bluuebunny/crossref_metadata_2025 huggingface dataset:
Proteomic Analysis of Bovine Nucleolus
Authors: Patel Amrutlal K. , Olson Doug , Tikoo Suresh K.
Published: October 2010

Nucleolus is the most prominent subnuclear structure, which performs a wide variety of functions in the eukaryotic cellular processes. In order to understand the structural and functional role of the nucleoli in bovine cells, we analyzed the proteomic composition of the bovine nucleoli. The nucleoli were isolated from Madin Darby bovine kidney cells and subjected to proteomic analysis by LC-MS/MS after fractionation by SDS-PAGE and strong cation exchange chromatography. Analysis of the data using the Mascot database search and the GPM database search identified 311 proteins in the bovine nucleoli, which contained 22 proteins previously not identified in the proteomic analysis of human nucleoli. Analysis of the identified proteins using the GoMiner software suggested that the bovine nucleoli contained proteins involved in ribosomal biogenesis, cell cycle control, transcriptional, translational and post-translational regulation, transport, and structural organization.
Follow the Leader: Preference for Specific Amino Acids Directly Following the Initial Methionine in Proteins of Different Organisms
Authors: Shemesh Ronen , Novik Amit , Cohen Yossi
Published: October 2010

It is well established that the vast majority of proteins of all taxonomical groups and species are initiated by an AUG codon, translated into the amino acid methionine (Met). Many attempts were made to evaluate the importance of the sequences surrounding the initiation codon, mostly focusing on the RNA sequence. However, the role and importance of the amino acids following the initiating Met residue were rarely investigated, mostly in bacteria and fungi. Herein, we computationally examined the protein sequences of all major taxonomical groups represented in the Swiss-Prot database, and evaluated the preference of each group to specific amino acids at the positions directly following the initial Met. The results indicate that there is a species-specific preference for the second amino acid of the majority of protein sequences. Interestingly, the preference for a certain amino acid at the second position changes throughout evolution from lysine in prokaryotes, through serine in lower eukaryotes, to alanine in higher plants and animals.
Instabilities of buoyancy-driven coastal currents and their nonlinear evolution in the two-layer rotating shallow water model. Part 2. Active lower layer
Authors: GULA J. , ZEITLIN V. , BOUCHUT F.
Published: October 2010

This paper is the second part of the work on linear and nonlinear stability of buoyancy-driven coastal currents. Part 1, concerning a passive lower layer, was presented in the companion paper Gula & Zeitlin (J. Fluid Mech., vol. 659, 2010, p. 69). In this part, we use a fully baroclinic two-layer model, with active lower layer. We revisit the linear stability problem for coastal currents and study the nonlinear evolution of the instabilities with the help of high-resolution direct numerical simulations. We show how nonlinear saturation of the ageostrophic instabilities leads to reorganization of the mean flow and emergence of coherent vortices. We follow the same lines as in Part 1 and, first, perform a complete linear stability analysis of the baroclinic coastal currents for various depths and density ratios. We then study the nonlinear evolution of the unstable modes with the help of the recent efficient two-layer generalization of the one-layer well-balanced finite-volume scheme for rotating shallow water equations, which allows the treatment of outcropping and loss of hyperbolicity associated with shear, Kelvin–Helmholtz type, instabilities. The previous single-layer results are recovered in the limit of large depth ratios. For depth ratios of order one, new baroclinic long-wave instabilities come into play due to the resonances among Rossby and frontal- or coastal-trapped waves. These instabilities saturate by forming coherent baroclinic vortices, and lead to a complete reorganization of the initial current. As in Part 1, Kelvin fronts play an important role in this process. For even smaller depth ratios, short-wave shear instabilities with large growth rates rapidly develop. We show that at the nonlinear stage they produce short-wave meanders with enhanced dissipation. However, they do not change, globally, the structure of the mean flow which undergoes secondary large-scale instabilities leading to coherent vortex formation and cutoff.
Neural reuse implies distributed coding
Authors: Bridgeman Bruce
Published: October 2010

Both distributed coding, with its implication of neural reuse, and more specialized function have been recognized since the beginning of brain science. A controversy over imageless thought threw introspection into disrepute as a scientific method, making more objective methods dominate. It is known in information science that one element, such as a bit in a computer, can participate in coding many independent states; in this commentary, an example is given.
Neural reuse and cognitive homology
Authors: Bergeron Vincent
Published: October 2010

Neural reuse theories suggest that, in the course of evolution, a brain structure may acquire or lose a number of cognitive uses while maintaining its cognitive workings (or low-level operations) fixed. This, in turn, suggests that homologous structures may have very different cognitive uses, while sharing the same workings. And this, essentially, is homology thinking applied to brain function.
The Leabra architecture: Specialization without modularity
Authors: Petrov Alexander A. , Jilk David J. , O'Reilly Randall C.
Published: October 2010

