bluuebunny/crossref_metadata_2025 huggingface dataset:
Stress reactivity in war-exposed young children with and without posttraumatic stress disorder: Relations to maternal stress hormones, parenting, and child emotionality and regulation
Authors: Feldman Ruth , Vengrober Adva , Eidelman-Rothman Moranne , Zagoory-Sharon Orna
Published: November 2013

The current study examined biomarkers of stress in war-exposed young children and addressed maternal and child factors that may correlate with children's stress response. Participants were 232 Israeli children aged 1.5–5 years, including 148 children exposed to continuous war. Similarly, 56 were diagnosed with posttraumatic stress disorder (PTSD) and 92 were defined as exposed-no-PTSD. Child cortisol (CT) and salivary alpha amylase (sAA), biomarkers of the hypothalamic–pituitary–adrenal and sympathetic–adrenal–medullary arms of the stress response, were measured at baseline, following challenge, and at recovery. Maternal CT and sAA, PTSD symptoms, and reciprocal parenting, and child negative emotionality and regulatory strategies were assessed. Differences between war-exposed children and controls emerged, but these were related to child PTSD status. Children with PTSD exhibited consistently low CT and sAA, exposed-no-PTSD displayed consistently high CT and sAA, and controls showed increase in CT following challenge and decrease at recovery and low sAA. Exposed children showed higher negative emotionality; however, whereas exposed-no-PTSD children employed comfort-seeking strategies, children with PTSD used withdrawal. Predictors of child CT included maternal CT, PTSD symptoms, low reciprocity, and negative emotionality. Findings suggest that high physiological arousal combined with approach strategies may be associated with greater resilience in the context of early trauma.
Developmental timing and continuity of exposure to interparental violence and externalizing behavior as prospective predictors of dating violence
Authors: Narayan Angela J. , Englund Michelle M. , Egeland Byron
Published: November 2013

This study investigated the prospective pathways of children's exposure to interparental violence (EIPV) in early and middle childhood and externalizing behavior in middle childhood and adolescence as developmental predictors of dating violence perpetration and victimization at ages 23 and 26 years. Participants (N= 168) were drawn from a longitudinal study of low-income families. Path analyses examined whether timing or continuity of EIPV predicted dating violence and whether timing or continuity of externalizing behavior mediated these pathways. Results indicated that EIPV in early childhood directly predicted perpetration and victimization at age 23. There were significant indirect effects from EIPV to dating violence through externalizing behavior in adolescence and life stress at age 23. Independent of EIPV, externalizing behavior in middle childhood also predicted dating violence through externalizing behavior in adolescence and life stress at age 23, but this pathway stemmed from maltreatment. These results highlight that the timing of EIPV and both the timing and the continuity of externalizing behavior are critical risks for the intergenerational transmission of dating violence. The findings support a developmental perspective that negative early experiences and children's externalizing behavior are powerful influences for dating violence in early adulthood.
The efficacy of interpersonal psychotherapy for depression among economically disadvantaged mothers
Authors: Toth Sheree L. , Rogosch Fred A. , Oshri Assaf , Gravener-Davis Julie , Sturm Robin , Morgan-López Antonio Alexander
Published: November 2013

A randomized clinical trial was conducted to evaluate the efficacy of interpersonal psychotherapy (IPT) for ethnically and racially diverse, economically disadvantaged women with major depressive disorder. Non-treatment-seeking urban women (N = 128; M age = 25.40, SD = 4.98) with infants were recruited from the community. Participants were at or below the poverty level: 59.4% were Black and 21.1% were Hispanic. Women were screened for depressive symptoms using the Center for Epidemiologic Studies Depression Scale; the Diagnostic Interview Schedule was used to confirm major depressive disorder diagnosis. Participants were randomized to individual IPT or enhanced community standard. Depressive symptoms were assessed before, after, and 8 months posttreatment with the Beck Depression Inventory—II and the Revised Hamilton Rating Scale for Depression. The Social Support Behaviors Scale, the Social Adjustment Scale—Self-Report, and the Perceived Stress Scale were administered to examine mediators of outcome at follow-up. Treatment effects were evaluated with a growth mixture model for randomized trials using complier-average causal effect estimation. Depressive symptoms trajectories from baseline through postintervention to follow-up showed significant decreases among the IPT group compared to the enhanced community standard group. Changes on the Perceived Stress Scale and the Social Support Behaviors Scale mediated sustained treatment outcome.
The development of thought problems: A longitudinal family risk study of offspring of bipolar, unipolar, and well parents
Authors: Klimes-Dougan Bonnie , Desjardins Christopher David , James Matthew G. , Narayan Angela J. , Long Jeffrey D. , Cullen Kathryn R. , Gold Philip W. , Martinez Pedro E.
Published: November 2013

