bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lipopolysaccharide O antigen size distribution is determined by a chain extension complex of variable stoichiometry inEscherichia coliO9a
Authors: King Jerry D. , Berry Scott , Clarke Bradley R. , Morris Richard J. , Whitfield Chris 
Published: April 2014

SignificanceLipopolysaccharides (LPSs) are unique glycolipids that are characteristic components of outer membranes in Gram negative bacteria and play important roles in pathogenesis. Many LPSs contain a long-chain polysaccharide (known as the O antigen) whose length can be an important factor in bacterial resistance to complement-mediated killing. While components involved in chain-length determination are known in many systems, the underlying regulatory mechanism is not. Here we apply a mathematical modeling approach that integrates the existing structural and biochemical data to develop a new model, variable geometry, for chain-length regulation using the prototype for O antigens whose synthesis involves the widespread ATP-binding cassette transporter-dependent pathway.
Mapping the stochastic response of nanostructures
Authors: Pattamatta Subrahmanyam , Elliott Ryan S. , Tadmor Ellad B. 
Published: April 2014

Significance
A challenge in nanotechnology is that nanoscale structures exhibit a rate-dependent and apparently random (stochastic) load-deflection behavior when repeated experimental measurements are compared. The variability in mechanical response is due to the extreme nonconvexity of the nanostructure’s energy versus structure function. The many minima of this function correspond to equilibrium states, accessible during loading, that create many possible pathways. Traditional atomistic simulation techniques cannot systematically address this complexity. Here, we explore a new method based on constructing an “equilibrium map” (akin to a phase diagram) that efficiently and systematically explores a nanostructure's stochastic, rate-dependent response to specified loading conditions. We demonstrate the method's capabilities and its surprisingly complex results for the case of a nanoslab of nickel under uniaxial compression.
Enhanced evolution by stochastically variable modification of epigenetic marks in the early embryo
Authors: Branciamore Sergio , Rodin Andrei S. , Riggs Arthur D. , Rodin Sergei N. 
Published: April 2014

Significance
In this paper we investigate by quantitative modeling the effect on evolution of epigenetic variation during a window of opportunity in the early embryo. It is generally accepted that generation of new functions is primarily driven by gene duplication. However, pseudogenization (degradation of a new gene copy) is statistically much more likely than gaining a new function, and thus this remains a serious conceptual problem. We find that epigenetic variation, even in a constant environment, can essentially eliminate the pseudogenization problem and dramatically improve the efficacy of evolution by gene duplication.
Assessing the effects of anthropogenic aerosols on Pacific storm track using a multiscale global climate model
Authors: Wang Yuan , Wang Minghuai , Zhang Renyi , Ghan Steven J. , Lin Yun , Hu Jiaxi , Pan Bowen , Levy Misti , Jiang Jonathan H. , Molina Mario J. 
Published: April 2014

SignificanceIncreasing levels of air pollutants in Asia have recently drawn considerable attention, but the effects of Asian pollution outflows on regional climate and global atmospheric circulation remain to be quantified. Using a multiscale global aerosol–climate model (GCM), we demonstrate long-range transport of the Asian pollution, large resulting variations in the aerosol optical depth, cloud droplet number concentration, and cloud and ice water paths; enhanced shortwave and longwave cloud radiative forcings; and increased precipitation and poleward heat transport. Our work provides, for the first time to the authors’ knowledge, a global multiscale perspective of the climatic effects of pollution outflows from Asia. The results reveal that the multiscale modeling framework is essential in simulating the aerosol invigoration effect of deep convective cloud systems by a GCM.
Defining modulatory inputs into CNS neuronal subclasses by functional pharmacological profiling
Authors: Raghuraman Shrinivasan , Garcia Alfredo J. , Anderson Tatiana M. , Twede Vernon D. , Curtice Kigen J. , Chase Kevin , Ramirez Jan-Marino , Olivera Baldomero M. , Teichert Russell W. 
Published: April 2014

Significance
We functionally profiled cells from a locus of the mouse brainstem that contains the neuronal network responsible for generating breathing patterns. By uncovering cell-specific constellations (i.e., distinctive combinations of receptors and ion channels that define each cell type), we identified specific neuronal classes and subclasses within the network. We discovered neuromodulators affecting the activity of specific neuronal subclasses within the functional network. This study provides proof-of-principle that a pharmacological strategy for altering the activity of a specific type of neuron can be developed which has potential as a parallel or complementary approach to genetic strategies for functionally perturbing a specific neuronal cell type in vivo. Additionally, unlike genetic approaches, this pharmacological approach is directly applicable to nonmodel organisms.
Glioblastoma cellular architectures are predicted through the characterization of two-cell interactions
Authors: Kravchenko-Balasha Nataly , Wang Jun , Remacle Francoise , Levine R. D. , Heath James R. 
Published: April 2014

