bluuebunny/crossref_metadata_2025 huggingface dataset:
Magnetotransport in nanostructures: The role of inhomogeneous currents
Authors: Machado Tiago S. , Argollo de Menezes M. , Rappoport Tatiana G. , Sampaio Luiz C.
Published: May 2011

In the study of electronic transport in nanostructures, electric current is commonly considered homogeneous along the sample. We use a method to calculate the magnetoresistance of magnetic nanostructures where the current density may vary in space. The current distribution is numerically calculated by combining micromagnetic simulations with an associated resistor network and by solving the latter with a relaxation method. As an example, we consider a Permalloy disk exhibiting a vortex-like magnetization profile. We find that the current density is inhomogeneous along the disk, and that during the core magnetization reversal it is concentrated toward the center of the vortex and is repelled by the antivortex. We then consider the effects of the inhomogeneous current density on spin-torque transfer. The numerical value of the critical current density necessary to produce a vortex core reversal is smaller than the one that does not take the inhomogeneity into account.
Design of high birefringence and low confinement loss photonic crystal fibers with five rings hexagonal and octagonal symmetry air-holes in fiber cladding
Authors: Yang Kuang-Yu , Chau Yuan-Fong , Huang Yao-Wei , Yeh Hsiao-Yu , Ping Tsai Din
Published: May 2011

We present a new cladding design for high birefringence and low confinement loss photonic crystal fibers (PCFs) using a full-vector finite element method with anisotropic perfectly matched boundary layer. Six cases of PCFs are proposed for comparison. The proposed cladding in PCFs is composed of five rings of air-holes. Air-holes on the inner two rings are arranged in a hexagonal symmetry whereas, air-holes on the outer three rings are arranged in an octagonal symmetry in fused silica. Results show that suitable design air-holes on the inner two rings will significantly increase the birefringence, whereas, elliptical holes with major axis along x-axis on the outer three rings will provide strong confinement ability. The highest modal birefringence and lowest confinement loss of our proposed case five structure at the excitation wavelength of λ = 1550 nm can be achieved at a magnitude of 0.87 × 10−2 and less than 0.01 dB/km with only five rings of air-holes in fiber cladding.
Effects of film thickness and mismatch strains on magnetoelectric coupling in vertical heteroepitaxial nanocomposite thin films
Authors: Chen H. T. , Hong L. , Soh A. K.
Published: May 2011

The phase field model is adopted to study the magnetoelectric coupling effects in vertical heteroepitaxial nanocomposite thin films. Both the lateral epitaxial strains between the film and the substrate and the vertical epitaxial strains between the ferroelectric and ferromagnetic phases are accounted for in the model devised. The effects of the film thickness on the magnetic-field-induced electric polarization (MIEP) are investigated. The results obtained show that the MIEP is strongly dependent on the film thickness, as well as on the vertical and lateral epitaxial strains.
First-principles study on the electronic and magnetic properties of hydrogenated CdS nanosheets
Authors: Zhang Chang-wen , Yan Shi-shen , Wang Pei-ji , Li Ping , Zheng Fu-bao
Published: May 2011

Based on first-principles calculations, we study the electronic structures and magnetic properties of a two-dimensional CdS nanostructure upon hydrogenation adsorption. The results show that the hydrogen atoms can adsorb on Cd atoms within the graphenelike Cd layers with favorable formation energies, and the resulting semihydrogenated CdS systems are expected to show semimetallic properties with Curie temperatures above room temperature. These studies demonstrate that the decoration II-VI group semiconductor with hydrogen might be an efficient route for realizing the interesting long-range ferromagnetism in nanostructure materials.
Comparison between chemical vapor deposited and physical vapor deposited WSi2 metal gate for InGaAs n-metal-oxide-semiconductor field-effect transistors
Authors: Ong B. S. , Pey K. L. , Ong C. Y. , Tan C. S. , Antoniadis D. A. , Fitzgerald E. A.
Published: May 2011

We compare chemical vapor deposition (CVD) and physical vapor deposition (PVD) WSi2 metal gate process for In0.53Ga0.47As n-metal-oxide-semiconductor field-effect transistors using 10 and 6.5 nm Al2O3 as dielectric layer. The CVD-processed metal gate device with 6.5 nm Al2O3 shows enhanced transistor performance such as drive current, maximum transconductance and maximum effective mobility. These values are relatively better than the PVD-processed counterpart device with improvement of 51.8%, 46.4%, and 47.8%, respectively. The improvement for the performance of the CVD-processed metal gate device is due to the fluorine passivation at the oxide/semiconductor interface and a nondestructive deposition process.
Epitaxial graphene prepared by chemical vapor deposition on single crystal thin iridium films on sapphire
Authors: Vo-Van Chi , Kimouche Amina , Reserbat-Plantey Antoine , Fruchart Olivier , Bayle-Guillemaud Pascale , Bendiab Nedjma , Coraux Johann
Published: May 2011

Uniform single layer graphene was grown on single-crystal Ir films a few nanometers thick which were prepared by pulsed laser deposition on sapphire wafers. These graphene layers have a single crystallographic orientation and a very low density of defects, as shown by diffraction, scanning tunnelling microscopy, and Raman spectroscopy. Their structural quality is as high as that of graphene produced on Ir bulk single crystals, i.e., much higher than on metal thin films used so far.
An inverse problem of temperature estimation for the combination of the linear and nonlinear resistances
Authors: Perovich Slavica M. , Bauk Sanja I.
Published: May 2011

