bluuebunny/crossref_metadata_2025_split huggingface dataset:
Self-similar transport of inertial particles in a turbulent boundary layer
Authors: Sardina G. , Schlatter P. , Picano F. , Casciola C. M. , Brandt L. , Henningson D. S. 
Published: July 2012

AbstractResults are presented from a direct numerical simulation of a particle-laden spatially developing turbulent boundary layer up to ${\mathit{Re}}_{\theta } = 2500$. The peculiar feature of a boundary-layer flow seeded with heavy particles is the variation of the local dimensionless parameters defining the fluid–particle interactions along the streamwise direction. Two different Stokes numbers can be defined, one using inner flow units and the other with outer units. Since these two Stokes numbers exhibit different decay rates in the streamwise direction, we find a decoupled particle dynamics between the inner and the outer region of the boundary layer. Preferential near-wall particle accumulation is similar to that observed in turbulent channel flow, while different behaviour characterizes the outer region. Here the concentration and the streamwise velocity profiles are found to be self-similar and to depend only on the local value of the outer Stokes number and the rescaled wall-normal distance. These new results are powerful in view of engineering and environmental applications and corresponding flow modelling.
Nagata compactification for algebraic spaces
Authors: Conrad Brian , Lieblich Max , Olsson Martin 
Published: July 2012

AbstractWe prove the Nagata compactification theorem for any separated map of finite type between quasi-compact and quasi-separated algebraic spaces, generalizing earlier results of Raoult. Along the way we also prove (and use) absolute noetherian approximation for such algebraic spaces, generalizing earlier results in the case of schemes.
Use of Bioelectric Impedance Analysis to Assess Total‐Body Condition and Predict Energy Density in Juvenile Atlantic Croaker
Authors: Garner S. B. , van der Ham J. L. , Boswell K. M. , Cowan J. H. 
Published: July 2012

AbstractBioelectric impedance analysis (BIA) uses the conductive properties of biological tissues to provide whole‐body resistance (R) and reactance (Xc) data through direct measurements of intracellular and extracellular water content. The application of BIA to fish remains relatively novel, and the relationship between condition and impedance is not fully understood. We sought to test the efficacy of BIA in assessing total‐body condition and energy content in juvenile fish. We present results from a laboratory tank experiment using juvenile Atlantic croaker Micropogonias undulatus to investigate the BIA‐condition relationship and compare BIA with traditional condition measures (i.e., relative condition and energy‐content analysis). Atlantic croaker were held in large recirculation tanks and subjected to either a starvation or ad libitum feeding treatment for 45 d. Relative condition, energy content, phase angle, and the composition index all showed significant differences between treatments. However, trends observed in the BIA‐derived condition measures (phase angle and the composition index) displayed contradictory results. When regressed against energy content, phase angle yielded consistently lower r2 values than relative condition, while both were much lower than literature‐derived r2 values for predictive equations of proximate components. Two explanations are possible for the weak relationships observed among BIA measures in this experiment: (1) relatively high‐metabolic rates and low energy storage capacities of juvenile fish may have disrupted normal impedance relationships, and (2) an electrode array placed in muscle tissue may not have detected compositional changes if the primary centers for fat storage and mobilization occurred in the liver or viscera.
Feeding Response of Sport Fish after Electrical Immobilization, Chemical Sedation, or Both
Authors: Fredricks Kim T. , Meinertz Jeffery R. , Ambrose Ryan D. , Jackan Leanna M. , Wise Jeremy K. , Gaikowski Mark P. 
Published: July 2012