The posterior cortex, hippocampus, and prefrontal cortex in the Leabra architecture are specialized in terms of various neural parameters, and thus are predilections for learning and processing, but domain-general in terms of cognitive functions such as face recognition. Also, these areas are not encapsulated and violate Fodorian criteria for modularity. Anderson's terminology obscures these important points, but we applaud his overall message.
Reuse of molecules and of neural circuits
Authors: Reimers Mark
Published: October 2010

Reuse is well established in molecular evolution; some analogies from this better understood field may help suggest specific aspects of reuse of neural circuits.
How and over what timescales does neural reuse actually occur?
Authors: Donnarumma Francesco , Prevete Roberto , Trautteur Giuseppe
Published: October 2010

We isolate some critical aspects of the reuse notion in Anderson's massive redeployment hypothesis (MRH). We notice that the actual rearranging of local neural circuits at a timescale comparable with the reactivity timescale of the organism is left open. We propose the concept of programmable neural network as a solution.
Implications of neural reuse for brain injury therapy: Historical note on the work of Kurt Goldstein
Authors: Lia Barry
Published: October 2010

This commentary suggests how the target article raises new implications for brain injury therapies, which may have been anticipated by the neurologist Kurt Goldstein, though he worked in and earlier era of fervent localization of brain function.
Multi-use and constraints from original use
Authors: Jungé Justin A. , Dennett Daniel C.
Published: October 2010

Anderson's theory is plausible and largely consistent with the data. However, it remains underspecified on several fronts, and we highlight areas for potential improvement. Reuse is described as duplicating a functional component, preserving one function and tinkering to add another function. This is a promising model, but Anderson neglects other reasonable alternatives and we highlight several. Evidence cited in support of reuse fails to uniquely support it among a broader set of multi-use theories. We suggest that a more stringent criterion for direct support of reuse may be satisfied by focusing on previous adaptive functions (original use).
Let us redeploy attention to sensorimotor experience
Authors: Michaux Nicolas , Pesenti Mauro , Badets Arnaud , Di Luca Samuel , Andres Michael
Published: October 2010

With his massive redeployment hypothesis (MRH), Anderson claims that novel cognitive functions are likely to rely on pre-existing circuits already possessing suitable resources. Here, we put forward recent findings from studies in numerical cognition in order to show that the role of sensorimotor experience in the ontogenetical development of a new function has been largely underestimated in Anderson's proposal.
Competence: What's in? What's out? Who knows?
Authors: Alexander Joshua , Mallon Ronald , Weinberg Jonathan M.
Published: October 2010

Knobe's argument rests on a way of distinguishing performance errors from the competencies that delimit our cognitive architecture. We argue that other sorts of evidence than those that he appeals to are needed to illuminate the boundaries of our folk capacities in ways that would support his conclusions.
Reasoning asymmetries do not invalidate theory-theory
Authors: Bartsch Karen , Young Tess N.
Published: October 2010

In this commentary we suggest that asymmetries in reasoning associated with moral judgment do not necessarily invalidate a theory-theory account of naïve psychological reasoning. The asymmetries may reflect a core knowledge assumption that human nature is prosocial, an assumption that heightens vigilance for antisocial dispositions, which in turn leads to differing assumptions about what is the presumed topic of conversation.
The social origin and moral nature of human thinking
Authors: Carpendale Jeremy I. M. , Hammond Stuart I. , Lewis Charlie
Published: October 2010

Knobe's laudable conclusion that we make sense of our social world based on moral considerations requires a development account of human thought and a theoretical framework. We outline a view that such a moral framework must be rooted in social interaction.
Morals, beliefs, and counterfactuals
Authors: Girotto Vittorio , Surian Luca , Siegal Michael
Published: October 2010

We have found that moral considerations interact with belief ascription in determining intentionality judgment. We attribute this finding to a differential availability of plausible counterfactual alternatives that undo the negative side-effect of an action. We conclude that Knobe's thesis does not account for processes by which counterfactuals are generated and how these processes affect moral evaluations.
Person as moral scientist
Authors: Humphrey Nicholas
Published: October 2010

Scientists are generally more moral, and moralists more scientific, than Knobe suggests. His own experiments show that people, rather than making unscientific judgements about the moral intentions of others, are behaving as good Bayesians who take account of prior knowledge.
The cultural capital of the moralist and the scientist
Authors: Kang Min Ju , Glassman Michael
Published: October 2010

In this commentary we explore Knobe's ideas of moral judgments leading to moral intuitions in the context of the moral thought and moral action debate. We suggest that Knobe's primary moral judgment and the setting of a continuum with a default point is in essence a form of cultural capital, different from moral action, which is more akin to social capital.
Scientists and the folk have the same concepts
Authors: Levy Neil
Published: October 2010

If Knobe is right that ordinary judgments are normatively suffused, how do scientists free themselves from these influences? I suggest that because science is distributed and externalized, its claims can be manipulated in ways that allow normative influences to be hived off. This allows scientists to deploy concepts which are not normatively suffused. I suggest that there are good reasons to identify these normatively neutral concepts with the folk concepts.
Expectations and morality: A dilemma
Authors: Mandelbaum Eric , Ripley David
Published: October 2010