The subject of the theoretical analysis presented in this paper is an analytical approach to the temperature estimation, as an inverse problem, for different thermistors – linear resistances structures: series and parallel ones, by the STFT - Special Trans Functions Theory (S.M. Perovich). The mathematical formulae genesis of both cases is given. Some numerical and graphical simulations in MATHEMATICA program have been realized. The estimated temperature intervals for strongly determined values of the equivalent resistances of the nonlinear structures are given, as well.
Sex difference in the near-24-hour intrinsic period of the human circadian timing system
Authors: Duffy Jeanne F. , Cain Sean W. , Chang Anne-Marie , Phillips Andrew J. K. , Münch Mirjam Y. , Gronfier Claude , Wyatt James K. , Dijk Derk-Jan , Wright Kenneth P. , Czeisler Charles A.
Published: May 2011

The circadian rhythms of melatonin and body temperature are set to an earlier hour in women than in men, even when the women and men maintain nearly identical and consistent bedtimes and wake times. Moreover, women tend to wake up earlier than men and exhibit a greater preference for morning activities than men. Although the neurobiological mechanism underlying this sex difference in circadian alignment is unknown, multiple studies in nonhuman animals have demonstrated a sex difference in circadian period that could account for such a difference in circadian alignment between women and men. Whether a sex difference in intrinsic circadian period in humans underlies the difference in circadian alignment between men and women is unknown. We analyzed precise estimates of intrinsic circadian period collected from 157 individuals (52 women, 105 men; aged 18–74 y) studied in a month-long inpatient protocol designed to minimize confounding influences on circadian period estimation. Overall, the average intrinsic period of the melatonin and temperature rhythms in this population was very close to 24 h [24.15 ± 0.2 h (24 h 9 min ± 12 min)]. We further found that the intrinsic circadian period was significantly shorter in women [24.09 ± 0.2 h (24 h 5 min ± 12 min)] than in men [24.19 ± 0.2 h (24 h 11 min ± 12 min);
P
< 0.01] and that a significantly greater proportion of women have intrinsic circadian periods shorter than 24.0 h (35% vs. 14%;
P
< 0.01). The shorter average intrinsic circadian period observed in women may have implications for understanding sex differences in habitual sleep duration and insomnia prevalence.
Fossil evidence for Cretaceous escalation in angiosperm leaf vein evolution
Authors: Feild Taylor S. , Brodribb Timothy J. , Iglesias Ari , Chatelet David S. , Baresch Andres , Upchurch Garland R. , Gomez Bernard , Mohr Barbara A. R. , Coiffard Clement , Kvacek Jiri , Jaramillo Carlos
Published: May 2011

The flowering plants that dominate modern vegetation possess leaf gas exchange potentials that far exceed those of all other living or extinct plants. The great divide in maximal ability to exchange CO
2
for water between leaves of nonangiosperms and angiosperms forms the mechanistic foundation for speculation about how angiosperms drove sweeping ecological and biogeochemical change during the Cretaceous. However, there is no empirical evidence that angiosperms evolved highly photosynthetically active leaves during the Cretaceous. Using vein density (
D
V
) measurements of fossil angiosperm leaves, we show that the leaf hydraulic capacities of angiosperms escalated several-fold during the Cretaceous. During the first 30 million years of angiosperm leaf evolution, angiosperm leaves exhibited uniformly low vein
D
V
that overlapped the
D
V
range of dominant Early Cretaceous ferns and gymnosperms. Fossil angiosperm vein densities reveal a subsequent biphasic increase in
D
V
. During the first mid-Cretaceous surge, angiosperm
D
V
first surpassed the upper bound of
D
V
limits for nonangiosperms. However, the upper limits of
D
V
typical of modern megathermal rainforest trees first appear during a second wave of increased
D
V
during the Cretaceous-Tertiary transition. Thus, our findings provide fossil evidence for the hypothesis that significant ecosystem change brought about by angiosperms lagged behind the Early Cretaceous taxonomic diversification of angiosperms.
Quantifying the Waddington landscape and biological paths for development and differentiation
Authors: Wang Jin , Zhang Kun , Xu Li , Wang Erkang
Published: May 2011

We developed a theoretical framework to prove the existence and quantify the Waddington landscape as well as chreode-biological paths for development and differentiation. The cells can have states with the higher probability ones giving the different cell types. Different cell types correspond to different basins of attractions of the probability landscape. We study how the cells develop from undifferentiated cells to differentiated cells from landscape perspectives. We quantified the Waddington landscape through construction of underlying probability landscape for cell development. We show the developmental process proceeds as moving from undifferentiated to the differentiated basins of attractions. The barrier height of the basins of attractions correlates with the escape time that determines the stability of cell types. We show that the developmental process can be quantitatively described and uncovered by the biological paths on the quantified Waddington landscape from undifferentiated to the differentiated cells. We found the dynamics of the developmental process is controlled by a combination of the gradient and curl force on the landscape. The biological paths often do not follow the steepest descent path on the landscape. The landscape framework also quantifies the possibility of reverse differentiation process such as cell reprogramming from differentiated cells back to the original stem cell. We show that the biological path of reverse differentiation is irreversible and different from the one for differentiation process. We found that the developmental process described by the underlying landscape and the associated biological paths is relatively stable and robust against the influences of environmental perturbations.
Higher categories, colimits, and the blob complex
Authors: Morrison Scott , Walker Kevin
Published: May 2011

