bluuebunny/crossref_metadata_2025 huggingface dataset:
Visualising the Structure of Document Search Results: A Comparison of Graph Theoretic Approaches
Authors: Cribbin Timothy
Published: April 2009

Previous work has shown that distance-similarity visualisation or ‘spatialisation’ can provide a potentially useful context in which to browse the results of a query search, enabling the user to adopt a simple local foraging or ‘cluster growing’ strategy to navigate through the retrieved document set. However, faithfully mapping feature-space models to visual space can be problematic owing to their inherent high dimensionality and non-linearity. Conventional linear approaches to dimension reduction tend to fail at this kind of task, sacrificing local structural in order to preserve a globally optimal mapping. In this paper the clustering performance of a recently proposed algorithm called isometric feature mapping (Isomap), which deals with non-linearity by transforming dissimilarities into geodesic distances, is compared to that of non-metric multidimensional scaling (MDS). Various graph pruning methods, for geodesic distance estimation, are also compared. Results show that Isomap is significantly better at preserving local structural detail than MDS, suggesting it is better suited to cluster growing and other semantic navigation tasks. Moreover, it is shown that applying a minimum-cost graph pruning criterion can provide a parameter-free alternative to the traditional K-neighbour method, resulting in spatial clustering that is equivalent to or better than that achieved using an optimal- K criterion.
A Framework for Work-Life Balance Practices: Addressing the Needs of the Tourism Industry
Authors: Deery Margaret , Jago Leo
Published: April 2009

This paper examines the key issues associated with work-life balance (WLB) with a particular focus on practices within the tourism industry. It provides an overview of the general literature and then the research that relates specifically to WLB in the tourism industry. It builds on previous research in this area to present an adapted framework for addressing the key variables of WLB that can be tested in subsequent research.
Extracting the multiscale backbone of complex weighted networks
Authors: Serrano M. Ángeles , Boguñá Marián , Vespignani Alessandro
Published: April 2009

A large number of complex systems find a natural abstraction in the form of weighted networks whose nodes represent the elements of the system and the weighted edges identify the presence of an interaction and its relative strength. In recent years, the study of an increasing number of large-scale networks has highlighted the statistical heterogeneity of their interaction pattern, with degree and weight distributions that vary over many orders of magnitude. These features, along with the large number of elements and links, make the extraction of the truly relevant connections forming the network's backbone a very challenging problem. More specifically, coarse-graining approaches and filtering techniques come into conflict with the multiscale nature of large-scale systems. Here, we define a filtering method that offers a practical procedure to extract the relevant connection backbone in complex multiscale networks, preserving the edges that represent statistically significant deviations with respect to a null model for the local assignment of weights to edges. An important aspect of the method is that it does not belittle small-scale interactions and operates at all scales defined by the weight distribution. We apply our method to real-world network instances and compare the obtained results with alternative backbone extraction techniques.
Rapid repetitive element-mediated expansion of piRNA clusters in mammalian evolution
Authors: Assis Raquel , Kondrashov Alexey S.
Published: April 2009

Piwi-interacting RNAs (piRNAs) are ≈30 nucleotide noncoding RNAs that may be involved in transposon silencing in mammalian germline cells. Most piRNA sequences are found in a small number of genomic regions referred to as clusters, which range from 1 to hundreds of kilobases. We studied the evolution of 140 rodent piRNA clusters, 103 of which do not overlap protein-coding genes. Phylogenetic analysis revealed that 14 clusters were acquired after rat–mouse divergence and another 44 after rodent–primate divergence. Most clusters originated in a process analogous to the duplication of protein-coding genes by ectopic recombination, via insertions of long sequences that were mediated by flanking chromosome-specific repetitive elements (REs). Source sequences for such insertions are often located on the same chromosomes and also harbor clusters. The rate of piRNA cluster expansion is higher than that of any known gene family and, in contrast to other large gene families, there was not a single cluster loss. These observations suggest that piRNA cluster expansion is driven by positive selection, perhaps caused by the need to silence the ever-expanding repertoire of mammalian transposons.
Evidentiality
Authors: Boye Kasper , Harder Peter
Published: April 2009

This article takes up two closely connected theoretical unclarities: the questions of what a linguistic category is, and what it means for linguistic elements to have grammatical rather than lexical status. The two issues are discussed with reference to the case of evidentiality.

The point of departure is the problem of how to define a category: Definitions of categories like evidentiality tend to mix up the question of what unifies the category with distinctions between pragmatic and semantic meaning, between lexical and grammatical coding, and between main predication and ancillary modification. In this article, we try to demonstrate the drawbacks of a conception of evidentiality as a strictly semantic, grammatical or modification phenomenon. We argue that evidentiality should be understood basically as a functional-conceptual substance domain.

