bluuebunny/crossref_metadata_2025 huggingface dataset:
XML Essence Testing
Authors: Becker Abraham , Beck Jeff
Published: July 2010

SYNOPSIS:
PubMed Central (PMC) is the U.S. National Institutes of Health free digital archive, gathering together biomedical and life sciences journal literature from diverse sources. When an article arrives at PMC, it conforms to one of over 40 evolving DTDs. An ingestion process applies appropriate "Modified Local" and "Production" XSLT style sheets to produce two instances of the common NLM Archiving and Interchange DTD. In the "Essence Testing" phase, the essential nodes of these XML instances, as specified by some 60 XPath expressions, are compared. This method allows the reliable detection of unintentional changes to an XSLT style sheet that can have negative impacts on product quality.

OBJECTIVE: Create an easy-to-use tool that allows tracking, reporting, and qualitative analysis to monitor the effects of changes to existing XSLT style sheets on the content of XML articles. The tool should have the ability to look beyond differences in the XML structures of those articles, focusing on essential data and its semantics (the document’s Essence).

RESULTS: A Guided User Interface was created using CGI, which invokes 2 PERL scripts (sampler [SQL, UNIX], and converter [Saxon 9.1.0.5J]). A test and a control NXML document are created. The Essence is extracted from those documents using XPath expressions, and a JAVA program compares and formulates a report of the differences in the Essence documents.

SIGNIFICANCE: Quality control reports on XSLT style sheets are now run on a weekly basis, or any time significant changes are made to the XSLT style sheets. The level of control and the granularity of tracking has increased, and has had a very positive effect on quality of the XML output.
I say XSLT, you say XQuery: let's call the whole thing off
Authors: Birnbaum David J.
Published: July 2010

XSLT and XQuery can both be used for extracting information from XML resources and transforming it for presentation in a different form. The same task can be performed entirely with XSLT, entirely with XQuery, or using a combination of the two, and there seems to be no general consensus or guidelines concerning best practice for choosing among the available approaches. The author solved a specific problem initially (and satisfactorily) with XSLT because XQuery was not a sufficiently mature technology at the time the task first arose, but years later began to suspect that XQuery might be, in some ineffable way, a better fit than XSLT for the data and the task. Both the exclusively XSLT approach and the exclusively XQuery approach were comparable in functionality, efficiency, ease of development, and ease of maintenance, and they also shared (of course) an XPath addressing component, but they were nonetheless profoundly different in the way they interacted with the same source XML files. The goal of this presentation is to consider why one or the other technology may be a better fit for a particular combination of data and task, and to suggest guidelines for making decisions of that sort.
On Implementing string-range() for TEI
Authors: Cayless Hugh A. , Soroka Adam
Published: July 2010

The Text Encoding Initiative Guidelines specify a number of pointer schemes for use in implementing standoff markup. This paper reports on an implementation of one of these pointer schemes, string-range(), and discusses the issues surrounding standoff markup in the context of TEI.
Processing Arbitrarily Large XML using a Persistent DOM
Authors: Probst Martin
Published: July 2010

As the adoption of XML reaches more and more application domains, data sizes increase, and efficient XML handling gets more and more important. Many applications face scalability problems due to the overhead of XML parsing, the difficulty of effectively finding particular XML nodes, or the sheer size of XML documents, which nowadays can easily exceed gigabytes of data.

In particular the latter issue can make certain tasks seemingly impossible to handle, as many applications depend on parsing XML documents completely into a Document Object Model (DOM) memory structure. Parsing XML into a DOM typically requires close to or even more memory as the serialized XML would consume, thus making it prohibitively expensive to handle XML documents in the gigabyte range. Recent research and development suggests that it is possible to modify these applications to run a wide range of tasks in a streaming fashion, thus limiting the memory consumption of individual applications. However this requires not only changes in the underlying tools, but often also in user code, such as XSLT style sheets. These required changes can often be unintuitive and complicate user code.

A different approach is to run applications against an efficient, persistent, hard-disk backed DOM implementation that does not require entire documents to be in memory at a time. This talk will discuss such a DOM implementation, EMC's xDB, showing how to use binary XML and efficient backend structures to provide a standards compliant, non-memory-backed, transactional DOM implementation, with little overhead compared to regular memory-based DOMs. It will also give performance comparisons and show how to run existing applications transparently against xDB's DOM implementation, using XSLT stylesheets as an example.
Direct measurement of diffusivity within diatom aggregates containing transparent exopolymer particles
Authors: Ploug Helle , Passow Uta
Published: July 2010

We present the first direct measurements of apparent diffusivity within diatom aggregates using a diffusivity microsensor. Transparent exopolymer particles (TEP) and aggregate dry mass (TEP and cells) were determined in the same aggregates after diffusivity measurements. Carbon in TEP comprised 8‐12% of aggregate dry mass. The (wet) volume fraction of TEP in aggregates, however, was on average 7.2‐fold larger than that of cells, and it decreased with increasing aggregate size similar to that of cells. The exchangeable pore‐water content occupied 87‐98% of the aggregate volume. The average apparent diffusivities of gases within aggregates ranged between 0.90 and 0.95 times the free diffusion coefficient in seawater. Using a diffusion‐reaction model, we analyzed silicic acid concentrations within marine snow. An apparent diffusivity of silicic acid within marine snow being 0.9 times its free diffusion coefficient in seawater, and a specific net silica dissolution rate of 0.002 h21 could explain the observation that concentrations of silicic acid are significantly higher within marine snow compared to that of the ambient water.
Efficiency of a phytoplankton‐based and a bacterial‐based food web in a pelagic marine system
Authors: Berglund Johnny , Müren Umut , Båmstedt Ulf , Andersson Agneta
Published: July 2010