We summarize our axioms for higher categories, and describe the “blob complex.” Fixing an
n
-category

, the blob complex associates a chain complex

to any
n
-manifold
W
. The zeroth homology of this chain complex recovers the usual topological quantum field theory invariants of
W
. The higher homology groups should be viewed as generalizations of Hochschild homology (indeed, when
W
 = 
S
1
, they coincide). The blob complex has a very natural definition in terms of homotopy colimits along decompositions of the manifold
W
. We outline the important properties of the blob complex and sketch the proof of a generalization of Deligne’s conjecture on Hochschild cohomology and the little discs operad to higher dimensions.
Unique system of photoreceptors in sea urchin tube feet
Authors: Ullrich-Lüter Esther M , Dupont Sam , Arboleda Enrique , Hausen Harald , Arnone Maria Ina
Published: May 2011

Different sea urchin species show a vast variety of responses to variations in light intensity; however, despite this behavioral evidence for photosensitivity, light sensing in these animals has remained an enigma. Genome information of the recently sequenced purple sea urchin (
Strongylocentrotus purpuratus
) allowed us to address this question from a previously unexplored molecular perspective by localizing expression of the rhabdomeric opsin
Sp-opsin4
and
Sp-pax6
, two genes essential for photoreceptor function and development, respectively. Using a specifically designed antibody against Sp-Opsin4 and in situ hybridization for both genes, we detected expression in two distinct groups of photoreceptor cells (PRCs) located in the animal's numerous tube feet. Specific reactivity of the Sp-Opsin4 antibody with sea star optic cushions, which regulate phototaxis, suggests a similar visual function in sea urchins. Ultrastructural characterization of the sea urchin PRCs revealed them to be of a microvillar receptor type. Our data suggest that echinoderms, in contrast to chordates, deploy a microvillar, r-opsin–expressing PRC type for vision, a feature that has been so far documented only in protostome animals. Surprisingly, sea urchin PRCs lack any associated screening pigment. Indeed, one of the tube foot PRC clusters may account for directional vision by being shaded through the opaque calcite skeleton. The PRC axons connect to the animal internal nervous system, suggesting an integrative function beyond local short circuits. Because juveniles display no phototaxis until skeleton completion, we suggest a model in which the entire sea urchin, deploying its skeleton as PRC screening device, functions as a huge compound eye.
Resetting the evolution of marine reptiles at the Triassic-Jurassic boundary
Authors: Thorne Philippa M. , Ruta Marcello , Benton Michael J.
Published: May 2011

Ichthyosaurs were important marine predators in the Early Jurassic, and an abundant and diverse component of Mesozoic marine ecosystems. Despite their ecological importance, however, the Early Jurassic species represent a reduced remnant of their former significance in the Triassic. Ichthyosaurs passed through an evolutionary bottleneck at, or close to, the Triassic-Jurassic boundary, which reduced their diversity to as few as three or four lineages. Diversity bounced back to some extent in the aftermath of the end-Triassic mass extinction, but disparity remained at less than one-tenth of pre-extinction levels, and never recovered. The group remained at low diversity and disparity for its final 100 Myr. The end-Triassic mass extinction had a previously unsuspected profound effect in resetting the evolution of apex marine predators of the Mesozoic.
Autoregulation of an RNA polymerase II promoter by the RNA polymerase III transcription factor III C (TF
III
C) complex
Authors: Kleinschmidt Richard A. , LeBlanc Kimberly E. , Donze David
Published: May 2011

E
xtra
T
F
III
C
(
ETC
) sites are chromosomal locations bound in vivo by the RNA polymerase III (Pol III) transcription factor III C (TF
III
C) complex, but are not necessarily associated with Pol III transcription. Although the location of
ETC
sequences are conserved in budding yeast, and similar sites are found in other organisms, their functions are largely unstudied. One such site,
ETC6
in
Saccharomyces cerevisiae
, lies upstream of
TFC6
, a gene encoding a subunit of the TF
III
C complex itself. Promoter analysis shows that the
ETC6
B-box sequence is involved in autoregulation of the
TFC6
promoter. Mutation of
ETC6
increases
TFC6
mRNA levels, whereas mutation immediately upstream severely weakens promoter activity. A temperature-sensitive mutation in
TFC3
that weakens DNA binding of TF
III
C also results in increased
TFC6
mRNA levels; however, no increase is observed in mutants of TF
III
B or Pol III subunits, demonstrating a specific role for the TF
III
C complex in
TFC6
promoter regulation. Chromatin immunoprecipitation shows an inverse relationship of TF
III
C occupancy at
ETC6
versus
TFC6
mRNA levels. Overexpression of
TFC6
increases association of TF
III
C at
ETC6
(and other loci) and results in reduced expression of a
TFC6
promoter-
URA3
reporter gene. Both of these effects are dependent on the
ETC6
B-box. These results demonstrate that the
TFC6
promoter is directly regulated by the TF
III
C complex, a demonstration of an RNA polymerase II promoter being directly responsive to a core Pol III transcription factor complex. This regulation could have implications in controlling global tRNA expression levels.
Structural context for mobilization of a human tRNA synthetase from its cytoplasmic complex
Authors: Fang Pengfei , Zhang Hui-Min , Shapiro Ryan , Marshall Alan G. , Schimmel Paul , Yang Xiang-Lei , Guo Min
Published: May 2011

