[Book review] Quality Planning for the Life Science Researcher: Meeting Quality Assurance Requirements, by Amy Cross-Smiecinski and Linda D. Stetzenbach
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Journal of Wildlife Management↗
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Cx-02 Program, workshop on modeling complex systems
This publication contains the abstracts and program for the workshop on complex systems that was held on November 19-21, 2002, in Reno, Nevada. Complex systems are ubiquitous within the realm of the earth sciences. Geological systems consist of a multiplicity of linked components with nested feedback loops; the dynamics of these systems are non-linear, iterative, multi-scale, and operate far from equilibrium. That notwithstanding, It appears that, with the exception of papers on seismic studies, geology and geophysics work has been disproportionally underrepresented at regional and national meetings on complex systems relative to papers in the life sciences. This is somewhat puzzling because geologists and geophysicists are, in many ways, preadapted to thinking of complex system mechanisms. Geologists and geophysicists think about processes involving large volumes of rock below the sunlit surface of Earth, the accumulated consequence of processes extending hundreds of millions of years in the past. Not only do geologists think in the abstract by virtue of the vast time spans, most of the evidence is out-of-sight. A primary goal of this workshop is to begin to bridge the gap between the Earth sciences and life sciences through demonstration of the universality of complex systems science, both philosophically and in model structures.
Open-File Report↗
The web of life: Natural science information on the Internet
As society has come to equate economic prosperity with the health of our living resources, national science policy has called for the development of a comprehensive digital knowledge base to support informed decision making and wise resource management. The Internet and World Wide Web demonstrate the earliest stages of this evolving virtual library of the natural world, offering an increasing array of high-quality, innovative resources and services in the natural science arena. This article discusses the leading providers of natural science information on the Internet and highlights some of the exemplary resources they are delivering online. The discussion concludes with a brief discussion of the role of the librarian in developing the Web of natural science knowledge online and provides a short Webliography of starting points for further exploration of this subject area. PDF
Journal of Library Administration↗
Decision science as a framework for combining geomorphological and ecological modeling for the management of coastal systems
The loss of ecosystem services due to climate change and coastal development is projected to have significant impacts on local economies and conservation of natural resources. Consequently, there has been an increase in coastal management activities such as living shorelines, oyster reef restoration, marsh restoration, beach and dune nourishment, and revegetation projects. Coastal management decisions are complex and include challenging trade-offs. Decision science offers a useful framework to address such complex problems. Here, we provide a synthesis about how decision science can help to integrate research from multiple disciplines (physical and life sciences) with management of coastal and marine systems. Specifically, we discuss the importance of considering concepts and techniques from ecology, coastal geology, geomorphology, climate science, oceanography, and decision analysis when developing conservation plans for coastal restoration. We illustrate the process with several coastal restoration studies. Our capstone example is based on a recent barrier island restoration assessment project at Dauphin Island, Alabama, which included the development of geomorphological and ecological models. We show how decision science can be used as a framework to combine geomorphological and ecological modeling to help inform management decisions while considering uncertainty about system changes and risk tolerance. We also build on our examples through a review of recently developed techniques for spatial conservation planning for land acquisition decisions and the application of adaptive management for sequential decisions.
Alabama↗
Succession in ecological education
As complex and dynamic systems, wetlands offer the opportunity to investigate and incorporate the ecological concept of succession in educational settings. For example, the well-known, classic hydrosere concept is illustrated in numerous ecology and life-science textbooks. In this chapter, the drawbacks of using the hydrosere successional concept are assessed, and two examples of using wetlands to illustrate the process of succession for educational purposes are described. In each case, the premise and approach is that students best “learn ecology by doing ecology.”