Significance
Microscopic analysis of cellular architectures within a diseased tissue often provides an independent assay relative to measurements of molecular biomarkers from that same tissue. Both methods may point to the same disease state, but the relationship between the two is often not clear. We explore a connection by investigating how growth factor-driven protein signaling depends upon the distance separating pairs of cancer cells. A thermodynamic-derived theory identifies the intercellular separation that corresponds to the steady state of the signaling. That length scale is found to be the dominant cell separation distance in bulk tissue culture. The approach is tested in one cell line and validated in another, and may provide insight into the diffusive nature of certain brain cancer phenotypes.
Thalamocortical rhythms during a vibrotactile detection task
Authors: Haegens Saskia , Vázquez Yuriria , Zainos Antonio , Alvarez Manuel , Jensen Ole , Romo Ranulfo 
Published: April 2014

SignificanceWhen a near-threshold sensory stimulus is presented, a sensory percept may or may not be produced. The exact process by which neural activity elicits subjective perception is a long-standing open question. Here, we ask what role brain oscillations in early sensory regions play in this cognitive process, as oscillations are thought to reflect population dynamics, indicative of the state of a brain network. We found task-related modulations in oscillatory activity in both the somatosensory thalamus and primary sensory cortex, which were correlated with the perceptual decision process and subsequent behavioral response. We conclude that these early sensory regions, in addition to their primary sensory functions, may be actively involved in perceptual decision making.
Effects of Streamflow Diversion on a Fish Population: Combining Empirical Data and Individual-Based Models in a Site-Specific Evaluation
Authors: Harvey Bret C. , White Jason L. , Nakamoto Rodney J. , Railsback Steven F. 
Published: April 2014

Abstract
Resource managers commonly face the need to evaluate the ecological consequences of specific water diversions of small streams. We addressed this need by conducting 4 years of biophysical monitoring of stream reaches above and below a diversion and applying two individual-based models of salmonid fish that simulated different levels of behavioral complexity. The diversion of interest captured about 24% of streamflow between June and October but had little or no effect over the remainder of the year. The change in biomass of Rainbow Trout Oncorhynchus mykiss and steelhead (anadromous Rainbow Trout) over the dry season (June–October) favored the upstream control over the downstream diversion reach over 4 years (2008–2011). Dry-season growth did not differ consistently between the two reaches but did exhibit substantial annual variation. Longer-term observations revealed that in both reaches most fish growth occurred outside the period of dry-season diversion. After calibration to the upstream control reach, both individual-based models predicted the observed difference in fish biomass between control and diversion reaches at the ends of the dry seasons. Both models suggested the difference was attributable in part to differences in habitat structure unrelated to streamflow that favored the upstream reach. The two models both also reproduced the large seasonal differences in growth, small differences between reaches in individual growth, and natural distributions of growth among individuals. Both the empirical data and simulation modeling suggested that the current level of diversion does not threaten the persistence of the salmonid population. In multiyear simulations using the two models, the model incorporating greater flexibility in fish behavior exhibited weaker population-level responses to more extreme reductions in dry-season streamflow. We believe the application of individual-based models in this case has placed resource managers in a relatively strong position to forecast the consequences of future environmental alterations at the study site.
Received March 22, 2013; accepted October 17, 2013
Measuring the Economic Value of Increased Precision in Scientific Estimates of Marine Mammal Abundance and Bycatch: Harbor Porpoise Phocoena phocoena in the Northeast U.S. Gill-Net Fishery
Authors: Bisack Kathryn D. , Magnusson Gisele 
Published: April 2014

Abstract
Marine mammal stock assessments provide information that is valuable to public sector management and the private fishing sector; however, data are costly to collect. The precautionary approach, which is widely used in fishery and marine mammal management, advocates a conservative management decision with priority to the resource when there is uncertainty regarding the impact on the resource from human activity. The potential biological removal (PBR) control rule of the U.S. Marine Mammal Protection Act explicitly incorporates uncertainty in input variables into the determination of allowable levels of human-induced mortality for a stock. Less uncertainty results in higher PBR values for a given stock level. Variations in government funding levels can disrupt the scientific data collection that is necessary for PBR calculation. We present an economic net benefit framework that examines the indirect value of information from marine mammal stock assessments to the commercial fishing industry. Using the harbor porpoise Phocoena phocoena and the U.S. Atlantic sink gill-net fishery as a case study, we estimated the difference between total public sector data collection costs and total private sector benefits from increased profits. Net benefits represent a measure of the value of information to society, while the difference in profits measures the value of the information to the private sector. Several results are forthcoming. First, the optimal allocation of funding showed that abundance surveys are a more cost-effective means to reduce uncertainty in PBR input variables than increasing observer coverage of the fishing industry. Second, for all levels of PBR in this empirical example, total benefits to the private sector for a higher PBR exceeded the costs of collecting additional scientific data to increase the precision of input variables and thus increase PBR. Since net benefits are positive, the private sector may consider funding of scientific data collection for marine mammals as a way to reduce uncertainty, thereby allowing a higher PBR value.
Received March 19, 2013; accepted November 14, 2013
Evaluation of Calcein for Estimating Abundance of Lake Trout Alevins on a Spawning Reef
Authors: Marsden J. Ellen , Kelsey Kevin P. , Riley Jacob W. , Hatt Joanna 
Published: April 2014