There is growing evidence that many offspring of parents with bipolar disorder (BD) will develop moderate to severe forms of psychopathology during childhood and adolescence, including thought problems. The purpose of this study was to evaluate the developmental progression of thought problems within the context of a family risk study. Repeated assessments of thought problems, spanning approximately 15 years, were conducted in offspring (N= 192 from 98 families) of parents diagnosed with BD (O-BD), unipolar depression (O-UNI), or no significant psychiatric or medical problems (O-WELL). Survival analysis showed that the O-BD group had the greatest estimated probability of developing thought problems over time, followed by O-UNI, and then O-WELL and O-BD exhibiting higher levels of persistence than O-WELL. Parent-reported thought problems in childhood and adolescence predicted a range of problems in young adulthood. Disturbances in reality testing and other atypical behaviors are likely to disrupt progression through important developmental periods and to associate with poor outcomes. These findings are likely relevant to preventing the occurrence or progression of problems in offspring of bipolar parents. The study of thought problems across development represents an important area of continued research in children at risk for development of affective disorders.
A SECOND PHILOSOPHY OF ARITHMETIC
Authors: MADDY PENELOPE
Published: November 2013

This paper outlines a second-philosophical account of arithmetic that places it on a distinctive ground between those of logic and set theory.
Reduced nephron endowment in the neonates of Indigenous Australian peoples
Authors: Kandasamy Y. , Smith R. , Wright I. M. R. , Lumbers E. R.
Published: November 2013

Rates of chronic kidney disease (CKD) among Indigenous groups in Australia exceed non-Indigenous rates eight-fold. Using kidney volume as a surrogate for nephron number, we carried out a study to determine if Indigenous neonates have a smaller kidney volume (and thus a reduced nephron number) from birth compared with non-Indigenous neonates. We recruited term and preterm neonates (<32 weeks) at a tertiary care neonatal unit over a 12 months period. Preterm neonates were assessed (renal sonography and renal function measurement) at 32 weeks corrected age (CA) and again at 38 weeks CA when blood pressure was also measured. All term neonates were assessed in the first post-natal week, including renal sonography, renal function and blood pressure measurement. The primary outcome measured was total kidney volume (TKV) and estimated glomerular filtration rate (eGFR) was a secondary outcome. Data was available for 44 preterm (11 Indigenous) and 39 term (13 Indigenous) neonates. TKV of Indigenous neonates was significantly lower at 32 weeks [12.0 (2.0)v.15.4 (5.1) ml;P=0.03] and 38 weeks CA [18.6 (4.0)v.22.6 (5.9) ml;P=0.04] respectively. Term Indigenous neonates also had smaller kidney volumes compared with non-Indigenous neonates. Despite a smaller kidney volume (and reduced nephron number), Indigenous neonates did not have a significantly lower eGFR. Indigenous neonates achieve similar eGFRs to Non-Indigenous neonates, presumably through a higher single nephron filtration rate. This places Indigenous neonates at a greater risk of long-term kidney damage later in life.
From promise to practice
Authors: Nielsen David R , Moon Tae Seok
Published: November 2013

Synthetic biology has the potential to profoundly change the way we produce many chemicals, as well as to reduce the environmental impact of the chemical industry.
Karrikins from plant smoke modulate bacterial quorum sensing
Authors: Mandabi Aviad , Ganin Hadas , Krief Pnina , Rayo Josep , Meijler Michael M.
Published: November 2013

The discovery that plant smoke contains germination stimuli, named karrikins, has now led to the identification of a new role for these signals as quorum sensing modulators.
Generalised method of current excitation reconstruction from near‐field data of planar, cylindrical and spherical antenna arrays
Authors: Sen Ritika , Jerome‐Surendran Thomas D. , Trivedi Dhara Kiritkumar , Qayyum Mazher Abdul , Kumar Balasubramaniam Preetham
Published: November 2013

Currently chemotherapy, radiation and surgery are the widely accepted treatments for cancer. A fourth modality, hyperthermia, or heat treatment, is emerging as an adjuvant cancer treatment along with radiation or chemotherapy, and works as a booster, sometimes even doubling the effects of these standard treatments. Hyperthermia essentially heats the cancer region to around 42°C by precisely controlled electromagnetic radiation in the 27, 900 or 2400 MHz frequency range. The re‐emergence of hyperthermia is primarily due to advanced antenna technology, which can precisely target the tumour volume, while delivering minimal energy to neighbouring healthy tissue. The precise focusing of the electromagnetic beam is realised either by focusing plates or lenses, or by conformal antenna arrays. In order to achieve efficient array near‐field control for hyperthermia applications, electronic control of the array currents is essential to control the beam over the tumour volume and achieve uniform heating. This paper reports a generalised analytical technique to reconstruct the array currents from a specific near‐zone electric field profile. This reconstruction technique is applicable to conformal arrays with planar, cylindrical or spherical geometry. Several simulations have been carried out to test the validity and accuracy of the reconstruction algorithm.
Influence of total gas flow on carbon nanotube forests synthesised by water‐assisted chemical vapour deposition
Authors: Liang Youxuan , Jiang Chuan , Zhao Bin , Yang Junhe
Published: November 2013