Book chapter↗
Advances in the simulation and automated measurement of well-sorted granular material: 1. Simulation
1. In this, the first of a pair of papers which address the simulation and automated measurement of well-sorted natural granular material, a method is presented for simulation of two-phase (solid, void) assemblages of discrete non-cohesive particles. The purpose is to have a flexible, yet computationally and theoretically simple, suite of tools with well constrained and well known statistical properties, in order to simulate realistic granular material as a discrete element model with realistic size and shape distributions, for a variety of purposes. The stochastic modeling framework is based on three-dimensional tessellations with variable degrees of order in particle-packing arrangement. Examples of sediments with a variety of particle size distributions and spatial variability in grain size are presented. The relationship between particle shape and porosity conforms to published data. The immediate application is testing new algorithms for automated measurements of particle properties (mean and standard deviation of particle sizes, and apparent porosity) from images of natural sediment, as detailed in the second of this pair of papers. The model could also prove useful for simulating specific depositional structures found in natural sediments, the result of physical alterations to packing and grain fabric, using discrete particle flow models. While the principal focus here is on naturally occurring sediment and sedimentary rock, the methods presented might also be useful for simulations of similar granular or cellular material encountered in engineering, industrial and life sciences.
Journal of Geophysical Research F: Earth Surface↗
“One Health” or three? Publication silos among the One Health disciplines
The One Health initiative is a global effort fostering interdisciplinary collaborations to address challenges in human, animal, and environmental health. While One Health has received considerable press, its benefits remain unclear because its effects have not been quantitatively described. We systematically surveyed the published literature and used social network analysis to measure interdisciplinarity in One Health studies constructing dynamic pathogen transmission models. The number of publications fulfilling our search criteria increased by 14.6% per year, which is faster than growth rates for life sciences as a whole and for most biology subdisciplines. Surveyed publications clustered into three communities: one used by ecologists, one used by veterinarians, and a third diverse-authorship community used by population biologists, mathematicians, epidemiologists, and experts in human health. Overlap between these communities increased through time in terms of author number, diversity of co-author affiliations, and diversity of citations. However, communities continue to differ in the systems studied, questions asked, and methods employed. While the infectious disease research community has made significant progress toward integrating its participating disciplines, some segregation—especially along the veterinary/ecological research interface—remains.
PLoS Biology↗
A review of methods to estimate cause-specific mortality in presence of competing risks
Estimating cause-specific mortality is often of central importance for understanding the dynamics of wildlife populations. Despite such importance, methodology for estimating and analyzing cause-specific mortality has received little attention in wildlife ecology during the past 20 years. The issue of analyzing cause-specific, mutually exclusive events in time is not unique to wildlife. In fact, this general problem has received substantial attention in human biomedical applications within the context of biostatistical survival analysis. Here, we consider cause-specific mortality from a modern biostatistical perspective. This requires carefully defining what we mean by cause-specific mortality and then providing an appropriate hazard-based representation as a competing risks problem. This leads to the general solution of cause-specific mortality as the cumulative incidence function (CIF). We describe the appropriate generalization of the fully nonparametric staggered-entry Kaplan–Meier survival estimator to cause-specific mortality via the nonparametric CIF estimator (NPCIFE), which in many situations offers an attractive alternative to the Heisey–Fuller estimator. An advantage of the NPCIFE is that it lends itself readily to risk factors analysis with standard software for Cox proportional hazards model. The competing risks–based approach also clarifies issues regarding another intuitive but erroneous “cause-specific mortality” estimator based on the Kaplan–Meier survival estimator and commonly seen in the life sciences literature.
Journal of Wildlife Management↗
Current trends and future directions in swan research: Insights from the 6th International Swan Symposium
Given their popularity with researchers and public alike, together with their welldocumented importance in aquatic and terrestrial ecosystems, fundamental and applied research on swans continues to develop in the 21st century. The 6th International Swan Symposium (6th ISS), was held at the Estonian University of Life Sciences in Tartu, Estonia, in October 2018. The symposium brought together 101 delegates from 17 countries, with presentations on a range of topics on Cygnus and Coscoroba species, including monitoring, habitat and resource use, demography, movements and migration, and threats and conservation. The proceedings of the 6th ISS in this special issue of Wildfowl include select papers on swan research presented at the 6th ISS, covering a wide range of species, systems and issues. This paper presents a synthesis of the 6th ISS and an overview of current trends and future directions in swan research. Despite progress on many topics, southern hemisphere swan species continue to receive less attention than their northern hemisphere counterparts, whilst facing many of the same pressures. It is clear that, given the challenges facing swan researchers in the twenty-first century, international cooperation will continue to be vital. Swans are highly mobile animals and many populations undertake migrations spanning thousands of kilometres, and crucially do not recognise human geographic and political borders. Such international collaborations will be particularly important in coordinating future monitoring and conservation activities. The IUCN-SSC/Wetlands International Swan Specialist Group (SSG) will continue to facilitate international collaborations and communication among the global network of swan researchers, through its activities, website and annual newsletter. Given the substantial challenges and knowledge gaps documented here, there is no doubt that swan researchers will continue to benefit from regular symposia to share information and develop collaborations towards understanding and addressing emerging conservation issues. As such, we recommend holding International Swan Symposia every 4–5 years.
