bluuebunny/crossref_metadata_2025 huggingface dataset:
Iron oxide nanoparticles fabricated by electric explosion of wire: focus on magnetic nanofluids
Authors: Beketov I. V. , Safronov A. P. , Medvedev A. I. , Alonso J. , Kurlyandskaya G. V. , Bhagat S. M.
Published: June 2012

Nanoparticles of iron oxides (MNPs) were prepared using the electric explosion of wire technique (EEW). The main focus was on the fabrication of de-aggregated spherical nanoparticles with a narrow size distribution. According to XRD the major crystalline phase was magnetite with an average diameter of MNPs, depending on the fraction. Further separation of air-dry EEW nanoparticles was performed in aqueous suspensions. In order to provide the stability of magnetite suspension in water, we found the optimum concentration of the electrostatic stabilizer (sodium citrate and optimum pH level) based on zeta-potential measurements. The stable suspensions still contained a substantial fraction of aggregates which were disintegrated by the excessive ultrasound treatment. The separation of the large particles out of the suspension was performed by centrifuging. The structural features, magnetic properties and microwave absorption of MNPs and their aqueous solutions confirm that we were able to obtain an ensemble in which the magnetic contributions come from the spherical MNPs. The particle size distribution in fractionated samples was narrow and they showed a similar behaviour to that expected of the superparamagnetic ensemble. Maximum obtained concentration was as high as 5 % of magnetic material (by weight). Designed assembly of de-aggregated nanoparticles is an example of on-purpose developed magnetic nanofluid.
Recognising Faces Seen Alone or with Others: Why are Two Heads Worse Than One?
Authors: Bindemann Markus , Sandford Adam , Gillatt Katherine , Avetisyan Meri , Megreya Ahmed M
Published: June 2012

The ability to identify an unfamiliar target face from an identity lineup declines when the target is accompanied by a second face during visual encoding. This two-face disadvantage is still little studied and its basis remains poorly understood. We investigated several possible explanations for this phenomenon. Experiments 1 and 2 varied the number of potential targets (1 or 2) and the number of faces in a lineup (5 or 10) to explore if this effect arises from the number of identity comparisons that need to be made to detect a target in a lineup. We also explored if this effect arises from an uncertainty concerning which is the to-be-identified target in two-face displays, by cueing the relevant face during encoding. In experiment 3 we then examined whether the two-face disadvantage reflects the depth of face encoding or a memory effect. The results show that this effect arises from the additional comparisons that are necessary to compare two potential targets to an identity lineup when memory demands are minimised (experiment 1), but it reflects a difficulty in remembering several faces when targets and lineups cannot be viewed simultaneously (experiments 2 and 3). However, in both cases the two-face disadvantage could not be eliminated fully by cueing the target. This hints at a further possible locus for this effect, which might reflect perceptual interference during the initial encoding of the target. The implications of these findings are discussed.
The Interaction between Time and Number in a Temporal Bisection Task: A Reply to Vicario (2011)
Authors: Grassi Massimo , Bonato Mario
Published: June 2012

We discuss the results of Vicario (2011, Perception40 23–29), in the light of an experiment designed to bypass some of the limits of that study. There, participants were asked to perform a temporal bisection on numerical stimuli (small or large digits) presented either for 700/900 ms or 2000/2200 ms. For the two longest durations only, bisections of larger digits occurred later than those of smaller digits. Here, subjects judged the temporal position of a flick occurring during the visual presentation of a digit (1, 5, or 9) which lasted on the screen for either 700 ms or 2000 ms. Results revealed no difference in the perceived temporal midpoints of large compared to small digits. In contrast, they showed a response bias: only with the shortest-duration stimuli the digit's magnitude affected the subject's response.
Stare in the Crowd: Frontal Face Guides Overt Attention Independently of its Gaze Direction
Authors: Shirama Aya
Published: June 2012

Whether or not a stare in the midst of many faces can guide visual attention is a controversial issue. Two experiments are reported that investigate the hypothesis that visual attention is guided toward a frontal face in the search for a stare among faces with varied head angles. The participants were required to search for a face with a direct gaze in a context where the target could be at any of various head angles and the target's head angle was unpredictable in one trial. The search performance was better for a frontal-face target than for deviated-face targets. Furthermore, eye-movement analyses revealed that a frontal-face stimulus tended to be initially fixated prior to deviated-face stimuli, and many of the initially fixated frontal-face stimuli had an averted gaze. The findings suggest that a frontal face guides overt attention independently of its gaze direction in the search for a stare in a crowd. The validity of prioritising a frontal face in order to find a direct gaze among faces and the characteristics of a human-face detection system are discussed.
An Odorant Congruent with a Colour Cue is Selectively Perceived in an Odour Mixture
Authors: Arao Mari , Suzuki Maya , Katayama Jun'ich , Yagi Akihiro
Published: June 2012

Odour identification can be influenced by colour cues. This study examined the mechanism underlying this colour context effect. We hypothesised that a specific odour component congruent with a colour would be selectively perceived in preference to another odour component in a binary odour mixture. We used a ratio estimation method under two colour conditions, a binary odour mixture (experiment 1) and single chemicals presented individually (experiment 2). Each colour was congruent with one of the odour components. Participants judged the perceived mixture ratio in each odour container on which a colour patch was pasted. An influence of colour was not observed when the odour stimulus did not contain the odour component congruent with the colour (experiment 2); however, the odour component congruent with the colour was perceived as more dominant when the odour stimulus did contain the colour-congruent odorant (experiment 1). This pattern indicates that a colour-congruent odour component is selectively perceived in an odour mixture. This finding suggests that colours can enhance the perceptual representation of the colour-associated component in an odour mixture.
Galileo Perceptionist
Authors: Sinico Michele
Published: June 2012