The influence of total gas flow on the growth of carbon nanotube (CNT) forests in water‐assisted chemical vapour deposition has been investigated. It was found that the average height of the CNT forests decreased gradually from 996.53 to 696.8 μm, and the growth yield decreased notably from 2.91 to 1.98 mg/cm2 as the total flow increased, but the crystallinity and thermostability of CNT forests increased with increasing total flow. Investigation on CNT growth kinetics suggested that increasing the total flow could decrease the growth rate and shorten catalyst lifetime because of decreased gas dwell time and enhanced subsurface diffusion of Fe catalyst.
Chemically synthesized nanowire TiO2/ZnO core-shell p-n junction array for high sensitivity ultraviolet photodetector
Authors: Dao T. D. , Dang C. T. T. , Han G. , Hoang C. V. , Yi W. , Narayanamurti V. , Nagao T.
Published: November 2013

A sol-gel-based ultrathin TiO2 lamination coating was adapted to a hydrothermally grown ZnO nanowire array to realize an all-oxide ultra-sensitive p-n photodiode. The core-shell heterojunction—the key component of the device—is composed of a 5–10 nm thick p-type Cr-doped TiO2 nanoshell and n-type single-crystalline ZnO nanowires (50 nm radius). Owing to the enhanced light scattering and carrier separation in the core-shell architecture, this device exhibits the highest performance among the ZnO nanowire-based photodetectors. At a moderate reverse bias of −5 V and under ultraviolet light illumination at 104 μW, it shows a switch current ratio of 140 and a responsivity as large as 250 A/W, while it shows nearly no response to the infrared and visible light.
A high-current electron gun for the electron beam ion trap at the National Superconducting Cyclotron Laboratory
Authors: Schwarz S. , Baumann T. M. , Kittimanapun K. , Lapierre A. , Snyder A.
Published: November 2013

The Electron Beam Ion Trap (EBIT) in NSCL’s reaccelerator ReA uses continuous ion injection and accumulation. In order to maximize capture efficiency and minimize breeding time into high charge states, the EBIT requires a high-current/high current-density electron beam. A new electron gun insert based on a concave Ba-dispenser cathode has been designed and built to increase the current transmitted through the EBIT’s superconducting magnet. With the new insert, stable EBIT operating conditions with 0.8 A of electron beam have been established. The design of the electron gun is presented together with calculated and measured perveance data. In order to assess the experimental compression of the electron beam, a pinhole CCD camera has been set up to measure the electron beam radius. The camera observes X-rays emitted from highly charged ions, excited by the electron beam. Initial tests with this camera setup will be presented. They indicate that a current density of 640 A/cm2 has been reached when the EBIT magnet was operated at 4 T.
Interaction of TiO2− with water: Photoelectron spectroscopy and density functional calculations
Authors: Li Ren-Zhong , Xu Hong-Guang , Cao Guo-Jin , Xu Xi-Ling , Zheng Wei-Jun
Published: November 2013

The interactions of titania with water molecules were studied via photoelectron spectroscopy and density functional calculations of TiO(OH)2− and Ti(OH)4(H2O)n− (n = 0–5) clusters which are corresponding to the TiO2(H2O)− and TiO2(H2O)n+2− (n = 0–5) systems, respectively. Experimental observation and theoretical calculations confirmed that TiO(OH)2− was produced when TiO2− interacts with one water molecule, and Ti(OH)4(H2O)n− (n = 0–5) were produced successively when TiO2− interacts with two or more water molecules. The structures of Ti(OH)4(H2O)n− with n = 4, 5 are slightly different from those of n = 1–3. The structures of Ti(OH)4(H2O)1-3− can be viewed as the water molecules interacting with the Ti(OH)4− core through hydrogen bonds; however, in Ti(OH)4(H2O)4,5−, one of the water molecules interacts directly with the Ti atom via its oxygen atom instead of a hydrogen bond and distorted the Ti(OH)4− core.
Identifying Dirac cones in carbon allotropes with square symmetry
Authors: Wang Jinying , Huang Huaqing , Duan Wenhui , Liu Zhirong
Published: November 2013

A theoretical study is conducted to search for Dirac cones in two-dimensional carbon allotropes with square symmetry. By enumerating the carbon atoms in a unit cell up to 12, an allotrope with octatomic rings is recognized to possess Dirac cones under a simple tight-binding approach. The obtained Dirac cones are accompanied by flat bands at the Fermi level, and the resulting massless Dirac-Weyl fermions are chiral particles with a pseudospin of S = 1, rather than the conventional S = 1/2 of graphene. The spin-1 Dirac cones are also predicted to exist in hexagonal graphene antidot lattices.
Study of second phase in bioabsorbable magnesium alloys: Phase stability evaluation via Dmol3 calculation
Authors: Yang Huazhe , Liu Chen , Wan Peng , Tan Lili , Yang Ke
Published: November 2013

Thermodynamical stabilities of four conventional second phases as well as magnesium matrix in bioabsorbable magnesium alloys were investigated theoretically via computer calculation method. Model of individual phase and systems including phase and four water molecular (phase-4H2O) were established to simulate the in vitro and in vivo environment. Local orbital density functional theory approach was applied to calculate the total energy for the individual phase and phase-4H2O system. The results demonstrated that all the second phases possessed higher phase stability compared with magnesium matrix, but the phase stability was quite different for different types of second phases or second phase-4H2O systems. Furthermore, a schematic process of inflammation reaction caused by magnesium alloy implants was proposed for the further evaluation on biocompatibility of different second phases.
Electron impact excitation of the low-lying 3s[3/2]1 and 3s′[1/2]1 levels in neon for incident energies between 20 and 300 eV
Authors: Hoshino M. , Murai H. , Kato H. , Brunger M. J. , Itikawa Y. , Tanaka H.
Published: November 2013

