bluuebunny/crossref_metadata_2025 huggingface dataset:
Stratospheric polar vortex influence on Northern Hemisphere winter climate variability
Authors: Douville H.
Published: September 2009

Given the low skill of seasonal forecasts in the Northern Hemisphere, it is important to look for extra sources of long‐range predictability in addition to the global distribution of sea surface temperature (SST). Former studies have suggested the potential contribution of the stratosphere but have never really quantified this influence and compared it to the SST forcing. In the present study, two ensembles of global atmospheric simulations driven by observed SST and radiative forcings have been performed over the 1971–2000 period. In the perturbed experiment, the stratospheric dynamics and temperature is nudged towards the ERA40 reanalyses north of 25°N in order to mimic a “perfect” polar vortex. The comparison with the control experiment reveals a strong improvement in the simulation of the Arctic and North Atlantic Oscillation, with obvious positive impacts on the interannual variability of winter surface air temperature and precipitation, especially over Europe.
Potential roles of myosin VI in cell motility
Authors: Chibalina Margarita V. , Puri Claudia , Kendrick-Jones John , Buss Folma
Published: September 2009

There is now increasing evidence that myosin motor proteins, together with the dynamic actin filament machinery and associated adhesion proteins, play crucial roles in the events leading to motility at the leading edge of migrating cells. Myosins exist as a large superfamily of diverse ATP-dependent motors, and in the present review, we focus on the unique minus-end-directed myosin VI, briefly discussing its potential functions in cell motility.
Regulation of kinetochore–microtubule attachments by Aurora B kinase
Authors: Liu Dan , Lampson Michael A.
Published: September 2009

Accurate segregation of chromosomes in mitosis requires that spindle microtubules attach sister kinetochores to opposite poles of the mitotic spindle (biorientation). To achieve biorientation of all chromosomes, incorrect attachments are selectively destabilized, providing a fresh opportunity to biorient, whereas correct attachments are stabilized. Tension across the centromere may be the signal that distinguishes different attachment states, as spindle microtubules pull bioriented sister kinetochores in the opposite direction. Destabilization of incorrect attachments requires the Ipl1/Aurora B kinase, which phosphorylates kinetochore substrates that directly interact with microtubules. The present review focuses on how Aurora B regulates attachments in response to centromere tension.
The dynamic Rab11-FIPs
Authors: Horgan Conor P. , McCaffrey Mary W.
Published: September 2009

The Rab11-FIPs (Rab11-family interacting proteins; also known as FIPs) constitute an evolutionarily conserved protein family that act as effector molecules for multiple Rab and Arf (ADP-ribosylation factor) GTPases. They were initially characterized by their ability to bind Rab11 subfamily members via a highly-conserved C-terminal RBD (Rab11-binding domain). Resolution of the crystal structure of Rab11 in complex with FIPs revealed that the RBD mediates homodimerization of the FIP molecules, creating two symmetrical interfaces for Rab11 binding and leading to the formation of a heterotetrameric complex between two FIP and two Rab11 molecules. The FIP proteins are encoded by five genes and alternative splicing has been reported. Based on primary structure, the FIPs were subcategorized into two classes: class I [Rip11, FIP2 and RCP (Rab-coupling protein)] and class II (FIP3 and FIP4). Recent studies have identified the FIPs as key players in the regulation of multiple distinct membrane trafficking events. In this mini-review, we summarize the Rab11-FIP field and discuss, at molecular and cellular levels, the recent findings on FIP function.
Employing multiple models, methods and mechanisms in bipolar disorder research
Authors: Williams Robin S.B.
Published: September 2009

BD (bipolar disorder) is a devastating condition, giving rise to debilitating mood swings and a greatly increased likelihood of suicide. Research into the origins, progression and treatment of BD has been slow, primarily due to lack of suitable model systems for BD research. However, the complexity of the neurological basis for mood, variability in patient populations and the lack of clear readouts for BD diagnosis also provide significant problems for research in this area. In this Biochemical Society Focused Meeting, held at Royal Holloway University of London, approx. 40 national and international delegates met to discuss current research into understanding BD. The talks presented at this conference covered research examining the genetic basis of the disorder, changes in patient populations, pharmacological actions of BD drugs and the development of new models systems for this research. The focus of these talks and the following papers is to help to unify and disseminate research into this important but poorly understood medical condition.
PtdIns(3,4,5)P3 and inositol depletion as a cellular target of mood stabilizers
Authors: Teo Regina , King Jason , Dalton Emma , Ryves Jonathan , Williams Robin S.B. , Harwood Adrian J.
Published: September 2009