The present paper focuses on Galileo's conception of perception. I take as my starting point the interpretation of the Galilean text by Piccolino and Wade (2008, Perception37 1312–1340): Galileo's eye: a new vision of the senses in the work of Galileo Galilei. Three points are discussed: the criticism of naive realism, the theoretical role of perceptual laws, and the distinction between different qualities of experience. The conclusions support an alternative interpretation which underscores the crucial role of phenomenology of perception in Galileo's epistemology.
Vection Can Be Induced without Global-Motion Awareness
Authors: Seno Takeharu , Palmisano Stephen , Ito Hiroyuki , Sunaga Shoji
Published: June 2012

A new vection illusion is reported. Vection was induced even though there was no consciously perceived global display motion corresponding to the self-motion. The resulting experience can be summarised as: “I feel that I am moving but I do not know why”.
Effects of a gradient in river regulation on the longitudinal trends in water quality and benthic algal and macroinvertebrate assemblages in the Hunter River, Australia
Authors: Cortez Daniela P. , Growns Ivor O. , Mitrovic Simon M. , Lim Richard P.
Published: June 2012

River regulation impacts lotic ecosystem processes; however, the effect of a gradient of regulation on these attributes has rarely been studied. This study examined the effects of a river regulation gradient on longitudinal trends in water quality and benthic algal and macroinvertebrate assemblages in three tributaries of the Hunter River, New South Wales, Australia. Longitudinal patterns were expected to differ across rivers, with recovery being proportional to its regulation gradient. Significant differences in longitudinal trends were tested using permutational multivariate analysis of variance (PERMANOVA) through exploration of the river by distance from source interaction. Multi-dimensional scaling (MDS) ordination plots identified sites responsible for any significant interaction observed. Similarity percentage analysis (SIMPER) analyses identified variables/taxa responsible for differences at sites below dams. BEST analyses identified environmental variables best explaining biological assemblage patterns. Significant differences in longitudinal trends were observed for all attributes. Increases in the regulation gradient most affected macroinvertebrate assemblages, followed by water quality and benthic algal assemblages respectively. Downstream recovery was absent in the heavily regulated river at its most downstream site, whereas recovery was observed on corresponding sites of the moderately regulated river. The study suggests that a gradient in river regulation increases the magnitude of disruption of lotic ecosystems, with recovery dependent on this gradient.
Trimodal low-dose X-ray tomography
Authors: Zanette I. , Bech M. , Rack A. , Le Duc G. , Tafforeau P. , David C. , Mohr J. , Pfeiffer F. , Weitkamp T.
Published: June 2012

X-ray grating interferometry is a coherent imaging technique that bears tremendous potential for three-dimensional tomographic imaging of soft biological tissue and other specimens whose details exhibit very weak absorption contrast. It is intrinsically trimodal, delivering phase contrast, absorption contrast, and scattering (“dark-field”) contrast. Recently reported acquisition strategies for grating-interferometric phase tomography constitute a major improvement of dose efficiency and speed. In particular, some of these techniques eliminate the need for scanning of one of the gratings (“phase stepping”). This advantage, however, comes at the cost of other limitations. These can be a loss in spatial resolution, or the inability to fully separate the three imaging modalities. In the present paper we report a data acquisition and processing method that optimizes dose efficiency but does not share the main limitations of other recently reported methods. Although our method still relies on phase stepping, it effectively uses only down to a single detector frame per projection angle and yields images corresponding to all three contrast modalities. In particular, this means that dark-field imaging remains accessible. The method is also compliant with data acquisition over an angular range of only 180° and with a continuous rotation of the specimen.
Intermittent depolymerization of actin filaments is caused by photo-induced dimerization of actin protomers
Authors: Niedermayer Thomas , Jégou Antoine , Chièze Lionel , Guichard Bérengère , Helfer Emmanuèle , Romet-Lemonne Guillaume , Carlier Marie-France , Lipowsky Reinhard
Published: June 2012

Actin, one of the most abundant proteins within eukaryotic cells, assembles into long filaments that form intricate cytoskeletal networks and are continuously remodelled via cycles of actin polymerization and depolymerization. These cycles are driven by ATP hydrolysis, a process that also acts to destabilize the filaments as they grow older. Recently, abrupt dynamical changes during the depolymerization of single filaments have been observed and seemed to imply that old filaments are more stable than young ones [Kueh HY, et al. (2008)
Proc Natl Acad Sci USA
105:16531–16536]. Using improved experimental setups and quantitative theoretical analysis, we show that these abrupt changes represent actual pauses in depolymerization, unexpectedly caused by the photo-induced formation of actin dimers within the filaments. The stochastic dimerization process is triggered by random transitions of single, fluorescently labeled protomers. Each pause represents the delayed dissociation of a single actin dimer, and the statistics of these single molecule events can be determined by optical microscopy. Unlabeled actin filaments do not exhibit pauses in depolymerization, which implies that, in vivo, older filaments become destabilized by ATP hydrolysis, unless this aging effect is overcompensated by actin-binding proteins. The latter antagonism can now be systematically studied for single filaments using our combined experimental and theoretical method. Furthermore, the dimerization process discovered here provides a molecular switch, by which one can control the length of actin filaments via changes in illumination. This process could also be used to locally “freeze” the dynamics within networks of filaments.
Identification of the kinase that activates a nonmetazoan STAT gives insights into the evolution of phosphotyrosine-SH2 domain signaling
Authors: Araki Tsuyoshi , Kawata Takefumi , Williams Jeffrey G.
Published: June 2012

