spatial distribution and abundance in Gulf of Mexico waters were investigated. Ages determined from whole otoliths ranged from 0 to 7 years, and von Bertalanffy growth models for males and females were not significantly different. Von Bertalanffy growth model parameters were L∞=219.9 mm SL, k =0.33/yr, and t0 =–1.10 years for all fish combined. High gonadosomatic indices during October–December indicated that some spawning may occur in Tampa Bay. Estimated lengths at 50% maturity were 132 mm SL for males and 131 mm SL for females. Total instantaneous mortality rates derived from the Chapman-Robson estimator ranged from 0.88 to 1.08/yr, and natural mortality was estimated to be 0.78/yr. In Gulf of Mexico waters, pinfish catch rates declined with increasing depth, and most pinfish were caught in <17 m of water. Length distributions showed that pinfish segregate by size with increasing depth.

Simulation and diagnosis of large-scale atmospheric moisture and surface hydrology over North America

We describe a preliminary investigation into large-scale atmospheric and surface moisture variations over North America. We compare large-scale hydrologic budgets in the Los Alamos general circulation model (GCM) to observed precipitation and vertically integrated atmospheric moisture fluxes derived from the National Meteorological Center's operational analyses. THe GCM faithfully simulates the integrated flux divergence and P-E differences. However, the integrated moisture content is too low, and precipitation and evaporation are too high. The model produces summertime soil moisture dryness, which supports previous studies showing increased droughts under warmer conditions.

The Los Alamos General Circulation Model hydrologic cycle

As the global population has increased, so have human influences on the global environment. ... How can we better understand and predict these natural and potential anthropogenic variations? One way is to develop a model that can accurately describe all the components of the hydrologic cycle, rather than just the end result variables such as precipitation and soil moisture. If we can predict and simulate variations in evaporation and moisture convergence, as well as precipitation, then we will have greater confidence in our ability to at least model precipitation variations. Therefore, we describe here just how well we can model relevant aspects of the global hydrologic cycle. In particular, we determine how well we can model the annual and seasonal mean global precipitation, evaporation, and atmospheric water vapor transport.

Chronological records of climate-related events and societal consequences [abstract]

EXTRACT (SEE PDF FOR FULL ABSTRACT): A chronology of documented regional and global warm and cold event records is collated along with documented ecosystem response records and health threat/sequellae records for the historical period. Patterns of societal response to cold periods punctuated by warm periods have been associated with considerable human health impacts, stimulated by blooms in disease vectors such as rodents and insects.

Association of early growth response-1 gene polymorphisms with total IgE and atopy in asthmatic children

Early growth response-1 (Egr-1) is expressed in human airways and found to modulate tumor necrosis factor, immunoglobulin E (IgE), airway responsiveness, and interleukin-13-induced inflammation in mice. We investigated the effects of Chinese-tagging singl

When Does a Polynomial Over a Finite Field Permute the Elements of the Field?

We present a class of indecomposable polynomials of non prime-power degree over the finite field of two elements which are permutation polynomials on infinitely many finite extensions of the field. The associated geometric monodromy groups are the simple ...

A Global Crisis for Seagrass Ecosystems

Seagrasses, marine flowering plants, have a long evolutionary history but are now challenged with rapid environmental changes as a result of coastal human population pressures. Seagrasses provide key ecological services, including organic carbon production and export, nutrient cycling, sediment stabilization, enhanced biodiversity, and trophic transfers to adjacent habitats in tropical and temperate regions. They also serve as “coastal canaries,” global biological sentinels of increasing anthropogenic influences in coastal ecosystems, with large-scale losses reported worldwide. Multiple stressors, including sediment and nutrient runoff, physical disturbance, invasive species, disease, commercial fishing practices, aquaculture, overgrazing, algal blooms, and global warming, cause seagrass declines at scales of square meters to hundreds of square kilometers. Reported seagrass losses have led to increased awareness of the need for seagrass protection, monitoring, management, and restoration. However, seagrass science, which has rapidly grown, is disconnected from public awareness of seagrasses, which has lagged behind awareness of other coastal ecosystems. There is a critical need for a targeted global conservation effort that includes a reduction of watershed nutrient and sediment inputs to seagrass habitats and a targeted educational program informing regulators and the public of the value of seagrass meadows.

Transition Space

Informal causal descriptions of physical systems abound in sources such as encyclopedias, reports and user's manuals. Yet these descriptions remain largely opaque to computer processing. This paper proposes a representational framework in which such descriptions are viewed as providing partial specifications of paths in a space of possible transitions, or transition space. In this framework, the task of comprehending informal causal descriptions emerges as one of completing the specifications of paths in transition space---filling causal gaps and relating accounts of activity varied by analogy and abstraction. The use of the representation and its operations is illustrated in the context of a simple description concerning rocket propulsion.