We propose Knobe's explanation of his cases encounters a dilemma: Either his explanation works and, counterintuitively, morality is not at the heart of these effects; or morality is at the heart of the effects and Knobe's explanation does not succeed. This dilemma is then used to temper the use of the Knobe paradigm for discovering moral norms.
Norms, causes, and alternative possibilities
Authors: Menzies Peter
Published: October 2010

I agree with Knobe's claim in his “Person as Scientist, Person as Moralist” article that moral considerations are integral to the workings of people's competence in making causal judgments. However, I disagree with the particular explanation he gives of the way in which moral considerations influence causal judgments. I critically scrutinize his explanation and outline a better one.
Ambiguity of “intention”
Authors: Scanlon Thomas M.
Published: October 2010

Knobe reports that subjects' judgments of whether an agent did something intentionally vary depending on whether the outcome in question was seen by them as good or as bad. He concludes that subjects' moral views affect their judgments about intentional action. This conclusion appears to follow only if different meanings of “intention” are overlooked.
Alternatives and defaults: Knobe's two explanations of how moral judgments influence intuitions about intentionality and causation
Authors: Sinnott-Armstrong Walter
Published: October 2010

Knobe cites both relevant alternatives and defaults on a continuum to explain how moral judgments influence intuitions about certain apparently non-moral notions. I ask (1) how these two accounts are related, (2) whether they exclude or supplement supposedly competing theories, and (3) how to get positive evidence that people consider relevant alternatives when applying such notions.
Fixing the default position in Knobe's competence model
Authors: Ulatowski Joseph , Johnson Justus
Published: October 2010

Although we agree with the spirit of Knobe's competence model, our aim in this commentary is to argue that the default position should be made more precise. Our quibble with Knobe's model is that we find it hard to ascribe a coherent view to some experimental subjects if the default position is not clearly defined.
Understanding the adult moralist requires first understanding the child scientist
Authors: Kushnir Tamar , Chernyak Nadia
Published: October 2010

Children learnfrompeople andaboutpeople simultaneously; that is, children consider evidentiary qualities of human actions which cross traditional domain boundaries. We propose that Knobe's moral asymmetries are a natural consequence of this learning process: the way “child scientists” gather evidence for causation, intention, and morality through early social experiences.
The person as moralist account and its alternatives
Authors: Knobe Joshua
Published: October 2010

The commentators offer helpful suggestions at three levels: (1) explanations for the particular effects discussed in the target article; (2) implications of those effects for our understanding of the role of moral judgment in human cognition; and (3) more theoretical questions about the overall relationship between ordinary cognition and systematic science. The present response takes up these three issues in turn.
The spatial dimension in environmental and resource economics
Authors: XEPAPADEAS ANASTASIOS
Published: October 2010

Mechanisms generating patterns in spatial domains have been extensively studied in biology, but also in economics in the context of new economic geography. The Turing mechanism or Turing diffusion-induced instability has been central to the understanding of forces which endogenously generate spatial patterns, but in a context where agents do not explicitly optimize an objective. The present paper reviews tools to study, in the spirit of Turing's analysis, a mechanism generating optimal diffusion-induced instability where optimizing agents generate optimal agglomerations. By extending the maximum principle to the optimal control of partial differential equations, it is shown how under certain conditions it will be optimal to design controls so that the price-quantity system implied by the costate–state functions of the optimal control of distributed parameter systems induces optimal spatial patterns. These methods might be useful in studying pattern formation both in problems of resource management and of economic development.
ENDOGENOUS TIME PREFERENCE AND PUBLIC POLICY: GROWTH AND FISCAL IMPLICATIONS
Authors: Dioikitopoulos Evangelos V. , Kalyvitis Sarantis
Published: October 2010

This paper studies the growth and fiscal policy implications of the assumption that public policy generates an externality in the individual rate of time preference through the aggregate public capital stock. We examine the competitive equilibrium properties and we solve for endogenous growth–maximizing fiscal policy. We investigate the behavior of the government size and the growth rate to the sensitivity of time preference to public capital and the magnitude of public capital externality on production. We find that the Barro taxation rule [Barro, Robert J.,Journal of Political Economy98 (1990), 103–125], which states that the elasticity of public capital in the production function should equal the government size, is suboptimal. We show that the government does not necessarily have to increase income taxation following a rise in public capital intensity because of the externality of public capital on time preference and, in turn, on growth and the tax base of the economy.
Advantages of Clustering in the Phase Classification of Hyperspectral Materials Images
Authors: Stork Christopher L. , Keenan Michael R.
Published: October 2010

