bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modelling invasion probability of giant hogweed (
Heracleum mantegazzianum
) with logistic GLMM.
Authors: Thiele J. , Markussen B. 
Published: July 2012

Abstract

In this worked example of the application of
generalized linear mixed models
, we model the invasion probability of an invasive plant species, giant hogweed (
Heracleum mantegazzianum
), based on field surveys of 20 study areas of 1 km2 which were situated in areas of Germany most invaded by this species This forms Supplement B to Thiele J, Markussen B. Potential of GLMM in modelling invasive spread.
Age and Population Size Estimates of Overwintering Shortnose Sturgeon in the Saint John River, New Brunswick, Canada
Authors: Usvyatsov Sima , Watmough James , Litvak Matthew K. 
Published: July 2012

AbstractThe densities and overall abundances of overwintering shortnose sturgeon Acipenser brevirostrum were estimated using underwater video at the Kennebecasis River overwintering site in 2009 and 2011. In 2009, underwater cameras coupled with lasers provided image‐based estimates of fish lengths (and therefore ages). The precision and accuracy of laser‐based measurements were estimated by laboratory experiments. In total, 362 and 222 overwintering shortnose sturgeon were counted in the 0.02‐km2 area during 2009 and 2011, respectively. The fork lengths of 83 overwintering shortnose sturgeon measured in 2009 ranged from 54 to 119 cm, corresponding to ages of 11–57 years (20.3 ± 7.9 years [mean ± SD]). Length measurement accuracy was highest (±10% fork length) when fish were positioned at 0 ± 30° or 180 ± 30° to the camera's lens. Three different models of spatial fish density estimated a total of 3,852–5,222 shortnose sturgeon in 2009 and 2011, similar to the 2005 local population estimate of 4,836 shortnose sturgeon. The consistent, high‐density aggregation of subadults and adults at this small site between 2005 and 2011 suggests that the site is important for protection of shortnose sturgeon in the Saint John River system.
The Use of Fluorescent Randomly Amplified Polymorphic DNA Markers to Identify Hybrids: A Case Study Evaluating the Origins of Saugeye following the Cessation of Stocking in an Ohio Reservoir
Authors: Sovic Michael G. , Denlinger Jonathan C. , Fuerst Paul A. 
Published: July 2012

Abstract
Hybridization and introgression continue to gain recognition as important issues in the management and conservation of native fishes. It is often necessary to identify hybrids in natural populations and to distinguish among individuals of various hybrid categories. Molecular methods are important for these purposes, and it is valuable if researchers have a range of molecular methods to apply, since each method has unique advantages and disadvantages. The determination of the best class of marker for a particular study depends on various factors, including the goals of the study, the resolution required, and the genomic and marker information already available for the taxa of interest. We modified a protocol to generate fluorescent randomly amplified polymorphic DNA (FRAPD) markers for hybridization studies. To our knowledge, this type of marker has not previously been used for hybrid identification. To demonstrate the utility of the modified methods, FRAPD markers were used to evaluate potential reproduction by saugeye (female walleye Sander vitreus × male sauger Sander canadensis) in a central Ohio reservoir. Our approach successfully generated a battery of diagnostic genetic markers that were used to test the hypothesis that young-of-year saugeye were later-generation offspring of saugeye cohorts previously stocked into the reservoir. Alternatively, the fish may have been immigrant first-generation saugeye from other sources. Data obtained from the FRAPD markers provided strong support favoring the alternative hypothesis. These methods provide a very useful tool for distinguishing between pure parentals and various classes of hybrid individuals, both in Sander spp. and in other taxa, offering a powerful and easily developed alternative to other molecular methods of generating informative genetic markers for hybridization studies.
Received September 20, 2011; accepted April 5, 2012
Use of Night Video to Enumerate Adult Pacific Lamprey Passage at Hydroelectric Dams: Challenges and Opportunities to Improve Escapement Estimates
Authors: Clabough Tami S. , Keefer Matthew L. , Caudill Christopher C. , Johnson Eric L. , Peery Christopher A. 
Published: July 2012