Absolute differential cross sections (DCSs) for electron impact of the two lower-lying 3s[3/2]1 (3P0) and 3s′[1/2]1 (1P1) electronic states in neon (Ne) have been determined for eight incident electron energies in the range 20–300 eV. Comparisons between our results and previous measurements and calculations, where possible, are provided with best agreement being found with the recent large-scale B-spline R-matrix computations [O. Zatsarinny and K. Bartschat, Phys. Rev. A 86, 022717 (2012)]. Based on these DCSs at 100, 200, and 300 eV, a generalised oscillator strength analysis enabled us to determine estimates for the optical oscillator strengths of the 3s[3/2]1 and 3s′[1/2]1 levels. In this case, excellent agreement was found with a range of independent experiments and calculations, giving us some confidence in the validity of our measurement and analysis procedures. Integral cross sections, derived from the present DCSs, were presented graphically and discussed elsewhere [M. Hoshino, H. Murai, H. Kato, Y. Itikawa, M. J. Brunger, and H. Tanaka, Chem. Phys. Lett. 585, 33 (2013)], but are tabulated here for completeness.
Laser assisted crystallization of ferromagnetic amorphous ribbons: A multimodal characterization and thermal model study
Authors: Katakam Shravana , Devaraj Arun , Bowden Mark , Santhanakrishnan S. , Smith Casey , Ramanujan R. V. , Thevuthasan Suntharampillai , Banerjee Rajarshi , Dahotre Narendra B.
Published: November 2013

This paper focuses on laser-based de-vitrification of amorphous soft magnetic Fe-Si-B ribbons and its consequent influence on the magnetic properties. Laser processing resulted in a finer scale of crystallites due to rapid heating and cooling during laser annealing compared to conventional furnace annealing process. A significant increase in saturation magnetization is observed for laser-annealed ribbons compared to both as-received and furnace annealed samples coupled with an increase in coercivity compared to the as received samples. The combined effect of thermal histories and stresses developed during laser annealing results in the formation of nano-crystalline phase along the laser track. The phase evolution is studied by micro-XRD and TEM analysis. Solute partitioning and compositional variation within the phases are obtained by Local Electrode Atom probe analysis. The evolution of microstructure is rationalized using a Finite Element based heat transfer multi-physics model.
Self-organized topology of recurrence-based complex networks
Authors: Yang Hui , Liu Gang
Published: November 2013

With the rapid technological advancement, network is almost everywhere in our daily life. Network theory leads to a new way to investigate the dynamics of complex systems. As a result, many methods are proposed to construct a network from nonlinear time series, including the partition of state space, visibility graph, nearest neighbors, and recurrence approaches. However, most previous works focus on deriving the adjacency matrix to represent the complex network and extract new network-theoretic measures. Although the adjacency matrix provides connectivity information of nodes and edges, the network geometry can take variable forms. The research objective of this article is to develop a self-organizing approach to derive the steady geometric structure of a network from the adjacency matrix. We simulate the recurrence network as a physical system by treating the edges as springs and the nodes as electrically charged particles. Then, force-directed algorithms are developed to automatically organize the network geometry by minimizing the system energy. Further, a set of experiments were designed to investigate important factors (i.e., dynamical systems, network construction methods, force-model parameter, nonhomogeneous distribution) affecting this self-organizing process. Interestingly, experimental results show that the self-organized geometry recovers the attractor of a dynamical system that produced the adjacency matrix. This research addresses a question, i.e., “what is the self-organizing geometry of a recurrence network?” and provides a new way to reproduce the attractor or time series from the recurrence plot. As a result, novel network-theoretic measures (e.g., average path length and proximity ratio) can be achieved based on actual node-to-node distances in the self-organized network topology. The paper brings the physical models into the recurrence analysis and discloses the spatial geometry of recurrence networks.
Neutral gas heating via non-resonant optical lattices
Authors: Cornella Barry M. , Gimelshein Sergey F. , Lilly Taylor C. , Ketsdever Andrew D.
Published: November 2013

Energy deposition from high intensity pulsed optical lattices to a neutral gas was experimentally recorded for molecular nitrogen at 300/500 K and methane at 300 K. The magnitude of acoustic waves generated by the interaction was experimentally measured and simulated using the direct simulation Monte-Carlo method. The relationship between the lattice velocity and the measured acoustic wave magnitude was compared to numerical simulation which both exhibited dependence on lattice velocity, indicating that the detected pressure wave was the result of gas heating from the optical lattice and not from other forms of laser energy deposition.
Self-assembly of compositionally modulated Ga1−xMnxAs multilayers during molecular beam epitaxy
Authors: Gallardo-Hernández S. , Martinez-Velis I. , Ramirez-Lopez M. , Kudriatsev Y. , Escobosa-Echavarria A. , Luiz Morelhao S. , Lopez-Lopez M.
Published: November 2013