Lithium (Li+) is the mood stabilizer most frequently used in the treatment of bipolar mood disorder; however, its therapeutic mechanism is unknown. In the 1980s, Berridge and colleagues proposed that Li+ treatment acts via inhibition of IMPase (inositol monophosphatase) to deplete the cellular concentration of myo-inositol. Inositol depletion is also seen with the alternative mood stabilizers VPA (valproic acid) and CBZ (carbamazepine), suggesting a common therapeutic action. All three drugs cause changes in neuronal cell morphology and cell chemotaxis; however, it is unclear how reduced cellular inositol modulates these changes in cell behaviour. It is often assumed that reduced inositol suppresses Ins(1,4,5)P3, a major intracellular signal molecule, but there are other important phosphoinostide-based signal molecules in the cell. In the present paper, we discuss evidence that Li+ has a substantial effect on PtdIns(3,4,5)P3, an important signal molecule within the nervous system. As seen for Ins(1,4,5)P3 signalling, suppression of PtdIns(3,4,5)P3 signalling also occurs via an inositol-depletion mechanism. This has implications for the cellular mechanisms controlling phosphoinositide signalling, and offers insight into the genetics underlying risk of bipolar mood disorder.
Knockout mice in understanding the mechanism of action of lithium
Authors: Agam Galila , Bersudsky Yuly , Berry Gerard T. , Moechars Diederik , Lavi-Avnon Yael , Belmaker R.H.
Published: September 2009

Lithium inhibits IMPase (inositol monophosphatase) activity, as well as inositol transporter function. To determine whether one or more of these mechanisms might underlie lithium's behavioural effects, we studied Impa1 (encoding IMPase) and Smit1 (sodium–myo-inositol transporter 1)-knockout mice. In brains of adult homozygous Impa1-knockout mice, IMPase activity was found to be decreased; however, inositol levels were not found to be altered. Behavioural analysis indicated decreased immobility in the forced-swim test as well as a strongly increased sensitivity to pilocarpine-induced seizures. These are behaviours robustly induced by lithium. In homozygous Smit1-knockout mice, free inositol levels were decreased in the frontal cortex and hippocampus. These animals behave like lithium-treated animals in the model of pilocarpine seizures and in the Porsolt forced-swim test model of depression. In contrast with O'Brien et al. [O'Brien, Harper, Jove, Woodgett, Maretto, Piccolo and Klein (2004) J. Neurosci. 24, 6791–6798], we could not confirm that heterozygous Gsk3b (glycogen synthase kinase 3β)-knockout mice exhibit decreased immobility in the Porsolt forced-swim test or decreased amphetamine-induced hyperactivity in a manner mimicking lithium's behavioural effects. These data support the role of inositol-related processes rather than GSK3β in the mechanism of the therapeutic action of lithium.
Validating GSK3 as an in vivo target of lithium action
Authors: Timothy O'Brien W. , Klein Peter S.
Published: September 2009

Lithium is widely used to treat bipolar disorder, but its mechanism of action in this disorder is unknown. Lithium directly inhibits GSK3 (glycogen synthase kinase 3), a critical regulator of multiple signal transduction pathways. Inhibition of GSK3 provides a compelling explanation for many of the known effects of lithium, including effects on early development and insulin signalling/glycogen synthesis. However, lithium also inhibits inositol monophosphatase, several structurally related phosphomonoesterases, phosphoglucomutase and the scaffolding function of β-arrestin-2. It is not known which of these targets is responsible for the behavioural or therapeutic effects of lithium in vivo. The present review discusses basic criteria that can be applied to model systems to validate a proposed direct target of lithium. In this context, we describe a set of simple behaviours in mice that are robustly affected by chronic lithium treatment and are similarly affected by structurally diverse GSK3 inhibitors and by removing one copy of the Gsk3b gene. These observations, from several independent laboratories, support a central role for GSK3 in mediating behavioural responses to lithium.
Treatment with IFN‐γ prevents insulin‐dependent PKB, p70S6k phosphorylation and protein synthesis in mouse C2C12 myogenic cells
Authors: Grzelkowska‐Kowalczyk Katarzyna , Wieteska‐Skrzeczyńska Wioletta
Published: September 2009

The purpose of the present study was to examine the potential effect of IFN‐γ (interferon‐γ) on the cellular content and phosphorylation of PKB (protein kinase B), p70S6k (p70 S6 kinase) and MAPK (mitogen‐activated protein kinase), and on the ability of insulin to stimulate the glucose uptake and protein synthesis in mouse C2C12 myotubes. Insulin (100 nmol/l) stimulated glucose uptake in C2C12 myotubes by 203.4%. Glucose uptake in cells differentiated in the presence of IFN‐γ (10 ng/ml) was increased by 165.8% and was not further significantly modified by the addition of insulin (183.4% of control value). Insulin increased the rate of protein synthesis by 198.8%. The basal rate of protein synthesis was not affected by IFN‐γ; however, this cytokine abolished the insulin effect. Cellular levels of PKB, p70S6k, p42MAPK and p44MAPK were not modified by IFN‐γ. Insulin caused the phosphorylation of PKB and the activation of p70S6k, but not p42MAPK and p44MAPK. In cells differentiated in the presence of IFN‐γ, the insulin‐mediated PKB phosphorylation was significantly diminished, whereas the phosphorylation of p70S6k was completely prevented. Pretreatment of C2C12 myogenic cells with IFN‐γ led to the marked increase in p42MAPK phosphorylation. Exposure of C2C12 myoblasts to IFN‐γ impaired MyoD and myogenin expression and decreased the fusion index on the fifth day of differentiation. In conclusion, (i) IFN‐γ present in the extracellular environment during C2C12 myoblast differentiation prevents the stimulatory action of insulin on protein synthesis; (ii) IFN‐γ‐induced insulin resistance of protein synthesis in myogenic cells can be associated with the decreased phosphorylation of PKB and p70S6k, as well as with the augmented basal phosphorylation of p42MAPK; (iii) this cytokine effect can be partly explained by alterations in the differentiation process.
Transition of spiral calcium waves between multiple stable patterns can be triggered by a single calcium spark in a fire-diffuse-fire model
Authors: Tang Ai-Hui , Wang Shi-Qiang
Published: September 2009

