Estimating and exploring the proportions of inter- and intrastate cattle shipments in the United States

Mathematical models are key tools for the development of surveillance, preparedness and response plans for the potential events of emerging and introduced foreign animal diseases. Creating these types of plans requires data; when data are incomplete, mathematical models can help fill in missing information, provided they are informed by the data that are available. In the United States, the most complete national-scale data available on cattle shipments are based on Interstate Certificates of Veterinary Inspection, which track the shipment of cattle between states; data on intrastate cattle shipments are lacking. Here we develop four new datasets on intrastate cattle shipments in the U.S., including an expert elicitation survey covering 19 states and territories and three state-level brand inspection data sets. The expert elicitation survey provides estimates on the proportion of shipments that travel interstate over multiple regions of the U.S. These survey data also identify differences in shipment patterns between regions, cattle commodity types, and sectors of the cattle industry. These survey data cover more states than any other source of intrastate data; however, one limitation of these data is the small number of participating experts in many of the states, only seven of the 19 responding states and territories had a group size of three or larger. The brand data sets include origin and destination information for both intra- and interstate shipments. These data, therefore, also provide detailed information on the proportion of interstate shipments in three Western states, including the temporal and geographic variation in shipments. Because the survey and brand data overlap in the Western U.S., they can be compared. We find that in the Western U.S. the expert estimates of the overall proportion of cattle shipments matched the brand data well. However, the experts estimated that there would be larger differences in beef and dairy shipments than the brand data show. This suggests the cattle industries in the West may be sending similar proportions of commodity specific cattle shipments over state lines. We additionally used the expert survey data to explore how differences in the proportion of interstate shipments can change predictions about cattle shipment patterns using the example of model-guided suggestions for targeted surveillance in Texas. Together these four data sets are the most extensive and geographically comprehensive information to date on intrastate cattle shipments. Additionally, our analyses on predicted shipment patterns suggest that assumptions about intrastate shipments could have consequences for targeted surveillance

Progress and challenges in coupled hydrodynamic-ecological estuarine modeling

© The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Estuaries and Coasts 39 (2016): 311-332, doi:10.1007/s12237-015-0011-y.Numerical modeling has emerged over the last several decades as a widely accepted tool for investigations in environmental sciences. In estuarine research, hydrodynamic and ecological models have moved along parallel tracks with regard to complexity, refinement, computational power, and incorporation of uncertainty. Coupled hydrodynamic-ecological models have been used to assess ecosystem processes and interactions, simulate future scenarios, and evaluate remedial actions in response to eutrophication, habitat loss, and freshwater diversion. The need to couple hydrodynamic and ecological models to address research and management questions is clear because dynamic feedbacks between biotic and physical processes are critical interactions within ecosystems. In this review, we present historical and modern perspectives on estuarine hydrodynamic and ecological modeling, consider model limitations, and address aspects of model linkage, skill assessment, and complexity. We discuss the balance between spatial and temporal resolution and present examples using different spatiotemporal scales. Finally, we recommend future lines of inquiry, approaches to balance complexity and uncertainty, and model transparency and utility. It is idealistic to think we can pursue a “theory of everything” for estuarine models, but recent advances suggest that models for both scientific investigations and management applications will continue to improve in terms of realism, precision, and accuracy.NKG, ALA, and RPS acknowledge support from the USGS Coastal and Marine Geology Program. DKR gratefully acknowledges support from NSF (OCE-1314642) and NIEHS (1P50-ES021923-01). MJB and JMPV gratefully acknowledge support from NOAA NOS NCCOS (NA05NOS4781201 and NA11NOS4780043). MJB and SJL gratefully acknowledge support from the Strategic Environmental Research and Development Program—Defense Coastal/Estuarine Research Program (RC-1413 and RC-2245)

Effect of nutrient reductions on dissolved oxygen and pH: a case study of Narragansett bay