SH2 domains are integral to many animal signaling pathways. By interacting with specific phosphotyrosine residues, they provide regulatable protein–protein interaction domains.
Dictyostelium
is the only nonmetazoan with functionally characterized SH2 domains, but the cognate tyrosine kinases are unknown. There are no orthologs of the animal tyrosine kinases, but there are very many tyrosine kinase-like kinases (TKLs), a group of kinases which, despite their family name, are classified mainly as serine-threonine kinases. STATs are transcription factors that dimerize via phosphotyrosine–SH2 domain interactions. STATc is activated by phosphorylation on Tyr922 when cells are exposed to the prestalk inducer differentiation inducing factor (DIF-1), a chlorinated hexaphenone. We show that in a null mutant for Pyk2, a tyrosine-specific TKL, exposure to DIF-1 does not activate STATc. Conversely, overexpression of Pyk2 causes constitutive STATc activation. Pyk2 phosphorylates STATc on Tyr922 in vitro and complexes with STATc both in vitro and in vivo. This demonstration that a TKL directly activates a STAT has significant implications for understanding the evolutionary origins of SH2 domain–phosphotyrosine signaling. It also has mechanistic implications. Our previous work suggested that a predicted constitutive STATc tyrosine kinase activity is counterbalanced in vivo by the DIF-1–regulated activity of PTP3, a Tyr922 phosphatase. Here we show that the STATc-Pyk2 complex is formed constitutively by an interaction between the STATc SH2 domain and phosphotyrosine residues on Pyk2 that are generated by autophosphorylation. Also, as predicted, Pyk2 is constitutively active as a STATc kinase. This observation provides further evidence for this highly atypical, possibly ancestral, STAT regulation mechanism.
High-throughput genomic sequencing of cassava bacterial blight strains identifies conserved effectors to target for durable resistance
Authors: Bart Rebecca , Cohn Megan , Kassen Andrew , McCallum Emily J. , Shybut Mikel , Petriello Annalise , Krasileva Ksenia , Dahlbeck Douglas , Medina Cesar , Alicai Titus , Kumar Lava , Moreira Leandro M. , Neto Júlio Rodrigues , Verdier Valerie , Santana María Angélica , Kositcharoenkul Nuttima , Vanderschuren Hervé , Gruissem Wilhelm , Bernal Adriana , Staskawicz Brian J.
Published: June 2012

Cassava bacterial blight (CBB), incited by
Xanthomonas axonopodis
pv.
manihotis
(
Xam
), is the most important bacterial disease of cassava, a staple food source for millions of people in developing countries. Here we present a widely applicable strategy for elucidating the virulence components of a pathogen population. We report Illumina-based draft genomes for 65
Xam
strains and deduce the phylogenetic relatedness of
Xam
across the areas where cassava is grown. Using an extensive database of effector proteins from animal and plant pathogens, we identify the effector repertoire for each sequenced strain and use a comparative sequence analysis to deduce the least polymorphic of the conserved effectors. These highly conserved effectors have been maintained over 11 countries, three continents, and 70 y of evolution and as such represent ideal targets for developing resistance strategies.
Response of Migratory Sea Lampreys to Artificial Lighting in Portable Traps
Authors: Stamplecoskie Keith M. , Binder Thomas R. , Lower Nicola , Cottenie Karl , McLaughlin Robert L. , McDonald D. Gordon
Published: June 2012

This study evaluated responses by migratory spawning-phase sea lampreys Petromyzon marinus to artificial trap lighting in the laboratory and field with the aim of improving trapping as a method of sea lamprey control in the Laurentian Great Lakes. We hypothesized that lighting would improve trap success by increasing the attraction to, entrance into, or retention within portable sea lamprey traps. The responses of migratory sea lampreys to nocturnal lighting were complex and situation dependent. In the laboratory, where two traps were placed side by side, more sea lampreys were caught in the lit trap than in the unlit trap (80% versus 20%), largely because of increased attraction to the lit trap (75% of trap funnel entries by sea lampreys were in lit traps). In the field, where two traps were set 9 m apart and located against a barrier to upstream movement, there was no consistent difference in the numbers of sea lampreys caught in lit versus unlit traps. We provide two hypotheses for the variability in response to trap lighting between the laboratory and field, but overall the inconsistency of sea lamprey response to trap lighting leads us to conclude that the benefits of implementing trap lighting for sea lamprey control are limited. Lighting traps may be beneficial in situations where lighting is implemented in conjunction with other trap modifications that attract sea lampreys to within close proximity of traps or when traps are operated in stream locations that already encounter high volumes of sea lampreys.

