bluuebunny/crossref_metadata_2025 huggingface dataset:
Propositions, attitudinal objects, and the distinction between actions and products
Authors: Moltmann Friederike
Published: June 2016

Propositions as mind-independent abstract objects raise serious problems such as their cognitive accessibility and their ability to carry essential truth conditions, as a number of philosophers have recently pointed out. This paper argues that ‘attitudinal objects’ or kinds of them should replace propositions as truth bearers and as the (shared) objects of propositional attitudes. Attitudinal objects, entities like judgments, beliefs, and claims, are not states or actions, but rather their (spatio-temporally coincident) products, following the distinction between actions and products introduced by Twardowski (1912). The paper argues that the action–product distinction is not tied to particular terms in a particular language, but is to be understood as the more general distinction between an action and the (abstract or physically realized) artifact that it creates. It thus includes the distinction between the passing of a law and the law itself and an act of artistic creation and the created work of art.
Survival, Tag Retention, and Growth of Spot and Mummichog following PIT Tag Implantation
Authors: Brewer Melissa A. , Rudershausen Paul J. , Sterba-Boatwright Blair D. , Merrell Jeffery H. , Buckel Jeffrey A.
Published: June 2016

We conducted three laboratory studies to determine the effects of surgically implanted, passive integrated transponder (PIT) tags on survival, tag retention, and growth in two abundant estuarine fishes. The effects of the 12.5-mm PIT tags were examined in Spot Leiostomus xanthurus, and the effects of the 12.5-mm and 8.4-mm tags were examined in Mummichog Fundulus heteroclitus. For each experiment, Spot and Mummichogs were divided into three size-groups: small, medium, and large. Tagged Spot had lower survival rates than the untagged conspecifics with the exception of the larger Spot, where there was no difference in survival rates. Large Spot also had the highest tag retention (86%) and tagging “success” (i.e., 80% survived and retained their tag). There was no significant difference in the survival rate between the 12.5-mm tagged and untagged Mummichogs; there was no significant effect of Mummichog size on survival, tag retention, or success; and success for all 12.5-mm tagged Mummichogs was 87%. Survival estimates were 90%, 95%, and 100% for the small, medium, and large 8.4-mm tagged Mummichogs; and tag retention was 100% for the survivors. Within the medium and large sized Spot and Mummichogs (for both 8.4-mm and 12.5-mm tags), there was no effect of PIT tag presence on growth (length or weight). Spot should be >68 mm TL to obtain a tag success of >90% using 12.5-mm PIT tags. Tagging was successful for Mummichogs in the smallest sized groups examined but there was also an indication of lower growth rates for Mummichogs <50 mm marked with 12.5-mm PIT tags. Mummichogs should thereby be >50 mm when initially tagged with 12.5-mm PIT tags and more than ~36 mm TL when tagged with 8.4-mm PIT tags. PIT tags can be used to successfully mark relatively small Spot and Mummichogs, potentially allowing for robust estimates of their demographic rates.

Received April 2, 2015; accepted December 16, 2015 Published online May 31, 2016
Isolation, Migration, and Local Recruitment Drive Persistence of Cutthroat Trout in Tributaries near American Falls Reservoir
Authors: Bingham Daniel M. , Buckskin Preston , Osborne Hunter
Published: June 2016

We analyzed 67 SNPs to describe the genetics of Yellowstone Cutthroat Trout Oncorhynchus clarkii bouvieri in seven tributaries near American Falls Reservoir, Idaho. We detected Yellowstone Cutthroat Trout in all but one site despite significant historical stocking of Rainbow Trout O. mykiss. Three of four relatively low-elevation sites near the reservoir contained Yellowstone Cutthroat Trout in sympatry with early-generation hybrids and Rainbow Trout yet contained no physical barriers to admixture. A posteriori assignment tests suggested that migrants from a nearby headwater population in Ross Fork Creek and possibly recruitment by local-origin Yellowstone Cutthroat Trout with fluvial or adfluvial life histories drive persistence in these sites. In contrast, hybridization was rare or absent in headwater populations and was associated with complete or apparent physical isolation. We also compared genetic diversity of our samples with Yellowstone basin Yellowstone Cutthroat Trout and Bear River Bonneville Cutthroat Trout O. c. utah to examine possible historical gene flow resulting from hydrogeological connections during the Pleistocene. Multivariate analysis showed that most genetic variation among individuals was explained by divergence of Yellowstone basin Yellowstone Cutthroat Trout from our samples and Bear River Bonneville Cutthroat Trout, which supports recent mtDNA studies and a possible change in taxonomic nomenclature. Our results indicate that, due to relative isolation and downstream emigration, headwater populations are critical to the persistence of Yellowstone Cutthroat Trout and thus loss of such populations would likely threaten the subspecies throughout the region. Management actions to reduce threats from established, nonnative Rainbow Trout populations will likely have to be multifaceted and may include a combination of targeted removal of Rainbow Trout and hybrids and the use of physical barriers to prevent further dispersal.