Abstract
Fishery managers frequently capture wild fish for a variety of fishery management activities. Though some activities can be accomplished without immobilizing the fish, others are accomplished more readily, humanely, and safely (for both the handler and the fish) when fish are immobilized by physical (e.g., electrical immobilization) or chemical sedation. A concern regarding the use of chemical sedatives is that chemical residues may remain in the fillet tissue after the fish recovers from sedation. If those residues are harmful to humans, there is some risk that a postsedated fish released to public waters may be caught and consumed by an angler. To characterize this risk, a series of four trials were conducted. Three trials assessed feeding activity after hatchery-reared fish were electrically immobilized, chemically sedated, or both, and one trial assessed the likelihood of an angler catching a wild fish that had been electrically immobilized and chemically sedated. Results from the first trial indicated that the feeding activity of laboratory habituated fish was variable among and within species after electrical immobilization, chemical sedation, or both. Results from the second trial indicated that the resumption of feeding activity was rapid after being mildly sedated for 45 min. Results from the third trial indicated that the feeding activity of outdoor, hatchery-reared fish was relatively aggressive after fish had been chemically sedated. Results from the fourth trial indicated that the probability of capturing wild fish in a more natural environment by angling after fish had been electrically immobilized and chemically sedated is not likely, i.e., in a group of five fish caught, 3 out of 100 times one would be a fish that had been sedated.
Received October 17, 2011; accepted April 13, 2012
The Relationship between Age-0 Walleye Density and Adult Year-Class Strength across Northern Wisconsin
Authors: Hansen Jonathan F. , Fayram Andrew H. , Hennessy Joseph M. 
Published: July 2012

Abstract
Walleyes Sander vitreus are an important cultural and economic resource in northern Wisconsin, both as a recreational fishery and a tribal subsistence fishery. Understanding the recruitment of age-0 walleyes to the adult population could be of great utility in effectively managing harvest and informing stocking efforts in this mixed-use fishery. Our objective was to determine the relationship between abundance of age-0 walleyes in the fall and the subsequent adult year-class 4 years later and to explain additional residual variation related to environmental variables. Since 1986, fall electrofishing surveys have been conducted to estimate the densities of age-0 walleyes and spring mark–recapture surveys to estimate spawning adult walleyes. We fit a gamma stock–recruitment curve to a data set of 104 paired surveys (age-0 survey with adult survey conducted 4 years later) on 58 lakes and attempted to explain residual variation related to additional environmental variables. Our analysis suggests that the maximum number of age-4 fish (3.36/ha) is not produced by the maximum number of age-0 fish but by a somewhat intermediate density (243/ha) and that this relationship varies with the complexity of the shoreline. This density-dependent relationship should help managers refine models forecasting walleye abundance, as well as optimize stocking rates.
Received December 28, 2011; accepted April 27, 2012
How and Why 1 Year Differs from 365 Days: A Conversational Logic Analysis of Inferences from the Granularity of Quantitative Expressions
Authors: Zhang Y. Charles , Schwarz Norbert 
Published: July 2012

Abstract
The same quantity can be expressed at different levels of granularity, for example, “1 year,” “12 months,” or “365 days.” Consumers attend to the granularity chosen by a communicator and draw pragmatic inferences that influence judgment and choice. They consider estimates expressed in finer granularity more precise and have more confidence in their accuracy (studies 1–4). This effect is eliminated when consumers doubt that the communicator complies with Gricean norms of cooperative conversational conduct (studies 2–3). Based on their pragmatic inferences, consumers perceive products as more likely to deliver on their promises when the promise is described in fine-grained rather than coarse terms and choose accordingly (study 4). These findings highlight the role of pragmatic inferences in consumer judgment and have important implications for the design of marketing communications.
“I Don’t” versus “I Can’t”: When Empowered Refusal Motivates Goal-Directed Behavior
Authors: Patrick Vanessa M. , Hagtvedt Henrik 
Published: July 2012

Abstract
This research is based on the insight that the language we use to describe our choices serves as a feedback mechanism that either enhances or impedes our goal-directed behavior. Specifically, we investigate the influence of a linguistic element of self-talk, in which a refusal may be framed as “I don’t” (vs. “I can’t”), on resisting temptation and motivating goal-directed behavior. We present a set of four studies to demonstrate the efficacy of the “don’t” (vs. “can’t”) framing (studies 1–3) when the source of the goal is internal (vs. external; studies 2A and 2B), as well as the mediating role of psychological empowerment (studies 1, 2A, and 2B). We demonstrate this novel and effective refusal strategy with actual choice (study 1) and with behavioral intent (studies 2A and 2B) and also illustrate its applicability in the real world in a longitudinal intervention-based field study (study 3).
Psychological Distance and Subjective Experience: How Distancing Reduces the Feeling of Difficulty
Authors: Thomas Manoj , Tsai Claire I. 
Published: July 2012