Spiral patterns have been found in various nonequilibrium systems. The Ca2+-induced Ca2+ release system in single cardiac cells is unique for highly discrete reaction elements, each giving rise to a Ca2+ spark upon excitation. We imaged the spiral Ca2+ waves in isolated cardiac cells and numerically studied the effect of system excitability on spiral patterns using a two-dimensional fire-diffuse-fire model. We found that under certain conditions, the system was able to display multiple stable patterns of spiral waves, each exhibiting different periods and distinct routines of spiral tips. Transition between these different patterns could be triggered by an internal fluctuation in the form of a single Ca2+ spark.
Intermolecular vibrational energy exchange directly probed with ultrafast two dimensional infrared spectroscopy
Authors: Bian Hongtao , Zhao Wei , Zheng Junrong
Published: September 2009

Ultrafast two dimensional infrared (2D IR) spectroscopy has been applied to probe the intermolecular vibrational energy exchange between two model molecules, benzonitrile and acetonitrile-d3. The vibrational energy exchange between these two molecules is manifested through the growth of cross peaks in their 2D IR spectra. In experiments, their nitrile groups (CN) are not involved in the energy exchange but serve as reporters of the process. Our experiments demonstrate that intermolecular vibrational energy transfer can be directly probed with the 2D IR method. Results also show that the mode specific energy transfer can be important in intermolecular vibrational energy transfers.
Reducing thermal conductivity of thermoelectric materials by using a narrow wire geometry
Authors: Hasegawa Yasuhiro , Murata Masayuki , Nakamura Daiki , Komine Takashi
Published: September 2009

The dependence of the thermal conductivity of narrow wires made from bismuth and covalently bonded materials on wire diameter was numerically calculated by considering contributions of mean free paths of carriers and phonons. The results suggest that a reduction in the thermal conductivity should be observable in a bismuth wire having a diameter of less than 1 μm sample. A reduction of nearly 20% in the temperature range of 150–300 K is expected due to the use of a narrow wire geometry. Such a geometry reduces the mobility and the thermal conductivity of the carriers, which is the dominant component, while the thermal conductivity due to phonons was dramatically reduced by using narrow wires at temperatures under 50 K due to the longer mean free path phonons. The thermal conductivity of materials with covalent bonding such as silicon was also estimated, and it is expected that the thermal conductivity of a silicon wire could be reduced due to the mean free path of phonons being longer than that of the carriers. The results suggest that it should be possible to enhance the figure of merit by reducing the thermal conductivity through using wire geometries having diameters of less than 100 nm in materials having low mobilities, high thermal conductivities, and high Debye temperatures.
ZnO nanowire arrays grown on Al:ZnO buffer layers and their enhanced electron field emission
Authors: Chen Z. H. , Tang Y. B. , Liu Y. , Yuan G. D. , Zhang W. F. , Zapien J. A. , Bello I. , Zhang W. J. , Lee C. S. , Lee S. T.
Published: September 2009

Arrays of highly ordered ZnO nanowires have been synthesized on polycrystalline Al-doped ZnO (AZO) buffer layers prepared on p-Si substrates (7–13 Ω cm) with assistance of a thermal deposition method. The diameter and interspacing of the nanowires have been controlled by the growth conditions and properties of AZO films. The optimized array of ZnO nanowires shows low turn-on and threshold fields (∼1.1 and ∼3.0 V/μm, respectively) and displays exceptional time stability of electron field emission. The time-fluctuation instability was found to be less than 0.6% at a current density of 10 mA/cm2, as measured for 500 min. The low turn-on and threshold fields as well as the stable electron emission current suggest that the arrays of ZnO nanowires could be considered in some electron field emission applications.
Kinetic-fluid dynamics modeling of I2 dissociation in supersonic chemical oxygen-iodine lasers
Authors: Waichman K. , Barmashenko B. D. , Rosenwaks S.
Published: September 2009

The mechanism of I2 dissociation in supersonic chemical oxygen-iodine lasers (COILs) is studied applying kinetic-fluid dynamics modeling, where pathways involving the excited species I2(X Σ1g+,10≤v<25), I2(X Σ1g+,25≤v≤47), I2(A′ Π32u), I2(A Π31u), O2(X Σ3g−,v), O2(a Δ1g,v), O2(b Σ1g+,v), and I(P21/2) as intermediate reactants are included. The gist of the model is adding the first reactant and reducing the contribution of the second as compared to previous models. These changes, recently suggested by Azyazov, et al. [J. Chem. Phys. 130, 104306 (2009)], significantly improve the agreement with the measurements of the gain in a low pressure supersonic COIL for all I2 flow rates that have been tested in the experiments. In particular, the lack of agreement for high I2 flow rates, which was encountered in previous models, has been eliminated in the present model. It is suggested that future modeling of the COIL operation should take into account the proposed contribution of the above mentioned reactants.
The role of copper in ZnO/Cu/ZnO thin films for flexible electronics
Authors: Sivaramakrishnan K. , Theodore N. D. , Moulder J. F. , Alford T. L.
Published: September 2009