Received November 2, 2011; accepted February 17, 2012
Magnetodielectric effect from the onset of ferrimagnetic transition in CoCr2O4
Authors: Yang S , Bao H X , Xue D Z , Zhou C , Gao J H , Wang Y , Wang J Q , Song X P , Sun Z B , Ren X B , Otsuka K
Published: June 2012

Multiferroicity in CoCr2O4 is generally regarded to emerge from the onset of noncollinear spiral magnetic order (T
s ≈ 28 K) due to the inverse Dzyaloshinskii–Moriya interaction, far below the temperature of collinear ferrimagnetic transition (T
c ≈ 96 K). So far, the possibility of multiferroicity appearing in collinear magnetic order has been rarely explored. Here, we report a magnetodielectric effect emerging from the onset of collinear ferrimagnetic transition T
c in CoCr2O4. Based on the postulation of non-centric crystal symmetry and Landau theory, we deduce that such a magnetodielectric effect is attributed to the coexistence of electric and magnetic ordering by the magnetoelectric coupling below T
c. Our results suggest that CoCr2O4 is a natural multiferroic in both noncollinear spiral and collinear magnetic ordering.
Complete fabrication study of InAs/GaSb superlattices for long-wavelength infrared detection
Authors: Wang Guowei , Xu Yingqiang , Wang Lijuan , Ren Zhengwei , He Zhenhong , Xing Junliang , Niu Zhichuan
Published: June 2012

We report a complete fabrication process of InAs/GaSb type-II superlattice long-wavelength infrared photodiodes with band structure modelling, materials growth and device fabrication. The optoelectronic property of InAs/GaSb type-II superlattices is simulated by the modified empirical tight binding model for interface stoichiometry. We chose target superlattices from the simulation results. To obtain good lattice matched and high interface quality material, a two-step strain balance method of migration-enhanced epitaxy is applied in the growth of superlattices. The property of superlattices is matched well with the simulation results. Finally, photodiodes with 50% cutoff wavelength of 8.72 µm and peak detectivity of 8.1 × 1010 cm Hz1/2 W−1 at 77 K are demonstrated.
Rectification effect in La1.89Ce0.11CuO4/SrTiO3/La0.67Sr0.33MnO3 heterostructure
Authors: Xia F J , Yuan J , Xie Z , Xu B , Cao L X , Zhao B R , Zhu B Y
Published: June 2012

Perovskite oxide junctions of p-type colossal magneto-resistance material La0.67Sr0.33MnO3 (LSMO), strontium titanate insulator SrTiO3 (STO) and n-type high-T
c superconductor La1.89Ce0.11CuO4 (LCCO) were deposited on STO (001) substrates by the pulsed laser deposition method. The current–voltage (I–V) characteristics were measured at room temperature and pronounced rectifying characteristics were observed. The trilayer junctions with different thicknesses of the middle STO insulator were investigated and the measurement exhibits a remarkable insulator thickness dependence in their I–V characteristics. We attribute the rectification of the trilayer junctions to the interfaces between different materials by energy band analysis.
Free-standing electrospun carbon nanofibres—a high performance anode material for lithium-ion batteries
Authors: Suresh Kumar P , Sahay R , Aravindan V , Sundaramurthy J , Ling Wong Chui , Thavasi V , Mhaisalkar S G , Madhavi S , Ramakrishna Seeram
Published: June 2012

Free-standing carbon nanofibres (CNFs) are prepared by the carbonization of poly-acrylonitrile using a simple electro-spinning technique. The electro-spun fibres are studied as an anode material for lithium-ion batteries in half-cell configurations. The fibres showed an initial discharge capacity of 826 mAh g−1 at a current density of 200 mA g−1 and exhibited an appreciable capacity profile during cycling. The Li-storage mechanism has been explained based on the cyclic voltametric and galvanostatic cycling results.
On the norm closure problem for complex symmetric operators
Authors: Garcia Stephan , Poore Daniel
Published: June 2012

We prove that the set of all complex symmetric operators on a separable, infinite-dimensional Hilbert space is not norm closed.
On the asymptotics of determinant of Laplacian at the principal boundary of the principal stratum of the moduli space of Abelian differentials
Authors: Kokotov A.
Published: June 2012

Let

X

\mathcal {X}

be a translation surface of genus

g
>
1

g>1

with

2
g
−
2

2g-2

conical points of angle

4
π

4\pi

and let

γ
\gamma

,

γ
′

\gamma ’

be two homologous saddle connections of length

s
s

joining two conical points of

X

\mathcal {X}

and bounding two surfaces

S
+

S^+

and

S
−

S^-

with boundaries

∂

S
+

=
γ
−

γ
′

\partial S^+=\gamma -\gamma ’

and

∂

S
−

=

γ
′

−
γ

\partial S^-=\gamma ’-\gamma

. Gluing the opposite sides of the boundary of each surface

S
+

S^+

,

S
−

S^-

one gets two (closed) translation surfaces

X

+

\mathcal {X}^+

,

X

−

\mathcal {X}^-

of genera

g
+

g^+

,

g
−

g^-

;

g
+

+

g
−

=
g

g^++g^-=g

. Let

Δ
\Delta

,

Δ
+

\Delta ^+

and

Δ
−

\Delta ^-

be the Friedrichs extensions of the Laplacians corresponding to the (flat conical) metrics on

X

\mathcal {X}

,

X

+

\mathcal {X}^+

and

X

−

\mathcal {X}^-

respectively. We study the asymptotical behavior of the (modified, i.e. with zero modes excluded) zeta-regularized determinant

det

∗

Δ

\textrm {det}^*\, \Delta

as

γ
\gamma

and

γ
′

\gamma ’

shrink. We find the asymptotics
\[
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="det Superscript asterisk Baseline normal upper Delta tilde kappa s Superscript 1 slash 2 Baseline StartFraction Area left-parenthesis script upper X right-parenthesis Over Area left-parenthesis script upper X Superscript plus Baseline right-parenthesis Area left-parenthesis script upper X Superscript minus Baseline right-parenthesis EndFraction det Superscript asterisk Baseline normal upper Delta Superscript plus Baseline det Superscript asterisk Baseline normal upper Delta Superscript minus">

det

∗

Δ
∼
κ

s

1

/

2

Area

(

X

)

Area

(

X

+

)