GaMnAs structures were grown on GaAs(100) substrates by molecular beam epitaxy employing different growth parameters. We studied manganese incorporation employing secondary ion mass spectrometry (SIMS). At a growth temperature of 300 °C, we observed a self-assembled modulation of the manganese concentration. SIMS depth profiles were analyzed employing a depth resolution function taking into account sputtering-induced broadening of the original distribution and segregation. We found a Mn segregation length along the growth direction of ∼4 nm. The presence of GaMnAs multilayers was corroborated by high-resolution x-ray diffraction. Spinodal decomposition is a possible mechanism for the spontaneous formation of the multilayer structure.
Does woodland condition influence the diversity and abundance of small mammal communities?
Authors: Moore T. L. , Valentine L. E. , Craig M. D. , Hardy G. E. St J. , Fleming P. A.
Published: November 2013

Loss of mammal species in Australia in the last 200 years has been attributed to many factors including habitat removal and altered fire regimes. Decline in tree condition could contribute further to the ongoing decline of mammals. Eucalyptus wandoo trees are currently undergoing a decline in condition that can result in a loss of canopy and other changes to the habitat. This paper examines the relationships between E. wandoo tree condition, habitat characteristics and small mammal species richness and abundance. Live-capture trapping was conducted at 24 E. wandoo sites at Dryandra State Forest and Wandoo Conservation Park, Western Australia. Condition and microhabitat variables of E. wandoo were recorded for each site. Generalised additive mixed models revealed a range of habitat and tree condition characteristics that influenced small mammal abundance and species richness, including site litter cover, crown dieback, understorey vegetation cover and tree density. The availability of coarse woody debris played a large role in explaining the abundance of Cercartetus concinnus and Antechinus flavipes, along with other microhabitat and tree condition variables, such as tree leaf litter and crown dieback. Epicormic growth, crown density and the distance to the drift fence from E. wandoo trees were the common variables in the best model for the abundance of Sminthopsis griseoventer. The decline in condition of E. wandoo and the subsequent modifications to the microhabitat are correlated with changes in the small mammal community. A better understanding of how the decline of E. wandoo impacts small mammal communities could improve management practices in E. wandoo woodlands.
Detection of single photons by toad and mouse rods
Authors: Reingruber Jürgen , Pahlberg Johan , Woodruff Michael L. , Sampath Alapakkam P. , Fain Gordon L. , Holcman David
Published: November 2013

Significance

Amphibian and mammalian rods both detect single photons of light even though mammalian rods are much smaller in diameter. To understand how this is possible, we combined electrical recordings with computations. We show that changes in the rod diameter go hand in hand with changes in the biochemistry to allow for single-photon detection.
School choice research in five European countries: the circulation of Stephen Ball's concepts and interpretations
Authors: van Zanten Agnès , Kosunen Sonja
Published: November 2013

This article analyzes the influence of Stephen Ball's work on research on markets and school choice in five European countries (Finland, France, Norway, Spain, and Sweden). The main focus is on the intellectual circulation of ideas, but the authors also take into account the relationship
between ideas and social and political changes, as well as between ideas and the organization of research communities. Concepts derived from policy sociology are used to examine the dissemination of concepts and interpretations. Three areas of study are taken into account (school choice policies,
choice as a class strategy, and choice within local education markets). The conclusion points out differences between countries and underlines the need to take into account processes of migration of ideas between national research communities in a more integrated European research area.
Globalization, edu-business and network governance: the policy sociology of Stephen J. Ball and rethinking education policy analysis
Authors: Lingard Bob , Sellar Sam
Published: November 2013

This paper traces developments across Stephen J. Ball's policy sociology in education oeuvre and considers their implications for doing research on education policy today. It begins with an account of his policy sociology trilogy from the 1990s, which outlined his conception of the
policy cycle consisting of the contexts of influence, text production and policy practice. It then considers the emergence of a strengthening focus on the global in Ball's work, noting the significance of the 1998 paper, 'Big policies/small world', which demonstrated how policy problems and
solutions circulate through global discourses, but are always recontextualized within national policies and practices. Next, the paper reflects on two recent books: Global Education Inc and Networks, New Governance and Education. The former is concerned with the rescaling of the contexts
of policy and the enhanced significance of both international organizations and global edu-business in the education policy cycle and the implications for doing policy analysis. The latter employs a network ethnography approach and provides an account of the new network governance in education:
the rise of heterarchies, a melange of bureaucracy, markets and networks. The paper concludes by suggesting this account is indicative of the topological turn in culture and social theory. The conclusion gestures towards the implications of this for the policy cycle conception and for doing
education policy analysis today, suggesting that Ball's recent work provides the scaffolds of such an approach.
Membrane damage-induced vesicle–vesicle fusion of dysferlin-containing vesicles in muscle cells requires microtubules and kinesin
Authors: McDade Joel R. , Michele Daniel E.
Published: November 2013