To assess the consequences of nutrient reduction strategies on water quality under climate change, we investigated the long-term dynamics of dissolved oxygen (DO) and pH in Narragansett Bay (NB), a warming urbanized estuary in Rhode Island, where nitrogen loads have declined due to extensive wastewater treatment plant upgrades. We use 15 years (January 2005-December 2019) of measurements from the Narragansett Bay Fixed Site Monitoring network. Nutrient-enhanced phytoplankton growth can increase DO in the upper water column while subsequent respiration can reduce water column DO and enhance bottom water acidification, and vice-versa. We observed significant decreases in surface DO levels, concurrent with a significant increase in bottom DO, associated with the nitrogen load reduction. Surface DO decline was primarily attributed to reduced intensity of primary productivity, supported by a concurrent decrease in surface chlorophyll concentrations. Meanwhile, the influence of reduced organic matter respiration led to the increase of bottom DO levels by 9 µmol kg-1 (approximately 0.2 mg L-1 for typical summer temperature and salinity) over a 15-year period, which overcame the opposite influence of oxygen reduction from solubility decreases due to warming temperatures. In contrast, long-term changes in surface pH have not exhibited discernible trends beyond natural variability, likely due to the complex and sometimes opposing influences of biological activity and changing river flow conditions. We observed a slight increase in bottom pH, associated with the increase in DO in bottom water. Notably, future variations in freshwater discharge, particularly linked to extreme precipitation events, may further influence water carbonate chemistry and thereby impact pH dynamics. This study highlights the necessity of long-term time series measurements in helping understand the impacts of environmental management practices in improving water quality in coastal regions during a changing climate

We’re All Infected: Legal Personhood, Bare Life and The Walking Dead

This article argues that greater theoretical attention should be paid to the figure of the zombie in the fields of law, cultural studies and philosophy. Using The Walking Dead as a point of critical departure concepts of legal personhood are interrogated in relation to permanent vegetative states, bare life and the notion of the third person. Ultimately, the paper recommends a rejection of personhood; instead favouring a legal and philosophical engagement with humanity and embodiment. Personhood, it is suggested, creates a barrier in law allowing individuals in certain contexts (and in certain embodied states) to be rendered non-persons and thus outside the scope of legal rights. An approach that rejects personhood in favour of embodiment would allow individuals to enjoy their rights without being subject to such discrimination. It is also suggested that the concept of the human, itself complicated by the figure of the zombie, allows for legal engagement with a greater number of putative rights claimants including admixed embryos, cyborgs and the zombie

Ocean and coastal acidification off New England and Nova Scotia

Author Posting. © The Oceanography Society, 2015. This article is posted here by permission of The Oceanography Society for personal use, not for redistribution. The definitive version was published in Oceanography 28, no. 2 (2015): 182-197, doi:10.5670/oceanog.2015.41.New England coastal and adjacent Nova Scotia shelf waters have a reduced buffering capacity because of significant freshwater input, making the region’s waters potentially more vulnerable to coastal acidification. Nutrient loading and heavy precipitation events further acidify the region’s poorly buffered coastal waters. Despite the apparent vulnerability of these waters, and fisheries’ and mariculture’s significant dependence on calcifying species, the community lacks the ability to confidently predict how the region’s ecosystems will respond to continued ocean and coastal acidification. Here, we discuss ocean and coastal acidification processes specific to New England coastal and Nova Scotia shelf waters and review current understanding of the biological consequences most relevant to the region. We also identify key research and monitoring needs to be addressed and highlight existing capacities that should be leveraged to advance a regional understanding of ocean and coastal acidification.This project was supported in part by an appointment to the Internship/Research Participation Program at the Office of Water, US Environmental Protection Agency (EPA), administered by the Oak Ridge Institute for Science and Education through an interagency agreement between the US Department of Energy and the EPA. JS acknowledges support from NASA grant from NNX14AL84G NASA-CCS