Abstract
Reproduction by stocked Lake Trout Salvelinus namaycush is generally estimated as the relative abundance of fry, that is, catch per unit effort in emergent fry traps and in beam trawls, but these estimates have high variance due to spatially heterogeneous distributions of fry. We used calcein, which produces a fluorescent mark in calcified structures, to batch-mark fry and generate a mark–recapture estimate of fry abundance on a small, shallow spawning reef. Eggs collected from feral Lake Trout in Lake Champlain, Vermont were reared at ambient lake temperatures, and fry were marked 7 d after hatching. Fry were immersed in a salt solution for osmotic induction and then placed for 4 min in a calcein solution. After marking, 18,000 fry were released on a spawning reef, and 2,000 fry were maintained in the hatchery. Wild-caught fry and hatchery fry were checked for marks every 2–9 d. Mark clarity was highest in the mandible and tail rays. Marks may have faded, but they did not disappear: marks were visible in the mandible in 100% of hatchery fry after 68 d. An average of 37% of wild-caught fry had marks, yielding a Chapman population estimate (±SD) of 47,486±2,301. The mark–recapture estimate was within the range of fry abundance estimated over 6 years based on egg density data and estimates of hatching success but was substantially higher than estimated for the same year-class. This work supports prior estimates of fry abundance and provides a potential method for assessing fry abundance on deep reefs and the success of fry stocking.
Received June 4, 2013; accepted November 20, 2013
Population Structure and Run Timing of Sockeye Salmon in the Skeena River, British Columbia
Authors: Beacham Terry D. , Cox-Rogers Steven , MacConnachie Cathy , McIntosh Brenda , Wallace Colin G. 
Published: April 2014

Abstract
Determination of run timing is an important component of salmonid fisheries management and was the major focus of the current study. Population structure of Sockeye Salmon Oncorhynchus nerka was examined in the Skeena River, northern British Columbia. Variation at 14 microsatellites was surveyed for 27 populations in the drainage. There were 9,473 individuals sampled in a lower river test fishery during 2000–2011 in order to provide information on relative abundance and time of arrival of specific populations or stocks near the mouth of the river. Within-lake or within-river tributary structuring of populations was the general pattern observed, with 10 populations from Babine Lake clustering together in 91% of dendrograms evaluated, and two populations from Lakelse Lake clustering together in 100% of dendrograms evaluated. The 27 populations sampled were arranged in 12 reporting groups for genetic stock identification applications. The estimated stock composition of known-origin mixtures was within 2% of the correct estimate for all 12 reporting groups present in the mixtures. Sockeye Salmon typically began arriving at the test fishery on the lower Skeena River by June 10, peaking in daily abundance in late July or early August, and finished migrating past the test fishery by mid-September. Relative timing of the 12 reporting groups, from earliest to latest, was as follows: Lakelse Lake, Alastair Lake, Zymoetz River, Morice Lake, Kispiox River, Sustut Lake, Babine Lake, Slamgeesh Lake, Motase Lake, Bear Lake, Kitsumkalum Lake, and Kitwanga Lake. Genetic mixed-stock analysis, coupled with a test fishery in the lower river, can assist managers in regulating fisheries directed at Skeena River Sockeye Salmon.
Received February 12, 2013; accepted December 4, 2013
Impacts of External and Surgery-Based Tagging Techniques on Small Northern Pike Under Field Conditions
Authors: Hühn Daniel , Klefoth Thomas , Pagel Thilo , Zajicek Petr , Arlinghaus Robert 
Published: April 2014