The food web efficiency in two contrasting food webs, one phytoplankton based and one bacteria based, was studied in a mesocosm experiment using seawater from the northern Baltic Sea. Organisms included in the experiment were bacteria, phytoplankton, protozoa, and mesozooplankton (copepods). A phytoplankton‐based food web was generated by incubating at a high light level with the addition of nitrogen and phosphorus (NP). A bacteria‐based food web was created by adding carbon, nitrogen, and phosphorus (CNP) and incubating at a lower light level. In the CNP treatment bacteria dominated the productivity (91%), while in the NP treatment phytoplankton were dominant producers (74%). The phytoplankton community in the NP treatment was dominated by autotrophic nanoflagellates. The food web efficiency, defined as mesozooplankton productivity per basal productivity (phytoplankton + bacteria), was 22% in the phytoplankton‐based food web and 2% in the bacteria‐based food web. This discrepancy could be explained by 1‐2 extra trophic levels in the bacteria‐based food web where carbon passed through flagellates and ciliates before reaching mesozooplankton, while in the phytoplankton‐based food web there was a direct pathway from phytoplankton to mesozooplankton. The results were supported by stable isotope analysis of mesozooplankton. We propose that climate change, with increased precipitation and river runoff in the Baltic Sea, might favor a bacteria‐based food web and thereby reduce pelagic productivity at higher trophic levels.
Photochemically produced bioavailable nitrogen from biologically recalcitrant dissolved organic matter stimulates production of a nitrogen‐limited microbial food web in the Baltic Sea
Authors: Vähätalo Anssi V. , Järvinen Marko
Published: July 2010

Experiments were designed to assess whether the photochemical production of bioavailable nitrogen (N) from biologically recalcitrant dissolved organic nitrogen (DON) stimulates growth of N‐limited plankton. Filtered Baltic Sea water was exposed to solar radiation for 12‐19 days. Along with dark controls, samples were inoculated with an indigenous nanoplankton (<10 µm) community and incubated under photosynthetically active radiation and N‐limiting conditions (molar dissolved inorganic nitrogen to PO43‐ ratio of 0.2). The concentration of particulate nitrogen, chlorophyll a (Chl a), and the biomass of phytoplankton and protozoa increased more in the solar radiation‐exposed waters than in dark controls, showing that the photochemical transformation of dissolved organic matter (DOM) supported both heterotrophic and autotrophic plankton. In order to calculate the apparent quantum yield (AQY) for the photochemical reactions, the experimentally determined photoproduced bioavailable N (the formed particulate N and mineralized DON) and the phytoplankton biomass stimulated by DOM photochemistry were related to the number of photons absorbed by chromophoric DOM. Model calculations based on AQY indicated that DOM photochemistry produces 22‐ 26 µmol bioavailable N m‐2 d‐1 and stimulates phytoplankton biomass by 12‐14 µg Chl a m‐2 d‐1 during summer in the northern Baltic Sea. Photoproduced bioavailable N potentially supports 1.2% and 3.6% of the new primary production and its N‐demand, respectively, in this study region during summer. In N‐limited surface waters, the photoproduction of bioavailable N from biologically recalcitrant, but photoreactive DOM can provide a new source of N and sustain the background productivity of a nanoplankton community, including phytoplankton.
Experiments linking nitrogenase gene expression to nitrogen fixation in the North Pacific subtropical gyre
Authors: Zehr Jonathan P. , Montoya Joseph P. , Jenkins Bethany D. , Hewson Ian , Mondragon Elizabeth , Short Cindy M. , Church Matthew J. , Hansen Andrew , Karl David M.
Published: July 2010

We examined diazotroph activity in controlled experiments containing natural populations of nitrogen (N2)‐fixing microbes collected offshore from Kane'ohe Bay, Hawai'i, and from Station ALOHA (A Long‐term Oligotrophic Habitat Assessment) in the North Pacific subtropical gyre. Quantitative polymerase chain reaction and reverse transcription‐polymerase chain reaction approaches showed that the abundances of the major phylotypes did not change substantially during experimental incubations. Diel phasing of nifH gene expression in the experiments was similar to that documented for natural populations. Cell‐specific N2 fixation rates, calculated as 15N2 incorporation rate divided by specific phylotype abundance (gene copy number), varied between the experiments, but generally agreed with the abundance and levels of nifH expression of each group of diazotrophs. Phosphorus additions had little effect on the abundance, gene expression, or N2 fixation activity of diazotrophs across the course of the 36‐h experiments, indicating that other factors may limit the growth, gene expression, and activity of diazotrophs in the North Pacific subtropical gyre.
Direct determination of total and fresh groundwater discharge and nutrient loads from a sandy beachface at low tide (Cape Henlopen, Delaware)
Authors: Hays Rebecca L. , Ullman William J.
Published: July 2010