Human lysyl-tRNA synthetase is bound to the multi-tRNA synthetase complex (MSC) that maintains and regulates the aminoacylation and nuclear functions of LysRS. The p38 scaffold protein binds LysRS to the MSC and, only with the appropriate cue, mobilizes LysRS for redirection to the nucleus to interact with the microphthalmia associated transcription factor (MITF). In recent work, an (
α
2
)
2
LysRS tetramer crystallized to yield a high-resolution structure and raised the question of how LysRS is arranged (dimer or tetramer) in the MSC to interact with p38. To understand the structural organization of the LysRS-p38 complex that regulates LysRS mobilization, we investigated the complex by use of small angle X-ray scattering and hydrogen-deuterium exchange with mass spectrometry in solution. The structure revealed a surprising
α
2
β
1
∶
β
1
α
2
organization in which a dimeric p38 scaffold holds two LysRS
α
2
dimers in a parallel configuration. Each of the
N
-terminal 48 residues of p38 binds one LysRS dimer and, in so doing, brings two copies of the LysRS dimer into the MSC. The results suggest that this unique geometry, which reconfigures the LysRS tetramer from
α
2
∶
α
2
to
α
2
β
1
∶
β
1
α
2
, is designed to control both retention and mobilization of LysRS from the MSC.
Molecular evidence for a single evolutionary origin of domesticated rice
Authors: Molina Jeanmaire , Sikora Martin , Garud Nandita , Flowers Jonathan M. , Rubinstein Samara , Reynolds Andy , Huang Pu , Jackson Scott , Schaal Barbara A. , Bustamante Carlos D. , Boyko Adam R. , Purugganan Michael D.
Published: May 2011

Asian rice,
Oryza sativa
, is one of world's oldest and most important crop species. Rice is believed to have been domesticated ∼9,000 y ago, although debate on its origin remains contentious. A single-origin model suggests that two main subspecies of Asian rice,
indica
and
japonica
, were domesticated from the wild rice
O. rufipogon
. In contrast, the multiple independent domestication model proposes that these two major rice types were domesticated separately and in different parts of the species range of wild rice. This latter view has gained much support from the observation of strong genetic differentiation between
indica
and
japonica
as well as several phylogenetic studies of rice domestication. We reexamine the evolutionary history of domesticated rice by resequencing 630 gene fragments on chromosomes 8, 10, and 12 from a diverse set of wild and domesticated rice accessions. Using patterns of SNPs, we identify 20 putative selective sweeps on these chromosomes in cultivated rice. Demographic modeling based on these SNP data and a diffusion-based approach provide the strongest support for a single domestication origin of rice. Bayesian phylogenetic analyses implementing the multispecies coalescent and using previously published phylogenetic sequence datasets also point to a single origin of Asian domesticated rice. Finally, we date the origin of domestication at ∼8,200–13,500 y ago, depending on the molecular clock estimate that is used, which is consistent with known archaeological data that suggests rice was first cultivated at around this time in the Yangtze Valley of China.
Whole-genome phylogeny ofEscherichia coli/Shigellagroup by feature frequency profiles (FFPs)
Authors: Sims Gregory E. , Kim Sung-Hou
Published: May 2011

A whole-genome phylogeny of theEscherichia coli/Shigellagroup was constructed by using the feature frequency profile (FFP) method. This alignment-free approach uses the frequencies ofl-mer features of whole genomes to infer phylogenic distances. We present two phylogenies that accentuate different aspects ofE. coli/Shigellagenomic evolution: (i) one based on the compositions ofallpossible features of lengthl= 24 (∼8.4 million features), which are likely to reveal the phenetic grouping and relationship among the organisms and (ii) the other based on the compositions ofcorefeatures with low frequency and low variability (∼0.56 million features), which account for ∼69% of all commonly shared features among 38 taxa examined and are likely to have genome-wide lineal evolutionary signal.Shigellaappears as a single clade when all possible features are used without filtering of noncore features. However, results using core features show thatShigellaconsists of at least two distantly related subclades, implying that the subclades evolved into a single clade because of a high degree of convergence influenced by mobile genetic elements and niche adaptation. In both FFP trees, the basal group of theE. coli/Shigellaphylogeny is the B2 phylogroup, which contains primarily uropathogenic strains, suggesting that theE. coli/Shigellaancestor was likely a facultative or opportunistic pathogen. The extant commensal strains diverged relatively late and appear to be the result of reductive evolution of genomes. We also identify clade distinguishing features and their associated genomic regions within each phylogroup. Such features may provide useful information for understanding evolution of the groups and for quick diagnostic identification of each phylogroup.
Regulation of angiogenesis and choroidal neovascularization by members of microRNA-23∼27∼24 clusters
Authors: Zhou Qinbo , Gallagher Rachel , Ufret-Vincenty Rafael , Li Xinyu , Olson Eric N. , Wang Shusheng
Published: May 2011

MicroRNAs (miRNAs) modulate complex physiological and pathological processes by repressing expression of multiple components of cellular regulatory networks. Here we demonstrate that miRNAs encoded by the miR-23∼27∼24 gene clusters are enriched in endothelial cells and highly vascularized tissues. Inhibition of miR-23 and miR-27 function by locked nucleic acid-modified anti-miRNAs represses angiogenesis in vitro and postnatal retinal vascular development in vivo. Moreover, miR-23 and miR-27 are required for pathological angiogenesis in a laser-induced choroidal neovascularization mouse model. MiR-23 and miR-27 enhance angiogenesis by promoting angiogenic signaling through targeting Sprouty2 and Sema6A proteins, which exert antiangiogenic activity. Manipulating miR-23/27 levels may have important therapeutic implications in neovascular age-related macular degeneration and other vascular disorders.
Isolation and function of mouse tissue resident vascular precursors marked by myelin protein zero
Authors: Kubota Yoshiaki , Takubo Keiyo , Hirashima Masanori , Nagoshi Narihito , Kishi Kazuo , Okuno Yuji , Nakamura-Ishizu Ayako , Sano Keigo , Murakami Masato , Ema Masatsugu , Omatsu Yoshiki , Takahashi Satoru , Nagasawa Takashi , Shibuya Masabumi , Okano Hideyuki , Suda Toshio
Published: May 2011