Abstract
In Northern Pike Esox lucius negligible effects of external tags on growth and survival have commonly been reported, but no studies exist for age-0 fish. We tested the impacts of fin clipping, PIT tags, and three external tags (T-bar anchor, opercular, and streamer tags) on age-0 Northern Pike in a pond. We also examined the impacts of surgically implanted transmitters on small adult Northern Pike in a natural lake. The loss of PIT tags was lowest among all tags and close to 0%. Of the external tags, T-bar anchor tags performed best. Loss of these tags was initially low (on average 5.7% after 195 d) increasing to about 20.0% by 520 d posttagging. Tagging-induced mortality of a few percent was present in all tags tested within the first 195 d posttagging in the pond environment but not present afterwards. The PIT tags, fin clips, and external tags did not affect the growth or condition of surviving fish. Surgically implanted transmitters reduced the growth of small adult Northern Pike with total lengths &lt;480 mm, but no effects were found for larger individuals. We conclude that PIT tagging is the most suitable marking technique for age-0 Northern Pike. If external visibility is required, T-bar anchor tags are also useful, as long as tagging-induced mortality and tag loss rates are accounted for at the analysis stage. Our study raises a cautionary note about surgically implanted transmitters in small adult Northern Pike, as they may negatively affect behavior and fitness.
Received March 27, 2013; accepted November 26, 2013
Risk-Based Management of Viral Hemorrhagic Septicemia Virus in Minnesota
Authors: Phelps Nicholas B. D. , Craft Meggan E. , Travis Dominic , Pelican Katharine , Goyal Sagar M. 
Published: April 2014

Abstract
Viral hemorrhagic septicemia virus (VHSV; strain VHSV-IVb) is an emergent and serious disease of fish in the Great Lakes region of North America. In addition to the numerous large-scale mortality events in wild fish, the emergence of VHSV has resulted in a major regulatory response to protect both farm-raised and wild fish populations. However, characterizing and mitigating risk factors for the continued transmission of VHSV is a difficult task. A semiquantitative risk assessment model was used to focus VHSV management efforts in Minnesota. The risk of VHSV introduction into major watersheds in Minnesota was directly correlated to their proximity to Lake Superior, the only VHSV-positive body of water in the state. Although the current regulations are uniform across Minnesota, the risk varied for specific locations within the watersheds. For example, the introduction of game fish for stock enhancement (a common fisheries management practice) is a significant factor in determining the risk of VHSV introduction into public waters, as is the movement of baitfish. In this analysis, aquaculture facilities with strict biosecurity programs and frequent health inspections received the lowest risk scores and were largely considered as protective or at low risk for VHSV introduction. These results suggest that the current management strategy, based on political boundaries, should be reevaluated. We recommend the creation of a risk-based management strategy based upon the identification of higher-risk watersheds and specific bodies of water, thus allowing managers to efficiently target surveillance and response activities in Minnesota.
Received July 22, 2013; accepted November 27, 2013
Limit Reference Points for Pacific Salmon Fisheries
Authors: Portley Nicole , Geiger Harold J. 
Published: April 2014

Abstract
“Limit reference points” define a state at which fishery management has reached overfishing, overfished stock status, or some other regulatory or conservation point of concern. In many Pacific salmon Oncorhynchus spp. fishery jurisdictions, management only uses “target reference points”—the specific numerical management objective intended to bring about some fishery benefit. There are several reasons to adopt limit reference points, and jurisdictions without previously defined limit reference points could adopt them in order to align better with the Magnuson–Stevens Act (American fisheries) or, more importantly, to facilitate cross-jurisdiction sustainability assessments, which are increasingly needed for certifications of sustainability. In actual practice, the stock size of 0.5 times a target reference point has been used as a limit reference point for some Pacific salmon fisheries, or at least as a proxy for a limit reference point. We term this point the “minimum stock size threshold,” following a convention already in use, and we note that limit reference points defined this way are increasingly being accepted as a standard either because of justification based on simulation and fishery principles or for purely pragmatic reasons.
Received July 2, 2013; accepted January 6, 2014
Coded Wire Tag and Passive Integrated Transponder Tag Implantations in Juvenile Burbot
Authors: Ashton Neil K. , Anders Paul J. , Young Shawn P. , Cain Kenneth D. 
Published: April 2014

Abstract
Regional stakeholders in various nations are investigating the restoration of imperiled and extirpated Burbot Lota lota populations via the stocking of hatchery-produced fish. Although stocking programs routinely tag fish for monitoring and evaluation projects, there is currently only limited information available regarding effective tagging techniques for use with juvenile Burbot. We identified two anatomical locations (dorsal muscle and peritoneum) that were suitable for PIT tag implantation and six body sites (snout, periocular region, nape, pectoral fin base, dorsal fin base, and ventral [anal fin base]) that were suitable for coded wire tag batch marking of age-0 Burbot (88–144 mm TL). Our evaluation of these implantation methods generally revealed a high rate of tag retention (&gt;95%) and no significant tagging effects on fish survival or growth. A follow-up study also demonstrated satisfactory mass-marking rates for both tag types. Coded wire tags and PIT tags should provide harmless, affordable, long-term identification of hatchery Burbot juveniles.
Received August 27, 2013; accepted December 27, 2013