Abstract
Reliable estimates of adult Pacific lamprey Entosphenus tridentatus escapement are critically needed to improve management of this declining and ecologically important species. The longest time series of Pacific lamprey counts are from count stations at Columbia River basin dams designed to enumerate adult salmonids during the day, but many Pacific lamprey pass at night. To estimate their total escapement, we used video to monitor nighttime lamprey passage in combination with daytime counts at two count stations at Bonneville Dam and two at The Dalles Dam in 2007–2008. We examined relationships among day and night counts and evaluated the potential for using expansion factors to estimate total escapement from past and future daytime count data. As expected, daytime counts systematically underestimated total lamprey passage, and day and night counts were positively correlated in most comparisons. Unexpectedly, ratios of night: day counts varied widely among sites and years because patterns of upstream and downstream movements past count stations varied. We highlight challenges associated with enumerating cryptic and nocturnal species, such as Pacific lamprey, the potential impact of species-specific behaviors on enumeration efforts, and the importance of appropriate count station location and structure for video monitoring of fish passage.
Received August 9, 2011; accepted April 27, 2012
Prebiotics Have Limited Effects on Nutrient Digestibility of a Diet Based on Fish Meal and Soybean Meal in Goldfish
Authors: Raggi Thiago , Gatlin Delbert M 
Published: July 2012

Abstract
This study evaluated four prebiotics: GroBiotic-A (a mixture of partially autolyzed brewers yeast, dairy ingredient components and dried fermentation products), mannanoligosaccharide (MOS), galactooligosaccharide (GOS), and the fructooligosaccharide (FOS) inulin on digestibility of diets based on fish meal and soybean meal by goldfish Carassius auratus. A basal diet was formulated with 50% of the protein provided by dehulled, solvent-extracted, soybean meal and the other 50% by menhaden Brevoortia sp. fish meal. Each prebiotic was supplemented to the basal diet at 1% by weight. A diet containing all of its protein from menhaden fish meal also was prepared as a control diet. Chromic oxide was added to the diets at 1% by weight. Each diet was fed to adult goldfish in duplicate 110-L aquaria for 8 weeks. The dried fecal material from each aquarium was pooled over time and analyzed for protein, lipid, organic matter, and chromium in order to compute coefficients of apparent digestibility. Genomic DNA of luminal gut microbiota also was isolated from the fecal samples of goldfish fed the various diets and was subjected to PCR using bacteria-specific PCR primers. Then, denaturing gradient gel electrophoresis (DGGE) of the resulting amplicons was conducted as a means of assessing diversity of microbiota in the gastrointestinal (GI) tract. Results revealed that none of the prebiotics affected apparent digestibility coefficients of the diet based on fish meal and soybean meal compared with the basal diet, although the diet supplemented with MOS consistently yielded the lowest values. In addition, goldfish digested the fish-meal–soybean-meal-based diets as well as the control diet. No differences in microbiota of goldfish fed the various prebiotics were revealed by DGGE. These results are in contrast to those obtained with carnivorous fish species such as the red drum Sciaenops ocellatus in which the prebiotics increased digestibility coefficients of diets based on fish meal and soybean meal and altered GI tract microbiota.
Pilot Field Trial to Evaluate SLICE (0.2% Emamectin Benzoate)–Medicated Feed to Reduce a Natural Infestation of Salmincola californiensis in Freshwater-Reared Rainbow Trout
Authors: Gunn Carolyn , Carty Daniel , Walker Peter G , Colburn Patricia A , Bowker James D 
Published: July 2012