Cross-species transmission potential between wild pigs, livestock, poultry, wildlife, and humans: implications for disease risk management in North America

Cross-species disease transmission between wildlife, domestic animals and humans is an increasing threat to public and veterinary health. Wild pigs are increasingly a potential veterinary and public health threat. Here we investigate 84 pathogens and the host species most at risk for transmission with wild pigs using a network approach. We assess the risk to agricultural and human health by evaluating the status of these pathogens and the co-occurrence of wild pigs, agriculture and humans. We identified 34 (87%) OIE listed swine pathogens that cause clinical disease in livestock, poultry, wildlife, and humans. On average 73% of bacterial, 39% of viral, and 63% of parasitic pathogens caused clinical disease in other species. Non-porcine livestock in the family Bovidae shared the most pathogens with swine (82%). Only 49% of currently listed OIE domestic swine diseases had published wild pig surveillance studies. The co-occurrence of wild pigs and farms increased annually at a rate of 1.2% with as much as 57% of all farms and 77% of all agricultural animals co-occurring with wild pigs. The increasing co-occurrence of wild pigs with livestock and humans along with the large number of pathogens shared is a growing risk for cross-species transmission

Estimating and exploring the proportions of inter- and intrastate cattle shipments in the United States

Mathematical models are key tools for the development of surveillance, preparedness and response plans for the potential events of emerging and introduced foreign animal diseases. Creating these types of plans requires data; when data are incomplete, mathematical models can help fill in missing information, provided they are informed by the data that are available. In the United States, the most complete national-scale data available on cattle shipments are based on Interstate Certificates of Veterinary Inspection, which track the shipment of cattle between states; data on intrastate cattle shipments are lacking. Here we develop four new datasets on intrastate cattle shipments in the U.S., including an expert elicitation survey covering 19 states and territories and three state-level brand inspection data sets. The expert elicitation survey provides estimates on the proportion of shipments that travel interstate over multiple regions of the U.S. These survey data also identify differences in shipment patterns between regions, cattle commodity types, and sectors of the cattle industry. These survey data cover more states than any other source of intrastate data; however, one limitation of these data is the small number of participating experts in many of the states, only seven of the 19 responding states and territories had a group size of three or larger. The brand data sets include origin and destination information for both intra- and interstate shipments. These data, therefore, also provide detailed information on the proportion of interstate shipments in three Western states, including the temporal and geographic variation in shipments. Because the survey and brand data overlap in the Western U.S., they can be compared. We find that in the Western U.S. the expert estimates of the overall proportion of cattle shipments matched the brand data well. However, the experts estimated that there would be larger differences in beef and dairy shipments than the brand data show. This suggests the cattle industries in the West may be sending similar proportions of commodity specific cattle shipments over state lines. We additionally used the expert survey data to explore how differences in the proportion of interstate shipments can change predictions about cattle shipment patterns using the example of model-guided suggestions for targeted surveillance in Texas. Together these four data sets are the most extensive and geographically comprehensive information to date on intrastate cattle shipments. Additionally, our analyses on predicted shipment patterns suggest that assumptions about intrastate shipments could have consequences for targeted surveillance

