bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mechanisms driving recruitment variability in fish: comparisons between the Laurentian Great Lakes and marine systems
Authors: Pritt Jeremy J. , Roseman Edward F. , O'Brien Timothy P. 
Published: May 2014

AbstractIn his seminal work, Hjort (in Fluctuations in the great fisheries of Northern Europe. Conseil Parmanent International Pour L'Exploration De La Mar. Rapports et Proces-Verbaux, 20: 1–228, 1914) observed that fish population levels fluctuated widely, year-class strength was set early in life, and egg production by adults could not alone explain variability in year-class strength. These observations laid the foundation for hypotheses on mechanisms driving recruitment variability in marine systems. More recently, researchers have sought to explain year-class strength of important fish in the Laurentian Great Lakes and some of the hypotheses developed for marine fisheries have been transferred to Great Lakes fish. We conducted a literature review to determine the applicability of marine recruitment hypotheses to Great Lakes fish. We found that temperature, interspecific interactions, and spawner effects (abundance, age, and condition of adults) were the most important factors in explaining recruitment variability in Great Lakes fish, whereas relatively fewer studies identified bottom-up trophodynamic factors or hydrodynamic factors as important. Next, we compared recruitment between Great Lakes and Baltic Sea fish populations and found no statistical difference in factors driving recruitment between the two systems, indicating that recruitment hypotheses may often be transferable between Great Lakes and marine systems. Many recruitment hypotheses developed for marine fish have yet to be applied to Great Lakes fish. We suggest that future research on recruitment in the Great Lakes should focus on forecasting the effects of climate change and invasive species. Further, because the Great Lakes are smaller and more enclosed than marine systems, and have abundant fishery-independent data, they are excellent candidates for future hypothesis testing on recruitment in fish.
Suppression of Photosynthetic Gene Expression in Roots Is Required for Sustained Root Growth under Phosphate Deficiency
Authors: Kang Jun , Yu Haopeng , Tian Caihuan , Zhou Wenkun , Li Chuanyou , Jiao Yuling , Liu Dong 
Published: May 2014

Abstract
Plants cope with inorganic phosphate (Pi) deficiencies in their environment by adjusting their developmental programs and metabolic activities. For Arabidopsis (Arabidopsis thaliana), the developmental responses include the inhibition of primary root growth and the enhanced formation of lateral roots and root hairs. Pi deficiency also inhibits photosynthesis by suppressing the expression of photosynthetic genes. Early studies showed that photosynthetic gene expression was also suppressed in Pi-deficient roots, a nonphotosynthetic organ; however, the biological relevance of this phenomenon remains unknown. In this work, we characterized an Arabidopsis mutant, hypersensitive to Pi starvation7 (hps7), that is hypersensitive to Pi deficiency; the hypersensitivity includes an increased inhibition of root growth. HPS7 encodes a tyrosylprotein sulfotransferase. Accumulation of HPS7 proteins in root tips is enhanced by Pi deficiency. Comparative RNA sequencing analyses indicated that the expression of many photosynthetic genes is activated in roots of hps7. Under Pi deficiency, the expression of photosynthetic genes in hps7 is further increased, which leads to enhanced accumulation of chlorophyll, starch, and sucrose. Pi-deficient hps7 roots also produce a high level of reactive oxygen species. Previous research showed that the overexpression of GOLDEN-like (GLK) transcription factors in transgenic Arabidopsis activates photosynthesis in roots. The GLK overexpressing (GLK OX) lines also exhibit increased inhibition of root growth under Pi deficiency. The increased inhibition of root growth in hps7 and GLK OX lines by Pi deficiency was completely reversed by growing the plants in the dark. Based on these results, we propose that suppression of photosynthetic gene expression is required for sustained root growth under Pi deficiency.
Structure of tomato wound-induced leucine aminopeptidase sheds light on substrate specificity
Authors: Duprez Kevin , Scranton Melissa A. , Walling Linda L. , Fan Li 
Published: May 2014