Vasculogenesis describes the process of de novo vessel formation from vascular precursor cells. Although formation of the first major vessels, such as the dorsal aorta and cardinal veins, occurs during embryonic vasculogenesis, the contribution of precursor cell populations to postnatal vessel development is not well understood. Here, we identified a novel population of postnatal vascular precursor cells in mice. These cells express the Schwann cell protein myelin protein zero (Po) and exhibit a CD45−CD31−VEcad−c-kit+CXCR4+ surface phenotype. Po+ vascular precursors (PVPs) are recruited into the growing vasculature, and comprise a minor population of arterial endothelial cells in adult mice. Recruitment of PVPs into growing vessels is mediated by CXCL12–CXCR4 signaling, and is enhanced during vascular expansion induced by Notch inhibition. Po-specific ablation of Flk1, a receptor for VEGF, results in branching defects and insufficient arterial patterning in the retina, as well as reduced neovascularization of tumors and ischemic tissues. Thus, in postnatal mice, although growing vessels are formed primarily by angiogenesis from preexisting vessels, a minor population of arterial endothelia may be derived from tissue-resident vascular precursor cells.
Exercise Promotion in Primary Care
Authors: Rolfe Alexandra , Boyce Stephen H.
Published: May 2011

Physical activity levels have been decreasing significantly for at least 50 years as advances in technology have allowed our lives to become more sedentary. Physical inactivity is a known risk factor for many diseases and regular exercise is known to have significant benefits. Promotion of physical activity by doctors can be limited, often by time and lack of knowledge. Additionally, practitioners' own participation has a significant effect on both exercise promotion and ability to provide a credible role model.
An Autoactive Mutant of the M Flax Rust Resistance Protein Has a Preference for Binding ATP, Whereas Wild-Type M Protein Binds ADP
Authors: Williams Simon J. , Sornaraj Pradeep , deCourcy-Ireland Emma , Menz R. Ian , Kobe Bostjan , Ellis Jeffrey G. , Dodds Peter N. , Anderson Peter A.
Published: May 2011

Resistance (R) proteins are key regulators of the plant innate immune system and are capable of pathogen detection and activation of the hypersensitive cell death immune response. To understand the molecular mechanism of R protein activation, we undertook a phenotypic and biochemical study of the flax nucleotide binding (NB)-ARC leucine-rich repeat protein, M. Using Agrobacterium-mediated transient expression in flax cotyledons, site-directed mutations of key residues within the P-loop, kinase 2, and MHD motifs within the NB-ARC domain of M were shown to affect R protein function. When purified using a yeast expression system and assayed for ATP and ADP, these mutated proteins exhibited marked differences in the quantity and identity of the bound nucleotide. ADP was bound to recombinant wild-type M protein, while the nonfunctional P-loop mutant did not have any nucleotides bound. In contrast, ATP was bound to an autoactive M protein mutated in the highly conserved MHD motif. These data provide direct evidence supporting a model of R protein function in which the “off” R protein binds ADP and activation of R protein defense signaling involves the exchange of ADP for ATP.
First Report of the Golden Potato Cyst Nematode, Globodera rostochiensis, in Bosnia and Herzegovina
Authors: Ostojić I. , Grubišić D. , Zovko M. , Miličević T. , Gotlin Čuljak T.
Published: May 2011

The golden potato cyst nematode, Globodera rostochiensis (Wollenweber, 1923) Behrens, 1975, is the most problematic pest of potato (Solanum tuberosum L. subsp. tuberosum) worldwide and it is recognized as an A1 plant health quarantine species. In Bosnia and Herzegovina, there have been no surveys for the presence of potato cyst nematodes (PCN) in ware potato lands, although they have been documented in the nearby countries of Serbia and Croatia (3). To determine the presence and distribution of PCN and to prevent further spread or increase of PCN populations, a survey in ware potato land was undertaken in 2008, 2009, and 2010. Soil samples consisting of 100 cores of 4 to 5 ml of soil were taken in a grid pattern throughout the plots. Samples of approximately 500 g were processed in the laboratory. The samples were air dried and cysts were extracted using a Spears's flotation method (4) from a 100-ml subsample. Species identification was based on morphometrical characters (2) and real-time PCR where the ribosomal internal transcribed spacer (ITS5, PITSr3) region was amplified and detected by the Sequence Dection Software v1.3 (Applied Biosystems, Carlsbad, CA) (1). In 2008, soil sampling was conducted in five locations and PCN were not detected in any of 10 soil samples taken. In June 2009, 17 soil samples were collected from seven locations. Two viable cysts of G. rostochiensis were detected in one soil sample from Tihaljina (Zaside; E 6447659.560, N 4797392.101, altitude 130 m). A total of 110 soil samples were collected from 90 locations in May and June 2010. Five viable cysts of G. rostochiensis were detected in one soil sample taken from Čapljina (Opličići – Turajlovina; E 6485169, N 4775964, altitude 222 m). On the basis of the survey results, G. rostochiensis is not widely spread but the cysts are detectable, indicating that the infestation is relatively recent and that there is a threat of further spread of this quarantine species. Consequently, producers need to grow resistant potato cultivars and implement additional control measures to keep the nematode populations below damaging levels.