Received April 19, 2015; accepted February 7, 2016 Published online May 31, 2016
Linking Oceanographic Modeling and Benthic Mapping with Habitat Suitability Models for Pink Shrimp on the West Florida Shelf
Authors: Rubec Peter J. , Lewis Jesse , Reed David , Santi Christi , Weisberg Robert H. , Zheng Lianyuan , Jenkins Chris , Ashbaugh Charles F. , Lashley Curt , Versaggi Salvatore
Published: June 2016

Research was undertaken to model and map the spatial distributions and abundances of pink shrimp Farfantepenaeus duorarum on the West Florida Shelf (WFS) using habitat suitability modeling (HSM). Data loggers and electronic logbook systems on three shrimp boats were used to gather catch and effort data along with bottom temperature, salinity, and depth data at the fishing locations. Vessel monitoring system (VMS) data supplied by the fishing company helped delineate areas with high fishing activity. For the vessels participating in this study, significantly higher mean catch per unit effort (CPUE) of pink shrimp was realized on the WFS during June–September 2004 and October–December 2004 than during January–March 2005 and April–June 2005. Suitability functions were created to predict CPUE in relation to depth, aspect, bottom type, bottom temperature, current speed, current direction, and VMS zone. Oceanographic modeling was conducted monthly from March 2004 to June 2005. Bottom current speed and direction indicated marked upwelling onto the WFS during 2004 and downwelling during 2005. The HSM linked to GIS was used to predict the spatial distributions and abundances of pink shrimp monthly from March 2004 to June 2005. While seven factors contributed to the HSM, current speed and current direction appeared to be most important during June–December 2004. The areas with the most pronounced upwelling were also the areas that the HSM predicted would have the highest mean CPUEs. This relationship was verified by overlaying the observed CPUE from the fishing vessels onto the suitability zones predicted by the HSM.

Received January 6, 2015; accepted August 1, 2015
Evaluation of Alternatives to Winter Closure of Black Sea Bass Pot Gear: Projected Impacts on Catch and Risk of Entanglement with North Atlantic Right Whales Eubalaena glacialis
Authors: Farmer Nicholas A. , Gowan Timothy A. , Powell Jessica R. , Zoodsma Barbara J.
Published: June 2016

Time–area closures have been widely used in fisheries management to prevent overfishing and reduce the bycatch of protected species. Due to quota overages and concerns about entanglement of federally protected North Atlantic right whales Eubalaena glacialis, the commercial harvest of Black Sea Bass Centropristis striata using pot gear has been prohibited in the southeastern United States in winter since 2009. Following the rebuilding of the Black Sea Bass stock and a change to the start date of the fishing year, the South Atlantic Fishery Management Council (SAFMC) increased the commercial annual catch limit (ACL) and is considering twelve alternatives to the pot gear closure that would revise the timing and/or spatial extent of the closure. Changes to this closure could affect the annual catch of Black Sea Bass and increase the risk of right whale entanglement in pot gear. Using historical fishing effort, landings, and right whale sightings data, we projected Black Sea Bass landings and the relative risk of right whale entanglement for each closure alternative, expressed in relative risk units (RRU). We predict that the ACL would be caught, resulting in an in-season closure for most of the proposed SAFMC closure alternatives. The relative risk of entanglement, estimated from the spatial and temporal overlap of Black Sea Bass pot gear fishing effort and right whale relative abundance, was lower for some alternatives than for others, and the relative differences between alternatives were consistent among uncertainty scenarios. The SAFMC's preferred alternative is projected to result in a relatively low increase in risk to North Atlantic right whales (3–15 RRU off North Carolina and 1–12 RRU off Florida–South Carolina). This framework demonstrates the use of temporally dynamic spatial overlays in assessing the impacts of time–area closures with multiple objectives.

Received April 23, 2015; accepted January 15, 2016
Orbit full groups for locally compact groups
Authors: Carderi A. , Le Maître F.
Published: June 2016

We show that the topological rank of an orbit full group generated by an ergodic, probability measure-preserving free action of a non-discrete unimodular locally compact Polish group is two. For this, we use the existence of a cross section and show that for a locally compact Polish group, the full group generated by any dense subgroup is dense in the orbit full group of the action of the group.

We prove that the orbit full group of a free action of a locally compact Polish group is extremely amenable if and only if the acting group is amenable, using the fact that the full group generates the von Neumann algebra of the action.
Fungicide Resistance Profiling inBotrytis cinereaPopulations from Blueberry in California and Washington and Their Impact on Control of Gray Mold
Authors: Saito S. , Michailides T. J. , Xiao C. L.
Published: June 2016