Despite the many demonstrated applications of factor analysis (FA) in analyzing hyperspectral materials images, FA does have inherent mathematical limitations, preventing it from solving certain materials characterization problems. A notable limitation of FA is its parsimony restriction, referring to the fact that in FA the number of components cannot exceed the chemical rank of a dataset. Clustering is a promising alternative to FA for the phase classification of hyperspectral materials images. In contrast with FA, the phases extracted by clustering do not have to be parsimonious. Clustering has an added advantage in its insensitivity to spectral collinearity that can result in phase mixing using FA. For representative energy dispersive X-ray spectroscopy materials images, namely a solder bump dataset and a braze interface dataset, clustering generates phase classification results that are superior to those obtained using representative FA-based methods. For the solder bump dataset, clustering identifies a Cu-Sn intermetallic phase that cannot be isolated using FA alone due to the parsimony restriction. For the braze interface sample that has collinearity among the phase spectra, the clustering results do not exhibit the physically unrealistic phase mixing obtained by multivariate curve resolution, a commonly utilized FA algorithm.
Early Spreading and Propagation of Human Bone Marrow Stem Cells on Isotropic and Anisotropic Topographies of Silica Thin Films Produced via Microstamping
Authors: Pelaez-Vargas A. , Gallego-Perez D. , Ferrell N. , Fernandes M.H. , Hansford D. , Monteiro F.J.
Published: October 2010

While there has been rapid development of microfabrication techniques to produce high-resolution surface modifications on a variety of materials in the last decade, there is still a strong need to produce novel alternatives to induce guided tissue regeneration on dental implants. High-resolution microscopy provides qualitative and quantitative techniques to study cellular guidance in the first stages of cell-material interactions. The purposes of this work were (1) to produce and characterize the surface topography of isotropic and anisotropic microfabricated silica thin films obtained by sol-gel processing, and (2) to compare the in vitro biological behavior of human bone marrow stem cells on these surfaces at early stages of adhesion and propagation. The results confirmed that a microstamping technique can be used to produce isotropic and anisotropic micropatterned silica coatings. Atomic force microscopy analysis was an adequate methodology to study in the same specimen the sintering derived contraction of the microfabricated coatings, using images obtained before and after thermal cycle. Hard micropatterned coatings induced a modulation in the early and late adhesion stages of cell-material and cell-cell interactions in a geometry-dependent manner (i.e., isotropic versus anisotropic), as it was clearly determined, using scanning electron and fluorescence microscopies.
Convective heat transfer over thin ice covered coastal polynyas
Authors: Fiedler E. K. , Lachlan‐Cope T. A. , Renfrew I. A. , King J. C.
Published: October 2010

Polynyas play an important role in the regional meteorology and oceanography of the high latitudes and in the global ocean circulation. Unique low‐level observations of an Antarctic coastal polynya, the Ronne Polynya, were conducted using an instrumented aircraft. At the time of the observations, the polynya was mostly covered with thin ice perforated with holes and was composed of two distinct regimes: an inner region of newly formed and thin ice and an outer region of thicker more consolidated ice. The sensible heat flux over the polynya was ∼100 W m−2 and decreased with fetch, primarily as a result of the thickening ice cover. The mean sensible heat transfer and drag coefficients over the polynya were CHN10 = (0.7 ± 0.1) × 10−3 and CDN10 = (1.1 ± 0.2) × 10−3, respectively. The heat transfer coefficient is similar to that found over heterogeneous sea ice and is significantly lower than has been used in previous studies of heat fluxes over polynyas, which are often assumed to be open water. The transfer coefficients were not found to be a function of fetch or ice conditions as represented by the surface temperature and albedo. The data were used in an investigation of the output of sensible heat flux, potential temperature, and boundary layer depth from a simple fetch‐dependent model. For this case study, surface temperatures and transfer coefficients appropriate to an ice‐covered surface were required for an accurate simulation.
Evidence for decadal variation in global terrestrial evapotranspiration between 1982 and 2002: 1. Model development
Authors: Wang Kaicun , Dickinson Robert E. , Wild Martin , Liang Shunlin
Published: October 2010

Estimating interannual to decadal variability of terrestrial evapotranspiration (ET) requires use of standard meteorological data complemented with some high‐resolution satellite data. A semiempirical expression for this purpose is developed and validated with data from 2000 to 2007. These data were collected at 64 globally distributed sites, including the continuous measurements collected by the Atmospheric Radiation Measurement (ARM) and FLUXNET projects, and are the longest available, with continuous worldwide multisite measurements of ET, and a total of 274 site years. The sites are mainly located in North America and Asia, with the exception of three sites in Australia, two in Europe, and one in Africa. The climates of the sites vary from tropical to subarctic and from arid to humid. The land cover types of the sites vary from desert, croplands, grasslands, and shrub land to forests. On average, the 16 day average daily ET can be estimated with an error (standard deviation) of 17 W m−2 (25% in relative value), and with an average correlation coefficient of 0.94. The standard deviation of the comparison between measured and predicted site‐averaged daily ET is 9 W m−2 (14%), with a correlation coefficient of 0.93. The model is also satisfactory in reproducing the interannual variability at sites with 5 years of data in both humid and arid regions. The correlation coefficient between measured and predicted annual ET anomalies is 0.85. This simple but accurate method permits us to investigate decadal variation in global ET over the land as will be demonstrated in part two of this paper series.
Searching for the Oldest Ice
Authors: Severinghaus Jeff , Wolff Eric. W. , Brook Edward J.
Published: October 2010

It is generally accepted that variations in the precession and eccentricity of Earth's orbit, and Earth's axial tilt, influence long‐term climate fluctuations; the combined variations are referred to as Milankovitch cycles. Precession varies with a mean period of about 23,000 years, axial tilt varies between about 22° and 25° on a 41,000‐year cycle, and the small orbital eccentricity variations have cycles of about 100,000 and 400,000 years.