Abstract
Salmincola spp. infestations can adversely affect freshwater-reared salmonids. Control methods tested to date have had limited success; consequently, we conducted a pilot field trial to evaluate SLICE (0.2% emamectin benzoate [EB])–medicated feed to reduce a natural infestation of S. californiensis in freshwater-reared rainbow trout Oncorhynchus mykiss. Before the trial started, 96 of 1,500 rainbow trout broodstock held in a flow-through raceway were impartially captured, sedated, uniquely tagged, and returned to the raceway. Pretreatment S. californiensis infestation prevalence and intensity were 97% and 10.4 ± 7.6 (mean ± SD) adult female parasites per fish, respectively. Treatment was administered at 50 μg EB·kg fish−1·d−1 for 7 d. By the end of the trial (43 d posttreatment), infestation prevalence and intensity had decreased to 32% and 1.6 ± 1.1 adult female parasites per fish, respectively. These results suggest that SLICE-medicated feed can be used to reduce natural infestations of S. californiensis in freshwater-reared rainbow trout.
How Economic Contractions and Expansions Affect Expenditure Patterns
Authors: Kamakura Wagner A. , Yuxing Du Rex 
Published: July 2012

Abstract
In this study, we attempt to understand how household budget allocations across various expenditure categories change when the economy is in recession or expansion. The common assumption is that a household’s tastes would not change as a function of economic conditions and therefore any adjustments in expenditure patterns during economic contractions/expansions would simply be due to changes in the consumption budget. Standard economic models translate these budgetary effects into lateral movements along a set of fixed Engel curves, which relate category expenditure shares to total expenditures. We propose and test a conceptual framework based on the notion of relative consumption, which prescribes that, for any given total consumption budget, expenditure shares for positional goods/services will decrease during a recession, while shares for nonpositional goods/services will increase (i.e., shifting the entire Engel curve upward or downward, depending on the nature of the expenditure category and the economic conditions).
Plate Size and Color Suggestibility: The Delboeuf Illusion’s Bias on Serving and Eating Behavior
Authors: Van Ittersum Koert , Wansink Brian 
Published: July 2012

Abstract
Despite the challenged contention that consumers serve more onto larger dinnerware, it remains unclear what would cause this and who might be most at risk. The results of five studies suggest that the neglected Delboeuf illusion may explain how the size of dinnerware creates two opposing biases that lead people to overserve on larger plates and bowls and underserve on smaller ones. A countercyclical sinus-shaped relationship is shown to exist between these serving biases and the relative gap between the edge of the food and the edge of the dinnerware. Although these serving biases are difficult to eliminate with attention and education, changing the color of one’s dinnerware or tablecloth may help attenuate them. By showing that the Delboeuf illusion offers a mechanistic explanation for how dinnerware size can bias serving and intake, we open new theoretical opportunities for linking illusions to eating behavior and suggest how simple changes in design can improve consumer welfare.
How Happiness Affects Choice
Authors: Mogilner Cassie , Aaker Jennifer , Kamvar Sepandar D. 
Published: July 2012

AbstractConsumers want to be happy, and marketers are increasingly trying to appeal to consumers’ pursuit of happiness. However, the results of six studies reveal that what happiness means varies, and consumers’ choices reflect those differences. In some cases, happiness is defined as feeling excited, and in other cases, happiness is defined as feeling calm. The type of happiness pursued is determined by one’s temporal focus, such that individuals tend to choose more exciting options when focused on the future, and more calming options when focused on the present moment. These results suggest that the definition of happiness, and consumers’ resulting choices, are dynamic and malleable.
Consumer Response to Versioning: How Brands’ Production Methods Affect Perceptions of Unfairness
Authors: Gershoff Andrew D. , Kivetz Ran , Keinan Anat 
Published: July 2012

Abstract
Marketers often extend product lines by offering limited-capability models that are created by removing or degrading features in existing models. This production method, called versioning, has been lauded because of its ability to increase both consumer and firm welfare. According to rational utility models, consumers weigh benefits relative to their costs in evaluating a product. So the production method should not be relevant. Anecdotal evidence suggests otherwise. Six studies show how the production method of versioning may be perceived as unfair and unethical and lead to decreased purchase intentions for the brand. Building on prior work in fairness, the studies show that this effect is driven by violations of norms and the perceived similarity between the inferior, degraded version of a product and the full-featured model offered by the brand.
Paving the future: finding suitable ISMB venues
Authors: Rost Burkhard , Gaasterland Terry , Lengauer Thomas , Linial Michal , Markel Scott , Morrison McKay B.J. , Schneider Reinhard , Horton Paul , Kelso Janet 
Published: July 2012