ZnO/Cu/ZnO multilayer structures with very high conductivity have been obtained by magnetron sputtering. The Hall resistivity of the films was as low as 6.9×10−5 Ω-cm with a carrier concentration of 1.2×1022 cm−3 at the optimum copper layer thickness. The conduction mechanism has been explained in terms of metal to oxide carrier injection at low copper thickness and metal layer conduction at higher Cu thicknesses. The peak transmittance of the films is 88% and the photopic averaged transmittance is 75%. Optical transmission behavior of the films involves absorption by copper due to d-band to Fermi-surface transitions at short wavelengths and reflectance combined with scattering losses at long wavelengths. A Burstein–Moss shift in the band gap of the films is seen to take place with increase in thickness of the copper layer. The Haacke figure of merit has been calculated for the films with the best value being 8.7×10−3 Ω−1. Pole figure results reveal that the copper midlayer acts as a hindrance to (002) ZnO texturing rather than as a seed layer. These results also confirm the mechanism of conduction. The results of the study assume further significance because annealing at 150 °C for up to 24 h in a reducing (Ar+5% H2) ambient was found to have negligible effect on the properties of the films.
Correlation between surface chemistry and ion energy dependence of the etch yield in multicomponent oxides etching
Authors: Bérubé P.-M. , Poirier J.-S. , Margot J. , Stafford L. , Ndione P. F. , Chaker M. , Morandotti R.
Published: September 2009

The influence of surface chemistry in plasma etching of multicomponent oxides was investigated through measurements of the ion energy dependence of the etch yield. Using pulsed-laser-deposited CaxBa(1−x)Nb2O6 (CBN) and SrTiO3 thin films as examples, it was found that the etching energy threshold shifts toward values larger or smaller than the sputtering threshold depending on whether or not ion-assisted chemical etching is the dominant etching pathway and whether surface chemistry is enhancing or inhibiting desorption of the film atoms. In the case of CBN films etched in an inductively coupled Cl2 plasma, it is found that the chlorine uptake is inhibiting the etching reaction, with the desorption of nonvolatile NbCl2 and BaCl2 compounds being the rate-limiting step.
Enhanced absorption of metals over ultrabroad electromagnetic spectrum
Authors: Vorobyev A. Y. , Topkov A. N. , Gurin O. V. , Svich V. A. , Guo Chunlei
Published: September 2009

Metals are usually highly reflective for electromagnetic waves, especially at far-infrared and terahertz frequencies. Using a femtosecond laser structuring technique, near-perfectly reflective metals are transformed to highly absorptive over an ultrabroad electromagnetic spectrum, ranging from ultraviolet to terahertz. Absorptance of the processed metal is directly measured in the terahertz region using a calorimetry technique, and the measurements show that absorptance of the processed metal is enhanced by more than thirty times over its intrinsic value.
Microscopic Faraday rotation measurement system using pulsed magnetic fields
Authors: Egami Shigeki , Watarai Hitoshi
Published: September 2009

Microscopic Faraday rotation measurement system using a pulsed magnetic field has been constructed, which can be applied to micron sized diamagnetic and paramagnetic materials. A pulsed magnetic coil could generate a maximum magnetic flux density of about 12 T. The performance of the microscopic Faraday rotation apparatus was demonstrated by the measurement of the Verdet constant V of a polystyrene particle, after the calibration of the pulsed magnetic flux density using a glass plate as a standard material. Also, the magneto-optical rotation dispersion of some diamagnetic substances have been measured and analyzed with V=aλ−2+b. The values of a and b were compared to their magnetic susceptibilities.
Capturing transition features around a wing by reduced-order modeling based on compressible Navier–Stokes equations
Authors: Bourguet Rémi , Braza Marianna , Sévrain Alain , Bouhadji Abdellatif
Published: September 2009

The three-dimensional transition in the flow around a NACA0012 wing of constant spanwise section at Mach number 0.3, Reynolds number 800, and incidence 20° is investigated by direct numerical simulation and reduced-order modeling. The interaction between the von Kármán and the secondary instabilities is analyzed. Irregular events in the flow transition modulating the spanwise undulation are highlighted and quantified. These transition features, including “local intermittencies” in the secondary instability pattern, are efficiently captured by a reduced-order model derived by means of the Galerkin projection of the compressible flow Navier–Stokes equations onto a truncated proper orthogonal decomposition basis.
Surfactant formation efficiency of fluorocarbon-hydrocarbon oligomers in supercritical CO2
Authors: Can Hatice , Kacar Gokhan , Atilgan Canan
Published: September 2009

We use dissipative particle dynamics simulations to explore the phase behavior and solution properties of ABCBA type model surfactants in near-supercritical CO2 environment. We present design guidelines for functional surfactants with tunable properties. The block co-oligomers used in this study are made up of a CO2-phobic block having ethyl propionate and nine different types of ethylene monomers, flanked on either side by eight repeat units of fluorinated CO2-philic blocks. The most promising design block co-oligomer in the series is that with the longest CO2-phobic group in the ethylene monomers. For this particular oligomer, we systematically analyze the effect of concentration on the self-assembly behavior. Spherical micelles form in the 5%–65% volume fraction range for this oligomer, with the highest number of spherical micelles occurring at 45% surfactant in CO2. When the volume fraction of the surfactant is increased from 70% to 85%, cylindrical micelles occur. We further investigate the effect of the length of the solvophilic fluorinated segments on self-assembly and find that stable micelles occur in a window of 8–14 repeat units. We find that the most critical contribution to stability is due to the mixing free energy between the chain tails residing in the outer layers and the interpenetrating molecules.
Macroinvertebrates on coarse woody debris in the littoral zone of a boreal lake
Authors: Glaz Patricia N. , Nozais Christian , Arseneault Dominique
Published: September 2009