Abstract
Psychological distance can reduce the subjective experience of difficulty caused by task complexity and task anxiety. Four experiments were conducted to test several related hypotheses. Psychological distance was altered by activating a construal mind-set and by varying bodily distance from a given task. Activating an abstract mind-set reduced the feeling of difficulty. A direct manipulation of distance from the task produced the same effect: participants found the task to be less difficult when they distanced themselves from the task by leaning back in their seats. The experiments not only identify psychological distance as a hitherto unexplored but ubiquitous determinant of task difficulty but also identify bodily distance as an antecedent of psychological distance.
Self-Affirmation through the Choice of Highly Aesthetic Products
Authors: Townsend Claudia , Sood Sanjay 
Published: July 2012

Abstract
Just as good looks bestow an unconscious “beauty premium” on people, high aesthetics bestows an unrecognized benefit on consumer goods. Specifically, choosing a product with good design affirms the consumer’s sense of self. Choice of a highly aesthetic product was compared with choice of products superior on other attributes including function, brand, and hedonics to show that only aesthetics influences a consumer’s personal values. In study 1 a prior self-affirming task leads to a decrease in choice share of a highly aesthetic option. Studies 2 and 3 mimic prior research on self-affirmation with, however, choice of a highly aesthetic product replacing a traditional self-affirmation manipulation. Choosing a product with good design resulted in increased openness to counter-attitudinal arguments and reduced propensity to escalate commitment toward a failing course of action. There are numerous implications of this form of self-affirmation, from public policy to retail therapy.
Bayesian sampling of evolutionarily conserved RNA secondary structures with pseudoknots
Authors: Doose Gero , Metzler Dirk 
Published: July 2012

Abstract
Motivation: Today many non-coding RNAs are known to play an active role in various important biological processes. Since RNA's functionality is correlated with specific structural motifs that are often conserved in phylogenetically related molecules, computational prediction of RNA structure should ideally be based on a set of homologous primary structures. But many available RNA secondary structure prediction programs that use sequence alignments do not consider pseudoknots or their estimations consist on a single structure without information on uncertainty.
Results: In this article we present a method that takes advantage of the evolutionary history of a group of aligned RNA sequences for sampling consensus secondary structures, including pseudoknots, according to their approximate posterior probability. We investigate the benefit of using evolutionary history and demonstrate the competitiveness of our method compared with similar methods based on RNase P RNA sequences and simulated data.
Availability: PhyloQFold, a C + + implementation of our method, is freely available from http://evol.bio.lmu.de/_statgen/software/phyloqfold/
Contact: gero@bioinf.uni-leipzig.de, metzler@bio.lmu.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Gene and translation initiation site prediction in metagenomic sequences
Authors: Hyatt Doug , LoCascio Philip F. , Hauser Loren J. , Uberbacher Edward C. 
Published: July 2012

Abstract
Motivation: Gene prediction in metagenomic sequences remains a difficult problem. Current sequencing technologies do not achieve sufficient coverage to assemble the individual genomes in a typical sample; consequently, sequencing runs produce a large number of short sequences whose exact origin is unknown. Since these sequences are usually smaller than the average length of a gene, algorithms must make predictions based on very little data.
Results: We present MetaProdigal, a metagenomic version of the gene prediction program Prodigal, that can identify genes in short, anonymous coding sequences with a high degree of accuracy. The novel value of the method consists of enhanced translation initiation site identification, ability to identify sequences that use alternate genetic codes and confidence values for each gene call. We compare the results of MetaProdigal with other methods and conclude with a discussion of future improvements.
Availability: The Prodigal software is freely available under the General Public License from http://code.google.com/p/prodigal/.
Contact: hyattpd@ornl.gov
Supplementary Information: Supplementary data are available at Bioinformatics online.
SQID-XLink: implementation of an intensity-incorporated algorithm for cross-linked peptide identification
Authors: Li Wenzhou , O’Neill Heather A. , Wysocki Vicki H. 
Published: July 2012