Gray mold caused by Botrytis cinerea is a major postharvest disease of blueberry grown in the Central Valley of California and western Washington State. Sensitivities to boscalid, cyprodinil, fenhexamid, fludioxonil, and pyraclostrobin, representing five different fungicide classes, were examined for 249 (California) and 106 (Washington) B. cinerea isolates recovered from decayed blueberry fruit or flowers. In California and Washington, 7 and 17 fungicide-resistant phenotypes, respectively, were detected: 66 and 49% of the isolates were resistant to boscalid, 20 and 29% were moderately resistant to cyprodinil, 29 and 29% were resistant to fenhexamid, and 66 and 55% were resistant to pyraclostrobin. All isolates from California were sensitive to fludioxonil, whereas 70% of the isolates from Washington showed reduced sensitivity to fludioxonil. In California, 26 and 30% of the isolates were resistant to two and three classes of fungicides, respectively. In Washington, 31, 14, 16, and 9% of the isolates were resistant to two, three, four, and five classes of fungicides, respectively. Inherent risk of the development of resistance to quinone outside inhibitor (QoI) fungicides was assessed by detecting the presence of the Bcbi-143/144 intron in gene cytb. The intron was detected in 11.8 and 40% of the isolates in California and Washington, respectively, suggesting that the risk of QoI resistance is higher in California than in Washington. On detached blueberry fruit inoculated with 11 isolates exhibiting different fungicide-resistant phenotypes, most fungicides failed to control gray mold on fruit inoculated with the respective resistant phenotypes but the mixture of cyprodinil and fludioxonil was effective against all fungicide-resistant phenotypes tested. Our findings would be useful in designing and implementing fungicide resistance management spray programs for control of gray mold in blueberry.
Sensitivity of Phytophthora nicotianae From Tobacco to Fluopicolide, Mandipropamid, and Oxathiapiprolin
Authors: Qu Tianli , Shao Yuanyuan , Csinos Alexander S. , Ji Pingsheng
Published: June 2016

Black shank incited by Phytophthora nicotianae is a devastating disease in the production of tobacco. Fungicides have been commonly used for managing the disease; however, there is only a narrow pool of effective fungicides. A few new fungicides became available in recent years, including fluopicolide, mandipropamid, and oxathiapiprolin, which reduced diseases incited by oomycetes under field conditions. Limited information is available regarding sensitivity of P. nicotianae isolates to these new fungicides. Research was conducted to determine effects of the three new fungicides on P. nicotianae isolates from tobacco in Georgia. Studies with 106 isolates indicated that they did not grow when agar medium was amended with the fungicides at the rate of 1 μg/ml. Twenty isolates were used for in vitro studies to determine sensitivity to the fungicides. Fluopicolide, mandipropamid, and oxathiapiprolin inhibited mycelial growth of the isolates with mean EC50 values (effective concentrations that provide 50% growth reduction) of 0.09, 0.04, and 0.001 μg/ml, respectively. EC50 values of fluopicolide, mandipropamid, and oxathiapiprolin for inhibiting sporangial formation were 0.15, 0.03, and 0.0002 μg/ml, respectively. EC50 values for suppressing zoospore germination averaged 0.16, 0.04, and 0.002 μg/ml for fluopicolide, mandipropamid, and oxathiapiprolin, respectively. Results from the study indicated that P. nicotianae isolates from tobacco in Georgia were sensitive to the fungicides, with lower EC50 for oxathiapiprolin than for fluopicolide and mandipropamid. The information on effectiveness and baseline sensitivity of fungicides on P. nicotianae will facilitate monitoring of resistance development in the pathogen population.
Identification and Differentiation of Monilinia Species Causing Brown Rot of Pome and Stone Fruit using High-Resolution Melting (HRM) Analysis
Authors: Papavasileiou Antonios , Madesis Panagiotis B. , Karaoglanidis George S.
Published: June 2016

Brown rot is a devastating disease of stone fruit caused by Monilinia spp. Among these species, Monilinia fructicola is a quarantine pathogen in Europe but has recently been detected in several European countries. Identification of brown rot agents relies on morphological differences or use of molecular methods requiring fungal isolation. The current study was initiated to develop and validate a high-resolution melting (HRM) method for the identification of the Monilinia spp. and for the detection of M. fructicola among other brown rot pathogens. Based on the sequence of the cytb intron from M. laxa, M. fructicola, M. fructigena, M. mumecola, M. linhartiana, and M. yunnanensis isolates originating from several countries, a pair of universal primers for species identification and a pair of primers specific to M. fructicola were designed. The specificity of the primers was verified to ensure against cross-reaction with other fungal species. The melting curve analysis using the universal primers generated six different HRM curve profiles, each one specific for each species. Τhe HRM analysis primers specific to M. fructicola amplified a 120-bp region with a distinct melt profile corresponding to the presence of M. fructicola, regardless of the presence of other species. HRM analysis can be a useful tool for rapid identification and differentiation of the six Monilinia spp. using a single primer pair. This novel assay has the potential for simultaneous identification and differentiation of the closely related Monilinia spp. as well as for the differentiation of M. fructicola from other common pathogens or saprophytes that may occur on the diseased fruit.
Reduced Virulence of Azoxystrobin-Resistant Zymoseptoria tritici Populations in Greenhouse Assays
Authors: Hagerty Christina H. , Mundt Christopher C.
Published: June 2016