Wildfowl↗
Role of intestinal microflora in the degradation of DDT by rainbow trout ( Salmo gairdneri )
Though liver homogenates show apparent microsomal enzyme DDT-dehydrochlorinase activity, in the intact fish the intestinal microflora play a major role in DDT detoxication. Since the presence of this microflora in fish depends on the recent intake of food (12), the rate of detoxication and hence the toxicity of ingested DDT to the rainbow trout will probably depend somewhat on the available food supply.
Life Sciences↗
The value of scientific information — An overview
Introduction The U.S. Geological Survey (USGS) provides reliable science, data, information, and models (hereafter collectively referred to as “information”) to describe and understand the Earth. This information is used to minimize loss of life and property from natural disasters; manage water, biological, energy, and mineral resources; and enhance and protect quality of life. USGS science informs public and private decisions, operations, and risk management in all major United States economic sectors, as defined by the Bureau of Economic Analysis, and provides critical information for natural resource and natural hazard management and stewardship decisions. Understanding the value of scientific information supports applications of USGS science in land- and water-management decisions, and better informs the public about the return on investment of USGS programs. USGS economists, social scientists, and physical scientists are engaged in collaborative efforts to advance methods to estimate the value of information (VOI) produced by the USGS. These efforts involve collaborating with an international community to develop and refine estimation methods, establish best practices to determine VOI, develop a study repository, and conduct projects to assess the VOI of specific information products and their application. This report focuses on economic valuation conducted by USGS specifically, although the methodology has much broader applicability within the U.S. government, academia, and beyond. Noneconomic valuation techniques for assessing the VOI also exist but are not addressed in this report.
Open-File Report↗
Translating climate change effects on species into everyday language: an example of more driving and less fishing
Climate change is expected to result in widespread changes in species distributions (e.g., shifting, shrinking, expanding species ranges; e.g., Parmesan and Yohe, 2003), especially for freshwater fish species (Heino et al. 2009). Although anglers and other resource users could be greatly affected by changes in species distributions, predicted changes are rarely reported in ways that can be easily understood by the general public. In contrast, climate science that more directly affects human welfare or livelihoods is often more readily communicated to the general public because it is of greater concern or closely related to everyday life. For example, most people can readily interpret how increases in the number of “hot” days above a given temperature threshold might affect their lives, and property owners in coastal areas can use predictive maps to determine how they might be affected by sea level rise (for more examples, see the Third National Assessment of the U.S. Environmental Protection Agency at globalchange.gov ). However, the effects of climate change on species are usually reported to the general public using summary metrics or maps designed to communicate concepts that are not normally encountered in everyday life, including changes in habitat suitability, range shifts, or increasing risks from disease or extreme events (e.g., National Audubon Society 2009; Groffman et al. 2014). Though these metrics are necessary, meaningful, and understood by scientists, many people lack the necessary training and background to readily understand them. Further, scientists and nonscientists alike may struggle to convert these metrics into a currency that directly affects day-to-day life. Climate science is a complex issue, and we argue that when communicating potential responses of vegetation, fish, and wildlife to nonscientists, creative thinking with respect to the currency of communication will facilitate discussions between scientists, policy makers, and the public. We posit that with some additional thought and relatively simple summaries, the responses of fish and other species to climate change can be translated into everyday language that will facilitate climate science communication. Although such translations are rare, one example of this type of creativity is the translation from changes in habitat suitability for tree species to potential reductions in maple syrup production (West over 2012), which is arguably more interesting and understandable for the general public. Similar translations could be especially important for communicating climate change effects on game fish and other species that are socially and economically important to large groups of people. We demonstrate this translation by communicating the potential effects of climate change on the distribution of a coldwater fish species, the eastern Brook Trout Salvelinus fontinalis . Rather than communicating the potential forecasted contraction of the Brook Trout's distribution in terms of habitat loss, we report the predicted increases in the driving distance to streams likely offering Brook Trout angling opportunities under a climate change scenario. Travel costs based on distance have been widely used to value ecosystem services such as angling under climate change scenarios (e.g., Pendleton and Mendelsohn 1998; Mendelsohn and Markowski 1999; Ahn et al. 2000) but, to the best of our knowledge, have not been used for communicating potential changes to the public despite the intrinsic link to everyday life.