Mutations in the dysferlin gene resulting in dysferlin-deficiency lead to limb-girdle muscular dystrophy 2B and Myoshi myopathy in humans. Dysferlin has been proposed as a critical regulator of vesicle-mediated membrane resealing in muscle fibers, and localizes to muscle fiber wounds following sarcolemma damage. Studies in fibroblasts and urchin eggs suggest that trafficking and fusion of intracellular vesicles with the plasma membrane during resealing requires the intracellular cytoskeleton. However, the contribution of dysferlin-containing vesicles to resealing in muscle and the role of the cytoskeleton in regulating dysferlin-containing vesicle biology is unclear. Here, we use live-cell imaging to examine the behavior of dysferlin-containing vesicles following cellular wounding in muscle cells and examine the role of microtubules and kinesin in dysferlin-containing vesicle behavior following wounding. Our data indicate that dysferlin-containing vesicles move along microtubules via the kinesin motor KIF5B in muscle cells. Membrane wounding induces dysferlin-containing vesicle–vesicle fusion and the formation of extremely large cytoplasmic vesicles, and this response depends on both microtubules and functional KIF5B. In non-muscle cell types, lysosomes are critical mediators of membrane resealing, and our data indicate that dysferlin-containing vesicles are capable of fusing with lysosomes following wounding which may contribute to formation of large wound sealing vesicles in muscle cells. Overall, our data provide mechanistic evidence that microtubule-based transport of dysferlin-containing vesicles may be critical for resealing, and highlight a critical role for dysferlin-containing vesicle–vesicle and vesicle–organelle fusion in response to wounding in muscle cells.
P23H opsin knock-in mice reveal a novel step in retinal rod disc morphogenesis
Authors: Sakami Sanae , Kolesnikov Alexander V. , Kefalov Vladimir J. , Palczewski Krzysztof
Published: November 2013

Retinal rod photoreceptor cells have double membrane discs located in their outer segments (ROS) that are continuously formed proximally from connecting cilia (CC) and phagocytized distally by the retinal pigmented epithelium. The major component of these rod discs, the light-sensitive visual pigment rhodopsin (Rho), consists of an opsin protein linked to 11-cis-retinal. The P23H mutation of rod opsin (P23H opsin) is the most common cause of human blinding autosomal dominant retinitis pigmentosa (adRP). A mouse model of adRP with this mutation (RhoP23H/+) shows low levels of P23H opsin protein, partial misalignment of discs and progressive retinal degeneration. However, the impact of mutant P23H opsin on the formation of abnormal discs is unclear and it is still unknown whether this mutant pigment can mediate phototransduction. Using transretinal ERG recordings, we demonstrate that P23H mutant Rho can trigger phototransduction but RhoP23H/P23H rods are ∼17 000-fold less sensitive to light than Rho+/+ rods and produce abnormally fast photo-responses. By analyzing homozygous RhoP23H/P23H knock-in mice, we show that P23H opsin is transported to ciliary protrusions where it forms sagittally elongated discs. Transmission electron microscopy of postnatal day (PND) 14 RhoP23H/+ mouse retina revealed disordered sagittally oriented discs before the onset of retinal degeneration. Surprisingly, we also observed smaller, immature sagittally oriented discs in PND14 Rho+/− and Rho+/+ mice that were not seen in older animals. These findings provide fundamental insights into the pathogenesis of the P23H mutant opsin and reveal a novel early sagittally aligned disc formation step in normal ROS disc expansion.
Fe K lines in the nuclear region of M82
Authors: Liu Jiren , Gou Lijun , Yuan Weimin , Mao Shude
Published: November 2013

We study the spatial distribution of the Fe 6.4 and 6.7 keV lines in the nuclear region of M82 using the Chandra archival data with a total exposure time of 500 ks. The deep exposure provides a significant detection of the Fe 6.4 keV line. Both the Fe 6.4 and 6.7 keV lines are diffuse emissions with similar spatial extent, but their morphology do not exactly follow each other. Assuming a thermal collisional-ionization-equilibrium (CIE) model, the fitted temperatures are around 5–6 keV and the Fe abundances are about 0.4–0.6 solar value. We also report the spectrum of a point source, which shows a strong Fe 6.7 keV line and is likely a supernova remnant or a superbubble. The fitted Fe abundance of the point source is 1.7 solar value. It implies that part of the iron may be depleted from the X-ray emitting gases as the predicted Fe abundance is about 5 times solar value if assuming a complete mixing. If this is a representative case of the Fe enrichment, a mild mass-loading of a factor of 3 will make the Fe abundance of the point source in agreement with that of the hot gas, which then implies that most of the hard X-ray continuum (2–8 keV) of M82 has a thermal origin. In addition, the Fe 6.4 keV line is consistent with the fluorescence emission irradiated by the hard photons from nuclear point sources.
TFBSshape: a motif database for DNA shape features of transcription factor binding sites
Authors: Yang Lin , Zhou Tianyin , Dror Iris , Mathelier Anthony , Wasserman Wyeth W. , Gordân Raluca , Rohs Remo
Published: November 2013