The development of resistance to multiple fungicide classes is currently limiting disease management options for many pathogens, while the discovery of new fungicide classes may become less frequent. In light of this, more research is needed to quantify virulence trade-offs of fungicide resistance in order to more fully understand the implications of fungicide resistance on pathogen fitness. The purpose of this study was to measure the virulence of azoxystrobin-resistant and -sensitive Zymoseptoria tritici populations collected from North and South Willamette Valley, Oregon, in 2012 and 2015. Inoculum mixtures of known fungicide-resistant phenotypes were used to simulate natural field conditions, where multiple genotypes exist and interact in close proximity. Six greenhouse inoculations were conducted over 2 years, and virulence of the isolate mixtures was evaluated in planta. We considered virulence to be “the degree of pathology caused by the organism” and visually estimated the percent area of leaf necrosis as a measure of virulence. In greenhouse conditions, a consistent association of reduced virulence with azoxystrobin-resistant Z. tritici isolate mixtures was observed. North Willamette Valley and South Willamette Valley populations did not differ in virulence.
Pathways of information transmission among wild songbirds follow experimentally imposed changes in social foraging structure
Authors: Firth Josh A. , Sheldon Ben C. , Farine Damien R.
Published: June 2016

Animals regularly use information from others to shape their decisions. Yet, determining how changes in social structure affect information flow and social learning strategies has remained challenging. We manipulated the social structure of a large community of wild songbirds by controlling which individuals could feed together at automated feeding stations (selective feeders). We then provided novel ephemeral food patches freely accessible to all birds and recorded the spread of this new information. We demonstrate that the discovery of new food patches followed the experimentally imposed social structure and that birds disproportionately learnt from those whom they could forage with at the selective feeders. The selective feeders reduced the number of conspecific information sources available and birds subsequently increased their use of information provided by heterospecifics. Our study demonstrates that changes to social systems carry over into pathways of information transfer and that individuals learn from tutors that provide relevant information in other contexts.
Casting your network wide: a plea to scale-up phenological research
Authors: Thackeray Stephen J.
Published: June 2016

Accumulating scientific evidence has demonstrated widespread shifts in the biological seasons. These shifts may modify seasonal interspecific interactions, with consequent impacts upon reproductive success and survival. However, current understanding of these impacts is based upon a limited number of studies that adopt a simplified ‘bottom-up’ food-chain paradigm, at a local scale. I argue that there is much insight to be gained by widening the scope of phenological studies to incorporate food-web interactions and landscape-scale processes across a diversity of ecosystem types, with the ultimate goal of developing a generic understanding of the systems most vulnerable to synchrony effects in the future. I propose that co-location of predator and prey phenological monitoring at sentinel sites, acting as research platforms for detailed food-web studies, experimentation and match-up with earth observation data, would be an important first step in this endeavour.
Predicting plant attractiveness to pollinators with passive crowdsourcing
Authors: Bahlai Christie A. , Landis Douglas A.
Published: June 2016

Global concern regarding pollinator decline has intensified interest in enhancing pollinator resources in managed landscapes. These efforts frequently emphasize restoration or planting of flowering plants to provide pollen and nectar resources that are highly attractive to the desired pollinators. However, determining exactly which plant species should be used to enhance a landscape is difficult. Empirical screening of plants for such purposes is logistically daunting, but could be streamlined by crowdsourcing data to create lists of plants most probable to attract the desired pollinator taxa. People frequently photograph plants in bloom and the Internet has become a vast repository of such images. A proportion of these images also capture floral visitation by arthropods. Here, we test the hypothesis that the abundance of floral images containing identifiable pollinator and other beneficial insects is positively associated with the observed attractiveness of the same species in controlled field trials from previously published studies. We used Google Image searches to determine the correlation of pollinator visitation captured by photographs on the Internet relative to the attractiveness of the same species in common-garden field trials for 43 plant species. From the first 30 photographs, which successfully identified the plant, we recorded the number of
Apis
(managed honeybees), non-
Apis
(exclusively wild bees) and the number of bee-mimicking syrphid flies. We used these observations from search hits as well as bloom period (BP) as predictor variables in Generalized Linear Models (GLMs) for field-observed abundances of each of these groups. We found that non-
Apis
bees observed in controlled field trials were positively associated with observations of these taxa in Google Image searches (pseudo-
R
2
of 0.668). Syrphid fly observations in the field were also associated with the frequency they were observed in images, but this relationship was weak.
Apis
bee observations were not associated with Internet images, but were slightly associated with BP. Our results suggest that passively crowdsourced image data can potentially be a useful screening tool to identify candidate plants for pollinator habitat restoration efforts directed at wild bee conservation. Increasing our understanding of the attractiveness of a greater diversity of plants increases the potential for more rapid and efficient research in creating pollinator-supportive landscapes.
Facultative asexual reproduction and genetic diversity of populations in the humivorous termite
Cavitermes tuberosus
Authors: Fournier Denis , Hellemans Simon , Hanus Robert , Roisin Yves
Published: June 2016