Despite the known regularity of the cycles, many aspects of their manifestation in the geological record are puzzling. For example, why did the Earth slide into a period of ice ages about 3 million years ago? Why, about a million years ago, did the pace of ice ages change from a regular 41,000‐year period (the tilt period) to an irregular 100,000‐year period whose association with Milankovitch cycles is still unclear (Figure 1)? Was a gradual decrease in atmospheric CO2 the culprit, or was it some other slow change in the climate system? Why did global ice volume have only weak 23,000‐year cycles related to Earth's orbital precession during the time period when the 41,000‐year pattern dominated, even though those 23,000‐year cycles appear prominently during the past million years? Did the north and south polar ice caps oscillate in opposite cycles during the precession period, canceling the precession response [Raymo et al., 2006]? Answering these questions is important because they underscore our incomplete understanding of the climate system.
Workshop Examines Ways to Channel a Flood of Hydrological Data ; Collaborative Energy and Water Cycle Information Services Workshop; Greenbelt, Maryland, 15–16 June 2010
Authors: Acker James , Teng William , Kempler Steven
Published: October 2010

Blizzards, floods, droughts, and heat waves from January to July 2010 brought into sharp focus a primary expected manifestation of global climate change: significant alteration of Earth's hydrological cycle. Increased numbers of extreme events, and longer‐term and larger‐scale precipitation pattern shifts that will stress both natural ecosystems and human societal norms, are anticipated as consequences of this alteration.

For 25 years, NASA has orbited satellite sensors providing data on Earth's interconnected energy and hydrologic systems; new missions for this purpose are scheduled to launch in coming years, including the Global Precipitation Measurement mission in 2013. These missions, and complementary studies, have produced large and steadily increasing volumes of data, either archived at NASA data centers or held by investigators, particularly those in the NASA Energy and Water Cycle Study (NEWS) program. This increasing volume has induced a data management dilemma: Investigators encounter an increasingly complex process to locate, access, and utilize such data, especially when seeking to combine heterogeneous data sets for innovative research.
Key Outcomes From the Inaugural AGU Board of Directors Meeting
Authors: McPhaden Michael J.
Published: October 2010

The engagement and enthusiasm of Board members and senior staff were evident as we met for the first Board of Directors meeting on 20–21 September 2010 at AGU headquarters, and much was accomplished over the 1.5 days.

The meeting kicked off with a look to the future. Board members and staff had been asked to submit imagined headlines for 2019, the year that AGU will celebrate its 100th anniversary. This was a question raised by Executive Director Chris McEntee as she interacted with AGU leaders over the past several months. Board members and staff replied with a wide variety of headlines that inspired us to think about what is possible for AGU as we move forward as an organization. The headlines are posted on the AGU Web site (http://www.agu.org/about/presidents_msg/), and we encourage you to submit your own headline to agu_execdirector@agu.org.
Climate Adaptation Summit report released
Authors: Showstack Randy
Published: October 2010

“We understand from the science that we have no choice between mitigation and adaptation. We have to do both,” John Holdren, President Barack Obama's science and technology advisor, said at a 29 September meeting where he was presented with a new report about national and regional preparations for adapting to changing climate. The report is based on the National Climate Adaptation Summit, which was convened by the University Corporation for Atmospheric Research in May 2010.
Air pollution app
Authors: Showstack Randy
Published: October 2010

A new smartphone application takes advantage of various technological capabilities and sensors to help users monitor air quality. Tapping into smartphone cameras, Global Positioning System (GPS) sensors, compasses, and accelerometers, computer scientists with the University of Southern California's (USC) Viterbi School of Engineering have developed a new application, provisionally entitled “Visibility.”
Cryo‐hydrologic warming: A potential mechanism for rapid thermal response of ice sheets
Authors: Phillips Thomas , Rajaram Harihar , Steffen Konrad
Published: October 2010

Cryo‐Hydrologic (CH) warming is proposed as a potential mechanism for rapid thermal response of glaciers and ice sheets to climate warming. We present a simple parameterization to incorporate CH warming in thermal models of ice sheets using a dual‐continuum concept, which treats ice and the cryo‐hydrologic system (CHS) as overlapping continua with heat exchange between them. The presence of liquid water in the CHS due to surface melt leads to warming of the ice. The magnitude and time‐scale of CH warming is controlled by the average spacing between elements of the CHS, which is often of the order of just 10's of meters. The corresponding time‐scale of thermal response is of the order of years‐decades, in contrast to conventional estimates of thermal response time‐scales based on vertical conduction through ice (∼102–3 m thick), which are of the order of centuries to millennia. We show that CH warming is already occurring along the west coast of Greenland. Increased temperatures resulting from CH warming will reduce ice viscosity and thus contribute to faster ice flow.
Gamma distribution models for transit time estimation in catchments: Physical interpretation of parameters and implications for time‐variant transit time assessment
Authors: Hrachowitz M. , Soulsby C. , Tetzlaff D. , Malcolm I. A. , Schoups G.
Published: October 2010