Area

(

X

−

)

det

∗

Δ
+

det

∗

Δ
−

\textrm {det}^*\,\Delta \sim \kappa s^{1/2}\frac {\textrm {Area}\,(\mathcal {X})}{\textrm {Area}\,(\mathcal {X}^+)\textrm {Area}\,(\mathcal {X}^-)}\,\textrm {det}^*\,\Delta ^+\textrm {det}^*\,\Delta ^-

\]
as

s
→
0

s\to 0

; here

κ
\kappa

is a certain absolute constant admitting an explicit expression through spectral characteristics of some model operators. We use the obtained result to fix an undetermined constant in the explicit formula for

det

∗

Δ

\textrm {det}^*\, \Delta

found in an earlier work by the author and D. Korotkin.
Algebraic 𝐾-theory via binary complexes
Authors: Grayson Daniel
Published: June 2012

Motivated by work of Nenashev on

K
1

K_1

, we introduce acyclic binary multicomplexes and use them to provide generators and relations for the Quillen

K
K

-groups of an arbitrary exact category.
Perturbation-based analysis and modeling of combinatorial regulation in the yeast sulfur assimilation pathway
Authors: McIsaac R. Scott , Petti Allegra A. , Bussemaker Harmen J. , Botstein David
Published: June 2012

In yeast, the pathways of sulfur assimilation are combinatorially controlled by five transcriptional regulators (three DNA-binding proteins [Met31p, Met32p, and Cbf1p], an activator [Met4p], and a cofactor [Met28p]) and a ubiquitin ligase subunit (Met30p). This regulatory system exerts combinatorial control not only over sulfur assimilation and methionine biosynthesis, but also on many other physiological functions in the cell. Recently we characterized a gene induction system that, upon the addition of an inducer, results in near-immediate transcription of a gene of interest under physiological conditions. We used this to perturb levels of single transcription factors during steady-state growth in chemostats, which facilitated distinction of direct from indirect effects of individual factors dynamically through quantification of the subsequent changes in genome-wide patterns of gene expression. We were able to show directly that Cbf1p acts sometimes as a repressor and sometimes as an activator. We also found circumstances in which Met31p/Met32p function as repressors, as well as those in which they function as activators. We elucidated and numerically modeled feedback relationships among the regulators, notably feedforward regulation of Met32p (but not Met31p) by Met4p that generates dynamic differences in abundance that can account for the differences in function of these two proteins despite their identical binding sites.
Combinatorial control of diverse metabolic and physiological functions by transcriptional regulators of the yeast sulfur assimilation pathway
Authors: Petti Allegra A. , McIsaac R. Scott , Ho-Shing Olivia , Bussemaker Harmen J. , Botstein David
Published: June 2012

Methionine abundance affects diverse cellular functions, including cell division, redox homeostasis, survival under starvation, and oxidative stress response. Regulation of the methionine biosynthetic pathway involves three DNA-binding proteins—Met31p, Met32p, and Cbf1p. We hypothesized that there exists a “division of labor” among these proteins that facilitates coordination of methionine biosynthesis with diverse biological processes. To explore combinatorial control in this regulatory circuit, we deleted CBF1, MET31, and MET32 individually and in combination in a strain lacking methionine synthase. We followed genome-wide gene expression as these strains were starved for methionine. Using a combination of bioinformatic methods, we found that these regulators control genes involved in biological processes downstream of sulfur assimilation; many of these processes had not previously been documented as methionine dependent. We also found that the different factors have overlapping but distinct functions. In particular, Met31p and Met32p are important in regulating methionine metabolism, whereas Cbf1p functions as a “generalist” transcription factor that is not specific to methionine metabolism. In addition, Met31p and Met32p appear to regulate iron–sulfur cluster biogenesis through direct and indirect mechanisms and have distinguishable target specificities. Finally, CBF1 deletion sometimes has the opposite effect on gene expression from MET31 and MET32 deletion.
Clinical effects of cardiac contractility modulation (CCM) as a treatment for chronic heart failure
Authors: Borggrefe Martin , Burkhoff Daniel
Published: June 2012

Cardiac contractility modulation (CCM) signals are non‐excitatory signals applied during the absolute refractory period that have been shown to enhance the strength of left ventricular contraction without increasing myocardial oxygen consumption in studies carried out in animals and humans with heart failure and reduced ejection fraction. Studies from myocardial tissue of animals and humans with heart failure suggest that the mechanisms of these effects is that CCM drives expression of many genes that are abnormally expressed in heart failure towards normal, including proteins involved with calcium cycling and the myocardial contractile machinery. Clinical studies have primarily focused on patients with normal QRS durations in view of the fact that cardiac resynchronization (CRT) is a viable option for patients with prolonged QRS duration. These studies show that CCM improves exercise tolerance as indexed by peak oxygen consumption (VO2) and quality of life indexed by the Minnesota Living with Heart Failure Questionnaire. The device is currently available for clinical use in countries recognizing the CE mark and is undergoing additional testing in the USA under a protocol approved by the Federal Drug Administration.
Modelling the migration of post-smolt Atlantic salmon (Salmo salar) in the Northeast Atlantic
Authors: Mork Kjell Arne , Gilbey John , Hansen Lars Petter , Jensen Arne J. , Jacobsen Jan Arge , Holm Marianne , Holst Jens Christian , Ó Maoiléidigh Niall , Vikebø Frode , McGinnity Philip , Melle Webjørn , Thomas Katie , Verspoor Eric , Wennevik Vidar
Published: June 2012