Against this background, we reconsider the distinction between grammatical and lexical status. We present a functional account of grammaticalization according to which grammatical status arises when a meaning is coded as being secondary information. By separating the definition of functional-conceptual substance domains from the distinction between grammatical and lexical status, we try to show how a function-based approach can make the characteristics of categories and of grammatical status cohere without getting mixed up.
Evidentiality and epistemic modality
Authors: Cornillie Bert
Published: April 2009

This paper attempts to explain the terminological and conceptual confusion of evidentiality and epistemic modality. It presents a functionally oriented semantic analysis which does not belong to a specific theoretical framework. It shows that the alleged epistemic speaker commitment of evidential expressions does not come from the specific evidential value or mode of information, but rather boils down to the speaker’s and hearer’s interpretation of the source of information. A source of information can be attributed different degrees of reliability, but these should not automatically be translated into degrees of epistemic speaker commitment. The latter involves an evaluation of the likelihood, which is quite different from the evaluation of the reliability of the source of information. Thus, the account presented here challenges previous analyses in which the labels “epistemic” and “evidential” are applied to linguistic expressions either in too broad a way or in too exclusive a way. The analysis also contrasts with accounts based on the “inclusion” or the “overlap” of the two categories. Finally, the paper also discusses Nuyts’ (2004) claim that a clause can only have one qualification at a time.
Identity and belonging in social learning groups: The importance of distinguishing social, operational and knowledge‐related identity congruence
Authors: Hughes Gwyneth
Published: April 2009

Collaborative learning has much to offer but not all learners participate fully and peer groups can be exclusive. The article examines how belonging or ‘congruence’ in learning groups is related to identities of gender, age, ethnicity and socio‐economic status. A study of student experiences of collaborative learning on three different blended learning courses illustrated how learners negotiate identity congruence with peer groups to belong and engage. An analytical framework that distinguishes social, operational and knowledge‐related identity congruence has emerged. Contrary to received wisdom, the social aspect appears least important for learner engagement while knowledge‐related identity congruence is fundamental. Some of the consequences of identity incongruence, particularly concerning gender and maturity, are discussed and the article points towards the pedagogies which might enable identities of group members to shift so that collaborative learning can flourish.
CCTV, school surveillance and social control
Authors: Hope Andrew
Published: April 2009

Burgeoning fears for safety in UK schools have resulted in a rapid growth in the use of various security measures, most notably closed‐circuit television (CCTV) systems. Utilising semi‐structured interviews and non‐participant observation this research examines how CCTV is used in schools, explores the manner in which this facilitates social control and considers the wider implications of such surveillance technology. It is argued that this technology, which is predominantly focused on students, is effective in facilitating direct observation, but does little to foster self‐surveillance in the longer term. It is concluded that CCTV use in schools represents an underlying shift in values, away from exercising social control through enculturation towards system integration. This has important ethical implications.
There is no clam with coats in the calm coast: Delimiting the transposed-letter priming effect
Authors: Duñabeitia Jon Andoni , Perea Manuel , Carreiras Manuel
Published: April 2009

In this article, we explore the transposed-letter priming effect (e.g., jugde–JUDGE vs. jupte–JUDGE), a phenomenon that taps into some key issues on how the brain encodes letter positions and has favoured the creation of new input coding schemes. However, almost all the empirical evidence from transposed-letter priming experiments comes from nonword primes (e.g., jugde–JUDGE). Indeed, previous evidence when using word–word pairs (e.g., causal–CASUAL) is not conclusive. Here, we conducted five masked priming lexical decision experiments that examined the relationship between pairs of real words that differed only in the transposition of two of their letters (e.g., CASUAL vs. CAUSAL). Results showed that, unlike transposed-letter nonwords, transposed-letter words do not seem to affect the identification time of their transposed-letter mates. Thus, prime lexicality is a key factor that modulates the magnitude of transposed-letter priming effects. These results are interpreted under the assumption of the existence of lateral inhibition processes occurring within the lexical level—which cancels out any orthographic facilitation due to the overlapping letters. We examine the implications of these findings for models of visual-word recognition.
Performed or observed keyboard actions affect pianists’ judgements of relative pitch
Authors: Repp Bruno H. , Knoblich Günther
Published: April 2009

Action can affect visual perception if the action's expected sensory effects resemble a concurrent unstable or deviant event. To determine whether action can also change auditory perception, participants were required to play pairs of octave-ambiguous tones by pressing successive keys on a piano or computer keyboard and to judge whether each pitch interval was rising or falling. Both pianists and nonpianist musicians gave significantly more “rising” responses when the order of key presses was left-to-right than when it was right-to-left, in accord with the pitch mapping of the piano. However, the effect was much larger in pianists. Pianists showed a similarly large effect when they passively observed the experimenter pressing keys on a piano keyboard, as long as the keyboard faced the participant. The results suggest that acquired action–effect associations can affect auditory perceptual judgement.
The Bowel Prep Conundrum
Authors: Lee James T.
Published: April 2009