In hydrological tracer studies, the gamma distribution can serve as an appropriate transit time distribution (TTD) as it allows more flexibility to account for nonlinearities in the behavior of catchment systems than the more commonly used exponential distribution. However, it is unclear which physical interpretation can be ascribed to its two parameters (α, β). In this study, long‐term tracer data from three contrasting catchments in the Scottish Highlands were used for a comparative assessment of interannual variability in TTDs and resulting mean transit times (MTT = αβ) inferred by the gamma distribution model. In addition, spatial variation in the long‐term average TTDs from these and six additional catchments was also assessed. The temporal analysis showed that the β parameter was controlled by precipitation intensities above catchment‐specific thresholds. In contrast, the α parameter, which showed little temporal variability and no relationship with precipitation intensity, was found to be closely related to catchment landscape organization, notably the hydrological characteristics of the dominant soils and the drainage density. The relationship between β and precipitation intensity was used to express β as a time‐varying function within the framework of lumped convolution integrals to examine the nonstationarity of TTDs. The resulting time‐variant TTDs provided more detailed and potentially useful information about the temporal dynamics and the timing of solute fluxes. It was shown that in the wet, cool climatic conditions of the Scottish Highlands, the transit times from the time‐variant TTD were roughly consistent with the variations of MTTs revealed by interannual analysis.
SciNetS Search : Inference Search over an Integrated Life-sciences Database Based on the Semantic Web
Authors: Toyoda Tetsuro , Kobayashi Norio , Ishii Manabu , Yoshida Yuko , Makita Yuko , Matsushima Akihiro , Mochizuki Yoshiki
Published: October 2010

Integration of various omics databases is a fundamental approach for comprehensive understanding of life phenomena. Scientists’ Networking System (SciNetS) is a Semantic Web-based data repository that realises database integration by collecting metadata of databases described as a set of triples consisting of two bio-items such as gene and ontology terms and a semantically defined relationship between these bio-items. These triples are curated from various life-sciences databases including gene-publication relationships manually curated from MEDLINE and gene-phenotype relationships extracted from published databases by computer programs. SciNetS internally forms a metadata network by maximally concatenating triples.SciNetS Search realizes a cross-search over the integrated databases by traversing the metadata network managed by SciNetS. SciNetS Search allows a user to discover bio-items included in the ontological category specified by the user. The results include bio-items not only having a user’s keyword but also semantically inferred from these bio-items using metadata relationships, and are ranked using statistical scores computed on the basis of the metadata network. SciNetS Search is available via a user’s web browser and provides search service against over 30 million bio-items of 100 thousand categories and 100 million relationships curated from over 100 public omics databases of various species including human, mouse, rice and Arabidopsis.
Gas phase hydration, bond dissociation enthalpies, and acidity of aldehydes: A CBS-Q//B3, G4MP2, and G4 theoretical study of substituent effects
Authors: Rayne Sierra , Forest Kaya
Published: October 2010

CBS-Q//B3, G4MP2, and G4 composite method calculations were used to estimate gas phase standard state (298.15 K, 1 atm) free energies of hydration (Δ~hydr~G°~(g)~), hydration equilibrium constants (log K~hydr,(g)~), bond dissociation enthalpies (BDEs), and enthalpies (Δ~d~H°~(g)~) and free energies (Δ~d~G°~(g)~) of aldehydic proton acid dissociation for various substituted aldehydes with electron withdrawing and electron releasing groups. Good quality log K~hydr,(g)~ correlations with the Swain-Lupton resonance effect parameters R and R^+^ were found, allowing extension of the model to predict log K~hydr,(g)~ values for 487 substituted aldehydes having available R-values and 108 substituted aldehydes having available R^+^-values. Good correlations were also found between experimental aqueous phase hydration equilibrium constants (log K~hydr,(aq)~) and summative R/R^+^-values for peripheral substituents on a range of carbonyl derivatives (aldehydes, ketones, esters, and amides), suggesting the structure-reactivity modeling approach can be extended to include all possible combinations of R~1~C(O)R~2~ carbonyl substitution in both gas and aqueous systems. Computationally derived BDEs and Δ~d~H°~(g)~ / Δ~d~G°~(g)~ were in good agreement with the limited experimental and theoretical datasets. BDEs did not generally correlate with any of the Hammett substituent constants or Swain-Lupton parameters considered. Gas phase acidities exhibited high correlation coefficients with Hammett inductive substituent constants (σ~I~) and field effect parameters (F), allowing these to be employed as surrogates for estimating the gas phase aldehydic proton acidities of a larger potential compound range.
Automatic protein clustering as a basis of automatic annotation
Authors: Sato Naoki
Published: October 2010