Total groundwater discharge from a sandy seepage site to the Delaware Bay at Cape Henlopen, Delaware, was determined together with the associated nutrient loads by trapping the discharge from a length of the shoreline in a tidal pond at low tide and measuring the discharge of the trapped water through a weir at steady state. Salinity was used to parse the total groundwater discharge from the beachface at low tide into a “recycled” estuarine component and a “new” fresh groundwater component. Based on 16 measurements over 18 months, average total discharge and average freshwater discharge at low tide were found to be 2.76 ± 1.08 and 0.87 ± 0.43 L min−1 m−1 of shoreline, respectively. The estuarine component of discharge varied with the maximum height of the immediately preceding high tide. Owing to the control of freshwater discharge by the average upland hydraulic gradient away from the beach, individual measurements of freshwater discharge at low tide represent a good estimate of this discharge component over time scales of hours to days. Based on the nutrient concentrations in the discharge waters, nutrient loads from the beach to the adjacent estuary at low tide were 148 ± 79, 7.5 ± 5.1, and 197 ± 101 µmol min−1 m−1 of shoreline for total dissolved N, P, and Si, respectively. Groundwater discharge and these nutrient fluxes contribute significantly to the unusually productive benthic communities that inhabit the seepage and nearby intertidal zones.
Interannual dynamics and phenology of bacterial communities in a eutrophic lake
Authors: Shade Ashley , Kent Angela D. , Jones Stuart E. , Newton Ryan J. , Triplett Eric W. , McMahon Katherine D.
Published: July 2010

We investigated patterns of intra‐ and interannual change in pelagic bacterial community composition (BCC, assessed using automated ribosomal intergenic spacer analysis) over six years in eutrophic Lake Mendota, Wisconsin. A regular phenology was repeated across years, implying that freshwater bacterial communities are more predictable in their dynamics than previously thought. Seasonal events, such as water column mixing and trends in water temperature, were most strongly related to BCC variation. Communities became progressively less similar across years between the months of May and September, when the lake was thermally stratified. Dissolved oxygen and nitrate + nitrite concentrations were highly correlated to BCC change within and across seasons. The relationship between BCC and seasonal drivers suggests that trajectories of community change observed over long time series will reflect large‐scale climate variation.
Standing stocks and activity of Archaea and Bacteria in the western Arctic Ocean
Authors: Kirchman David L. , Elifantz Hila , Dittel Ana I. , Malmstrom Rex R. , Cottrell Matthew T.
Published: July 2010

This study examined the abundance, cell size, and activity of Bacteria and Archaea in the Chukchi Sea and the Canada Basin of the western Arctic Ocean in the spring (May—June) and summer (July—August) of 2002 and 2004. Data from fluorescence in situ hybridization (FISH) analyses indicate that bacterial abundance as a percent of total prokaryotes decreased with depth, whereas in contrast, Crenarchaeota increased from about 10%of prokaryotes in surface waters to as much as 40% in samples from 100 to 200 m. Euryarchaeota were detectable in only a few samples. Relative abundance of Crenarchaeota, expressed as a percent of total prokaryotes, correlated with ammonium concentrations, but relative bacterial abundance did not. Crenarchaeota cells were significantly larger than Bacteria by 1.5‐ to 2‐fold in the upper 200 m. Data collected from a combination of FISH and microautoradiography indicate that often the fraction of both Bacteria and Crenarchaeota assimilating organic compounds was high (up to 55%), and both microbial groups were more active in assimilating amino acids than other compounds. However, Crenarchaeota were usually less active than Bacteria in assimilating amino acids and glucose, but were nearly as active as Bacteria in assimilating protein and diatom extracellular polymers. The fraction of Bacteria and Crenarchaeota assimilating CO2 in surface waters was higher than expected by anaplerotic fixation alone, suggesting that many of these microbes are chemoautotrophic. These data add to a growing body of evidence indicating how the roles of Archaea and Bacteria differ in biogeochemical cycles of the oceans.
Viral infection plays a key role in extracellular DNA dynamics in marine anoxic systems
Authors: Corinaldesi Cinzia , Dell'Anno Antonio , Danovaro Roberto
Published: July 2010

To investigate the role of viruses in extracellular DNA production through cell lysis, we selected two systems where viruses are expected to be the main component controlling prokaryote dynamics. These systems include anoxic subsuperficial coastal sediments and water and sediments of two deep‐hypersaline anoxic basins (i.e., DHABs) of the eastern Mediterranean. Viral production was high in both places. Viruses were responsible for 10–60% of prokaryote mortality in anoxic sediments and up to 100% in deep‐anoxic waters. The daily contribution of DNA released by viral lysis to the total extracellular DNA pool was 2–11% in anoxic sediments and more than 100% in the brines of both deep‐sea basins. Extracellular DNA released by viral infection was rapidly degraded by deoxyribonucleases (DNases), which were also high in permanently anoxic conditions. Overall, our data suggest that DNA released by viral lysis, because of its high lability and fast turnover, may represent an important mechanism of trophic supply for prokaryotes, particularly in systems characterized by limited availability of external trophic sources.
Effect of the diffusive boundary layer on benthic mineralization and O2 distribution: A theoretical model analysis
Authors: Glud Ronnie N. , Berg Peter , Fossing Henrik , Jørgensen Bo B.
Published: July 2010