Transcription factor binding sites (TFBSs) are most commonly characterized by the nucleotide preferences at each position of the DNA target. Whereas these sequence motifs are quite accurate descriptions of DNA binding specificities of transcription factors (TFs), proteins recognize DNA as a three-dimensional object. DNA structural features refine the description of TF binding specificities and provide mechanistic insights into protein–DNA recognition. Existing motif databases contain extensive nucleotide sequences identified in binding experiments based on their selection by a TF. To utilize DNA shape information when analysing the DNA binding specificities of TFs, we developed a new tool, the TFBSshape database (available at http://rohslab.cmb.usc.edu/TFBSshape/), for calculating DNA structural features from nucleotide sequences provided by motif databases. The TFBSshape database can be used to generate heat maps and quantitative data for DNA structural features (i.e., minor groove width, roll, propeller twist and helix twist) for 739 TF datasets from 23 different species derived from the motif databases JASPAR and UniPROBE. As demonstrated for the basic helix-loop-helix and homeodomain TF families, our TFBSshape database can be used to compare, qualitatively and quantitatively, the DNA binding specificities of closely related TFs and, thus, uncover differential DNA binding specificities that are not apparent from nucleotide sequence alone.
First Report of Diaporthe neoviticola Associated with Wood Cankers of Grapevine in Turkey
Authors: Akgül D. S. , Mayorquin J. S. , Eskalen A.
Published: November 2013

In recent years, delayed bud bursting, cane bleaching, shoot dieback, and cankers in 1-year-old canes and perennial arms were observed in vineyards of the Aegean region (western Turkey). These symptoms were frequently observed on the following major table grape (Vitis vinifera) cultivars: ‘Alphonse Lavallée,’ ‘Cardinal,’ ‘Sultana Seedless,’ and ‘Trakya Ilkeren’ in 2012. To determine the causal agents, symptomatic woody tissues (0.5 cm2) were sampled from the canes of nine Manisa and four Salihli Cities (13 total) grapevine varieties and were plated onto potato dextrose agar amended with tetracycline (0.01%) (PDA-tet). A considerable amount of phomopsis-like fungi were isolated from the symptomatic tissues and fungal colonies were incubated for 2 to 3 weeks to induce sporulation. After incubation for 14 days at 24°C in the dark, white mycelial growth with undulating colony margins, and abundant pycnidia producing hyaline, ellipsoidal, fusoid α-conidia with invisible nuclei, and β-conidia, were observed on PDA, and they resembled species in the Diaporthaceae (1,2). The α-conidia dimensions were 9.3 to 10.2 × 1.9 to 2.9 μm (avg. 9.7 × 2.4 μm) and β-conidia were 19 to 24 × 0.5 to 1 μm (avg. 22 × 0.9 μm). For molecular identification, fungal DNA was extracted from mycelial mats and ribosomal DNA fragments (ITS1, 5.8S ITS2 rDNA, amplified with ITS4 and ITS5 primers) (3) were sequenced and the sequences were compared with those deposited in NCBI GenBank in a BLASTn search. The representative isolate (MBAi43AG) showed 99% homology with Diaporthe neoviticola isolate from New Zealand KC145831.1. The DNA sequence of the identified isolate was submitted to GenBank under accession number KF460427. Pathogenicity tests were conducted under controlled conditions (24°C, 16/8 h day/night, and 70% RH) on 1-cm-diameter, detached green grapevine cv. Cabernet Sauvignon canes (with leaves) using the isolate of D. neoviticola specified above. The shoots were wounded by creating a 5-mm-diameter incision with a sterile scalpel. An agar disc with mycelia and pycniospores was placed into each wound and covered with Parafilm. Sterile PDA plugs were used as mock inoculum for the control plants. There were 10 replicates per treatment and the experiment was repeated twice. After 1 month of incubation, the green shoots were examined for the extent of superficial blackish lesions. The average lesion length on inoculated shoots was 18.2 mm for D. neoviticola. No lesions were observed in the control shoots. The fungal isolate was successfully re-isolated from 96% of inoculated shoots to fulfill Koch's postulates. To our knowledge, this is the first report of D. neoviticola causing wood canker and dieback of shoots on grapevine in Turkey.

References: (1) R. R. Gomes. Persoonia 31:1, 2013. (2) D. Udayanga et al. Fungal Diversity 56:157, 2012. (3) J. M. van Niekerk et al. Australas. Plant Pathol. 34:27, 2005.
First Report of Stolbur Phytoplasma Affecting Cichorium intybus in Serbia
Authors: Pavlovic S. , Starović M. , Stojanovic S. D. , Kojic S. , Marinkovic J. , Josic D.
Published: November 2013