Development of new generation sequencers enabled genome sequencing feasible for every organism in a laboratory. A typical data flow of de novo seuqencing includes (1) assembly of sequence reads, (2) estimation of open reading frames, (3) annotation of proteins, and (4) finding RNA genes. The annotation is normally performed by BLASTP searches against several different databases. However, it is usually hard to find a plausible annotation by just looking at the results of BLASTP searches.Here I propose a potentially automatic method of annotation that exploits automatic protein clustering using the software GCLUST, which estimates proper similarity threshold for each list of homologs using ‘entropy-optimized organism count’ method (Sato 2009). The software has been used to construct a homolog database including both prokaryotic and eukaryotic proteins ("http://gclust.c.u-tokyo.ac.jp/":http://gclust.c.u-tokyo.ac.jp/). For use in genome annotation, we need de novo clustering including many genomes of related organisms as well as genomes of representative organisms. Application of protein clustering in the annotation in Arthrospira platensis was the first successful case (Fujisawa et al. 2010). I present here results of protein clustering of total predicted proteins in two draft genomes of cyanobacteria along with total predicted proteins of 41 cyanobacteria available at NCBI. For each of the resultant protein clusters, an alignment and a phylogenetic tree were also prepared for assistance in functional annotation. The quality of alignments was evaluated by counting ill-aligned proteins (missing N- or C-terminus, or insertion/deletion), which was 4-13% of total predicted proteins in most cyanobacterial genomes. Annotation may be automated by extracting significant key words alreadly assigned for member proteins of clusters or by comparison with reference protein clusters.
Integral presentation of Experimental Results and Bioinformatic Analyses on Ciona intestinalis Proteins
Authors: Yonezawa Kouki , Ueno Keisuke , Mineta Katsuhiko , Endo Toshinori
Published: October 2010

For the aim of facilitating biologists to find new knowledge through the comprehensive proteomic and transcriptomic data of Ciona intestinalis, we have been developing an intuitive and integral view of experimental and bioinformatic results for each protein, which, unlike on human proteins, was incomplete for Ciona proteins. In the presentation, we integrated in a view the experimental results of 2D-PAGE analyses done at Shimoda Marine Research Center, University of Tsukuba, 3D-view of expressions (3DPL) done by Hotta et al., and cross-references with JGI version 1 and ENSEMBL. A total of 1,673 entries of 2D-PAGE and 57 of 3DPL are currently contained in CIPRO database. The information is summarized in a single page for a protein. Together with BLAST results, comparative genomics, expression profiles, domain search results, localization, phylogeny etc., we provide biologists the highly integrated view amongst the existing databases, which facilitates to understand the protein. For example, the 2D-PAGE and the microarray results of the same protein are sometimes different, which implies the spatial or temporal gaps of the expressions between the mRNA and the protein. Besides, two functionalities are implemented. One is an improved 2D-PAGE viewer, which provides the compact view of spots and experimental information, and another is peptide fragment mass search functionality as improved PerMS algorithm by Hozumi et al., by enabling detection of seven kinds of modifications and suspected contaminants.
The Data Sharing Challenge. Learning Community From Consortia
Authors: Hide Winston , Altshuler Gabriel , Hofmann Oliver , Begley Kimberly
Published: October 2010

Today’s data generation and analysis environment is changing rapidly as the lure of technologies provide new opportunities to laboratory scientists. From physicians seeking rapid translation to the bedside, to environmentalists seeking new paradigms to understand the biome - large scale data generation is everywhere. How do we overcome the challenges of curation, management, interpretation and sharing of these data in the new multidisciplinary environment? One key approach is to leverage the expertise inherent in existing systems - bringing together tools and paradigms that work in subfields, and making them work together for the consortium. We will discuss the stem cell discovery engine. The approach brings together leading experts in stem cell biology, molecular profiles from stem cell systems, and seeks to combine data from diverse platforms under the unifying theme of common biology. We explore the use of gene lists and canonical pathways as a supervisor - and present pathway fingerprinting as a molecular approach to a broader problem. We explore how the community seeks to interact with its data - under the glare of reality.
Passive Participle Marking by African American English–Speaking Children Reared in Poverty
Authors: Pruitt Sonja L. , Oetting Janna B. , Hegarty Michael
Published: October 2010

Purpose

In this study, the authors examined the linguistic profile of African American English (AAE)-speaking children reared in poverty by focusing on their marking of passive participles and by comparing the results with the authors' previous study of homophonous forms of past tense (S. Pruitt & J. Oetting, 2009).

Method

The data were from 45 five- to six-year-olds who spoke AAE and who participated in the authors' earlier study. Fifteen were classified as low-income (LSES); the others were classified as middle-income and served as either age- or language-matched controls. The data came from a probe that was designed by S. M. Redmond (2003), but it was modified to examine the morphological and phonological characteristics of AAE.