References: (1) J. Bacic et al. Russ. J. Nematol. 16:1, 61, 2008. (2) C. C. Fleming and T. O. Powers. Potato Cyst Nematodes: Biology, Distribution and Control. R. J. Marks and B. B. Brodie, eds.CAB International, Wallingford, 1998. (3) D. Grubišic et al. J. Pest Sci. 80:21, 2007. (4) J. F. Spears. Agr. Handb. No. 353. U.S. Dep. Agric., 1968.
Identification of Brassica napus Lines with Partial Resistance to Sclerotinia sclerotiorum
Authors: Khot S. D. , Bilgi V. N. , del Río L. E. , Bradley C. A.
Published: May 2011

A collection of Brassica napus plant introduction (PI) lines was evaluated in a series of research trials to identify lines with resistance to Sclerotinia sclerotiorum, causal agent of Sclerotinia stem rot of canola. Five PI lines (169080, 286418, 436554, 458940, and 633119) were identified that consistently had SSR resistance levels equal to or greater than the partially resistant check cultivar Hyola 357. In addition, two of these lines (436554 and 458940) were found to exhibit SSR field resistance levels similar to Hyola 357. The PI lines identified from our research studies could be used in canola breeding programs to develop cultivars with improved resistance to S. sclerotiorum.

Accepted for publication 21 February 2011. Published 22 April 2011.
A Model of the Dynamic Relationship between Blood Flow and Volume Changes during Brain Activation
Authors: Kong Yazhuo , Zheng Ying , Johnston David , Martindale John , Jones Myles , Billings Steve , Mayhew John
Published: May 2011

The temporal relationship between changes in cerebral blood flow (CBF) and cerebral blood volume (CBV) is important in the biophysical modeling and interpretation of the hemodynamic response to activation, particularly in the context of magnetic resonance imaging and the blood oxygen level–dependent signal. Grubb et al. (1974) measured the steady state relationship between changes in CBV and CBF after hypercapnic challenge. The relationship CBVαCBFΦ has been used extensively in the literature. Two similar models, the Balloon ( Buxton et al., 1998 ) and the Windkessel ( Mandeville et al., 1999 ), have been proposed to describe the temporal dynamics of changes in CBV with respect to changes in CBF. In this study, a dynamic model extending the Windkessel model by incorporating delayed compliance is presented. The extended model is better able to capture the dynamics of CBV changes after changes in CBF, particularly in the return-to-baseline stages of the response.
Global Gene Expression in the Immature Brain after Hypoxia-Ischemia
Authors: Maj Hedtjärn , Mallard Carina , Eklind Saskia , Gustafson-Brywe Katarina , Hagberg Henrik
Published: May 2011

Ischemia induces a complex response of differentially expressed genes in the brain. In order to understand the specific mechanisms of injury in the developing brain, it is important to obtain information on global changes in the transcriptome after neonatal hypoxia-ischemia. In this study, oligonucleotide arrays were used to investigate genomic changes at 2, 8, 24, and 72 hours after neonatal hypoxia-ischemia, which was induced in 9-day-old mice by left carotid artery ligation followed by hypoxia (10% O2). In total, 343 genes were differentially expressed in cortex, hippocampus, thalamus, and striatum 2 to 72 hours after hypoxia-ischemia, when comparing ipsilateral with contralateral hemispheres and with controls, using the significance analysis for microarrays. A total of 283 genes were upregulated and 60 were downregulated, and 94% of the genes had not previously been shown after neonatal hypoxia-ischemia. Genes related to transcription factors and metabolism had mostly upregulated transcripts, whereas most downregulated genes belonged to the categories of ion and vesicular transport and signal transduction. Genes involved in transcription, stress, and apoptosis were induced early after the insult, and many new genes that may play important roles in the pathophysiology of neonatal hypoxiaischemia were identified.
Anti—Monocyte Chemoattractant Protein-1 Gene Therapy Protects against Focal Brain Ischemia in Hypertensive Rats
Authors: Kumai Yasuhiro , Ooboshi Hiroaki , Takada Junichi , Kamouchi Masahiro , Kitazono Takanari , Egashira Kensuke , Ibayashi Setsuro , Iida Mitsuo
Published: May 2011