Abstract
The International Society for Computational Biology, ISCB, organizes the largest event in the field of computational biology and bioinformatics, namely the annual international conference on Intelligent Systems for Molecular Biology, the ISMB. This year at ISMB 2012 in Long Beach, ISCB celebrated the 20th anniversary of its flagship meeting. ISCB is a young, lean and efficient society that aspires to make a significant impact with only limited resources. Many constraints make the choice of venues for ISMB a tough challenge. Here, we describe those challenges and invite the contribution of ideas for solutions.
Contact: assistant@rostlab.org
RIBFIND: a web server for identifying rigid bodies in protein structures and to aid flexible fitting into cryo EM maps
Authors: Pandurangan Arun Prasad , Topf Maya 
Published: July 2012

Abstract
Motivation: To better analyze low-resolution cryo electron microscopy maps of macromolecular assemblies, component atomic structures frequently have to be flexibly fitted into them. Reaching an optimal fit and preventing the fitting process from getting trapped in local minima can be significantly improved by identifying appropriate rigid bodies (RBs) in the fitted component.
Results: Here we present the RIBFIND server, a tool for identifying RBs in protein structures. The server identifies RBs in proteins by calculating spatial proximity between their secondary structural elements.
Availability: The RIBFIND web server and its standalone program are available at http://ribfind.ismb.lon.ac.uk.
Contact: a.pandurangan@mail.cryst.bbk.ac.uk
Supplementary Information: Supplementary data are available at Bioinformatics online.
A regression model for estimating DNA copy number applied to capture sequencing data
Authors: Rigaill Guillem J. , Cadot Sidney , Kluin Roelof J.C. , Xue Zheng , Bernards Rene , Majewski Ian J. , Wessels Lodewyk F.A. 
Published: July 2012

Abstract
Motivation: Target enrichment, also referred to as DNA capture, provides an effective way to focus sequencing efforts on a genomic region of interest. Capture data are typically used to detect single-nucleotide variants. It can also be used to detect copy number alterations, which is particularly useful in the context of cancer, where such changes occur frequently. In copy number analysis, it is a common practice to determine log-ratios between test and control samples, but this approach results in a loss of information as it disregards the total coverage or intensity at a locus.
Results: We modeled the coverage or intensity of the test sample as a linear function of the control sample. This regression approach is able to deal with regions that are completely deleted, which are problematic for methods that use log-ratios. To demonstrate the utility of our approach, we used capture data to determine copy number for a set of 600 genes in a panel of nine breast cancer cell lines. We found high concordance between our results and those generated using a single-nucleotide polymorphsim genotyping platform. When we compared our results with other log-ratio-based methods, including ExomeCNV, we found that our approach produced better overall correlation with SNP data.
Availability: The algorithm is implemented in C and R and the code can be downloaded from http://bioinformatics.nki.nl/ocs/
Contact: l.wessels@nki.nl
Supplementary information: Supplementary data are available at Bioinformatics online.
Is juvenile anchovy a feeding resource for the demersal community in the Bay of Biscay? On the availability of pelagic prey to demersal predators
Authors: López-López Lucía , Preciado Izaskun , Villamor Begoña , Velasco Francisco , Iglesias Magdalena , Nogueira Enrique , Gutierrez-Zabala Jose Luis , Olaso Ignacio 
Published: July 2012