Termite colonies are typically founded by a pair of sexually reproducing dispersers, which can sometimes be replaced by some of their offspring. Some
Reticulitermes
and
Embiratermes
species routinely practice asexual queen succession (AQS): the queen is replaced by neotenic daughters produced by parthenogenesis, which mate with the primary king. Here, to cast light on the evolution of AQS, we investigated another candidate species,
Cavitermes tuberosus
(Termitinae). Of 95 nests, 39 contained a primary queen and 28 contained neotenic females (2–667 individuals), usually with the primary king. Microsatellite analyses confirmed that colonies were initiated by single pairs after large dispersal flights. More than 80% of the neotenic females were of exclusively maternal origin and completely homozygous, suggesting automictic parthenogenesis with gamete duplication. Conversely, workers, soldiers, and most alates and primary reproductives were produced sexually. AQS often occurs late, after colonies have reached maturity, whereas early AQS in other species may boost the young colony's growth rate. We suggest additional benefits of AQS in
C. tuberosus
, related with a smaller size, lesser stability and higher mobility of colonies. Our data add to the phylogenetical dispersion and diversity of modalities of AQS in termites, supporting a multiple evolutionary origin of this process.
Hierarchical dynamics of informational patterns and decision-making
Authors: Varona Pablo , Rabinovich Mikhail I.
Published: June 2016

Traditional studies on the interaction of cognitive functions in healthy and disordered brains have used the analyses of the connectivity of several specialized brain networks—the functional connectome. However, emerging evidence suggests that both brain networks and functional spontaneous brain-wide network communication are intrinsically dynamic. In the light of studies investigating the cooperation between different cognitive functions, we consider here the dynamics of hierarchical networks in cognitive space. We show, using an example of behavioural decision-making based on sequential episodic memory, how the description of metastable pattern dynamics underlying basic cognitive processes helps to understand and predict complex processes like sequential episodic memory recall and competition among decision strategies. The mathematical images of the discussed phenomena in the phase space of the corresponding cognitive model are hierarchical heteroclinic networks. One of the most important features of such networks is the robustness of their dynamics. Different kinds of instabilities of these dynamics can be related to ‘dynamical signatures’ of creativity and different psychiatric disorders. The suggested approach can also be useful for the understanding of the dynamical processes that are the basis of consciousness.
Active dispersal in loggerhead sea turtles (
Caretta caretta
) during the ‘lost years’
Authors: Briscoe D. K. , Parker D. M. , Balazs G. H. , Kurita M. , Saito T. , Okamoto H. , Rice M. , Polovina J. J. , Crowder L. B.
Published: June 2016

Highly migratory marine species can travel long distances and across entire ocean basins to reach foraging and breeding grounds, yet gaps persist in our knowledge of oceanic dispersal and habitat use. This is especially true for sea turtles, whose complex life history and lengthy pelagic stage present unique conservation challenges. Few studies have explored how these young at-sea turtles navigate their environment, but advancements in satellite technology and numerical models have shown that active and passive movements are used in relation to open ocean features. Here, we provide the first study, to the best of our knowledge, to simultaneously combine a high-resolution physical forcing ocean circulation model with long-term multi-year tracking data of young, trans-oceanic North Pacific loggerhead sea turtles during their ‘lost years’ at sea. From 2010 to 2014, we compare simulated trajectories of passive transport with empirical data of 1–3 year old turtles released off Japan (29.7–37.5 straight carapace length cm). After several years, the at-sea distribution of simulated current-driven trajectories significantly differed from that of the observed turtle tracks. These results underscore current theories on active dispersal by young oceanic-stage sea turtles and give further weight to hypotheses of juvenile foraging strategies for this species. Such information can also provide critical geographical information for spatially explicit conservation approaches to this endangered population.
Sequence Entropy and the Absolute Rate of Amino Acid Substitutions
Authors: Goldstein Richard A. , Pollock David D.
Published: June 2016

The evolution of model proteins under selection for thermodynamic stability suggests parallels between evolutionary behavior and chemical reaction kinetics. We developed a statistical mechanics theory of protein evolution by dividing amino acid interactions into site-specific and ‘bath’ components, and show that substitutions between two amino acids occur when their site-specific contributions to stability are nearly identical. Fluctuating epistatic interactions drive stabilities into and out of these regions of near neutrality, with the time spent in the neutral region and thus the rate of substitution governed by physicochemical similarities between the amino acids. We derive a theoretical framework for how site-specific stabilities are determined, and demonstrate that substitution rates and the magnitude of the evolutionary Stokes shift can be predicted from biophysics and the effect of sequence entropy alone. Population genetics underlays our analysis, but population size does not determine the absolute rate of amino acid substitutions.
A Novel Algorithm for the Maximal Fit Problem in Boolean Networks
Authors: Karlebach Guy
Published: June 2016