On the basis of a dynamic diagenetic model, we evaluate and discuss the effect of the diffusive boundary layer (DBL) on benthic O2 exchange and O2 consuming pathways. The analysis documents that the DBL has only minor importance for the annual O2 uptake of coastal cohesive sediments. Imposing static DBL thicknesses of 300‐900 mm decreased the annual O2 uptake by only 2–10% in comparison to a situation without any DBL. Lower O2 availability as imposed by a thicker DBL, however, markedly reduced the aerobic heterotrophic respiration but enhanced aerobic reoxidation of solutes released by the stimulated anaerobic respiration. The 2–10% decrease in the annual O2 uptake was caused mainly by higher benthic release rates of NH4+ and Mn2+. The overall carbon degradation rate—and thus the carbon preservation—remained unaffected by the DBL thickness. Dynamic modeling revealed that abrupt changes in the DBL thickness caused an instantaneous change in the interstitial O2 distribution and in the benthic O2 uptake rate. However, conditions quickly reversed as the porewater profiles of reduced solutes and distribution of reduced solids readjusted even though full steady state was obtained only after several months. In nature the DBL is constantly changing, and thus in situ O2 microprofiles are transient by nature. Dynamic modeling showed that the benthic O2 concentration and the O2 uptake in Aarhus Bay could vary by 30% or more on time scales of a few hours or days solely because of changes in the DBL thickness. The integrated annual O2 uptake remained unaffected by these fluctuations.
Biodiversity and food web structure influence short‐term accumulation of sediment organic matter in an experimental seagrass system
Authors: Canuel Elizabeth A. , Spivak Amanda C. , Waterson Elizabeth J. , Emmett Duffy J.
Published: July 2010

We tested the effects of grazer diversity and food chain length on the quantity and quality of accumulated sediment organic matter (SOM) in experimental eelgrass (Zostera marina) mesocosms. By use of a factorial manipulation of crustacean grazer species richness and predator presence, we examined the effects of epibenthic consumers on SOM composition by using stable carbon isotopes (δ13C) and lipid biomarker compounds. Grazer species composition strongly influenced nearly all measures of SOM quantity and quality. In particular, increased densities of the grazing amphipod, Gammarus mucronatus, decreased accumulation of benthic microalgae (chlorophyll a) and the relative abundance of polyunsaturated fatty acids (FA, a proxy for labile algal organic matter) and branched FA (a proxy for bacterial biomass). On average, increasing grazer species richness decreased SOM quantity (percentage of total organic carbon). Increasing food chain length by addition of predatory blue crabs (Callinectes sapidus) resulted in a trophic cascade, increasing algal biomass and accumulation of algal organic matter in sediments, and enhancing the quality of SOM. Concomitantly, the relative proportion of bacterial branched FA increased. The identity and number of epibenthic consumers strongly influence accumulation and composition of SOM and the pathways by which it is processed, and these responses are not easily predictable from bulk measurements (δ13C, percentage of total organic carbon) alone.
Scaling of feeding in marine calanoid copepods
Authors: Saiz Enric , Calbet Albert
Published: July 2010

We describe patterns of body size scaling of feeding by marine calanoid copepods based on a literature review. Maximum feeding rates of calanoid copepods, determined in the laboratory, were temperature independent and scaled in conformity to the three‐quarters universal law followed by animals. Field feeding rates (log transformed) of marine calanoid copepods were dependent on food availability, temperature, and body size, and in combination, these three variables explained 81% of the variance. The scaling to body mass for field data, however, showed a much lower slope, indicating severe food limitation in the larger copepods. The direct effects of temperature in field feeding rates were difficult to ascertain because of the inherent association between body size, temperature, and trophic level in natural ecosystems.
Periodicity in the accumulation of gelatinous zooplankton during the summer season in the coastal area of Iyo‐Nada, Japan
Authors: Kaneda Atsushi , Kohama Takeshi , Kawamura Yuji , Takeoka Hidetaka
Published: July 2010

Gelatinous zooplankton collected and quantified daily at the sluice gate of the Ikata Nuclear Power Station along the coast of Iyo‐Nada in the Seto Inland Sea were analyzed for the period 1998‐2004 in an effort to correlate the number of these animals with the physical oceanographic conditions. Sudden periodic and nonperiodic increases of gelatinous zooplankton occur repeatedly from early summer to late autumn in nearshore areas. Periodic increases are synchronous with the spring tidal period. Nearshore tide‐induced eddy development may play an important role for the aggregation process of gelatinous zooplankton, and the spring‐neap tidal variation of the circulation induces increases of the gelatinous zooplankton population in coastal waters of the Iyo‐Nada. Nonperiodic increases are attributable to typhoons and other storms. The strong shoreward currents due to the winds caused by these events transport gelatinous zooplankton to nearshore areas.
Bio‐optical consequences of viral infection of phytoplankton: I. Experiments with the cyanobacterium, Synechococcus sp.
Authors: Balch W. M. , Vaughn J. M. , Goes J. I. , Novotny J. F. , Drapeau D. T. , Booth E. S. , Vining C. L.
Published: July 2010