Monocyte chemoattractant protein-1 (MCP-1) is expressed in the ischemic cortex after focal brain ischemia and appears to exacerbate ischemic damage. The authors examined the effect of gene transfer of dominant negative MCP-1, called 7ND, 90 minutes after induction of focal brain ischemia in hypertensive rats. Adenoviral vectors encoding mutant MCP-1 (Ad7ND; n = 11), or Escherichia coli β-galactosidase (AdlacZ; n = 17) as control were injected into the lateral ventricle of male spontaneously hypertensive rats. Both AdlacZ (n = 12) and Ad7ND (n = 6) administration provided transgene expression as early as 6 hours after injection and the expression further increased on day 1, followed by a sustained detection on day 5. Five days after ischemia, infarct volume (75 ± 13 mm3, n = 5, mean ± SD) significantly reduced to 72% of control (104 ± 22 mm3, n = 5, P < 0.05) by 7ND gene transfer. Numbers of leukocytes in the vessels (48.3 ± 32.9/cm2) and macrophage/monocyte infiltration (475.2 ± 125.5 /mm2) of the infarct area in the Ad7ND group were significantly less than those measured in the AdlacZ group (143.8 ± 72.1/cm2 and 671.8 ± 125.5/mm2, P < 0.05, respectively). In summary, the postischemic gene transfer of dominant negative MCP-1 attenuated the infarct volume and infiltration of inflammatory cells, suggesting potential usefulness of the anti–MCP-1 gene therapy.
Functional Magnetic Resonance Imaging and Somatosensory Evoked Potentials in Rats with a Neonatally Induced Freeze Lesion of the Somatosensory Cortex
Authors: Schwindt Wolfram , Burke Michael , Pillekamp Frank , Luhmann Heiko J. , Hoehn Mathias
Published: May 2011

Brain plasticity is an important mechanism for functional recovery from a cerebral lesion. The authors aimed to visualize plasticity in adult rats with a neonatal freeze lesion in the somatosensory cortex using functional magnetic resonance imaging (fMRI), and hypothesized activation outside the primary projection area. A freeze lesion was induced in the right somatosensory cortex of newborn Wistar rats (n = 12). Sham-operated animals (n = 7) served as controls. After 6 or 7 months, a neurologic examination was followed by recording of somatosensory evoked potentials (SSEPs) and magnetic resonance experiments (anatomical images, fMRI with blood oxygen level–dependent contrast and perfusion-weighted imaging) with electrical forepaw stimulation under α-chloralose anesthesia. Lesioned animals had no obvious neurologic deficits. Anatomical magnetic resonance images showed a malformed cortex or hyperintense areas (cysts) in the lesioned hemisphere. SSEPs were distorted and smaller in amplitude, and fMRI activation was significantly weaker in the lesioned hemisphere. Only in a few animals were cortical areas outside the primary sensory cortex activated. The results are discussed in respect to an apparent absence of plasticity, loss of excitable tissue, the excitability of the lesioned hemisphere, altered connectivity, and a disturbed coupling of increased neuronal activity to the hemodynamic response.
The Phosphodiesterase 3 Inhibitor Cilostazol Dilates Large Cerebral Arteries in Humans without Affecting Regional Cerebral Blood Flow
Authors: Birk Steffen , Kruuse Christina , Petersen Kenneth A. , Jonassen Olga , Tfelt-Hansen Peer , Olesen Jes
Published: May 2011

Cilostazol, an inhibitor of phosphodiesterase (PDE) type 3, is used clinically in peripheral artery disease. PDE3 inhibitors may be clinically useful in the treatment of delayed cerebral vasospasm after subarachnoid hemorrhage. The authors present the first results on the effect of cilostazol on cerebral hemodynamics in normal participants. In this double-blind, randomized, crossover study, 200 mg cilostazol or placebo was administered orally to 12 healthy participants. Cerebral blood flow was measured using 133Xe inhalation and single photon emission computerized tomography. Mean flow velocity in the middle cerebral arteries (VMCA) was measured with transcranial Doppler, and the superficial temporal and radial arteries diameters were measured with ultrasonography. During the 4-hour observation period, there was no effect on systolic blood pressure ( P = 0.28), but diastolic blood pressure decreased slightly compared with placebo ( P = 0.04). VMCA decreased 21.5 ± 5.7% after cilostazol and 5.5 ± 12.2% after placebo ( P = 0.02, vs. placebo), without any change in global or regional cerebral blood flow. The superficial temporal artery diameter increased 17.6 ± 12.3% ( P < 0.001 vs. baseline) and radial artery diameter increased 12.6 ± 8.6% ( P < 0.001 vs. baseline). Adverse events, especially headache, were common. The findings suggest that cilostazol is an interesting candidate for future clinical trials of delayed cerebral vasospasm.
De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics
Authors: Adamidi Catherine , Wang Yongbo , Gruen Dominic , Mastrobuoni Guido , You Xintian , Tolle Dominic , Dodt Matthias , Mackowiak Sebastian D. , Gogol-Doering Andreas , Oenal Pinar , Rybak Agnieszka , Ross Eric , Alvarado Alejandro Sánchez , Kempa Stefan , Dieterich Christoph , Rajewsky Nikolaus , Chen Wei
Published: May 2011

Freshwater planaria are a very attractive model system for stem cell biology, tissue homeostasis, and regeneration. The genome of the planarian Schmidtea mediterranea has recently been sequenced and is estimated to contain >20,000 protein-encoding genes. However, the characterization of its transcriptome is far from complete. Furthermore, not a single proteome of the entire phylum has been assayed on a genome-wide level. We devised an efficient sequencing strategy that allowed us to de novo assemble a major fraction of the S. mediterranea transcriptome. We then used independent assays and massive shotgun proteomics to validate the authenticity of transcripts. In total, our de novo assembly yielded 18,619 candidate transcripts with a mean length of 1118 nt after filtering. A total of 17,564 candidate transcripts could be mapped to 15,284 distinct loci on the current genome reference sequence. RACE confirmed complete or almost complete 5′ and 3′ ends for 22/24 transcripts. The frequencies of frame shifts, fusion, and fission events in the assembled transcripts were computationally estimated to be 4.2%–13%, 0%–3.7%, and 2.6%, respectively. Our shotgun proteomics produced 16,135 distinct peptides that validated 4200 transcripts (FDR ≤1%). The catalog of transcripts assembled in this study, together with the identified peptides, dramatically expands and refines planarian gene annotation, demonstrated by validation of several previously unknown transcripts with stem cell-dependent expression patterns. In addition, our robust transcriptome characterization pipeline could be applied to other organisms without genome assembly. All of our data, including homology annotation, are freely available at SmedGD, the S. mediterranea genome database.
Prioritizing candidate disease genes by network-based boosting of genome-wide association data
Authors: Lee Insuk , Blom U. Martin , Wang Peggy I. , Shim Jung Eun , Marcotte Edward M.
Published: May 2011