My prior essay in this section dissected recent European work that claimed an amazing surgical-site infection (SSI) prevention benefit of giving patients 80% oxygen by mask for a few hours perioperatively. Its authors proposed that using this simple adjunct halves SSI risk in colorectal operations. Besides addressing some specific methodology concerns, I asserted that the article had dubious impact on me because its authors had not used the “standard of care” in their control and treatment groups. The patients in both arms received no oral nonabsorbed antibiotic agents during preoperative preparation of the colon, but only systemic prophylactic agents. Local comments about my exegesis of the article were sparse. One of our research residents volunteered only that “mentioning your two dogs at the start of the article was cute”. A local surgeon, who casts a rather large shadow both literally and politically, displayed astonishing naiveté when he told me that “even if that oxygen work is valid, we will have to do the same number of operations that the article reported before any benefit could occur for our patients.”
Autophagic Elimination of Misfolded Procollagen Aggregates in the Endoplasmic Reticulum as a Means of Cell Protection
Authors: Ishida Yoshihito , Yamamoto Akitsugu , Kitamura Akira , Lamandé Shireen R. , Yoshimori Tamotsu , Bateman John F. , Kubota Hiroshi , Nagata Kazuhiro
Published: April 2009

Type I collagen is a major component of the extracellular matrix, and mutations in the collagen gene cause several matrix-associated diseases. These mutant procollagens are misfolded and often aggregated in the endoplasmic reticulum (ER). Although the misfolded procollagens are potentially toxic to the cell, little is known about how they are eliminated from the ER. Here, we show that procollagen that can initially trimerize but then aggregates in the ER are eliminated by an autophagy-lysosome pathway, but not by the ER-associated degradation (ERAD) pathway. Inhibition of autophagy by specific inhibitors or RNAi-mediated knockdown of an autophagy-related gene significantly stimulated accumulation of aggregated procollagen trimers in the ER, and activation of autophagy with rapamycin resulted in reduced amount of aggregates. In contrast, a mutant procollagen which has a compromised ability to form trimers was degraded by ERAD. Moreover, we found that autophagy plays an essential role in protecting cells against the toxicity of the ERAD-inefficient procollagen aggregates. The autophagic elimination of aggregated procollagen occurs independently of the ERAD system. These results indicate that autophagy is a final cell protection strategy deployed against ER-accumulated cytotoxic aggregates that are not able to be removed by ERAD.
Kinesin-1 and Cytoplasmic Dynein Act Sequentially to Move the Meiotic Spindle to the Oocyte Cortex inCaenorhabditis elegans
Authors: Ellefson Marina L. , McNally Francis J.
Published: April 2009

During female meiosis in animals, the meiotic spindle is attached to the egg cortex by one pole during anaphase to allow selective disposal of half the chromosomes in a polar body. In Caenorhabditis elegans, this anaphase spindle position is achieved sequentially through kinesin-1–dependent early translocation followed by anaphase-promoting complex (APC)-dependent spindle rotation. Partial depletion of cytoplasmic dynein heavy chain by RNA interference blocked spindle rotation without affecting early translocation. Dynein depletion also blocked the APC-dependent late translocation that occurs in kinesin-1–depleted embryos. Time-lapse imaging of green fluorescent protein-tagged dynein heavy chain as well as immunofluorescence with dynein-specific antibodies revealed that dynein starts to accumulate at spindle poles just before the initiation of rotation or late translocation. Accumulation of dynein at poles was kinesin-1 independent and APC dependent, just like dynein driven spindle movements. This represents a case of kinesin-1/dynein coordination in which these two motors of opposite polarity act sequentially and independently on a cargo to move it in the same direction.
ModLink+: improving fold recognition by using protein–protein interactions
Authors: Fornes Oriol , Aragues Ramon , Espadaler Jordi , Marti-Renom Marc A. , Sali Andrej , Oliva Baldo
Published: April 2009

Motivation:Several strategies have been developed to predict the fold of a target protein sequence, most of which are based on aligning the target sequence to other sequences of known structure. Previously, we demonstrated that the consideration of protein–protein interactions significantly increases the accuracy of fold assignment compared with PSI-BLAST sequence comparisons. A drawback of our method was the low number of proteins to which a fold could be assigned. Here, we present an improved version of the method that addresses this limitation. We also compare our method to other state-of-the-art fold assignment methodologies.

Results: Our approach (ModLink+) has been tested on 3716 proteins with domain folds classified in the Structural Classification Of Proteins (SCOP) as well as known interacting partners in the Database of Interacting Proteins (DIP). For this test set, the ratio of success [positive predictive value (PPV)] on fold assignment increases from 75% for PSI-BLAST, 83% for HHSearch and 81% for PRC to >90% for ModLink+at the e-value cutoff of 10−3. Under this e-value, ModLink+can assign a fold to 30–45% of the proteins in the test set, while our previous method could cover <25%. When applied to 6384 proteins with unknown fold in the yeast proteome, ModLink+combined with PSI-BLAST assigns a fold for domains in 3738 proteins, while PSI-BLAST alone covers only 2122 proteins, HHSearch 2969 and PRC 2826 proteins, using a threshold e-value that would represent a PPV >82% for each method in the test set.

Availability: The ModLink+server is freely accessible in the World Wide Web at http://sbi.imim.es/modlink/.