Four strains of the cyanobacteria, Synechococcus, were infected with viruses isolated and purified from coastal waters of the Gulf of Maine. Changes in host and virus concentration were observed in time course experiments, along with associated variability in inherent optical properties. There were strong optical shifts before and after lysis in inherent optical properties on time scales commensurate with the viral infection process. Specifically, both backscattering and absorption (particularly in visible wavelengths) increased slightly after infection, but decreased markedly after lysis. The most rapid optical change was seen in in vivo chlorophyll fluorescence, with a slight increase within 2 d after initial infection. Such changes likely reflect fundamental changes in host photophysiology after infection. After host lysis, there was a major drop in bulk Chl a fluorescence, synchronous with a major increase in the ratio of free viruses per host cell. The net effect of the changes in fluorescence and host concentration was an increase in the fluorescence per cell. These optical changes were accompanied by major changes in the submicron particle size spectra as cells were lysed, releasing their intracellular contents.
Investigation of the optical backscattering to scattering ratio of marine particles in relation to their biogeochemical composition in the eastern English Channel and southern North Sea
Authors: Loisel Hubert , Mériaux Xavier , Berthon Jean-François , Poteau Antoine
Published: July 2010

The variability of the backscattering to scattering ratio of marine particles, bbp : bp, is examined from in situ measurements performed during the spring and early summer of 2004 in the eastern English Channel and southern North Sea. This area is characterized by a quasi‐permanent background of mineral matter from direct inputs, or resuspension effects, and by relatively intense spring phytoplankton blooms (mainly diatoms and the prymnesiophyte Phaeocystis globosa). The bbp : bp surface values range between 0.0024 and 0.0417, with a mean value of 0.0138 ± 0.0083. In order to interpret such a great variability, simultaneous water samples were collected for the biogeochemical characterization of the bulk suspended particle population. We show that the bbp : bp variability is related to the composition of the particulate assemblage expressed by Chl a, the POC:SPM and POC: Chl a ratios, where Chl a, POC, and SPM are the concentrations of chlorophyll a, particulate organic carbon, and suspended particulate matter, respectively. Low bbp : bp values are observed for a particle population dominated by low refractive index material such as phytoplankton, whereas high bbp : bp values are generally observed in presence of relatively high concentration of inorganic particles. The amount of organic material (both living and nonliving, including phytoplankton) relative to phytoplankton has a strong (and sometimes the greatest) effect on the backscattering‐to‐scattering ratio. Assuming that phytoplankton and detritus have similar refractive index, this pattern is interpreted as resulting from changes in the particle size distribution as well as by aggregation of mineral and nonliving organic detrital material.
Dissolved iron speciation in two distinct river plumes and an estuary: Implications for riverine iron supply
Authors: Buck Kristen N. , Lohan Maeve C. , Berger Carolyn J. M. , Bruland Kenneth W.
Published: July 2010

Dissolved iron (Fe) speciation in the Columbia River plume, the San Francisco Bay plume, and the Columbia River estuary was investigated using competitive ligand exchange‐adsorptive cathodic stripping voltammetry (CLE‐ACSV) with the added ligand salicylaldoxime. A stronger L1‐type Fe‐binding ligand class was measured in all surface samples, and in the Columbia River estuary. A weaker L2‐type ligand class was present in the far‐field Columbia River plume and the San Francisco Bay plume but was not observed in the low‐salinity (S = 1.4‐22.5) waters of the near‐field Columbia River plume or estuary. Concentrations of total dissolved Fe were correlated with the concentrations of the stronger L1‐type ligand in nonestuarine (S > 13) surface samples. Leachable particulate (>0.4 µm) Fe concentrations in the Columbia River plume were measured to supplement existing data from the San Francisco Bay plume. There is a large concentration of readily leachable particulate Fe in the two plumes, yet it is the concentration of ambient L1‐type ligands that appears to dictate the concentration of dissolved Fe in these waters and, consequently, the supply of dissolved Fe to neighboring coastal waters. The correlation between dissolved Fe and L1 ligand concentrations in both plume waters, as well as in California Current and upwelled surface waters, suggests that this relationship will persist in other coastal environments and should be considered when evaluating and modeling coastal Fe cycling and supply.
Chemical warfare on coral reefs: Sponge metabolites differentially affect coral symbiosis in situ
Authors: Pawlik Joseph R. , Steindler Laura , Henkel Timothy P. , Beer Sven , Ilan Micha
Published: July 2010