Logging activity was a regular practice in the boreal forest of Quebec during the 19th century and may have had an impact on the temporal dynamics of aquatic coarse woody debris (CWD) and associated organisms. The dynamics of white cedar (Thuja occidentalis) CWD inputs from the riparian environment in a boreal lake in Eastern Quebec, Canada, over the past 350 years were reconstructed and differences in the macroinvertebate communities according to CWD age, season of sampling (spring, summer and autumn), depth and site were investigated. It was hypothesised that CWD macroinvertebrate community structure would change with CWD age, season and depth, but not among sites. No significant correlation was found between CWD age and macroinvertebrate densities and taxa number. The macroinvertebrate community was highly variable in space and time. Season was the main factor influencing taxa composition and the relative densities of individuals. The mean density was more than twofold greater in autumn than in spring and summer (1046, 1049 and 2335 individuals m–2 in spring, summer and autumn respectively). Density and taxa number decreased with depth, but site did not appear to influence the community. As CWD inputs increased during the log-driving period, impacts on macroinvertebrate communities were likely to be important and should be documented across the boreal zone.
Sources of nutrition supporting juvenile penaeid prawns in an Australian dry tropics estuary
Authors: Abrantes Kátya , Sheaves Marcus
Published: September 2009

Prawn fisheries are among the main sources of income in several tropical countries, where juveniles of many species inhabit estuarine wetlands. Although plants in these wetlands are considered to be essential food sources for juvenile prawns, some studies suggest that wetland producers are of limited importance. In the present study, δ13C and δ15N were used to identify differences in diet between penaeid species and size classes, and to determine if terrestrial wetland producers are important for nutrition. Two estuarine floodplain pools were sampled: one surrounded by mangroves and one surrounded by salt marsh. There were differences in diet between species and size classes. As mangrove δ13C (–29.7 to –26.3‰) was very different from salt marsh δ13C (–16.3 to –15.4‰), the importance of these producers was examined by comparing the isotopic composition of the prawns between sites and by using the IsoSource model. Although aquatic sources were the most important, salt marsh grass was also a significant contributor, supporting the hypothesis that these wetland producers are important for juvenile prawn nutrition. There was no evidence that mangrove material was of major importance for any species, suggesting that mangrove productivity is not the primary reason for the occurrence of penaeid prawns in mangrove habitats.
The effects of seeding sterile triticale on a native plant community after wildfire in a pinyon pine - mountain mahogany woodland
Authors: Waitman Benjamin A. , Draper Trent M. , Esque Todd C.
Published: September 2009

Post-fire seeding with grasses is a common practice for emergency rehabilitation of burned woodlands. However, most post-seeding monitoring does not address consequences to native flora. In November 2004, the US Forest Service hand-seeded triticale (×Triticosecale Wittm. ex A. Camus), a sterile wheat–rye hybrid, on a small burned area in the Spring Mountains of southern Nevada, United States. A monitoring project using paired plots was designed to quantify the effects of seeding triticale on density and species richness of native annual and perennial plants, cover of perennial plants, and aboveground production of annual plants. We did not find any effects of triticale seeding on annual plant species or most responses of perennial plants. However, the density of woody perennial seedlings was significantly lower 2 years after triticale was added. Although we found a smaller impact from seeding with exotic grass than other studies, quantifiable costs to native vegetation were observed. We caution against the use of non-native grass for seeding in areas with naturally low perennial recruitment.
Hutchinson's duality: The once and future niche
Authors: Colwell Robert K. , Rangel Thiago F.
Published: September 2009

The duality between “niche” and “biotope” proposed by G. Evelyn Hutchinson provides a powerful way to conceptualize and analyze biogeographical distributions in relation to spatial environmental patterns. Both Joseph Grinnell and Charles Elton had attributed niches to environments. Attributing niches, instead, to species, allowed Hutchinson's key innovation: the formal severing of physical place from environment that is expressed by the duality. In biogeography, the physical world (a spatial extension of what Hutchinson called the biotope) is conceived as a map, each point (or cell) of which is characterized by its geographical coordinates and the local values of
n
environmental attributes at a given time. Exactly the same
n
environmental attributes define the corresponding niche space, as niche axes, allowing reciprocal projections between the geographic distribution of a species, actual or potential, past or future, and its niche. In biogeographical terms, the realized niche has come to express not only the effects of species interactions (as Hutchinson intended), but also constraints of dispersal limitation and the lack of contemporary environments corresponding to parts of the fundamental niche. Hutchinson's duality has been used to classify and map environments; model potential species distributions under past, present, and future climates; study the distributions of invasive species; discover new species; and simulate increasingly more realistic worlds, leading to spatially explicit, stochastic models that encompass speciation, extinction, range expansion, and evolutionary adaptation to changing environments.
Tetramer opening in LacI-mediated DNA looping
Authors: Rutkauskas Danielis , Zhan Hongli , Matthews Kathleen S. , Pavone Francesco S. , Vanzi Francesco
Published: September 2009