Mork, K. A., Gilbey, J., Hansen, L. P., Jensen, A. J., Jacobsen, J. A., Holm, M., Holst, J. C., Ó Maoiléidigh, N., Vikebø, F., McGinnity, P., Melle, W., Thomas, K., Verspoor, E., and Wennevik, V. 2012. Modelling the migration of post-smolt Atlantic salmon (Salmo salar) in the Northeast Atlantic. – ICES Journal of Marine Science, 69: 1616–1624. The migration of post-smolt Atlantic salmon (Salmo salar) during their first 4 months at sea in the Northeast Atlantic was simulated using an individual-based model that combined a particle-tracking scheme with growth and behaviour routines. The migration was decomposed into both passive pelagic drift with the surface currents, provided by an ocean model, and active horizontal swimming behaviour. The active swimming direction was aligned with the surface current. Swimming speed was a function of body length and calculated from recaptured tagged salmon. Releases of particles in the model were made to the west of Ireland and to the southwest of Norway. The modelled post-smolt distributions were compared with the observed distributions, and a sensitivity analysis using different swimming speeds was performed. The strength and direction of the flow can transport the post-smolts towards areas with favourable feeding conditions. However, in some areas, the direction of migration was sensitive to interannual changes in the windforcing, leading the post-smolts to areas with a different environment and prey. Inclusion in the swimming behaviour of a preference for water with higher temperature and salinity displaced the northward migration more offshore, away from coastal areas.
Compound Poisson—Gamma Regression Models for Dollar Outcomes That Are Sometimes Zero
Authors: Lauderdale Benjamin E.
Published: June 2012

Political scientists often study dollar-denominated outcomes that are zero for some observations. These zeros can arise because the data-generating process is granular: The observed outcome results from aggregation of a small number of discrete projects or grants, each of varying dollar size. This article describes the use of a compound distribution in which each observed outcome is the sum of a Poisson—distributed number of gamma distributed quantities, a special case of the Tweedie distribution. Regression models based on this distribution estimate loglinear marginal effects without either the ad hoc treatment of zeros necessary to use a log-dependent variable regression or the change in quantity of interest necessary to use a tobit or selection model. The compound Poisson—gamma regression is compared with commonly applied approaches in an application to data on high-speed rail grants from the United States federal government to the states, and against simulated data from several data-generating processes.
Characterization of the Salmonella bacteriophage vB_SenS-Ent1
Authors: Turner Dann , Hezwani Mohammed , Nelson Shona , Salisbury Vyv , Reynolds Darren
Published: June 2012

The bacteriophage vB_SenS-Ent1 (Ent1) is a member of the family Siphoviridae of tailed bacteriophages and infects a broad range of serovars of the enteric pathogen Salmonella enterica. The virion particle is composed of an icosahedral head 64 nm in diameter and a flexible, non-contractile tail of 116 × 8.5 nm possessing terminal fibres. The adsorption rate constant at 37 °C is 6.73 × 10−9 ml min−1. Latent and eclipse periods are 25 and 20 min, respectively, and the burst size is 35 progeny particles per cell after 35 min at 37 °C. Sequencing revealed a circularly permuted, 42 391 bp dsDNA genome containing 58 ORFs organized into four major transcriptional units. Comparisons with the genome sequences of other bacteriophages revealed a high level of nucleotide sequence identity and shared orthologous proteins with the Salmonella phages SETP3, SE2 and KS7 (SS3e) and the Escherichia phages K1G, K1H, K1ind1 and K1ind3.
Worldwide emergence of multiple clades of enterovirus 68
Authors: Tokarz Rafal , Firth Cadhla , Madhi Shabir A. , Howie Stephen R. C. , Wu Winfred , Sall Amadou Alpha , Haq Saddef , Briese Thomas , Lipkin W. Ian
Published: June 2012

Human enterovirus 68 (EV-D68) is a historically rarely reported virus linked with respiratory disease. In the past 3 years, a large increase in respiratory disease associated with EV-D68 has been reported, with documented outbreaks in North America, Europe and Asia. In several outbreaks, genetic differences were identified among the circulating strains, indicating the presence of multiple clades. In this report, we analyse archived and novel EV-D68 strains from Africa and the USA, obtained from patients with respiratory illness. Phylogenetic analysis of all EV-D68 sequences indicates that, over the past two decades, multiple clades of the virus have emerged and spread rapidly worldwide. All clades appear to be currently circulating and contributing to respiratory disease.
Structural Variants in the Soybean Genome Localize to Clusters of Biotic Stress-Response Genes
Authors: McHale Leah K. , Haun William J. , Xu Wayne W. , Bhaskar Pudota B. , Anderson Justin E. , Hyten David L. , Gerhardt Daniel J. , Jeddeloh Jeffrey A. , Stupar Robert M.
Published: June 2012

Genome-wide structural and gene content variations are hypothesized to drive important phenotypic variation within a species. Structural and gene content variations were assessed among four soybean (Glycine max) genotypes using array hybridization and targeted resequencing. Many chromosomes exhibited relatively low rates of structural variation (SV) among genotypes. However, several regions exhibited both copy number and presence-absence variation, the most prominent found on chromosomes 3, 6, 7, 16, and 18. Interestingly, the regions most enriched for SV were specifically localized to gene-rich regions that harbor clustered multigene families. The most abundant classes of gene families associated with these regions were the nucleotide-binding and receptor-like protein classes, both of which are important for plant biotic defense. The colocalization of SV with plant defense response signal transduction pathways provides insight into the mechanisms of soybean resistance gene evolution and may inform the development of new approaches to resistance gene cloning.
Pentaguanidinium monohydrogendiphosphopentamolybdate(VI) 2.5-hydrate, (CH6N3)5[HP2Mo5O23]·2.5H2O: hydrogen bonding and π-stacking in guanidinium cations
Authors: Di Tondo Pietro , Pritchard Robin Gavin
Published: June 2012