Coral reef ecosystems are characterized by high species diversity and intense levels of biotic interaction, particularly competition for space among sessile benthic invertebrates. Using in situ pulse amplitude modulated fluorometry, we demonstrate that secondary metabolites present in the tissues of some Caribbean sponge species have rapid allelopathic effects on the symbiotic algae (zooxanthellae) that live in coral tissues and provide the energy for coral growth and reef formation. When incorporated into stable gels at natural concentrations and placed in contact with brain coral heads on shallow reefs for ~18 h, secondary metabolites of some sponge species caused a decrease in the photosynthetic potential of the symbiotic algae and bleaching of the coral tissue, whereas those of others interfered with algal photosynthesis without causing bleaching. Some sponges produce metabolites with different modes of action for competing with reef corals.
Isotopic heterogeneity and cycling of organic nitrogen in the oligotrophic ocean
Authors: Meador T. B. , Aluwihare L. I. , Mahaffey C.
Published: July 2010

We measured the nitrogen (N) isotopic composition (δ15N) of a large set (n = 38) of high‐molecular‐weight (HMW) dissolved organic nitrogen (DON) samples isolated from the tropical and subtropical North Atlantic and Pacific Oceans. The δ15N signature of surface HMW DON is relatively invariable in both oligotrophic basins (4.1 ± 0.6‰ in the Atlantic; 5.4 ± 0.8‰ in the Pacific) and shows little correlation with sources or concentrations of N supporting new production in the euphotic zone. While large variations in δ15N of bulk HMW DON are not apparent, δ15N of proteins isolated from sites with relatively high rates of N2 fixation (>80 µmol N m−2 d−1) were consistently depleted in 15N relative to bulk HMW DON and to proteins isolated from sites where N2 fixation does not routinely occur. This small component of HMW DON appears to be cycling more rapidly than bulk HMW DON and may be indicative of fresh DON contributed by organisms in the surface ocean. Furthermore, δ15N of DNA extracted from the bacterial size fraction (0.2‐0.5 µm) revealed that free‐living bacteria may be an important sink for isotopically depleted N produced during N2 fixation. We suggest that there exists a tight coupling between the production and uptake of DON contributed by diazotrophs (N2 fixers) in regions where N2 fixation provides a major input of new nitrogen.
Nutrient quality drives differential phytoplankton community composition on the southwest Florida shelf
Authors: Heil Cynthia A. , Revilla Marta , Glibert Patricia M. , Murasko Sue
Published: July 2010

During May 2003, the dry season, the southwest Florida shelf was surveyed for nutrient concentrations and phytoplankton community composition concurrently with plankton nutritional and physiological status (tracer techniques, enzyme assay, and biomass response bioassays). Inorganic nitrogen concentrations were low throughout the region, while dissolved organic nitrogen (DON) was elevated (>30 µmol N L−1) nearshore. Conversely, PO43‐ and dissolved organic phosphorus concentrations were high only in northern coastal areas adjacent to estuarine outflows. Nitrogen : phosphorus (N : P) ratios in the particulate material; gradients in NO3− and urea uptake rates; urease and alkaline phosphatase activities; and bioassay responses were indicative of a strong gradient from N to P limitation of plankton biomass from north to south. Nitrogen limitation was apparent in the northern region (N : Pparticulate < 8, Tampa to Sanibel), where PO43‐ and DON inputs dominated; balanced nutrient conditions were evident in the mid‐region (N : Pparticulate = 8−24, Sanibel to Shark River); and P limitation was evident south of the Shark River (N : Pparticulate > 24), where inorganic N input was greatest. Phytoplankton community composition varied along the same gradient, from a cyanobacteria and dinoflagellate community in the north, to a cyanobacteria‐dominated community in the mid‐region, and to a diatom community in the southern region. Percentages of NO3− uptake and diatoms in the total phytoplankton community were positively related, as were percentages of urea uptake and cyanobacteria. Inorganic and organic N and P fractions in the nearshore shelf region reflect longitudinal gradients in regional watershed characteristics, and their relative availability thus appeared to control both phytoplankton community composition and its physiological status.
Influence of the diversion of Bear River into Bear Lake (Utah and Idaho) on the environment of deposition of carbonate minerals
Authors: Dean Walter E. , Forester Richard M. , Bright Jordon , Anderson Roger Y.
Published: July 2010

Bear River, the largest river in the Great Basin, had some of its flow diverted into Bear Lake through a series of canals constructed between 1911 and 1918, turning Bear Lake into a reservoir. The prediversion lake had an unusually high Mg2+:Ca2+ ratio (38 by weight), which resulted in precipitation of CaCO3 as aragonite. The amount and mineralogy of the carbonate did not change immediately after the diversion, but during the middle of the 20th century, high‐Mg calcite began to precipitate. In contrast, at the time of diversion there were very distinct changes in the isotopic composition of the carbonate that clearly define the time of diversion within the sediments. Sedimenttrap studies show that the CaCO3 polymorph that precipitates in the epilimnion of the lake today is high‐Mg calcite. Samples in sediment traps placed 2 m above the bottom of the lake in 45 m of water (bottom traps) contain predominantly aragonite and quartz, with lesser amounts of high‐Mg and low‐Mg calcite and dolomite. Isotopic evidence from the sediments shows that the aragonite that accumulated in the bottom sediment traps and that constitutes the bulk of postdiversion sediments is reworked and redistributed from shallow sites to deep sites.
Effects of turbulence‐mediated larval behavior on larval supply and settlement in tidal currents
Authors: Fuchs Heidi L. , Neubert Michael G. , Mullineaux Lauren S.
Published: July 2010