Network “guilt by association” (GBA) is a proven approach for identifying novel disease genes based on the observation that similar mutational phenotypes arise from functionally related genes. In principle, this approach could account even for nonadditive genetic interactions, which underlie the synergistic combinations of mutations often linked to complex diseases. Here, we analyze a large-scale, human gene functional interaction network (dubbed HumanNet). We show that candidate disease genes can be effectively identified by GBA in cross-validated tests using label propagation algorithms related to Google's PageRank. However, GBA has been shown to work poorly in genome-wide association studies (GWAS), where many genes are somewhat implicated, but few are known with very high certainty. Here, we resolve this by explicitly modeling the uncertainty of the associations and incorporating the uncertainty for the seed set into the GBA framework. We observe a significant boost in the power to detect validated candidate genes for Crohn's disease and type 2 diabetes by comparing our predictions to results from follow-up meta-analyses, with incorporation of the network serving to highlight the JAK–STAT pathway and associated adaptors GRB2/SHC1 in Crohn's disease and BACH2 in type 2 diabetes. Consideration of the network during GWAS thus conveys some of the benefits of enrolling more participants in the GWAS study. More generally, we demonstrate that a functional network of human genes provides a valuable statistical framework for prioritizing candidate disease genes, both for candidate gene-based and GWAS-based studies.
The importance of incorporating age and sex when backcalculating length in bullhead Cottus gobio
Authors: Kielbassa J. , Charles S. , Delignette‐Muller M. L.
Published: May 2011

The present study backcalculated body length for a data set of a bullhead Cottus gobio population located at different sampling sites in a river network. Model comparison between various growth models, which included successively new parameters, showed the effect and importance of taking sex, age and the location in the river network into account. The data sets obtained by backcalculation were fitted by the von Bertalanffy growth function, which revealed the effect of the backcalculation formula on the estimation of the von Bertalanffy growth parameters. Fitting results and parameter estimates showed again the importance of incorporating age and sex when backcalculating body length in the C. gobio population studied.
Trophic ecology of Atlantic bluefin tuna Thunnus thynnus larvae
Authors: Catalán I. A. , Tejedor A. , Alemany F. , Reglero P.
Published: May 2011

Feeding intensity, diet composition, selectivity, energy ingestion and dietary niche breadth of larval Atlantic bluefin tuna Thunnus thynnus were studied on the eastern (Mediterranean) spawning grounds of the species. Larval T. thynnus were collected in the Balearic Archipelago (north‐west Mediterranean Sea) during 2004 and 2005 using surveys specific for larval scombrids. Larvae between 2·6 and 8·7 mm standard length (LS) are diurnal feeders, and 94% of the guts collected during daylight hours were full. The mean ±s.d. number of prey per gut was 7·1 ± 5·7, with mean ±s.d. ranging from 3·0 ± 1·6 in the smallest T. thynnus larvae to 11·1 ± 5·8 in 5·0–6·0 mm LS larvae. Up to 21 prey were found in a single larval gut (5·0–6·0 mm LS) at the end of the day. Larvae progressively selected larger prey and exhibited increased carbon content concurrent with preflexion development of feeding and locomotory structures. Larvae of 5·0–6·0 mm LS exhibited positive selection of cladocerans over other prey (Chesson's index), whereas copepod nauplii dominated the diets of earlier stages. The dietary niche breadth measured increased initially but decreased at c. 5·5 mm LS. Appendicularians were found in the diet of larger larval sizes, but no piscivory was observed. Results are discussed in light of the sparse existing data for larval T. thynnus and other larval tuna species.
Addiction Research Centres and the Nurturing of Creativity. Monitoring the European drug situation: the ongoing challenge for the European Monitoring Centre for Drugs and Drug Addiction (EMCDDA)
Authors: Griffiths Paul , Mounteney Jane , Lopez Dominique , Zobel Frank , Götz Wolfgang
Published: May 2011

The European Monitoring Centre for Drugs and Drug Addiction (EMCDDA) is the designated hub for drug‐related information in the European Union. The organization's role is to provide the European Union (EU) and its Member States with a factual overview of European drug problems and a common information framework to support the drugs debate. In order to achieve its mission, the EMCDDA coordinates and relies on a network of 30 national monitoring centres, the Reitox National Focal Points. The Centre publishes on a wide range of drug‐related topics, across epidemiology, interventions, laws and policies. Every November, the EMCDDA publishes its Annual Report, providing a yearly update on the European drug situation, translated into 23 EU languages. In line with its founding regulation, the EMCDDA has a role acting as an interface between the worlds of science and policy. While not a research centre in the formal sense, the results the Centre generates serve as catalysts for new research questions and help to identify priorities. Current challenges facing the agency include continuing to increase scientific standards while maintaining a strong institutional role, as well as supporting European efforts to identify, share and codify best practice in the drugs field.