Abstract
Summary: Peptide identification algorithm is a major bottleneck for mass spectrometry based chemical cross-linking experiments. Our lab recently developed an intensity-incorporated peptide identification algorithm, and here we implemented this scheme for cross-linked peptide discovery. Our program, SQID-XLink, searches all regular, dead-end, intra and inter cross-linked peptides simultaneously, and its effectiveness is validated by testing a published dataset. This new algorithm provides an alternative approach for high confidence cross-linking identification.
Availability: SQID-XLink program is freely available for download from http://quiz2.chem.arizona.edu/wysocki/bioinformatics.htm
Supplementary information: Supplementary data are available at Bioinformatics online.
Contact: vwysocki@email.arizona.edu
GAPIT: genome association and prediction integrated tool
Authors: Lipka Alexander E. , Tian Feng , Wang Qishan , Peiffer Jason , Li Meng , Bradbury Peter J. , Gore Michael A. , Buckler Edward S. , Zhang Zhiwu 
Published: July 2012

AbstractSummary: Software programs that conduct genome-wide association studies and genomic prediction and selection need to use methodologies that maximize statistical power, provide high prediction accuracy and run in a computationally efficient manner. We developed an R package called Genome Association and Prediction Integrated Tool (GAPIT) that implements advanced statistical methods including the compressed mixed linear model (CMLM) and CMLM-based genomic prediction and selection. The GAPIT package can handle large datasets in excess of 10 000 individuals and 1 million single-nucleotide polymorphisms with minimal computational time, while providing user-friendly access and concise tables and graphs to interpret results.Availability: http://www.maizegenetics.net/GAPIT.Contact: zhiwu.zhang@cornell.eduSupplementary Information: Supplementary data are available at Bioinformatics online.
Measuring and comparing structural fluctuation patterns in large protein datasets
Authors: Fuglebakk Edvin , Echave Julián , Reuter Nathalie 
Published: July 2012

Abstract
Motivation: The function of a protein depends not only on its structure but also on its dynamics. This is at the basis of a large body of experimental and theoretical work on protein dynamics. Further insight into the dynamics–function relationship can be gained by studying the evolutionary divergence of protein motions. To investigate this, we need appropriate comparative dynamics methods. The most used dynamical similarity score is the correlation between the root mean square fluctuations (RMSF) of aligned residues. Despite its usefulness, RMSF is in general less evolutionarily conserved than the native structure. A fundamental issue is whether RMSF is not as conserved as structure because dynamics is less conserved or because RMSF is not the best property to use to study its conservation.
Results: We performed a systematic assessment of several scores that quantify the (dis)similarity between protein fluctuation patterns. We show that the best scores perform as well as or better than structural dissimilarity, as assessed by their consistency with the SCOP classification. We conclude that to uncover the full extent of the evolutionary conservation of protein fluctuation patterns, it is important to measure the directions of fluctuations and their correlations between sites.
Contact: Nathalie.Reuter@mbi.uib.no
Supplementary Information: Supplementary data are available at Bioinformatics Online.
MALDIquant: a versatile R package for the analysis of mass spectrometry data
Authors: Gibb Sebastian , Strimmer Korbinian 
Published: July 2012