Gene regulatory networks (GRNs) are increasingly used for explaining biological processes with complex transcriptional regulation. A GRN links the expression levels of a set of genes via regulatory controls that gene products exert on one another. Boolean networks are a common modeling choice since they balance between detail and ease of analysis. However, even for Boolean networks the problem of fitting a given network model to an expression dataset is NP-Complete. Previous methods have addressed this issue heuristically or by focusing on acyclic networks and specific classes of regulation functions. In this paper we introduce a novel algorithm for this problem that makes use of sampling in order to handle large datasets. Our algorithm can handle time series data for any network type and steady state data for acyclic networks. Using in-silico time series data we demonstrate good performance on large datasets with a significant level of noise.
Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus
Authors: Vakirlis Nikolaos , Sarilar Véronique , Drillon Guénola , Fleiss Aubin , Agier Nicolas , Meyniel Jean-Philippe , Blanpain Lou , Carbone Alessandra , Devillers Hugo , Dubois Kenny , Gillet-Markowska Alexandre , Graziani Stéphane , Huu-Vang Nguyen , Poirel Marion , Reisser Cyrielle , Schott Jonathan , Schacherer Joseph , Lafontaine Ingrid , Llorente Bertrand , Neuvéglise Cécile , Fischer Gilles
Published: June 2016

Reconstructing genome history is complex but necessary to reveal quantitative principles governing genome evolution. Such reconstruction requires recapitulating into a single evolutionary framework the evolution of genome architecture and gene repertoire. Here, we reconstructed the genome history of the genus Lachancea that appeared to cover a continuous evolutionary range from closely related to more diverged yeast species. Our approach integrated the generation of a high-quality genome data set; the development of AnChro, a new algorithm for reconstructing ancestral genome architecture; and a comprehensive analysis of gene repertoire evolution. We found that the ancestral genome of the genus Lachancea contained eight chromosomes and about 5173 protein-coding genes. Moreover, we characterized 24 horizontal gene transfers and 159 putative gene creation events that punctuated species diversification. We retraced all chromosomal rearrangements, including gene losses, gene duplications, chromosomal inversions and translocations at single gene resolution. Gene duplications outnumbered losses and balanced rearrangements with 1503, 929, and 423 events, respectively. Gene content variations between extant species are mainly driven by differential gene losses, while gene duplications remained globally constant in all lineages. Remarkably, we discovered that balanced chromosomal rearrangements could be responsible for up to 14% of all gene losses by disrupting genes at their breakpoints. Finally, we found that nonsynonymous substitutions reached fixation at a coordinated pace with chromosomal inversions, translocations, and duplications, but not deletions. Overall, we provide a granular view of genome evolution within an entire eukaryotic genus, linking gene content, chromosome rearrangements, and protein divergence into a single evolutionary framework.
Exploratory Analysis of Biological Networks through Visualization, Clustering, and Functional Annotation in Cytoscape
Authors: Baryshnikova Anastasia
Published: June 2016

Biological networks define how genes, proteins, and other cellular components interact with one another to carry out specific functions, providing a scaffold for understanding cellular organization. Although in-depth network analysis requires advanced mathematical and computational knowledge, a preliminary visual exploration of biological networks is accessible to anyone with basic computer skills. Visualization of biological networks is used primarily to examine network topology, identify functional modules, and predict gene functions based on gene connectivity within the network. Networks are excellent at providing a bird’s-eye view of data sets and have the power of illustrating complex ideas in simple and intuitive terms. In addition, they enable exploratory analysis and generation of new hypotheses, which can then be tested using rigorous statistical and experimental tools. This protocol describes a simple procedure for visualizing a biological network using the genetic interaction similarity network for Saccharomyces cerevisiae as an example. The visualization procedure described here relies on the open-source network visualization software Cytoscape and includes detailed instructions on formatting and loading the data, clustering networks, and overlaying functional annotations.
CRISPR–Cas9 Genome Engineering in Saccharomyces cerevisiae Cells
Authors: Ryan Owen W. , Poddar Snigdha , Cate Jamie H.D.
Published: June 2016

This protocol describes a method for CRISPR–Cas9-mediated genome editing that results in scarless and marker-free integrations of DNA into Saccharomyces cerevisiae genomes. DNA integration results from cotransforming (1) a single plasmid (pCAS) that coexpresses the Cas9 endonuclease and a uniquely engineered single guide RNA (sgRNA) expression cassette and (2) a linear DNA molecule that is used to repair the chromosomal DNA damage by homology-directed repair. For target specificity, the pCAS plasmid requires only a single cloning modification: replacing the 20-bp guide RNA sequence within the sgRNA cassette. This CRISPR–Cas9 protocol includes methods for (1) cloning the unique target sequence into pCAS, (2) assembly of the double-stranded DNA repair oligonucleotides, and (3) cotransformation of pCAS and linear repair DNA into yeast cells. The protocol is technically facile and requires no special equipment. It can be used in any S. cerevisiae strain, including industrial polyploid isolates. Therefore, this CRISPR–Cas9-based DNA integration protocol is achievable by virtually any yeast genetics and molecular biology laboratory.
Staining Fission Yeast Filamentous Actin with Fluorescent Phalloidin Conjugates
Authors: Hagan Iain M.
Published: June 2016