Lactose repressor protein (LacI) controls transcription of the genes involved in lactose metabolism in bacteria. Essential to optimal LacI-mediated regulation is its ability to bind simultaneously to two operators, forming a loop on the intervening DNA. Recently, several lines of evidence (both theoretical and experimental) have suggested various possible loop structures associated with different DNA binding topologies and LacI tetramer structural conformations (adopted by flexing about the C-terminal tetramerization domain). We address, specifically, the role of protein opening in loop formation by employing the single-molecule tethered particle motion method on LacI protein mutants chemically cross-linked at different positions along the cleft between the two dimers. Measurements on the wild-type and uncross-linked LacI mutants led to the observation of two distinct levels of short tether length, associated with two different DNA looping structures. Restricting conformational flexibility of the protein by chemical cross-linking induces pronounced effects. Crosslinking the dimers at the level of the N-terminal DNA binding head (E36C) completely suppresses looping, whereas cross-linking near the C-terminal tetramerization domain (Q231C) results in changes of looping geometry detected by the measured tether length distributions. These observations lead to the conclusion that tetramer opening plays a definite role in at least a subset of LacI/DNA loop conformations.
Traffic-driven epidemic spreading in finite-size scale-free networks
Authors: Meloni Sandro , Arenas Alex , Moreno Yamir
Published: September 2009

The study of complex networks sheds light on the relation between the structure and function of complex systems. One remarkable result is the absence of an epidemic threshold in infinite-size, scale-free networks, which implies that any infection will perpetually propagate regardless of the spreading rate. The vast majority of current theoretical approaches assumes that infections are transmitted as a reaction process from nodes to all neighbors. Here we adopt a different perspective and show that the epidemic incidence is shaped by traffic-flow conditions. Specifically, we consider the scenario in which epidemic pathways are defined and driven by flows. Through extensive numerical simulations and theoretical predictions, it is shown that the value of the epidemic threshold in scale-free networks depends directly on flow conditions, in particular on the first and second moments of the betweenness distribution given a routing protocol. We consider the scenarios in which the delivery capability of the nodes is bounded or unbounded. In both cases, the threshold values depend on the traffic and decrease as flow increases. Bounded delivery provokes the emergence of congestion, slowing down the spreading of the disease and setting a limit for the epidemic incidence. Our results provide a general conceptual framework for the understanding of spreading processes on complex networks.
A progenitor cell origin of myeloid malignancies
Authors: Haeno Hiroshi , Levine Ross L. , Gilliland D. Gary , Michor Franziska
Published: September 2009

All cancers rely on cells that have properties of long-term self-renewal or “stemness” to maintain and propagate the tumor, but the cell of origin of most cancers is still unknown. Here, we design a stochastic mathematical model of hematopoietic stem and progenitor cells to study the evolutionary dynamics of cancer initiation. We consider different evolutionary pathways leading to cancer-initiating cells in JAK2V617F-positive myeloproliferative neoplasms (MPN): (
i
) the JAK2V617F mutation may arise in a stem cell; (
ii
) a progenitor cell may first acquire a mutation conferring self-renewal, followed by acquisition of the JAK2V617F mutation; (
iii
) the JAK2V617F mutation may first emerge in a progenitor cell, followed by a mutation conferring self-renewal; and (
iv
) a mutation conferring self-renewal to progenitors may arise in the stem cell population without causing a change in the stem cell's phenotype, followed by the JAK2V617F mutation emerging in a progenitor cell. We find mathematical evidence that a progenitor is the most likely cell of origin of JAK2V617F-mutant MPN. These results may also have relevance to other tumor types arising in tissues that are organized as a differentiation hierarchy.
Redox trapping of arsenic during groundwater discharge in sediments from the Meghna riverbank in Bangladesh
Authors: Datta S. , Mailloux B. , Jung H.-B. , Hoque M. A. , Stute M. , Ahmed K. M. , Zheng Y.
Published: September 2009

Groundwater arsenic (As) is elevated in the shallow Holocene aquifers of Bangladesh. In the dry season, the shallow groundwater discharges to major rivers. This process may influence the chemistry of the river and the hyporheic zone sediment. To assess the fate of As during discharge, surface (0–5 cm) and subsurface (1–3 m) sediment samples were collected at 9 sites from the bank of the Meghna River along a transect from its northern source (25° N) to the Bay of Bengal (22.5° N). Bulk As concentrations of surface sediment averaged 16 ± 7 mg/kg (
n
= 9). Subsurface sediment contained higher mean concentrations of As of 4,000 mg/kg (
n
= 14), ranging from 1 to 23,000 mg/kg As, with >100 mg/kg As measured at 8 sites. X-ray absorption near-edge structure spectroscopy indicated that As was mainly arsenate and arsenite, not As-bearing sulfides. We hypothesize that the elevated sediment As concentrations form as As-rich groundwater discharges to the river, and enters a more oxidizing environment. A significant portion of dissolved As sorbs to iron-bearing minerals, which form a natural reactive barrier. Recycling of this sediment-bound As to the Ganges-Brahmaputra-Meghna Delta aquifer provides a potential source of As to further contaminate groundwater. Furthermore, chemical fluxes from groundwater discharge from the Ganges-Brahmaputra-Meghna Delta may be less than previous estimates because this barrier can immobilize many elements.
Psychological Predictors of Help Needs in Male Dutch Prisoners
Authors: Bulten Erik , Nijman Henk , van der Staak Cees
Published: September 2009