The acidic leucine aminopeptidase (LAP-A) from tomato is induced in response to wounding and insect feeding. Although LAP-A showsin vitropeptidase activity towards peptides and peptide analogs, it is not clear what kind of substrates LAP-A hydrolyzesin vivo. In the current study, the crystal structure of LAP-A was determined to 2.20 Å resolution. Like other LAPs in the M17 peptidase family, LAP-A is a dimer of trimers containing six monomers of bilobal structure. Each monomer contains two metal ions bridged by a water or a hydroxyl ion at the active site. Modeling of different peptides or peptide analogs in the active site of LAP-A reveals a spacious substrate-binding channel that can bind peptides of five or fewer residues with few geometric restrictions. The sequence specificity of the bound peptide is likely to be selected by the structural and chemical restrictions on the amino acid at the P1 and P1′ positions because these two amino acids have to bind perfectly at the active site for hydrolysis of the first peptide bond to occur. The hexameric assembly results in the merger of the open ends of the six substrate-binding channels from the LAP-A monomers to form a spacious central cavity allowing the hexameric LAP-A enzyme to simultaneously hydrolyze six peptides containing up to six amino acids each. The hexameric LAP-A enzyme may also hydrolyze long peptides or proteins if only one such substrate is bound to the hexamer because the substrate can extend through the central cavity and the two major solvent channels between the two LAP-A trimers.
Butterfly-effect for massively separated flows
Authors: Lohner Rainald , Britto Dominic , Michailski Alexander , Haug Eberhard 
Published: May 2014

Purpose
– During a routine benchmarking and scalability study of CFD codes for typical large-scale wind engineering runs, it was observed that the resulting loads for buildings varied considerably with the number of parallel processors employed. The differences remained very small at the beginning of a typical run, and then grew progressively to a state of total dissimilitude. A “butterfly-effect” for such flows was suspected and later confirmed. The paper aims to discuss these issues.

Design/methodology/approach
– A series of numerical experiments was conducted for massively separated flows. The same geometry – a cube in front of an umbrella – was used to obtain the flowfields using different grids, different numbers of domains/processors, slightly different inflow conditions and different codes.

Findings
– In all of these cases the differences remained very small at the beginning of a typical run, they then grew progressively to a state of total dissimilitude. While the mean and maximum loads remained similar, the actual (deterministic) instantiations were completely different. The authors therefore suspect that for flows of this kind a “butterfly effect” is present, whereby even very small (roundoff) errors can have a pronounced effect on the actual deterministic instantiation of a flowfield.

Research limitations/implications
– This implies that for flows of this kind the CFD runs have to be carried out to much larger times than formerly expected (and done) in order to obtain statistically relevant ensembles.

Practical implications
– For practical calculations this implies running to much larger times in order to reach statistically relevant ensembles, with the associated much higher CPU time requirements.

Originality/value
– This is the first time such a finding has been reported in the numerical wind engineering context.
Does Lesson Study work?
Authors: Ming Cheung Wai , Yee Wong Wing 
Published: May 2014

Purpose– There has been rapid proliferation of Lesson Studies and Learning Studies over the world. Do they really help teachers’ professional development and student learning? The purpose of this paper is to review studies from 2000 to 2010 on Lesson Study and Learning Study to unravel their benefits on teachers and students.Design/methodology/approach– Relevant studies were screen and extracted on available electronic databases to evaluate outcome of Lesson Study and Learning Study. The results were based on nine studies which examined the achievement of Learning Study and Lesson Study.Findings– All reviews identified positive evidence supporting the benefits of Lesson Study and Learning Study as powerful tool to help teachers examine their practices and enhance student learning. Although all nine studies showed positive effects of Lesson Study and Learning Study on teaching, learning or both, different outcome measures were employed and the study designs varied in qualities.Originality/value– More well-controlled studies with consistent and validated outcome measures were recommended in the future to address the short- and long-term effects of Lesson Study on students, teachers, and school level. Efforts should be focussed on unveiling the relationship between what is taught and what is learned. Studies using these approaches with more vigorous procedures in randomization and blinding should be implemented.
The impact of transaction costs and institutional pressure on supplier environmental practices
Authors: L. Tate Wendy , M. Ellram Lisa , J. Dooley Kevin 
Published: May 2014