Intertidal gastropod larvae retract their vela and sink in strong turbulence, and this behavior potentially increases settlement in turbulent coastal habitats. We incorporated turbulence‐induced sinking behavior of mud snail larvae (Ilyanassa obsoleta) in a vertical advection‐diffusion model to characterize behavioral effects on larval supply and settlement in a tidal channel. Throughout flood and ebb tides, larvae that sink in turbulence have higher near‐bed concentrations than passive larvae. This high supply of larvae enables behaving larvae to settle more successfully than passive larvae in strong currents characteristic of tidal inlets. Unlike passive larvae, those that sink in turbulence settle more successfully in stronger currents than in weaker ones and would concentrate their settlement in energetic tidal zones. Turbulence‐mediated behavior may give intertidal larvae a greater ability to select habitats and may reduce larval mortality rates due to settlement failure.
Diel heat transport within the hyporheic zone of a pool‐riffle‐pool sequence of a losing stream and evaluation of models for fluid flux estimation using heat
Authors: Swanson Travis E. , Cardenas M. Bayani
Published: July 2010

Hyporheic water is thought to infiltrate at the head of a riffle, which in turn is complemented by upwelling back to the stream at the tail of the riffle in a pool‐riffle‐pool (PRP) sequence. Heat tracing is a potentially useful method to characterize these hyporheic flow paths and quantify associated fluxes. Temperature was monitored within a PRP sequence for several days. Temperature in the hyporheic zone reflected the diel temperature change in the river but not uniformly. The observed thermal pattern exhibited deeper penetration of thermal oscillations below the head pool and shallower penetration below the tail pool. This pattern is consistent with the conceptual model of hyporheic exchange over a PRP sequence. One‐dimensional analytical heat transport models were used at different points below the PRP sequence to estimate distributed vertical fluid fluxes. The calculated fluxes exhibit a trend that follows the expected distribution for a PRP sequence but modified for a losing stream (net fluid flux into the streambed). Deviation of both magnitude and distribution of fluxes from the conceptual “downwelling‐to‐upwelling” model is due partly to the dominantly losing conditions at the study site, but the trends are consistent with a losing stream undergoing hyporheic exchange. Violation of the assumptions in the analytical models most likely adds error to flux estimates. For this study, flux estimation methods using a temperature time‐series amplitude analysis more closely matched field measurements than phase methods.
The path to preservation: Using proteomics to decipher the fate of diatom proteins during microbial degradation
Authors: Nunn Brook L. , Ting Ying S. , Malmström Lars , Tsai Yihsuan S. , Squier Angela , Goodlett David R. , Harvey H. Rodger
Published: July 2010

We drew upon recent advances in tandem mass spectrometry‐based proteomic analyses in order to examine the proteins that remain after a diatom bloom enters the stationary phase, precipitates out of the photic zone, and is subjected to microbial degradation over a 23‐d period within a controlled laboratory environment. Proteins were identified from tandem mass spectra searched against three different protein databases in order to track proteins from Thalassiosira pseudonana and any potential bacterial contributions. A rapid loss of diatom protein was observed over the incubation period; 75% of the proteins initially identified were not detected after 72 h of exposure to a microbial population. By the 23rd day, peptides identified with high confidence correlated with only four T. pseudonana proteins. Five factors may have influenced the preservation of diatom proteins: (1) protection within organelles or structures with multiple membranes, (2) the relative cellular abundance in the photosynthetic apparatus, (3) the number of transmembrane domains in the protein sequence, (4) the presence of glycan modification motifs, and (5) the capability of proteins or peptides to aggregate into supramolecules.
Trace metal cycling in the surface water of the South China Sea: Vertical fluxes, composition, and sources
Authors: Ho Tung-Yuan , Chou Wen-Chen , Wei Ching-Ling , Lin Fei-Jan , Wong George T. F. , Line Hui-Ling
Published: July 2010

We deployed floating traps in the surface waters of the South China Sea on four occasions at depths of 30 m, 100 m, and 160 m from 2006 to 2007 to quantify vertical metal fluxes in the surface water and examine trace metal composition in the sinking particles to investigate their sources. The elements determined include 13 trace metals and 8 major elements. The fluxes for most of the bioactive elements at 30 m varied markedly during different seasons and strongly co‐varied with organic matter production, but the fluxes at 160 m were low and consistent under different seasons, showing that most of the elements were internally recycled in the surface water during productive seasons. Most of the bioactive trace metals in sinking particles were correlated with biogenic P, and their P‐normalized quotas were also strongly associated with lithogenic Al. The ratios of metals to Al and P for most of the bioactive trace metals were significantly higher than the ratios in lithogenic particles and than intracellular quotas in plankton, respectively, indicating that the trace metals in the sinking particles were abiogenic, nonlithogenic, and adsorbed on biogenic particles. The comparable fluxes between aeolian deposition and the sinking particles in the mixed layer demonstrate that the highly enriched trace metals in the sinking particles were attributed to input from anthropogenic aerosols. The coupling and transport of anthropogenic trace metals with biogenic particles in oceanic surface waters may be an important mechanism for trace metal cycling in global oceans.
Coexisting overwintering strategies in Daphnia pulex: A test of genetic differences and growth responses
Authors: Lampert Winfried , Lampert Kathrin P. , Larssona Petter
Published: July 2010