Early-Holocene environments in the Wadi Faynan, Jordan

Hunt, C. Elrishi, H. Gilbertson, D. Grattan, J. McLaren, S. Pyatt, B. Rushworth, G. Barker, G. Early-Holocene environments in the Wadi Faynan, Jordan. The Holocene. 2004. 14,6 pp 921-930

Debugging: the good, the bad, and the quirky -- a qualitative analysis of novices' strategies

Murphy, L., Lewandowski, G., McCauley, R., Simon, B., Thomas, L., and Zander, C. 2008. Debugging: the good, the bad, and the quirky -- a qualitative analysis of novices' strategies. SIGCSE Bull. 40, 1 (Feb. 2008), 163-167

3'-UTR SIRF: A database for identifying clusters of short interspersed repeats in 3' untranslated regions

BACKGROUND:Short (~5 nucleotides) interspersed repeats regulate several aspects of post-transcriptional gene expression. Previously we developed an algorithm (REPFIND) that assigns P-values to all repeated motifs in a given nucleic acid sequence and reliably identifies clusters of short CAC-containing motifs required for mRNA localization in Xenopus oocytes.DESCRIPTION:In order to facilitate the identification of genes possessing clusters of repeats that regulate post-transcriptional aspects of gene expression in mammalian genes, we used REPFIND to create a database of all repeated motifs in the 3' untranslated regions (UTR) of genes from the Mammalian Gene Collection (MGC). The MGC database includes seven vertebrate species: human, cow, rat, mouse and three non-mammalian vertebrate species. A web-based application was developed to search this database of repeated motifs to generate species-specific lists of genes containing specific classes of repeats in their 3'-UTRs. This computational tool is called 3'-UTR SIRF (Short Interspersed Repeat Finder), and it reveals that hundreds of human genes contain an abundance of short CAC-rich and CAG-rich repeats in their 3'-UTRs that are similar to those found in mRNAs localized to the neurites of neurons. We tested four candidate mRNAs for localization in rat hippocampal neurons by in situ hybridization. Our results show that two candidate CAC-rich (Syntaxin 1B and Tubulin beta4) and two candidate CAG-rich (Sec61alpha and Syntaxin 1A) mRNAs are localized to distal neurites, whereas two control mRNAs lacking repeated motifs in their 3'-UTR remain primarily in the cell body.CONCLUSION:Computational data generated with 3'-UTR SIRF indicate that hundreds of mammalian genes have an abundance of short CA-containing motifs that may direct mRNA localization in neurons. In situ hybridization shows that four candidate mRNAs are localized to distal neurites of cultured hippocampal neurons. These data suggest that short CA-containing motifs may be part of a widely utilized genetic code that regulates mRNA localization in vertebrate cells. The use of 3'-UTR SIRF to search for new classes of motifs that regulate other aspects of gene expression should yield important information in future studies addressing cis-regulatory information located in 3'-UTRs.

The Least of These: American Evangelical Parachurch Missions to the Poor, 1947-2005

This dissertation narrates the historical development of American evangelical missions to the poor from 1947-2005 and analyzes the discourse of its main parachurch proponents, especially World Vision, Compassion International, Food for the Hungry, Samaritan's urse, Sojourners, Evangelicals for Social Action, and the Christian Community Development Association. Although recent scholarship on evangelicalism has been prolific, much of the historical work has focused on earlier periods. Sociological and political scientific scholarship on the postwar period has been attracted mostly to controversies surrounding the Religious Right, leaving evangelicalism's resurgent concern for the poor relatively understudied. This dissertation addresses these lacunae. The study consists of three chronological parts, each marked by a distinctive model of mission to the poor. First, the 1950s were characterized by compassionate charity for individual emergencies, a model that cohered neatly with evangelicalism's individualism and emotionalism. This model should be regarded as the quintessential, bedrock evangelical theory of mission to the poor. It remained strong throughout the entire postwar period. Second, in the 1970s, a strong countercurrent emerged that advocated for penitent protest against structural injustice and underdevelopment. In contrast to the first model, it was distinguished by going against the grain of many aspects of evangelical culture, especially its reflexive patriotism and individualism. Third, in the 1990s, an important movement towards developing potential through hopeful holism gained prominence. Its advocates were confident that their integration of biblical principles with insights from contemporary economic development praxis would contribute to drastic, widespread reductions in poverty. This model signaled a new optimism in evangelicalism's engagement with the broader world. The increasing prominence of missions to the poor within American evangelicalism led to dramatic changes within the movement's worldview: by 2005, evangelicals were mostly unified in their expressed concern for the physical and social needs of the poor, a position that radically reversed their immediate postwar worldview of near-exclusive focus on the spiritual needs of individuals. Nevertheless, missions to the poor also paralleled, reinforced, and hastened the increasing fragmentation of evangelicalism's identity, as each missional model advocated for highly variant approaches to poverty amelioration that were undergirded by diverse sociological, political, and theological assumptions.