Purpose– Suppliers play a more significant role in the environmental footprint of supply chains than most final manufacturers. The purpose of this paper is to apply transaction costs and institutional theory to help understand why the more conservative, or reactive suppliers may or may not be likely to adopt environmental practices.Design/methodology/approach– This research builds on a prior conceptual paper and uses the results of a survey to test whether transaction costs and institutional theory can provide insight into supplier's adoption of environmental practices.Findings– This research finds that perceived transaction costs affect supplier cooperation in adopting environmental practices. Suppliers are more likely to adopt an environmental practice if information-seeking costs are low or the cost of adoption is considered necessary to maintain the relationship. Data did not support the hypotheses concerning institutional pressures.Originality/value– There is much research in the area of proactive adoption of environmental business practices. This research looks specifically at what influences the adoption of environmental business practices by suppliers that are more reactive or hesitant to be leaders in this area.
Exploring the educative potential of eating disorder memoirs
Authors: McAllister Margaret , Lee Brien Donna , Alexander June , Flynn Trudi 
Published: May 2014

Purpose– The purpose of this paper is to explore the potential benefits that books, and specifically memoirs, may offer mental health students, positing that first person testimonials may make the complex experiences of a mental health challenge, in this case eating disorders (ED), accessible to learners.Design/methodology/approach– The paper presents a pedagogical approach, based on transformative learning (TL), to assist in encouraging the development of a Recovery Approach in students. TL is a pedagogy that is interested in problematic practices that keep afflicting an area such as mental health, such as the imbalanced focus on learning illness rather than wellbeing, and in pondering and revising the educational solutions.Findings– The paper proposes that forward movement in this area will be based on considering and developing such innovative curricula, and researching its impact.Originality/value– By virtue of their accessibility, memoirs could offer to a large audience the benefits of universality, empathy, hope and guidance. Teachers and learners could be making use of these books in face-to-face or online activities. This paper explores the groundwork that is needed before ED memoirs can be confidently recommended as an empowering tool.
Psychological morbidity associated with ovarian cancer screening: results from more than 23 000 women in the randomised trial of ovarian cancer screening (UKCTOCS)
Authors: Barrett J , Jenkins V , Farewell V , Menon U , Jacobs I , Kilkerr J , Ryan A , Langridge C , Fallowfield L ,   UKCTOCS trialists
Published: May 2014

ObjectiveTo examine the psychological sequelae associated with abnormal screening in the United Kingdom Collaborative Trial of Ovarian Cancer Screening (UKCTOCS).DesignProspective, longitudinal randomised control trial.SettingSixteen UKCTOCS centres.SampleWomen aged 50–70 years randomised to annual multimodal screening, ultrasound screening or control groups.MethodsTwo groups were followed for 7 years: (1) a random sample (n = 1339), taken from all three study groups; and (2) an events sample (n = 22 035) of women with abnormal screens resulting in the need for repeat testing of either low or higher level intensity.Main outcome measuresPatient‐reported measures of anxiety (scores ranging from 20 to 80) and psychological morbidity.ResultsIn the random sample the mean difference between anxiety scores after a repeat screening and those following an annual screening was 0.4 (95% CI −0.46, 1.27), and in the events sample it was 0.37 (95% CI 0.23, 0.51). The risk of psychological morbidity was only increased in the event sample for women requiring higher level repeat screening (OR 1.28; 95% CI 1.18, 1.39). The risk of psychological morbidity in women with ovarian cancer was higher at both 6 weeks (OR 16.2; 95% CI 9.19, 28.54) and 6 months (OR 3.32; 95% CI 1.91, 5.77) following surgery.ConclusionsScreening does not appear to raise anxiety but psychological morbidity is elevated by more intense repeat testing following abnormal annual screens, and in women after surgical treatment for ovarian cancer.
Metamicrobiomics in herbivore beetles of the genus Cryptocephalus (Chrysomelidae): toward the understanding of ecological determinants in insect symbiosis
Authors: Montagna Matteo , Gómez‐Zurita Jesús , Giorgi Annamaria , Epis Sara , Lozzia Giuseppe , Bandi Claudio 
Published: May 2014