Results

Participle marking by all 3 groups was influenced by AAE phonology, but the LSES children marked the participles at lower rates than the controls. The LSES children’s rates of participle marking were also lower than their rates of marking for homophonous forms of past tense. Unlike the children’s rates of past-tense marking, their rates of participle marking were correlated to their vocabulary test scores.

Conclusions

AAE-speaking children reared in poverty present weaknesses in aspects of grammatical morphology that are related to their vocabulary weaknesses.
The Effects of Age and Infant Hearing Status on Maternal Use of Prosodic Cues for Clause Boundaries in Speech
Authors: Kondaurova Maria V. , Bergeson Tonya R.
Published: October 2010

Purpose

The present study examined the effects of age and hearing status of a child on maternal use of pitch change, preboundary vowel lengthening, and pause duration, all of which are prosodic cues correlated with clause boundaries in infant-directed speech.

Method

Mothers' speech to infants with normal hearing (NH;
n
= 18), infants who are profoundly deaf with a cochlear implant (HI;
n
= 9), and an adult experimenter were recorded at 2 time periods separated by 6 months. NH infants were matched to HI infants by chronological age or hearing experience. Fundamental frequency of pre- and postboundary vowels, vowel duration, and pause duration between utterances was measured.

Results

Results demonstrated that mothers (a) exaggerated prosodic characteristics in infant-directed speech regardless of infants' hearing status; (b) tailored preboundary vowel lengthening to infants' hearing experience rather than to chronological age; and (c) decreased exaggeration of pause duration over time.

Conclusions

The results suggest that acoustic cues correlated with clause boundaries are available in maternal speech to HI infants. Their exaggeration relative to adult-directed speech suggests that mothers' use of infant-directed speech is a natural behavior regardless of infant hearing status. Finally, mothers modify speech prosody according to their children’s age and hearing experience.
Lung Volume Measured During Sequential Swallowing in Healthy Young Adults
Authors: Wheeler Hegland Karen , Huber Jessica E. , Pitts Teresa , Davenport Paul W. , Sapienza Christine M.
Published: October 2010

Purpose

Outcomes from studying the coordinative relationship between respiratory and swallow subsystems are inconsistent for sequential swallows, and the lung volume at the initiation of sequential swallowing remains undefined. The first goal of this study was to quantify the lung volume at initiation of sequential swallowing ingestion cycles and to identify the respiratory pattern(s) surrounding each sequential swallow ingestion cycle. The second goal was to compare these results with existing data for single swallows.

Method

Twenty healthy young adults served as participants, 9 males and 11 females, between 19 and 28 years of age (
M
= 22 years of age). Participants completed 2 trials each of 100 mL of water self-delivered by cup and by straw. Calibrated respiratory inductance plethysmography, surface electromyography, and a contact throat microphone were used to detect respiratory parameters, identify swallow-related muscle contraction, and identify swallowing sounds, respectively.

Results

Significantly higher lung volume initiation for trials delivered by straw and more variable respiratory patterns surrounding cup and straw sequential swallowing ingestion cycles existed compared with single swallows.

Conclusions

Results show that as the physiologic demands of swallowing deviate from single, small bolus swallows, the integration of the swallowing and respiratory systems change. This may reflect obligate differences in airway protection strategy and prolonged competition for respiratory resources.
Examining Continuity of Early Expressive Vocabulary Development: The Generation R Study
Authors: Henrichs Jens , Rescorla Leslie , Schenk Jacqueline J. , Schmidt Henk G. , Jaddoe Vincent W. V. , Hofman Albert , Raat Hein , Verhulst Frank C. , Tiemeier Henning
Published: October 2010

Purpose

The authors investigated continuity and discontinuity of vocabulary skills in a population-based cohort in the Netherlands.

Method

Mothers of 3,759 children completed the Dutch version of the MacArthur Short Form Vocabulary Checklist (Zink & Lejaegere, 2003) at 18 months and a Dutch translation of the Language Development Survey (Rescorla, 1989) at 30 months. At both ages, expressive vocabulary delay was defined as vocabulary scores <10th age- and gender-specific percentile.

Results

Of the children, 85.2% had normal vocabulary development at both ages, 6.2% were “late bloomers,” 6.0% had late onset expressive vocabulary delay, and 2.6% had persistent expressive vocabulary delay. Word production and comprehension at 18 months explained 11.5% of the variance in 30-month vocabulary scores, with low birth weight, child age, gender and ethnicity, maternal age and education, and parenting stress explaining an additional 6.2%. Multinomial logistic regression was used to identify biological, demographic, and psychological factors associated with each of the vocabulary delay outcome groups relative to the typically developing group.

Conclusions

Although multiple perinatal, demographic, and maternal psychosocial factors significantly predicted vocabulary skills at 30 months, positive predictive value and sensitivity were low. Future studies should address to what extent additional factors, such as brain maturation and genetic influences, can improve the prediction and understanding of continuity and discontinuity of language delay.