We tested whether clones of Daphnia pulex in a mesotrophic lake differ with respect to overwintering strategies: either surviving the winter as parthenogenetic females with reduced metabolism in pelagic waters, or as sexually produced dormant embryos in ephippia. During winter 2007, we established two groups of clonal laboratory lines from females collected in the lake and neonates hatched from ephippia. Genetic relatedness and differentiation of the two clonal groups were studied with microsatellite markers, and compared to the genetic structure of a field reference population. Flow‐through experiments designed to measure the specific juvenile growth rate (gj) of individual clones (a good proxy of fitness) at low and at high food concentrations show that differences in gj indicate physiological adaptation of the different starting populations to improving food conditions in spring. Although gj differed significantly among individual clones, both below and above the incipient limiting food concentration, we found no significant differences between the clonal groups. There was considerable clonal variation for reaction norms of gj, but neither the group means of the slopes of reaction norms nor of the threshold food concentrations for growth differed significantly. The lack of differences in group means so far does not support the hypothesis that clones are specialized for either parthenogenetic or for dormant overwintering. It rather suggests a mixed strategy of individual females producing resting stages as insurance and then trying to survive the winter in an active state.
Forensic Economics: A Perspective and An Agenda for Research
Authors: Ward John O. , Olson Gerald W.
Published: July 2010

No abstract available.
How Economists Can Help in Litigation
Authors: Slesinger Reuben E.
Published: July 2010

No abstract available.
Valuing Illiquid Pension Benefits
Authors: Trout Robert R.
Published: July 2010

No abstract available.
The Effect of Compensation Awards upon Consumption and Savings
Authors: Slesnick Frank , Dolin Richard
Published: July 2010

No abstract available.
Pitfalls to using the Real-Rates or Age-Earnings Profile Models in Calculating Economic Loss
Authors: Abraham Fred J.
Published: July 2010

No abstract available.
The Consideration of Progressive Taxes in Present Value Calculations for Personal Injury and Wrongful Death Cases
Authors: Goodwin Randall , Paul Chris
Published: July 2010

No abstract available.
Addressing the Value of Household Services Through a Functional Vocational Analysis
Authors: Tierney John P. , Gamboa A. M. , Holland Gwendolyn H.
Published: July 2010

No abstract available.
Exploring Anabolic Androgenic Steroid Use Among Cisgender Gay, Bisexual, and Queer Men
Authors: Kutscher Eric , Arshed Arslaan , Greene Richard E. , Kladney Mat
Published: May 2024

Importance

Anabolic androgenic steroids (AAS) are disproportionately used by sexual minority men, with the physical and mental health implications of AAS use incompletely understood.

Objective

To understand the reasons for use and health care needs of gay, bisexual, and queer cisgender men using AAS.

Design, Setting, and Participants

This qualitative study was conducted from November 2021 to May 2023 using self-administered questionnaires and semistructured interviews that were transcribed and coded using reflexive thematic analysis. Participants were recruited through convenience and snowball sampling from lesbian, gay, bisexual, transgender, and queer clinical centers in New York, New York, as well as through online platforms. All patients self-identified as cisgender and gay, bisexual, or queer.

Exposures

History of nonprescribed AAS use for a minimum of 8 consecutive weeks was required.

Main Outcomes and Measures

The primary outcomes were reasons for and health implications of AAS use and interactions with health care practitioners, as determined through interviews. Interview transcripts were collected and analyzed.

Results

Thematic saturation was reached after interviews with 12 male participants (mean [SD] age, 44 [11] years), with the majority of participants identifying as gay (10 participants [83%]), White non-Hispanic (9 participants [75%]), being in their 30s and 40s (9 participants [75%]), holding a bachelor’s degree or higher (11 participants [92%]), and having used steroids for a mean (SD) of 7.5 (7.1) years. One participant (8%) self-identified as Black, and 2 (17%) identified as Hispanic. Seven men (58%) met the criteria for muscle dysmorphia on screening. Nine overarching themes were found, including internal and external motivators for initial use, continued use because of effectiveness or fear of losses, intensive personal research, physical and emotional harms experienced from use, using community-based harm reduction techniques, frustration with interactions with the medical community focused on AAS cessation, and concerns around the illegality of AAS.

Conclusions and Relevance

In this qualitative study, AAS use among cisgender gay, bisexual, and queer men was found to be associated with multifactorial motivators, including a likely AAS use disorder and muscle dysmorphia. Despite all participants experiencing harms from use, men seeking medical help found insufficient support with practitioners insistent on AAS cessation and, thus, developed their own harm reduction techniques. Further research is needed to assess the utility of practitioner education efforts, the safety and efficacy of community-developed harm reduction methods, and the impact of AAS decriminalization on health care outcomes for this patient population.