AbstractThe Cryptocephalus marginellus (Coleoptera: Chrysomelidae) complex is composed by six species that are supposed to have originated by events of allo‐ or parapatric speciation. In the present study we investigated the alternative hypotheses that the bacterial communities associated with six populations of this species complex are shaped by environmental factors, or reflect the proposed pattern of speciation. The microbiota associated with the six populations, from five species of the complex, have been characterized through 16S rRNA pyrotag sequencing. Based on a 97% sequence similarity threshold, data were clustered into 381 OTUs, which were analyzed using a variety of diversity indices. The microbiota of C. acquitanus and C. marginellus (Calanques) were the most diverse (over 100 OTUs), while that from C. zoiai yielded less bacterial diversity (45 OTUs). Taxonomic assignment revealed Proteobacteria, Tenericutes and Firmicutes as the dominant components of these beetles’ microbiota. The most abundant genera were Ralstonia, Sphingomonas, Rickettsia, and Pseudomonas. Different strains of Rickettsia were detected in C. eridani and C. renatae. The analysis of β‐diversity revealed high OTU turnover among the populations of C. marginellus complex, with only few shared species. Hierarchical clustering taking into account relative abundances of OTUs does not match the phylogeny of the beetles, therefore we hypothesize that factors other than phylogenetic constraints play a role in shaping the insects’ microbiota. Environmental factors that could potentially affect the composition of bacterial communities were tested by fitting them on the results of a multi‐dimensional scaling analysis. No significant correlations were observed towards the geographic distances or the host plants, while the composition of the microbiota appeared associated with altitude. The metabolic profiles of the microbiotas associated with each population were inferred from bacterial taxonomy, and interestingly, the obtained clustering pattern was consistent with the host phylogeny.
Distance, flow and PCR inhibition: eDNA dynamics in two headwater streams
Authors: Jane Stephen F. , Wilcox Taylor M. , McKelvey Kevin S. , Young Michael K. , Schwartz Michael K. , Lowe Winsor H. , Letcher Benjamin H. , Whiteley Andrew R. 
Published: May 2014

AbstractEnvironmental DNA (eDNA) detection has emerged as a powerful tool for monitoring aquatic organisms, but much remains unknown about the dynamics of aquatic eDNA over a range of environmental conditions. DNA concentrations in streams and rivers will depend not only on the equilibrium between DNA entering the water and DNA leaving the system through degradation, but also on downstream transport. To improve understanding of the dynamics of eDNA concentration in lotic systems, we introduced caged trout into two fishless headwater streams and took eDNA samples at evenly spaced downstream intervals. This was repeated 18 times from mid‐summer through autumn, over flows ranging from approximately 1–96 L/s. We used quantitative PCR to relate DNA copy number to distance from source. We found that regardless of flow, there were detectable levels of DNA at 239.5 m. The main effect of flow on eDNA counts was in opposite directions in the two streams. At the lowest flows, eDNA counts were highest close to the source and quickly trailed off over distance. At the highest flows, DNA counts were relatively low both near and far from the source. Biomass was positively related to eDNA copy number in both streams. A combination of cell settling, turbulence and dilution effects is probably responsible for our observations. Additionally, during high leaf deposition periods, the presence of inhibitors resulted in no amplification for high copy number samples in the absence of an inhibition‐releasing strategy, demonstrating the necessity to carefully consider inhibition in eDNA analysis.
Pipeliner: software to evaluate the performance of bioinformatics pipelines for next‐generation resequencing
Authors: Nevado B. , Perez‐Enciso M. 
Published: May 2014