New York, Pennsylvania↗
Bioavailability and toxicity models of copper to freshwater life: The state of regulatory science
Efforts to incorporate bioavailability adjustments into regulatory water quality criteria in the United States have included four major procedures: hardness-based single-linear regression equations, water-effect ratios (WERs), biotic ligand models (BLMs), and multiple-linear regression models (MLRs) that use dissolved organic carbon, hardness, and pH. The performance of each with copper (Cu) is evaluated, emphasizing the relative performance of hardness-based versus MLR-based criteria equations. The WER approach was shown to be inherently highly biased. The hardness-based model is in widest use, and the MLR approach is the US Environmental Protection Agency's (USEPA's) present recommended approach for developing aquatic life criteria for metals. The performance of criteria versions was evaluated with numerous toxicity datasets that were independent of those used to develop the MLR models, including olfactory and behavioral toxicity, and field and ecosystem studies. Within the range of water conditions used to develop the Cu MLR criteria equations, the MLR performed well in terms of predicting toxicity and protecting sensitive species and ecosystems. In soft waters, the MLR outperformed both the BLM and hardness models. In atypical waters with pH <5.5 or >9, neither the MLR nor BLM predictions were reliable, suggesting that site-specific testing would be needed to determine reliable Cu criteria for such settings. The hardness-based criteria performed poorly with all toxicity datasets, showing no or weak ability to predict observed toxicity. In natural waters, MLR and BLM criteria versions were strongly correlated. In contrast, the hardness-criteria version was often out of phase with the MLR and, depending on waterbody and season, could be either strongly overprotective or underprotective. The MLR-based USEPA-style chronic criterion appears to be more generally protective of ecosystems than other models.
Environmental Toxicology and Chemistry↗
Hepatic microsomal N-oxidation and N-demethylation of N,N-dimethylaniline in red-winged blackbird compared with rat and other birds
Hepatic microsomes prepared from red-winged blackbirds and albino rats were incubated with N,N-dimethylaniline (DMA)_in complete incubation mixtures at pH 7.9 and 37?C for 10 min. Formaldehyde and N,N-dimethylaniline--oxide produced from DMA were measured. Redwings were found to have significantly lower N-demethylation activities than rats, and redwings had only marginal or no N-oxidation activities. Hepatic microsomes from redwings did not further metabolize the N-oxide. The N-oxidation and N-demethylation activities of brown-headed cowbirds, common grackles, and starlings were similar to those of redwings.
Life Sciences↗
The hormonal control of osmoregulation in teleost fish
Hormones are critical to the physiological alterations necessary for ion homeostasis when fish move between freshwater and seawater. Cortisol promotes seawater acclimation through differentiation of salt-secreting mitochondrion-rich cells and ion transport proteins in the gill. The growth hormone/insulin-like growth factor I axis is also important in seawater acclimation and acts in synergy with cortisol. Prolactin (PRL) is important in freshwater acclimation through regulation of ion and water permeability in the gill, gut, and kidney. Cortisol also promotes ion uptake and may interact with PRL during freshwater acclimation. For many species of fish, growth hormone promotes acclimation to seawater, PRL promotes acclimation to freshwater, and cortisol interacts with both hormones, thus having a dual osmoregulatory function.