The asymmetric unit of the title compound consists of two crystallographically independent, but structurally identical, [HP2Mo5O23]5−anions, ten guanidinium cations and five water molecules. Each singly protonated diphosphopentamolybdate(VI) anion retains the typical geometry of a ring of five edge-sharing MoO6octahedra [Mo...Mo = 3.3265 (8)–3.4029 (10) Å], except for one corner-sharing link [Mo...Mo = 3.6642 (7) and 3.6826 (8) Å]. Two capping PO4tetrahedra share corners with the five octahedra. Despite being surrounded by an extensive network of hydrogen bonds, predominantly from the guanidinium cations, short P—O—H...O=P contacts [O...O = 2.519 (7) and 2.457 (7) Å] associate the anions into infinite columns generated by thec-glide. In addition to their heavy involvement in hydrogen bonding, with all N—H donors being utilized, the guanidinium cations assemble into extensive π-stacked columns with an average interplanar spacing of 3.53 Å.
Bis(2-amino-1H-benzimidazol-3-ium) tetrakis(μ-but-2-enoato)-κ4O:O′;κ3O,O′:O;κ3O:O,O′-bis[bis(but-2-enoato-κ2O,O′)holmium(III)]
Authors: Atria Ana María , Garland Maria Teresa , Baggio Ricardo
Published: June 2012

The title ionic compound, (C7H8N3)2[Ho2(C4H5O2)8], is constructed from two almost identical independent centrosymmetric anionic dimers balanced by two independent 2-amino-1H-benzimidazol-3-ium (Habim+) cations. The asymmetric part of each dimer is made up of one HoIIIcation and four crotonate (crot or but-2-enoate) anions, two of them acting in a simple η2-chelating mode and the remaining two acting in two different μ2:η2fashions,viz.purely bridging and bridging–chelating. Symmetry-related HoIIIcations are linked by two Ho—O—Ho and two Ho—O—C—O—Ho bridges which lead to rather short intracationic Ho...Ho distances [3.8418 (3) and 3.8246 (3) Å]. In addition to the obvious Coulombic interactions linking the cations and anions, the isolated [Ho2(crot)8]2−and Habim+ions are linked by a number of N—H...O hydrogen bonds, in which all N—H groups of the cation are involved as donors and all (simple chelating) crot O atoms are involved as acceptors. These interactions result in compact two-dimensional structures parallel to (110), which are linked to each other by weaker π–π contacts between Habim+benzene groups.
4-Carboxypyridinium perchlorate 18-crown-6 dihydrate clathrate and 4-carboxypyridinium tetrafluoroborate 18-crown-6 dihydrate clathrate
Authors: Shi Ping-ping , Zhang Li , Ye Qiong
Published: June 2012

Mixtures of 4-carboxypyridinium perchlorate or 4-carboxypyridinium tetrafluoroborate and 18-crown-6 (1,4,7,10,13,16-hexaoxacyclooctadecane) in ethanol and water solution yielded the title supramolecular salts, C6H6NO2+·ClO4−·C12H24O6·2H2O and C6H6NO2+·BF4−·C12H24O6·2H2O. Based on their similar crystal symmetries, unit cells and supramolecular assemblies, the salts are essentially isostructural. The asymmetric unit in each structure includes one protonated isonicotinic acid cation and one crown ether molecule, which together give a [(C6H6NO2)(18-crown-6)]+supramolecular cation. N—H...O hydrogen bonds between the protonated N atoms and a single O atom of each crown ether result in the 4-carboxypyridinium cations `perching' on the 18-crown-6 molecules. Further hydrogen-bonding interactions involving the supramolecular cation and both water molecules form a one-dimensional zigzag chain that propagates along the crystallographiccdirection. O—H...O or O—H...F hydrogen bonds between one of the water molecules and the anions fix the anion positions as pendant upon this chain, without further increasing the dimensionality of the supramolecular network.
Assessing footprints of selection in commercial Atlantic salmon populations using microsatellite data
Authors: Martinez V. , Dettleff P. , Lopez P. , Fernandez G. , Jedlicki A. , Yañez J. M. , Davidson W. S.
Published: June 2012

Relatively large rates of response to traits of economic importance have been observed in different selection experiments in salmon. Several QTL have been mapped in the salmon genome, explaining unprecedented levels of phenotypic variation. Owing to the relatively large selection intensity, individual loci may be indirectly selected, leaving molecular footprints of selection, together with increased inbreeding, as its likely relatives will share the selected loci. We used population differentiation and levels of linkage disequilibrium in chromosomes known to be harbouring QTL for body weight, infectious pancreatic necrosis resistance and infectious salmon anaemia resistance to assess the recent selection history at the genomic level in Atlantic salmon. The results clearly suggest that the marker
SSA0343BSFU
on chromosome 3 (body weight QTL) showed strong evidence of directional selection. It is intriguing that this marker is physically mapped to a region near the coding sequence of
DVL2

, making it an ideal candidate gene to explain the rapid evolutionary response of this chromosome to selection for growth in
Salmo salar. Weak evidence of diversifying selection was observed in the QTL associated with infectious pancreatic necrosis and infectious salmon anaemia resistance. Overall, this study showed that artificial selection has produced important changes in the Atlantic salmon genome, validating QTL in commercial salmon populations used for production purposes according to the recent selection history.
X chromosome gene methylation in peripheral lymphocytes from monozygotic twins discordant for scleroderma
Authors: Selmi C , Feghali-Bostwick C A , Lleo A , Lombardi S A , De Santis M , Cavaciocchi F , Zammataro L , Mitchell M M , LaSalle J M , Medsger T , Gershwin M E
Published: June 2012