AbstractThe choice of technology and bioinformatics approach is critical in obtaining accurate and reliable information from next‐generation sequencing (NGS) experiments. An increasing number of software and methodological guidelines are being published, but deciding upon which approach and experimental design to use can depend on the particularities of the species and on the aims of the study. This leaves researchers unable to produce informed decisions on these central questions. To address these issues, we developed pipeliner – a tool to evaluate, by simulation, the performance of NGS pipelines in resequencing studies. Pipeliner provides a graphical interface allowing the users to write and test their own bioinformatics pipelines with publicly available or custom software. It computes a number of statistics summarizing the performance in SNP calling, including the recovery, sensitivity and false discovery rate for heterozygous and homozygous SNP genotypes. Pipeliner can be used to answer many practical questions, for example, for a limited amount of NGS effort, how many more reliable SNPs can be detected by doubling coverage and halving sample size or what is the false discovery rate provided by different SNP calling algorithms and options. Pipeliner thus allows researchers to carefully plan their study's sampling design and compare the suitability of alternative bioinformatics approaches for their specific study systems. Pipeliner is written in C++ and is freely available from http://github.com/brunonevado/Pipeliner.
Evaluation of metatranscriptomic protocols and application to the study of freshwater microbial communities
Authors: Tsementzi Despina , Poretsky Rachel , Rodriguez‐R Luis M. , Luo Chengwei , Konstantinidis Konstantinos T. 
Published: May 2014

SummaryMetatranscriptomics of environmental samples enables the identification of community activities without a priori knowledge of taxonomic or functional composition. However, several technical challenges associated with the RNA preparation protocols can affect the relative representation of transcripts and data interpretation. Here, seven replicate metatranscriptomes from planktonic freshwater samples (Lake Lanier, USA) were sequenced to evaluate technical and biological reproducibility of different RNA extraction protocols. Organic versus bead‐beating extraction showed significant enrichment for low versus high G + C% mRNA populations respectively. The sequencing data were best modelled by a negative binomial distribution to account for the large technical and biological variation observed. Despite the variation, the transcriptional activities of populations that persisted in year‐round metagenomes from the same site consistently showed distinct expression patterns, reflecting different ecologic strategies and allowing us to test prevailing models on the contribution of both rare biosphere and abundant members to community activity. For instance, abundant members of the Verrucomicrobia phylum systematically showed low transcriptional activity compared with other abundant taxa. Our results provide a practical guide to the analysis of metatranscriptomes and advance understanding of the activity and ecology of abundant and rare members of temperate freshwater microbial communities.
Spatially constrained clustering of ecological networks
Authors: Miele Vincent , Picard Franck , Dray Stéphane 
Published: May 2014

Summary

Spatial ecological networks are widely used to model interactions between georeferenced biological entities (e.g. populations or communities). The analysis of such data often leads to a two‐step approach where groups containing similar biological entities are firstly identified and the spatial information is used afterwards to improve the ecological interpretation.

We develop an integrative approach to retrieve groups of nodes that are geographically close and ecologically similar. Our model‐based spatially constrained method embeds the geographical information within a regularization framework by adding some constraints to the maximum likelihood estimation of parameters.

A simulation study and the analysis of two real data sets demonstrate that our approach is able to detect complex spatial patterns that are ecologically meaningful.

The model‐based framework allows us to consider external information (e.g. geographical proximities, covariates) in the analysis of ecological networks and appears to be an appealing alternative to consider such data.
Effect of cricoid pressure on placement of the I‐gel™: a randomised study
Authors: Hashimoto Y. , Asai T. , Arai T. , Okuda Y. 
Published: May 2014

SummaryWe studied 40 adult patients to see if cricoid pressure affected placement of the I‐gel™. In a randomised crossover design, the i‐gel was placed with and without cricoid pressure, and we compared the success rate of adequate ventilation through the i‐gel, time to placement and the rate of optimal position of the device between the two circumstances. Cricoid pressure significantly decreased the success rate of adequate ventilation through the i‐gel (40 vs 34 patients) (p = 0.041, 95% CI for difference 4–26%), and significantly decreased the rate of the optimal position (39 vs 17 patients) (p < 0.001). The time to achieve adequate ventilation was significantly longer (p < 0.001) with cricoid pressure than without (median difference 8 s; 95%CIfor median difference 3–12 s). Cricoid pressure significantly decreases the success rate of ventilation through the i‐gel, but the success rate of ventilation through the i‐gel is reasonably high.