Contact:  boliva@imim.es.

Supplementary information:  Supplementary data are available at Bioinformatics online.
WebGBrowse—a web server for GBrowse
Authors: Podicheti Ram , Gollapudi Rajesh , Dong Qunfeng
Published: April 2009

Summary: The Generic Genome Browser (GBrowse) is one of the most widely used tools for visualizing genomic features along a reference sequence. However, the installation and configuration of GBrowse is not trivial for biologists. We have developed a web server, WebGBrowse that allows users to upload genome annotation in the GFF3 format, configure the display of each genomic feature by simply using a web browser and visualize the configured genomic features with the integrated GBrowse software.

Availability: WebGBrowse is accessible via http://webgbrowse.cgb.indiana.edu/ and the system is also freely available for local installations.

Contact:  dongq@indiana.edu
Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy
Authors: Tuncbag Nurcan , Gursoy Attila , Keskin Ozlem
Published: April 2009

Motivation:Hot spots are residues comprising only a small fraction of interfaces yet accounting for the majority of the binding energy. These residues are critical in understanding the principles of protein interactions. Experimental studies like alanine scanning mutagenesis require significant effort; therefore, there is a need for computational methods to predict hot spots in protein interfaces.

Results:We present a new intuitive efficient method to determine computational hot spots based on conservation (C), solvent accessibility [accessible surface area (ASA)] and statistical pairwise residue potentials (PP) of the interface residues. Combination of these features is examined in a comprehensive way to study their effect in hot spot detection. The predicted hot spots are observed to match with the experimental hot spots with an accuracy of 70% and a precision of 64% in Alanine Scanning Energetics Database (ASEdb), and accuracy of 70% and a precision of 73% in Binding Interface Database (BID). Several machine learning methods are also applied to predict hot spots. Performance of our empirical approach exceeds learning-based methods and other existing hot spot prediction methods. Residue occlusion from solvent in the complexes and pairwise potentials are found to be the main discriminative features in hot spot prediction.

Conclusion:Our empirical method is a simple approach in hot spot prediction yet with its high accuracy and computational effectiveness. We believe that this method provides insights for the researchers working on characterization of protein binding sites and design of specific therapeutic agents for protein interactions.

Availability:The list of training and test sets are available as Supplementary Data at http://prism.ccbb.ku.edu.tr/hotpoint/supplement.doc

Contact:  agursoy@ku.edu.tr; okeskin@ku.edu.tr

Supplementary information:  Supplementary data are available at Bioinformatics online.
Measurements of acoustic backscatter and density of captive Atlantic cod with synchronized 300-kHz multibeam and 120-kHz split-beam echosounders
Authors: Gurshin Christopher W. D. , Jech J. Michael , Howell W. Huntting , Weber Thomas C. , Mayer Larry A.
Published: April 2009

Gurshin, C. W. D., Jech, J. M., Howell, W. H., Weber, T. C., and Mayer, L. A. 2009. Measurements of acoustic backscatter and density of captive Atlantic cod with synchronized 300-kHz multibeam and 120-kHz split-beam echosounders. – ICES Journal of Marine Science, 66: 1303–1309. Effective management strategies for Atlantic cod (Gadus morhua) in the Gulf of Maine require stock assessments based on accurate estimates of its abundance and distribution. If multibeam echosounders are to provide data for such estimates, the relationship between acoustic backscatter and fish biology must be better understood. Working towards this goal, a series of acoustic measurements was made using a 120 kHz, split-beam echosounder (Simrad EK60) and a 300 kHz, multibeam echosounder (Kongsberg EM3002). The transducers from both systems were fixed to a platform over a submerged 98 m3 cage made of 5 cm stretched-nylon mesh. After standard-sphere calibrations, the cage was stocked with live, mature Atlantic cod, with a mean total length of 80.7 cm (range: 51.5–105.0 cm). The echosounders synchronously collected acoustic data, while the cod were monitored with two underwater video cameras. Cod were incrementally removed from the cage to provide a time-series of acoustic backscatter at four densities (n = 128, 116, 66, and 23). Backscatter measurements of cod are compared between echosounders and over time, and the factors affecting the acoustically derived density estimates are discussed. The benefits and limitations of the EM3002 are highlighted.
Modelling demersal fishing effort based on landings and days absence from port, to generate indicators of “activity”
Authors: Greenstreet S. P. R. , Holland G. J. , Fraser T. W. K. , Allen V. J.
Published: April 2009