Abstract
López-López, L., Preciado, I., Villamor, B., Velasco, F., Iglesias, M., Nogueira, E. Gutierrez-Zabala, J. L., and Olaso, I. 2012. Is juvenile anchovy a feeding resource for the demersal community in the Bay of Biscay? On the availability of pelagic prey to demersal predators. – ICES Journal of Marine Science, 69: . The role that juvenile anchovy (Engraulis encrasicolus) play as a food resource for the demersal community in the southern Bay of Biscay is assessed using 21 years of anchovy abundance data and demersal predator diets. During the study period, a total of 26 fish and elasmobranch species preyed on anchovy either frequently or occasionally. Predators with a crustacean-based diet targeted the smaller anchovy individuals. The size range of anchovy juveniles (centred at 7.5–8.9 cm) was comparable to that of the largest nektonic–benthic crustaceans, but generally smaller than other demersal and pelagic fish prey. Hake (Merluccius merluccius) and megrim (Lepidorhombus whiffiagonis) were the predators that consumed the highest number of anchovy, one of the main prey items driving the variability of their diets. Anchovy consumption conformed only partially to the abundance of anchovy in the southern Bay of Biscay, suggesting that factors other than abundance might condition its availability to demersal predators. Prey size could be one of them, as the size of the anchovy preyed on proved to be significantly smaller than the individuals collected with bottom trawls. However, other factors, such as the vertical position of the shoals of anchovy juveniles, could also constrain anchovy availability to demersal predators.
Are Anesthesia and Surgery during Infancy Associated with Altered Academic Performance during Childhood?
Authors: Block Robert I. , Thomas Joss J. , Bayman Emine O. , Choi James Y. , Kimble Karolie K. , Todd Michael M. 
Published: July 2012

Background
Although studies in neonatal animals show that anesthetics have neurotoxic effects, relevant human evidence is limited. We examined whether children who had surgery during infancy showed deficits in academic achievement.

Methods
We attempted to contact parents of 577 children who, during infancy, had one of three operations typically performed in otherwise healthy children. We compared scores on academic achievement tests with population norms.

Results
Composite scores were available for 287 patients. The mean normal curve equivalent score was 43.0±22.4 (mean±SD), lower than the expected normative value of 50, P<0.0001 by one-sample Student t test; and 35 (12%) had scores below the 5th percentile, more than expected, P<0.00001 by binomial test. Of 133 patients who consented to participate so that their scores could be examined in relation to their medical records, the mean score was 45.9±22.9, P=0.0411; and 15 (11%) scored below the 5th percentile, P=0.0039. Of 58 patients whose medical records showed no central nervous system problems/potential risk factors during infancy, 8 (14%) scored below the 5th percentile, P=0.008; however, the mean score, 47.6±23.4, was not significantly lower than expected, P=0.441. Duration of anesthesia and surgery correlated negatively with scores (r=-0.34, N=58, P=0.0101).

Conclusions
Although the findings are consistent with possible adverse effects of anesthesia and surgery during infancy on subsequent academic achievement, other explanations are possible and further investigations are needed.
Formation of Complex Extrachromosomal T-DNA Structures in Agrobacterium tumefaciens-Infected Plants
Authors: Singer Kamy , Shiboleth Yoel M. , Li Jianming , Tzfira Tzvi 
Published: July 2012

Abstract
Agrobacterium tumefaciens is a unique plant pathogenic bacterium renowned for its ability to transform plants. The integration of transferred DNA (T-DNA) and the formation of complex insertions in the genome of transgenic plants during A. tumefaciens-mediated transformation are still poorly understood. Here, we show that complex extrachromosomal T-DNA structures form in A. tumefaciens-infected plants immediately after infection. Furthermore, these extrachromosomal complex DNA molecules can circularize in planta. We recovered circular T-DNA molecules (T-circles) using a novel plasmid-rescue method. Sequencing analysis of the T-circles revealed patterns similar to the insertion patterns commonly found in transgenic plants. The patterns include illegitimate DNA end joining, T-DNA truncations, T-DNA repeats, binary vector sequences, and other unknown “filler” sequences. Our data suggest that prior to T-DNA integration, a transferred single-stranded T-DNA is converted into a double-stranded form. We propose that termini of linear double-stranded T-DNAs are recognized and repaired by the plant’s DNA double-strand break-repair machinery. This can lead to circularization, integration, or the formation of extrachromosomal complex T-DNA structures that subsequently may integrate.