Population genetic diversity and fitness in multiple environments

<p>Abstract</p> <p>Background</p> <p>When a large number of alleles are lost from a population, increases in individual homozygosity may reduce individual fitness through inbreeding depression. Modest losses of allelic diversity may also negatively impact long-term population viability by reducing the capacity of populations to adapt to altered environments. However, it is not clear how much genetic diversity within populations may be lost before populations are put at significant risk. Development of tools to evaluate this relationship would be a valuable contribution to conservation biology. To address these issues, we have created an experimental system that uses laboratory populations of an estuarine crustacean, <it>Americamysis bahia </it>with experimentally manipulated levels of genetic diversity. We created replicate cultures with five distinct levels of genetic diversity and monitored them for 16 weeks in both permissive (ambient seawater) and stressful conditions (diluted seawater). The relationship between molecular genetic diversity at presumptive neutral loci and population vulnerability was assessed by AFLP analysis.</p> <p>Results</p> <p>Populations with very low genetic diversity demonstrated reduced fitness relative to high diversity populations even under permissive conditions. Population performance decreased in the stressful environment for all levels of genetic diversity relative to performance in the permissive environment. Twenty percent of the lowest diversity populations went extinct before the end of the study in permissive conditions, whereas 73% of the low diversity lines went extinct in the stressful environment. All high genetic diversity populations persisted for the duration of the study, although population sizes and reproduction were reduced under stressful environmental conditions. Levels of fitness varied more among replicate low diversity populations than among replicate populations with high genetic diversity. There was a significant correlation between AFLP diversity and population fitness overall; however, AFLP markers performed poorly at detecting modest but consequential losses of genetic diversity. High diversity lines in the stressful environment showed some evidence of relative improvement as the experiment progressed while the low diversity lines did not.</p> <p>Conclusions</p> <p>The combined effects of reduced average fitness and increased variability contributed to increased extinction rates for very low diversity populations. More modest losses of genetic diversity resulted in measurable decreases in population fitness; AFLP markers did not always detect these losses. However when AFLP markers indicated lost genetic diversity, these losses were associated with reduced population fitness.</p

Expression of SORL1 and a novel SORL1 splice variant in normal and Alzheimers disease brain

<p>Abstract</p> <p>Background</p> <p>Variations in sortilin-related receptor (SORL1) expression and function have been implicated in Alzheimers Disease (AD). Here, to gain insights into SORL1, we evaluated SORL1 expression and splicing as a function of AD and AD neuropathology, neural gene expression and a candidate single nucleotide polymorphism (SNP).</p> <p>Results</p> <p>To identify SORL1 splice variants, we scanned each of the 46 internal SORL1 exons in human brain RNA samples and readily found SORL1 isoforms that lack exon 2 or exon 19. Quantification in a case-control series of the more abundant isoform lacking exon 2 (delta-2-SORL1), as well as the "full-length" SORL1 (FL-SORL1) isoform containing exon 2 showed that expression of FL-SORL1 was reduced in AD individuals. Moreover, FL-SORL1 was reduced in cognitively intact individuals with significant AD-like neuropathology. In contrast, the expression of the delta-2-SORL1 isoform was similar in AD and non-AD brains. The expression of FL-SORL1 was significantly associated with synaptophysin expression while delta-2-SORL1 was modestly enriched in white matter. Lastly, FL-SORL1 expression was associated with rs661057, a SORL1 intron one SNP that has been associated with AD risk. A linear regression analysis found that rs661057, synaptophysin expression and AD neuropathology were each associated with FL-SORL1 expression.</p> <p>Conclusion</p> <p>These results confirm that FL-SORL1 expression declines in AD and with AD-associated neuropathology, suggest that FL-SORL1 declines in cognitively-intact individuals with AD-associated neuropathology, identify a novel SORL1 splice variant that is expressed similarly in AD and non-AD individuals, and provide evidence that an AD-associated SNP is associated with SORL1 expression. Overall, these results contribute to our understanding of SORL1 expression in the human brain.</p

Advancing newborn health: The Saving Newborn Lives initiative

Until recently, newborn health was virtually absent from the global health agenda. Now, assistance agencies, national governments and non-governmental organisations are increasingly addressing this previously neglected issue of close to four million newborns dying every year. The experience of the Saving Newborn Lives initiative documents some of the progress that has been made and the challenges and opportunities that lie ahead. Since the start of the initiative in 2000, targeted research, focused on overcoming the key barriers to improved newborn survival, has demonstrated low-cost, community-based interventions and strategies that can significantly reduce newborn mortality. Building on what has been learned from this and other efforts to date, the challenge now is to reach the millions of newborns still at risk