Greenstreet, S. P. R., Holland, G. J., Fraser, T. W. K., and Allen, V. J. 2009. Modelling demersal fishing effort based on landings and days absence from port, to generate indicators of “activity”. – ICES Journal of Marine Science, 66: 886–901. For many components of marine ecosystems, the derivation of biologically significant, operational “pressure” indicators will rely on modelling fishing mortality from indicators of anthropogenic “activity”. This essentially expands the well established Pressure–State–Response framework to one of Activity–Pressure–State–Response. Within the Common Fisheries Policy, the reporting of fishing effort data, the basic indicator of activity, is not mandatory. A modelling approach is therefore developed that utilizes the data that fishers are obliged to report (days absence from port, landings from each rectangle fished, and the gear used) to provide modelled estimates of fishing effort. The model is parameterized for the Scottish demersal fishing fleet using data collected through the Scottish discards observer scheme, and fishing effort over the period 1997–2004 is modelled. Reported effort data for the period 1960–1998 allowed validation of the model through direct comparison of modelled with reported data in 1997 and 1998. Combining the modelled and reported datasets revealed that Scottish fishing activity levels, remarkably constant over four decades, had declined markedly since 2000. Temporal trends in UK quotas for the main targeted demersal species are considered to assess the effectiveness of catch limitation management as a means of regulating fishing activity. Spatial patterns in effort by the four main gear types used by the Scottish demersal fleet are described, and in general terms, these have changed little over the period 1960–2004. However, distinct spatial patterns emerged in the temporal trends in each ICES rectangle, associated with the recent overall decline in Scottish demersal fishing activity. These patterns were not intuitive, and the implications of this for an ecosystem approach to management are discussed.
The sensitivity of the Seychelles–Chagos thermocline ridge to large-scale wind anomalies
Authors: Hermes Juliet C. , Reason Chris J. C.
Published: April 2009

Hermes, J. C., and Reason, C. J. C. 2009. The sensitivity of the Seychelles–Chagos thermocline ridge to large-scale wind anomalies. – ICES Journal of Marine Science, 66: 1455–1466. The Seychelles–Chagos thermocline ridge (SCTR) in the southwest tropical Indian Ocean is important for regional climate, the Madden–Julian Oscillation, as well as upper-ocean nutrients and related phytoplankton and zooplankton densities. Subsurface variability in this region has been proved to influence the overlying sea surface temperatures, which in turn can influence eastern African rainfall. There is evidence that austral summers with a deeper (shallower) SCTR tend to have more (less) tropical cyclone (TC) days in the Southwest Indian Ocean. The importance of this relationship was underlined during the 2006/2007 austral summer, when areas of Madagascar and central Mozambique experienced devastating floods, because of ten named tropical storms, including several intense TCs, effecting on these areas. At the same time, the SCTR during this season was anomalously deep, partly because of a downwelling Rossby wave that propagated across the South Indian Ocean during the previous austral winter/spring. In this paper, a regional ocean model is used to investigate the effect of remote forcing on this region and to study the sensitivity of the SCTR to changes in the large-scale winds over the South Indian Ocean, with a particular focus on the events of the 2006/2007 austral summer.
A bottom-up approach to technological development and its management implications in a commercial fishery
Authors: Eigaard Ole Ritzau
Published: April 2009

Eigaard, O. R. 2009. A bottom-up approach to technological development and its management implications in a commercial fishery. – ICES Journal of Marine Science, 66: 916–927. Analyses of electronic equipment on board Danish trawlers and gillnetters show that newer, larger vessels have a significantly higher “technological level” than older, smaller vessels. A hypothesis of linkage between fish-finding and navigation technology on board and standard vessel characteristics was tested based on the definition of a technological index. Using a proportional odds model, vessel length accounted for most of the variation in technological level on board, with odds of 1.17 (95% confidence interval: 1.16–1.18) of a higher index value for each increase in vessel length of 1 m. Vessel age was also significantly correlated with index values. In considering the technological index as an indicator of fishing power, the results have important implications for capacity-reduction schemes intended to reduce harvest pressure on fish stocks. In the course of such structural management plans, older, smaller vessels of a fleet are often replaced with newer, larger vessels within a fixed or reduced nominal capacity limit (e.g. total fleet tonnage), but according to the findings presented, nominal capacity reduction in fleet level may be undermined by increases in individual vessel fishing power.
Measurements of acoustic-scattering spectra from the whole and parts of Atlantic mackerel
Authors: Nesse Tonje Lexau , Hobæk Halvor , Korneliussen Rolf J.
Published: April 2009

Nesse, T. L., Hobæk, H., and Korneliussen, R. J. 2009. Measurements of acoustic-scattering spectra from the whole and parts of Atlantic mackerel. – ICES Journal of Marine Science, 66: 1169–1175. Atlantic mackerel (Scomber scombrus) are weak sound scatterers compared with fish that have swimbladders. Accurate acoustic estimates of mackerel abundance require estimates of target strength. Different parts of mackerel may dominate the backscattering spectra. Mackerel schools are acoustically recognized mainly by backscatter four times stronger at 200 kHz than at 38 kHz. Simulations have established that backscatter from only the flesh and the backbone could explain this frequency response, although there are uncertainties in the model parameters and simplifications. In this paper, experiments conducted in a laboratory tank to investigate the complexity of mackerel backscatter are discussed. Acoustic backscatter was measured over the frequency range 65–470 kHz from individual dead mackerel, and their backbones, heads, and skulls. Backscatter from the backbones was measured at several angles of incidence. Grating lobes (Bragg scattering) appeared at different angles, depending on the acoustic frequency and the spacing of the vertebrae. These lobes were evident in backbone backscatter after propagating through the flesh and can be used, in principle, to determine mackerel size acoustically. The frequency response of individual, ex situ Atlantic mackerel estimated from these measurements did not match that from the measurements of in situ mackerel schools. Further investigation is warranted.
Sexually antagonistic chromosomal cuckoos
Authors: Rice William R. , Gavrilets Sergey , Friberg Urban
Published: April 2009