In which ways are the subjective help needs of prisoners associated with the levels of psychological distress, mental disorders, treatment fearfulness, personality factors, and criminal thinking styles? This study found that detainees who expressed a subjective need for help had more psychoneurotic complaints and had more positive views of psychological help in general. Their fear for treatment, however, also turned out to be higher. Inmates who consider themselves in no need of help estimate a low possibility of actually seeking help in a situation in which they might encounter psychological problems. A significant proportion of prisoners expressed a subjective need for help. This need is related to several internal and external factors, and is shaped by approach and avoidance tendencies. Influencing the approach and avoidance motivation toward psychological help could improve chances that help and treatment needs would be converted into actual help-seeking behavior.
OA and IP: open access, digital copyright and marketplace competition
Authors: HARPER Georgia
Published: September 2009

For over 200 years copyright law has enabled, and scholars and their publishers have depended on, a state‐granted monopoly, creating ‘artificial scarcity’ to give publishers a period during which they can charge higher prices than the market would otherwise dictate and thus recover their costs, plus (usually) a profit. But today we have instant access to digital works, and easy, worldwide distribution for almost no cost to the reader beyond those of computers, Internet access, and electricity. The monopolistic mechanism of ‘artificial scarcity’ now turns one of the most critical advantages of the digital world into something to be fought tooth and nail. The solution is not stronger and longer copyrights. It more likely will emerge from experimentation to find business models that can fund the creation of works, still a costly undertaking, without sacrificing the digital benefit of almost free distribution to everyone who might desire to access them.
Book reviews
Authors: BENNETT Linda
Published: September 2009

Library Use of E‐books: 2008–2009 Edition
New York, Primary Research Group, 2008, 120 pp. ISBN 0 1 57440 101 7, US$95, pbk
Book reviews
Authors: THATCHER Sanford G.
Published: September 2009

Campus‐based Publishing Partnerships: A Guide to Critical Issues
Raym Crow Washington, DC, Scholarly Publishing and Academic Resources Coalition, 2009, 72 pp. Freely available at http://www.arl.org/sparc/partnering
Book reviews
Authors: MÜLLER Marius A.
Published: September 2009

PoWR: The Preservation of Web Resources Handbook – Digital Preservation for the UK HE/FE Web Management Community
University of London Computer Centre JISC, 2008, 102 pp. e‐Book, free online at http://jiscpowr.jiscinvolve.org/files/2008/11/powrhandbookv1.pdf
Book reviews
Authors: BENNETT Linda
Published: September 2009

New Thinking for 21st‐century Publishers: Emerging Patterns and Evolving Strategies
Joost Kist Oxford, Chandos Publishing, 2009, 180 pp. ISBN 1843344459 £39.95, pbk
How and when should interactome-derived clusters be used to predict functional modules and protein function?
Authors: Song Jimin , Singh Mona
Published: September 2009

Motivation: Clustering of protein–protein interaction networks is one of the most common approaches for predicting functional modules, protein complexes and protein functions. But, how well does clustering perform at these tasks?

Results: We develop a general framework to assess how well computationally derived clusters in physical interactomes overlap functional modules derived via the Gene Ontology (GO). Using this framework, we evaluate six diverse network clustering algorithms using Saccharomyces cerevisiae and show that (i) the performances of these algorithms can differ substantially when run on the same network and (ii) their relative performances change depending upon the topological characteristics of the network under consideration. For the specific task of function prediction in S.cerevisiae, we demonstrate that, surprisingly, a simple non-clustering guilt-by-association approach outperforms widely used clustering-based approaches that annotate a protein with the overrepresented biological process and cellular component terms in its cluster; this is true over the range of clustering algorithms considered. Further analysis parameterizes performance based on the number of annotated proteins, and suggests when clustering approaches should be used for interactome functional analyses. Overall our results suggest a re-examination of when and how clustering approaches should be applied to physical interactomes, and establishes guidelines by which novel clustering approaches for biological networks should be justified and evaluated with respect to functional analysis.

Contact:  msingh@cs.princeton.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Antimicrobial and Antioxidant Activities of Plants from Northeast of Mexico
Authors: Salazar-Aranda Ricardo , Pérez-López Luis Alejandro , López-Arroyo Joel , Alanís-Garza Blanca Alicia , Waksman de Torres Noemí
Published: September 2009