Abstract
Summary: MALDIquant is an R package providing a complete and modular analysis pipeline for quantitative analysis of mass spectrometry data. MALDIquant is specifically designed with application in clinical diagnostics in mind and implements sophisticated routines for importing raw data, preprocessing, non-linear peak alignment and calibration. It also handles technical replicates as well as spectra with unequal resolution.
Availability: MALDIquant and its associated R packages readBrukerFlexData and readMzXmlData are freely available from the R archive CRAN (http://cran.r-project.org). The software is distributed under the GNU General Public License (version 3 or later) and is accompanied by example files and data. Additional documentation is available from http://strimmerlab.org/software/maldiquant/.
Contact: mail@sebastiangibb.de
Environmental and fisheries effects on Gracilechinus acutus (Echinodermata: Echinoidea) distribution: is it a suitable bioindicator of trawling disturbance?
Authors: González-Irusta J. M. , Punzón A. , Serrano A. 
Published: July 2012

AbstractGonzález-Irusta, J. M., Punzón, A., and Serrano, A. 2012. Environmental and fisheries effects on Gracilechinus acutus (Echinodermata: Echinoidea) distribution: is it a suitable bioindicator of trawling disturbance? – ICES Journal of Marine Science, 69: . Habitat preferences of Gracilechinus acutus in the southern Bay of Biscay were studied using data from autumn bottom-trawl surveys. Wet weight and number of specimens of G. acutus were obtained and related to environmental variables (depth, sediment type, and organic matter percentage) at each haul and to trawl fishing effort. With this information and the otter trawl effort data, the environmental requirements and the impact of the trawl fishery on G. acutus populations were analysed. Although the species was present in all depth strata and all sediment types studied, it had clear habitat preferences, as greater abundances and mean weight values were found at depths ranging from 71 to 200 m and in bottom sediments dominated by coarse and medium sands. The effect of disturbance by trawling on this echinoid was significant and clearly negative. Seabeds exposed to higher trawling disturbance showed lower values of urchin abundance and smaller urchins than areas with lower disturbance. Results of the present study confirm the initial hypothesis of the suitability of using this urchin as a bioindicator of trawling impact but only in areas with appropriate environmental conditions, highlighting the importance of attaining a wider knowledge on the essential habitat of the species.
Conservation of coastal stingrays: seasonal abundance and population structure of the short-tailed stingray Dasyatis brevicaudata at a Marine Protected Area
Authors: Le Port A. , Lavery S. , Montgomery J. C. 
Published: July 2012

AbstractLe Port, A., Lavery, S., and Montgomery, J. C. 2012. Conservation of coastal stingrays: seasonal abundance and population structure of the short-tailed stingray Dasyatis brevicaudata at a Marine Protected Area. – ICES Journal of Marine Science, 69: . Elasmobranch (shark, ray, and skate) populations around the world are in decline, and effective conservation measures are urgently needed. Marine Protected Areas (MPA) placed in locations important for key life-history stages may form part of an effective conservation strategy. In this context, we examined the seasonal abundance and population structure of the short-tailed stingray (Dasyatis brevicaudata) at an offshore MPA in northeastern New Zealand, and the reported use of this location as a mating ground. Diver surveys were conducted from 2004 to 2007 at the Poor Knights Islands Marine Reserve (PKIMR). During this time, we observed: (i) a substantial increase in adult and subadult numbers, particularly females during the suggested breeding season, and a corresponding increase in females bearing fresh mating scars; and (ii) large numbers of smaller (probably immature) D. brevicaudata individuals of both sexes from spring to autumn. These results suggest that the PKIMR acts as both a mating aggregation location and a nursery for this species. We suggest that for coastal stingrays such as D. brevicaudata, small MPAs may be effective at protecting key life-history stages, but that as movements outside of reserve boundaries also occur, additional management tools may also be necessary.
Size-related variation in fecundity of European eel (Anguilla anguilla)
Authors: MacNamara Ruairí , McCarthy T. Kieran 
Published: July 2012

Abstract
MacNamara, R., and McCarthy, T. K. 2012. Size-related variation in fecundity of European eel (Anguilla anguilla). – ICES Journal of Marine Science, 69: . Declining European eel (Anguilla anguilla) recruitment has focused attention on conservation of potential spawners leaving continental waters. Fecundity of wild, seaward-migrating silver-phase eels was shown to be size-related and higher than previously reported from artificial maturation experiments. Reliable information on fecundity is essential for stock modelling and future development of eel management policies.