The two kinds of sex chromosomes in the heterogametic parent are transmitted to offspring with different sexes, causing opposite-sex siblings to be completely unrelated for genes located on these chromosomes. Just as the nest-parasitic cuckoo chick is selected to harm its unrelated nest-mates in order to garner more shared resources, sibling competition causes the sex chromosomes to be selected to harm siblings that do not carry them. Here we quantify and contrast this selection on the X and Y, or Z and W, sex chromosomes. We also develop a hypothesis for how this selection can contribute to the decay of the non-recombining sex chromosome.
Skin of the Cretaceous mosasaur
Plotosaurus
: implications for aquatic adaptations in giant marine reptiles
Authors: Lindgren Johan , Alwmark Carl , Caldwell Michael W. , Fiorillo Anthony R.
Published: April 2009

The physical nature of water and the environment it presents to an organism have long been recognized as important constraints on aquatic adaptation and evolution. Little is known about the dermal cover of mosasauroids (a group of secondarily aquatic reptiles that occupied a wide array of predatory niches in the Cretaceous marine ecosystems 92–65 Myr ago), a lack of information that has hindered inferences about the nature and level of their aquatic adaptations. A newly discovered
Plotosaurus
skeleton with integument preserved in three dimensions represents not only the first documented squamation in a mosasaurine mosasaur but also the first record of skin in an advanced member of the Mosasauroidea. The dermal cover comprises keeled and possibly osteoderm-reinforced scales that presumably contributed to an anterior–posterior channelling of the water flow and a reduction of microturbulent burst activities along the surface of the skin. Thus, hydrodynamic requirements of life in the water might have influenced the evolution of multiple-keeled body scales in advanced mosasauroids.
Sonar-induced temporary hearing loss in dolphins
Authors: Mooney T. Aran , Nachtigall Paul E. , Vlachos Stephanie
Published: April 2009

There is increasing concern that human-produced ocean noise is adversely affecting marine mammals, as several recent cetacean mass strandings may have been caused by animals' interactions with naval ‘mid-frequency’ sonar. However, it has yet to be empirically demonstrated how sonar could induce these strandings or cause physiological effects. In controlled experimental studies, we show that mid-frequency sonar can induce temporary hearing loss in a bottlenose dolphin (Tursiops truncatus). Mild-behavioural alterations were also associated with the exposures. The auditory effects were induced only by repeated exposures to intense sonar pings with total sound exposure levels of 214 dB re: 1 μPa2 s. Data support an increasing energy model to predict temporary noise-induced hearing loss and indicate that odontocete noise exposure effects bear trends similar to terrestrial mammals. Thus, sonar can induce physiological and behavioural effects in at least one species of odontocete; however, exposures must be of prolonged, high sound exposures levels to generate these effects.
Intelligently deciphering unintelligible designs: algorithmic algebraic model checking in systems biology
Authors: Mishra Bud
Published: April 2009

Systems biology, as a subject, has captured the imagination of both biologists and systems scientists alike. But what is it? This review provides one researcher's somewhat idiosyncratic view of the subject, but also aims to persuade young scientists to examine the possible evolution of this subject in a rich historical context. In particular, one may wish to read this review to envision a subject built out of a consilience of many interesting concepts from systems sciences, logic and model theory, and algebra, culminating in novel tools, techniques and theories that can reveal deep principles in biology—seen beyond mere observations. A particular focus in this review is on approaches embedded in an embryonic program, dubbed ‘algorithmic algebraic model checking’, and its powers and limitations.
Rheological response and dynamics of the amphiphilic diamond phase from kinetic lattice–Boltzmann simulations
Authors: Saksena R.S. , Coveney P.V.
Published: April 2009

The purpose of the present paper is to report on the first computational study of the dynamical and rheological response of a self-assembled diamond mesophase under Couette flow in a ternary mixture composed of oil, water and an amphiphilic species. The amphiphilic diamond mesophase arises in a wide range of chemical and biological systems, and a knowledge of its rheological response has important implications in materials science and biotechnological applications. The simulations reported here are performed using a kinetic lattice–Boltzmann method. Lyotropic liquid crystals exhibit characteristic rheological responses in experiments that include shear-banding and a non-Newtonian flow curve as well as viscoelasticity under oscillatory shear. Their behaviour under steady and oscillatory shear is correctly reproduced in our simulations. On cessation of shear, as the morphology returns to the diamond phase, the relaxation of the stress response follows a stretched-exponential form for low initial strain rates.
The geometry of modified Riemannian extensions
Authors: Calviño-Louzao E. , García-Río E. , Gilkey P. , Vázquez-Lorenzo R.
Published: April 2009