Traditional medicine has a key role in health care worldwide. Obtaining scientific information about the efficacy and safety of the plants from our region is one of the goals of our research group. In this report, 17 plants were selected and collected in different localities from northeast Mexico. The dried plants were separated into leaves, flowers, fruit, stems, roots and bark. Each part was extracted with methanol, and 39 crude extracts were prepared. The extracts were tested for their antimicrobial activity using three Gram‐negative bacterial strains (Pseudomonas aeruginosa, Klebsiella pneumoniae and Acinetobacter baumannii), three Gram‐positive bacterial strains (Enterococcus faecalis and two Staphylococcus aureus strains), and seven clinically isolated yeasts (Candida albicans, C. krusei, C. tropicalis, C. parapsilosis and C. glabrata); their antioxidant activity was tested using a DPPH free radical assay. No activity against Gram‐negative bacteria was observed with any extract up to the maximum concentration tested, 1000 μg ml−1. We report here for the first time activity of Ceanothus coeruleus against S. aureus (flowers, minimal inhibitory concentration (MIC) 125 μg ml−1), C. glabrata (MICs 31.25 μg ml−1) and C. parapsilosis (MICs between 31.25 and 125 μg ml−1); Chrysanctinia mexicana against C. glabrata (MICs 31.25 μg ml−1); Colubrina greggii against E. faecalis (MICs 250 μg ml−1) and Cordia boissieri against C. glabrata (MIC 125 μg ml−1). Furthermore, this is the first report about antioxidant activity of extracts from Ceanothus coeruleus, Chrysanctinia mexicana, Colubrina greggii and Cyperus alternifolius. Some correlation could exist between antioxidant activity and antiyeast activity against yeasts in the species Ceanothus coeruleus, Schinus molle, Colubrina greggii and Cordia boissieri.
Milesian Measures: Time, Space, and Matter
Authors: White Stephen
Published: September 2009

Any attempt to trace the origin of Greek philosophy faces two complementary problems. One is the fact that evidence for the early philosophers is woefully meager. The other problem raises a question of what is to be counted as philosophy. Yet neither problem is insuperable. This article proposes to reorient the search for origins in two ways, corresponding to these two problems. First, rather than trying to reconstruct vanished work directly, this article focuses on a crucial stage in its ancient reception, in particular, the efforts by Aristotle and his colleagues in the latter half of the fourth century to collect, analyze, and assess the evidence then available for earlier attempts to understand the natural world. The other shift in focus this article makes is from philosophy to science; or rather, it focuses on evidence for the interplay between observation, measurement, and explanation in the work of three sixth-century Milesians.
Empedocles: Physical and Mythical Divinity
Authors: Primavesi Oliver
Published: September 2009

This article considers how the new finds have affected one's view of Empedocles, and suggests how interpretation of that material might help solve (or dissolve) some longstanding problems about the structure and content of Empedocles' writings. A basic account of the teachings of Empedocles would distinguish between two main components. On the one hand, there is a “Presocratic” physics, including a theory of principles, a cosmology, and a biology. On the other hand, there is a mythical law, clearly inspired by Orphic or Pythagorean legends, which imposes on guilty gods (called daimones) a punishment consisting in their transmigration through a series of mortal beings. The purpose of this article is to show that Empedocles has the habit of referring to divine entities of his physical system both in a physical and in a mythological way and that his uses of the word daimon form part of this twofold language.
The Sophists
Authors: Gagarin Michael , Woodruff Paul
Published: September 2009

This article shows that important questions remain to be answered about the topics the sophists studied and taught, and their views, both positive and negative, about truth, religion, and convention. The sophists are united more by common methods and attitudes than by common interests. All sophists, for example, challenged traditional thinking, often in ways that went far beyond questioning the existence of the gods, or the truth of traditional myths, or customary moral rules, all of which had been questioned before. Gorgias, for example argued that nothing exists; Protagoras found fault with Homer's Greek; and Antiphon presented arguments for the innocence of someone who seems obviously guilty. In challenging traditional views, the sophists liked to use deliberately provocative, sometimes paradoxical arguments that seem aimed at capturing the audience's attention rather than enlightening them.
Reason, Cause, and Explanation in Presocratic Philosophy
Authors: Hankinson R. J.
Published: September 2009

In the Archaic Geek world of epic poetry, the causes of things are shrouded in divine mystery; the gods intervene in human affairs, and bring about events, in a cruel and capricious fashion, according to their whims; Apollo visits the devastating plague of Iliad 1 on the Greek host to avenge Agamemnon's ill-treatment of one of his priests; Poseidon shakes the earth and angers the sea, bringing to destruction those who have incurred his ire, as does Zeus himself with his thunderbolts. The gods take on human shape and intervene in battle with devastating effect. In tragedy, the houses of Atreus and of Laius are brought low when men offend against the gods. This article focuses on the explorations of the fundamental concepts of reasons and causation, and the problems of explanation, and argues that it is indeed reasonable to see in Presocratic thought the foundations of Western scientific explanation.
The Humanizing of Knowledge in Presocratic Thought
Authors: Lesher J. H.
Published: September 2009

This article explores Presocratic epistemology, arguing that divine revelation is replaced as a warrant for knowledge with naturalistic accounts of how and what we humans can know; thus replacing earlier Greek pessimism about knowledge with a more optimistic outlook that allows for human discovery of the truth. A review of the relevant fragments and testimonia shows that Xenophanes, Alcmaeon, Heraclitus, and Parmenides—even Pythagoras and Empedocles—all moved some distance away from the older “god-oriented” view of knowledge toward a more secular and optimistic outlook. But to get some sense of the dynamics at work in this transition this article begins, as virtually every account of early Greek thought must begin, with Homer and Hesiod.