The Schizosaccharomyces pombe filamentous (F)-actin cytoskeleton drives cell growth, morphogenesis, endocytosis, and cytokinesis. The protocol described here reveals the distribution of F-actin in fixed cells through the use of fluorescently conjugated phalloidin. Simultaneous staining of cell wall landmarks (with calcofluor) and chromatin (with 4′,6-diamidino-2-phenylindole, or DAPI) makes this rapid staining procedure highly effective for staging cell cycle progression, monitoring morphogenetic abnormalities, and assessing the impact of environmental and genetic changes on the integrity of the F-actin cytoskeleton.
Long-Term Potentiation by Theta-Burst Stimulation Using Extracellular Field Potential Recordings in Acute Hippocampal Slices
Authors: Abrahamsson Therese , Lalanne Txomin , Watt Alanna J. , Sjöström P. Jesper
Published: June 2016

This protocol describes how to carry out theta-burst long-term potentiation (LTP) with extracellular field recordings in acute rodent hippocampal slices. This method is relatively simple and noninvasive and provides a way to sample many neurons simultaneously, making it suitable for applications requiring higher throughput than whole-cell recording.
Using Multiple Whole-Cell Recordings to Study Spike-Timing-Dependent Plasticity in Acute Neocortical Slices
Authors: Lalanne Txomin , Abrahamsson Therese , Sjöström P. Jesper
Published: June 2016

This protocol provides a method for quadruple whole-cell recording to study synaptic plasticity of neocortical connections, with a special focus on spike-timing-dependent plasticity (STDP). It also describes how to morphologically identify recorded cells from two-photon laser-scanning microscopy (2PLSM) stacks.
Strategies for Assaying Lysosomal Membrane Permeabilization
Authors: Repnik Urška , Hafner Česen Maruša , Turk Boris
Published: June 2016

Late endosomal organelles have an acidic pH and contain hydrolytic enzymes to degrade cargo delivered either from the extracellular environment by endocytosis or from within the cell itself by autophagy. In the event of lysosomal membrane permeabilization (LMP), the contents of late endosomes and lysosomes can be released into the cytosol and then initiate apoptosis. Compounds that can trigger LMP are therefore candidates for the induction of apoptosis, in particular in anticancer therapy. Alternatively, drug-delivery systems, such as nanoparticles, can have side effects that can include LMP, which has toxic consequences for the cells. To determine when, to what extent, and with what consequences LMP occurs is therefore of paramount importance for the evaluation of new potentially LMP-inducing compounds. In this introduction, we provide an overview of some basic assays for assessing LMP, such as staining with lysosomotropic dyes and measurement of cysteine cathepsin activity, and discuss additional strategies for the detection of the release of endogenous lysosomal molecules or preloaded exogenous tracers into the cytosol.
In Vitro Investigation of Synaptic Plasticity
Authors: Abrahamsson Therese , Lalanne Txomin , Watt Alanna J. , Sjöström P. Jesper
Published: June 2016

A classical in vitro model for investigation of information storage in the brain is based on the acute hippocampal slice. Here, repeated high-frequency stimulation of excitatory Schaeffer collaterals making synapses onto pyramidal cells in the hippocampal CA1 region leads to strengthening of evoked field-recording responses—long-term potentiation (LTP)—in keeping with Hebb’s postulate. This model remains tremendously influential for its reliability, specificity, and relative ease of use. More recent plasticity studies have explored various other brain regions including the neocortex, which often requires more laborious whole-cell recordings of synaptically connected pairs of neurons, to ensure that the identities of recorded cells are known. In addition, with this experimental approach, the spiking activity can be controlled with millisecond precision, which is necessary for the study of spike-timing-dependent plasticity (STDP). Here, we provide protocols for in vitro study of hippocampal CA1 LTP using field recordings, and of STDP in synaptically connected pairs of layer-5 pyramidal cells in acute slices of rodent neocortex.
Intrinsic Optical Imaging of Functional Map Development in Mammalian Visual Cortex
Authors: Bonhoeffer Tobias , Hübener Mark
Published: June 2016

Here we describe how intrinsic imaging of the visual cortex can be used as a chronic technique. This method allows the time course of the development of cortical maps to be studied in a single animal during a period of up to 1 yr.
Intellectual structure of trust in business and management: a co-citation analysis
Authors: Yang Keng-Chieh
Published: June 2016

Purpose

In the past few decades, there has been a lot of literature about trust research for business and management. However, few authors have applied co-citation analysis.

Design/methodology/approach

Trust is one of the most discussed issues in management, as it has proved to have an essential role in business operations. In this study, all citation documents are included in Thomson Reuters ISI Web of Knowledge database from 1992 to 2010.

Findings

By using statistics analysis including factor analysis, cluster analysis and multidimensional scaling, researchers identified four domains, including organizational behaviour, strategic alliance, marketing and social capital. Directions for future research are discussed.