We show that every paracomplex space form is locally isometric to a modified Riemannian extension and gives necessary and sufficient conditions for a modified Riemannian extension to be Einstein. We exhibit Riemannian extension Osserman manifolds of signature (3, 3), whose Jacobi operators have non-trivial Jordan normal form and which are not nilpotent. We present new four-dimensional results in Osserman geometry.
Stage-structured transmission of phocine distemper virus in the Dutch 2002 outbreak
Authors: Klepac Petra , Pomeroy Laura W. , Bjørnstad Ottar N. , Kuiken Thijs , Osterhaus Albert D.M.E. , Rijks Jolianne M.
Published: April 2009

Heterogeneities in transmission among hosts can be very important in shaping infectious disease dynamics. In mammals with strong social organization, such heterogeneities are often structured by functional stage: juveniles, subadults and adults. We investigate the importance of such stage-related heterogeneities in shaping the 2002 phocine distemper virus (PDV) outbreak in the Dutch Wadden Sea, when more than 40 per cent of the harbour seals were killed. We do this by comparing the statistical fit of a hierarchy of models with varying transmission complexity: homogeneous versus heterogeneous mixing and density- versus frequency-dependent transmission. We use the stranding data as a proxy for incidence and use Poisson likelihoods to estimate the ‘who acquires infection from whom’ (WAIFW) matrix. Statistically, the model with strong heterogeneous mixing and density-dependent transmission was found to best describe the transmission dynamics. However, patterns of incidence support a model of frequency-dependent transmission among adults and juveniles. Based on the maximum-likelihood WAIFW matrix estimates, we use the next-generation formalism to calculate anR0between 2 and 2.5 for the Dutch 2002 PDV epidemic.
Temperature change as a probe of muscle crossbridge kinetics: a review and discussion
Authors: Woledge R.C. , Barclay C.J. , Curtin N.A.
Published: April 2009

Following the ideas introduced by Huxley (Huxley 1957,
Prog. Biophys. Biophys. Chem.
7
, 255–318), it is generally supposed that muscle contraction is produced by temporary links, called crossbridges, between myosin and actin filaments, which form and break in a cyclic process driven by ATP splitting. Here we consider the interaction of the energy in the crossbridge, in its various states, and the force exerted. We discuss experiments in which the mechanical state of the crossbridge is changed by imposed movement and the energetic consequence observed as heat output and the converse experiments in which the energy content is changed by altering temperature and the mechanical consequences are observed. The thermodynamic relationship between the experiments is explained and, at the first sight, the relationship between the results of these two types of experiment appears paradoxical. However, we describe here how both of them can be explained by a model in which mechanical and energetic changes in the crossbridges occur in separate steps in a branching cycle.
Negative density-dependent emigration of males in an increasing red deer population
Authors: Loe Leif Egil , Mysterud Atle , Veiberg Vebjørn , Langvatn Rolf
Published: April 2009

In species with polygynous mating systems, females are regarded as food-limited, while males are limited by access to mates. When local density increases, forage availability declines, while mate access for males may increase due to an increasingly female-biased sex ratio. Density dependence in emigration rates may consequently differ between sexes. Here, we investigate emigration using mark-recovery data from 468 young red deerCervus elaphusmarked in Snillfjord, Norway over a 20-year period when the population size has increased sixfold. We demonstrate a strong negative density-dependent emigration rate in males, while female emigration rates were lower and independent of density. Emigrating males leaving the natal range settled in areas with lower density than expected by chance. Dispersing males moved 42 per cent longer at high density in 1997 (37 km) than at low density in 1977 (26 km), possibly caused by increasing saturation of deer in areas surrounding the marking sites. Our study highlights that pattern of density dependence in dispersal rates may differ markedly between sexes in highly polygynous species. Contrasting patterns reported in small-scale studies are suggestive that spatial scale of density variation may affect the pattern of temporal density dependence in emigration rates and distances.
In vitro
fertilization experiments using sockeye salmon reveal that bigger eggs are more fertilizable under sperm limitation
Authors: Macfarlane Christopher P. , Hoysak Drew J. , Liley N. Robin , Gage Matthew J.G.
Published: April 2009

Although theory and widespread evidence show that the evolution of egg size is driven primarily by offspring and maternal fitness demands, an additional explanation invokes sperm limitation as a selective force that could also influence egg size optima. Levitan proposed that constraints from gamete encounter in external fertilization environments could select for enlargement of ova to increase the physical size of the fertilization target. We test this theory using
in vitro
fertilization experiments in an externally fertilizing fish. Sockeye salmon (
Onchorhyncus nerka
) females show considerable between-individual variation in ovum size, and we explored the consequences of this natural variation for the fertilization success of individual eggs under conditions of sperm limitation. By engineering consistent conditions where
in vitro
fertilization rate was always intermediate, we were able to compare the sizes of fertilized and unfertilized eggs across 20 fertilization replicates. After controlling for any changes in volume through incubation, results showed that successfully fertilized eggs were significantly larger than the eggs that failed to achieve fertilization. Under conditions without sperm limitation, fertility was unaffected by egg size. Our findings therefore support Levitan's theory, demonstrating empirically that some element of egg size variation could be selected by fertilization demands under sperm limitation. However, further research on sperm limitation in natural spawnings is required to assess the selective importance of these results.
Unravelling theWolbachiaevolutionary role: the reprogramming of the host genomic imprinting
Authors: Negri Ilaria , Franchini Antonella , Gonella Elena , Daffonchio Daniele , Mazzoglio Peter John , Mandrioli Mauro , Alma Alberto
Published: April 2009