Scleroderma (SSc) is a rare connective tissue disease characterized by fibrosis, microvasculopathy and autoimmune features. The role of genetics is limited in SSc, as suggested by similar concordance rates in monozygotic and dizygotic twin pairs, while environmental factors may act through epigenetic changes, as demonstrated for specific genes. Further, sex chromosome changes have been reported in SSc and may explain the female preponderance. In the present study we compared the methylation profile of all X chromosome genes in peripheral blood mononuclear cells from monozygotic twins discordant (n = 7) and concordant (n = 1) for SSc. Methylated DNA immunoprecipitations from each discordant twin pair were hybridized to a custom-designed array included 998 sites encompassing promoters of all X chromosome genes and randomly chosen autosomal genes. Biostatistical tools identified sites with an elevated probability to be consistently hypermethylated (n = 18) or hypomethylated (n = 25) in affected twins. Identified genes include transcription factors (ARX, HSFX1, ZBED1, ZNF41) and surface antigens (IL1RAPL2, PGRMC1), and pathway analysis suggests their involvement in cell proliferation (PGK1, SMS, UTP14A, SSR4), apoptosis (MTM1), inflammation (ARAF) and oxidative stress (ENOX2). In conclusion, we propose that X chromosome genes with different methylation profiles in monozygotic twin pairs may constitute candidates for SSc susceptibility.
Heat shock protein bystander antigens for peptide immunotherapy in autoimmune disease
Authors: Zonneveld-Huijssoon E , Albani S , Prakken B J , van Wijk F
Published: June 2012

Mucosal administration of an antigen eliciting bystander suppression at the site of inflammation results in effective antigen-specific immunotherapy for autoimmune diseases. Heat shock proteins are bystander antigens that are effective in peptide-specific immunotherapy in both experimental and human autoimmune disease. The efficacy of preventive peptide immunotherapy is increased by enhancing peptide-specific immune responses with proinflammatory agents. Combining peptide-specific immunotherapy with general suppression of inflammation may improve its therapeutic effect.
Using DNA taxonomy to investigate the ecological determinants of plankton diversity: explaining the occurrence of Synchaeta spp. (Rotifera, Monogononta) in mountain lakes
Authors: OBERTEGGER ULRIKE , FONTANETO DIEGO , FLAIM GIOVANNA
Published: June 2012

1. The occurrence of unresolved complexes of cryptic species may hinder the identification of the main ecological drivers of biodiversity when different cryptic taxa have different ecological requirements.

2. We assessed factors influencing the occurrence of Synchaeta species (monogonont rotifers) in 17 waterbodies of the Trentino‐South Tyrol region in the Eastern Alps. To do so, we compared the results of using unresolved complexes of cryptic species, as is common practice in limnological studies based on morphological taxonomy, and having resolved cryptic complexes, made possible by DNA taxonomy.

3. To identify cryptic species, we used the generalised mixed Yule coalescent (GMYC) model. We investigated the relationship between the environment and the occurrence of Synchaeta spp. by multivariate ordination using two definitions of the units of diversity, namely (i) unresolved species complexes (morphospecies) and (ii) putative cryptic species (GMYC entities). Our expectation was that resolving complexes of cryptic species could provide more information than using morphospecies.

4. As expected, DNA taxonomy provided greater taxonomic resolution than morphological taxonomy. Further, environmental‐based multivariate ordination on cryptic species explained a significantly higher proportion of variance than that based on morphospecies. Occurrence of GMYC entities was related to total phosphorus (TP), whereas no relationship could be found between morphospecies and the environment. Moreover, different cryptic species within the same morphospecies showed different, and even opposite, preferences for TP. In addition, the wide geographical distribution of haplotypes and cryptic species indicated the absence of barriers to dispersal in Synchaeta.
Intensified organic carbon dynamics in the ground water of a restored riparian zone
Authors: PETER SIMONE , KOETZSCH STEFAN , TRABER JACQUELINE , BERNASCONI STEFANO M. , WEHRLI BERNHARD , DURISCH‐KAISER EDITH
Published: June 2012

1. River restoration projects usually aim at improving the physical habitat for aquatic organisms. The extent to which biogeochemical processes and microbial activities are intensified in restored river reaches remains uncertain.

2. Here, we investigated the relationships between the distribution and composition of organic carbon (OC), bacterial secondary carbon production and extracellular enzymatic activity (EEA) in the ground water below a restored riparian section of the River Thur, Switzerland, relative to a channelised section. The spatiotemporal variability in the stable C isotopic ratio, dissolved OC polydispersity (the distribution of molecular mass in a mixture of molecules) as well as bacterial abundance, EEA and secondary production were investigated in different process zones.

3. At high river discharge, humic as well as low molecular weight amphiphilic substances infiltrated into the subsurface in a zone dominated by the pioneer plants Salix viminalis (willow bush). Concurrently, bacterial abundance, EEA and secondary carbon production increased at this location.

4. The willow plants leached bioavailable substrates into the ground water when the water table was high. The flood‐driven soil–groundwater coupling stimulated EEA and bacterial secondary production of the suspended groundwater bacterial community.

5. Establishing riparian habitat diversity adds hot spots of OC inputs during flood events, potentially providing valuable ecosystem services (e.g. degradation of organic pollutants) that accompany.