Life Sciences↗
Quantification of 15 bile acids in lake charr feces by ultra-high performance liquid chromatography–tandem mass spectrometry
Many fishes are hypothesized to use bile acids (BAs) as chemical cues, yet quantification of BAs in biological samples and the required methods remain limited. Here, we present an UHPLC–MS/MS method for simultaneous, sensitive, and rapid quantification of 15 BAs, including free, taurine, and glycine conjugated BAs, and application of the method to fecal samples from lake charr ( Salvelinus namaycush ). The analytes were separated on a C 18 column with acetonitrile–water (containing 7.5 mM ammonium acetate and 0.1% formic acid) as mobile phase at a flow rate of 0.25 mL/min for 12 min. BAs were monitored with a negative electrospray triple quadrupole mass spectrometer (Xevo TQ-S™). Calibration curves of 15 BAs were linear over the concentration range of 1.00–5,000 ng/mL. Validation revealed that the method was specific, accurate, and precise. The method was applied to quantitative analysis of feces extract of fry lake charr and the food they were eating. The concentrations of analytes CA, TCDCA, TCA, and CDCA were 242.3, 81.2, 60.7, and 36.2 ng/mg, respectively. However, other taurine conjugated BAs, TUDCA, TDCA, and THDCA, were not detected in feces of lake charr. Interestingly, TCA and TCDCA were detected at high concentrations in food pellets, at 71.9 and 38.2 ng/mg, respectively. Application of the method to feces samples from lake charr supported a role of BAs as chemical cues, and will enhance further investigation of BAs as chemical cues in other fish species.
Journal of Chromatography B: Analytical Technologi↗
Liquid chromatographic determination of florfenicol in the plasma of multiple species of fish
A simple method was developed for determining florfenicol concentration in a small volume (250 μl) of plasma from five phylogenetically diverse species of freshwater fish. Florfenicol was isolated from the plasma matrix through C 18 solid-phase extraction and quantified by reversed-phase high-performance liquid chromatography with UV detection. The accuracy (84–104%), precision (%RSD⩽8), and sensitivity (quantitation limit <30 ng/ml) of the method indicate its usefulness for conducting pharmacokinetic studies on a variety of freshwater fish.
Journal of Chromatography B: Analytical Technologi↗
Arsenite as an electron donor for anoxygenic photosynthesis: Description of three strains of Ectothiorhodospria from Mono Lake, California, and Big Soda Lake, Nevada
Three novel strains of photosynthetic bacteria from the family Ectothiorhodospiraceae were isolated from soda lakes of the Great Basin Desert, USA by employing arsenite (As(III)) as the sole electron donor in the enrichment/isolation process. Strain PHS-1 was previously isolated from a hot spring in Mono Lake, while strain MLW-1 was obtained from Mono Lake sediment, and strain BSL-9 was isolated from Big Soda Lake. Strains PHS-1, MLW-1, and BSL-9 were all capable of As(III)-dependent growth via anoxygenic photosynthesis and contained homologs of arxA, but displayed different phenotypes. Comparisons were made with three related species: Ectothiorhodospira shaposhnikovii DSM 2111, Ectothiorhodospira shaposhnikovii DSM 243 T , and Halorhodospira halophila DSM 244. All three type cultures oxidized arsenite to arsenate but did not grow with As(III) as the sole electron donor. DNA–DNA hybridization indicated that strain PHS-1 belongs to the same species as Ect. shaposhnikovii DSM 2111 (81.1% sequence similarity), distinct from Ect. shaposhnikovii DSM 243 T (58.1% sequence similarity). These results suggest that the capacity for light-driven As(III) oxidation is a common phenomenon among purple photosynthetic bacteria in soda lakes. However, the use of As(III) as a sole electron donor to sustain growth via anoxygenic photosynthesis is confined to novel isolates that were screened for by this selective cultivation criterion.
Life Sciences↗