Environmental factors can induce significant epigenetic changes that may also be inherited by future generations. The maternally inherited symbiont of arthropodsWolbachia pipientisis an excellent candidate as an ‘environmental’ factor promoting trans-generational epigenetic changes: by establishing intimate relationships with germ-line cells, epigenetic effects ofWolbachiasymbiosis would be manifested as a ‘maternal effect’, in which infection of the mother modulates the offspring phenotype. In the leafhopperZyginidia pullula,Wolbachiafeminizes genetic males, leaving them as intersexes. With the exception of male chitinous structures that are present in the last abdominal segment, feminized males display phenotypic features that are typical of females. These include ovaries that range from a typical histological architecture to an altered structure. Methylation-sensitive random amplification of polymorphic DNA profiles show that they possess a female genomic imprint. On the other hand, some rare feminized males bear testes instead of ovaries. These specimens possess aWolbachiadensity approximately four orders of magnitude lower than feminized males with ovaries and maintain a male genome—methylation pattern. Our results indicate thatWolbachiainfection disrupts male imprinting, which dramatically influences the expression of genes involved in sex differentiation and development, and the alteration occurs only ifWolbachiaexceeds a density threshold. Thus, a newWolbachia's role as an environmental evolutionary force, inducing epigenetic trans-generational changes, should now be considered.
Dynamic Localization of the DNA Replication Proteins MCM5 and MCM7 in Plants
Authors: Shultz Randall W. , Lee Tae-Jin , Allen George C. , Thompson William F. , Hanley-Bowdoin Linda
Published: April 2009

Genome integrity in eukaryotes depends on licensing mechanisms that prevent loading of the minichromosome maintenance complex (MCM2-7) onto replicated DNA during S phase. Although the principle of licensing appears to be conserved across all eukaryotes, the mechanisms that control it vary, and it is not clear how licensing is regulated in plants. In this work, we demonstrate that subunits of the MCM2-7 complex are coordinately expressed during Arabidopsis (Arabidopsis thaliana) development and are abundant in proliferating and endocycling tissues, indicative of a role in DNA replication. We show that endogenous MCM5 and MCM7 proteins are localized in the nucleus during G1, S, and G2 phases of the cell cycle and are released into the cytoplasmic compartment during mitosis. We also show that MCM5 and MCM7 are topologically constrained on DNA and that the MCM complex is stable under high-salt conditions. Our results are consistent with a conserved replicative helicase function for the MCM complex in plants but not with the idea that plants resemble budding yeast by actively exporting the MCM complex from the nucleus to prevent unauthorized origin licensing and rereplication during S phase. Instead, our data show that, like other higher eukaryotes, the MCM complex in plants remains in the nucleus throughout most of the cell cycle and is only dispersed in mitotic cells.
Interaction Transcriptome Analysis Identifies Magnaporthe oryzae BAS1-4 as Biotrophy-Associated Secreted Proteins in Rice Blast Disease
Authors: Mosquera Gloria , Giraldo Martha C. , Khang Chang Hyun , Coughlan Sean , Valent Barbara
Published: April 2009

Biotrophic invasive hyphae (IH) of the blast fungus Magnaporthe oryzae secrete effectors to alter host defenses and cellular processes as they successively invade living rice (Oryza sativa) cells. However, few blast effectors have been identified. Indeed, understanding fungal and rice genes contributing to biotrophic invasion has been difficult because so few plant cells have encountered IH at the earliest infection stages. We developed a robust procedure for isolating infected-rice sheath RNAs in which ∼20% of the RNA originated from IH in first-invaded cells. We analyzed these IH RNAs relative to control mycelial RNAs using M. oryzae oligoarrays. With a 10-fold differential expression threshold, we identified known effector PWL2 and 58 candidate effectors. Four of these candidates were confirmed to be fungal biotrophy-associated secreted (BAS) proteins. Fluorescently labeled BAS proteins were secreted into rice cells in distinct patterns in compatible, but not in incompatible, interactions. BAS1 and BAS2 proteins preferentially accumulated in biotrophic interfacial complexes along with known avirulence effectors, BAS3 showed additional localization near cell wall crossing points, and BAS4 uniformly outlined growing IH. Analysis of the same infected-tissue RNAs with rice oligoarrays identified putative effector-induced rice susceptibility genes, which are highly enriched for sensor-transduction components rather than typically identified defense response genes.