Originality/value

This study is the first to apply co-citation techniques in the fields of trust. Therefore, the major contribution of this study is to provide an intellectual structure and trends within the field of trust from an objective and quantitative perspective.
Research on feature-based opinion mining using topic maps
Authors: Xia Lixin , Wang Zhongyi , Chen Chen , Zhai Shanshan
Published: June 2016

Purpose

Opinion mining (OM), also known as “sentiment classification”, which aims to discover common patterns of user opinions from their textual statements automatically or semi-automatically, is not only useful for customers, but also for manufacturers. However, because of the complexity of natural language, there are still some problems, such as domain dependence of sentiment words, extraction of implicit features and others. The purpose of this paper is to propose an OM method based on topic maps to solve these problems.

Design/methodology/approach

Domain-specific knowledge is key to solve problems in feature-based OM. On the one hand, topic maps, as an ontology framework, are composed of topics, associations, occurrences and scopes, and can represent a class of knowledge representation schemes. On the other hand, compared with ontology, topic maps have many advantages. Thus, it is better to integrate domain-specific knowledge into OM based on topic maps. This method can make full use of the semantic relationships among feature words and sentiment words.

Findings

In feature-level OM, most of the existing research associate product features and opinions by their explicit co-occurrence, or use syntax parsing to judge the modification relationship between opinion words and product features within a review unit. They are mostly based on the structure of language units without considering domain knowledge. Only few methods based on ontology incorporate domain knowledge into feature-based OM, but they only use the “is-a” relation between concepts. Therefore, this paper proposes feature-based OM using topic maps. The experimental results revealed that this method can improve the accuracy of the OM. The findings of this study not only advance the state of OM research but also shed light on future research directions.

Research limitations/implications

To demonstrate the “feature-based OM using topic maps” applications, this work implements a prototype that helps users to find their new washing machines.

Originality/value

This paper presents a new method of feature-based OM using topic maps, which can integrate domain-specific knowledge into feature-based OM effectively. This method can improve the accuracy of the OM greatly. The proposed method can be applied across various application domains, such as e-commerce and e-government.
The career decisions of professional women with dependent children
Authors: Woolnough Helen , Redshaw Jane
Published: June 2016

Purpose

The purpose of this exploratory qualitative study was to investigate anticipated and real career decisions made by two cohorts of professional women in the UK at differing stages of the lifespan.

Design/methodology/approach

Career decisions made by two cohorts of professional women following the birth of their first child at different stages of the lifespan and satisfaction with these choices in retrospect were investigated. Data analysis followed a thematic approach, and comparisons between the two cohorts were made.

Findings

The study revealed much similarity between the two cohorts. The decisions women make regarding whether to return to work or not and the extent to which they are satisfied with their working arrangements are constrained by similar individual and organisational factors despite the 15-20 year gap.

Research limitations/implications

Although mothers in the UK now experience strengthened legislation concerning maternity benefits and entitlements and there have been advances in flexible working, progress in relation to supporting women in reconciling work and home life when they return to work is arguably limited.

Originality/value

This paper offers insights into the extent to which the career decisions made by professional women following the birth of their first child and satisfaction with these choices in retrospect have changed (or not) among two cohorts of professional women (15-20 years apart). The findings stress the importance of understanding the complex issues faced by mothers in the workforce and providing appropriate organisational support.
A three factor model of followership: part 1– introduction to followership, leadership and the three factor model of leadership
Authors: Manning Tony , Robertson Bob
Published: June 2016

Purpose

– While there is an extensive body of theory and research on leadership, less attention has been paid to other work roles, including follower roles. The purpose of this paper is to explain and justify a three factor model of followership as a basis for exploring the role of followers, establishing what makes an effective follower and discussing the training and development of followers. This is the first part of a three part paper. It reviews previous theory and research on followership, before describing the three factor model of leadership and considering how it can be applied to followership.

Design/methodology/approach

– The first part of this paper consists mainly of a literature review on followership, and a description of the three factor model of leadership. The second and third parts of the paper outline the approach to the empirical research.

Findings

– The overall findings of this three part paper: provide empirical evidence to support the three factor model of leadership; justify the extension of the model to other work roles, including follower roles; allow the development of a three factor framework of follower behaviours.

Research limitations/implications

– The three factor model of followership shows that followership and leadership are not fundamentally different. Indeed, the skills that leaders need in their roles develop out of and build on those needed in follower roles. The essential difference is in the contrasting roles of leader and follower in which they are used. The research findings are based mainly on individuals in the public sector in the UK. Further research on other populations would be useful.

Practical implications

– Effective organisations need effective followers and effective leaders. Moreover, the skills of the effective leader develop out of and build on those of the effective follower.

Social implications

– The view of followership expressed in this paper is a challenge to the widely held pre-occupation with leadership and, more generally, to the cult of leadership.

Originality/value

– This is the first published attempt to apply the three factor model of leadership to followership. Evidence is presented on the internal reliability and external validity of measures of leadership and followership. Scales were developed to distinguish between leader and follower roles and used to describe behaviours characteristic of such roles, as well as behaviours valued in these roles, based on 360 degree assessments.