Chicory (Cichorium intybus, Asteraceae) is a typical Mediterranean plant indigenous to Europe, western Asia, Egypt, and North America (3). It is commonly consumed as a fresh vegetable in salads. In rural areas of Serbia it grows as a weed in crops, but it is used in folk medicine to treat skin disorders due to its antihepatotoxic activity (3). Methanol extracts of chicory leaves showed moderate antibacterial activity against enteric bacteria (3). A phytoplasma-like disease, expressed as proliferation of chicory shoots and flowers, was observed on wild plants for the first time in Obrenovac vicinity (44°40′ N, 20°20′ E) in July 2012. A flattening of the stem with a large number of filamentous leaves, contortion and abnormal growth of flowers on the stem (typical fasciation symptoms) were observed. Diseased plants did not produce seeds. Total DNA was extracted from the leaf midveins of 15 symptomatic and five symptomless plants (4). PCR amplification of 1.5-kb 16S rDNA fragment was performed using DreamTaq Green master mix (Thermo Scientific, Lithuania) and phytoplasma universal primer pairs P1/16S-Sr (1). Products of nested PCR (1.2 kb) were obtained using primer pair R16F2n/R2 (1). Both amplicons were detected in all diseased samples; however, DNA from symptomless samples yielded no amplicons. Restriction fragment length polymorphism (RFLP) analysis of R16F2n/R2 PCR products was performed in independent reactions using four endonucleases (AluI, TruI1, HhaI and HpaII). RFLP patterns from chicory samples were compared to those of Stolbur (STOL), Aster Yellows (AY), Flavescence Dorée-C (FD-C), Poinsettia Branch-Inducing (PoiBI), and Clover Yellow Edge (CYE) phytoplasmas (1). All RFLP profiles from the chicory samples were identical to STOL reference strain, indicating that diseased chicory was affected by a phytoplasma that belongs to ‘Candidatus Phytoplasma solani’ (16SrXII-A group). The 16S rDNA sequence of representative sample from symptomatic plant (Vp4) was deposited under accession number KF661322 in NCBI GenBank. It showed 100% identity to KF263684.1 from Iranian peach, JQ730742.1 from Serbian valerian, and JQ730750 from Serbian corn, all belonging to the ‘Ca. P. solani’ taxon. Puna chicory disease on C. intybus associated with a subgroup 16SrV-B of phytoplasma was detected in China (2). This is the first report of the Stolbur phytoplasma associated with fasciation of C. intybus in Serbia and worldwide.

References: (1) I. M. Lee et al. Int. J. Syst. Evol. Microbiol. 56:1593, 2006. (2) Z. N. Li et al. Can. J. Plant Pathol. 34:34, 2012. (3) J. Petrovic et al. Fitoterapia 75:737, 2004. (4) J. P. Prince. Phytopathology 83:1130, 1993.
Occurrence of a Fruit Spot Disease of Pear Caused by Septoria pyricola in Tyrnavos Larissa, Northern Greece
Authors: Thomidis T. , Katerinis S.
Published: November 2013

Pear tree (Pyrus communis) is an important crop in Greece. In 2012, fruits of the pear cv. Kontoula were observed in commercial fields located in Tirnavos, Prefecture of Larrisa, Greece, with symptoms of well-defined brown angular margins and their grayish white centers in which a few pycnidia (about 180 × 150 μm) were produced within the spots. Pycnidia were dark, separate, and globe-shaped with an ostiole (opening at the apex) from which conidia (about 40 to 60 × 3 μm) were extruded, and erupted through the surface of the infected tissue. Conidia were produced on short conidiophores. They were clear, narrowly elongated to filiform, and several-celled. The pathogen was isolated on acidified-PDA (2.5 ml 85% lactic acid per liter of nutrient medium) and incubated at 23°C for 7 days. The pathogen was identified as Septoria pyricola Desm. based on morphological characteristics. Koch's postulates were completed in the laboratory by placing a 40-μl drop of suspension (4 × 105 conidia ml−1 of water) on a wounded area of healthy fruits of cv. Kontoula. Fruits were surface sterilized with dipping in 0.1% chlorine solution, allowed to dry in a laminar flow hood. There were 15 inoculated and 15 control fruits (similarly inoculated with sterile distilled water) in a randomized design. Fruits were covered with perforated polythene bags to maintain a high humidity necessary for infection and these bags were removed 48 h after inoculation and maintained at room temperature (23 ± 2°C). Lesion development was recorded daily for each fruit. Koch's postulates were satisfied after re-isolating the fungus from inoculated fruit that developed symptoms similar to those observed on fruits collected from fields. Symptoms of this disease were found in all pear orchards cultivating the cv. Kontoula located in Tyrnavos (a municipality in the Prefecture of Larissa). Symptoms of septoria leaf spot were also observed in the above pear orchards. In contrast, no symptom of septoria fruit spot and septoria leaf spot was observed in apple orchards of the above regions. To our knowledge, this is the first report of the occurrence of S. pyricola as causal agent of fruit spot of pears in Greece. Fruit spotting is relatively uncommon; nevertheless, Sivanesan (3) gives two reports of conidia infecting pear fruits from Italy and South Africa (1,2).

References: (1) G. Florenzano. Int. Bull. Plant Prot. 20:17, 1946. (2) A. J. Louw. Farming in South Africa 23:737, 1948. (3) A. Sivanesan. IMI Descriptions of Fungi and Bacteria, vol. 99, sheet 989. CABI, Wallingford, UK, 1990.
Identification, quantification and subtyping of Gardnerella vaginalis in noncultured clinical vaginal samples by quantitative PCR
Authors: Balashov Sergey V. , Mordechai Eli , Adelson Martin E. , Gygax Scott E.
Published: November 2013

Gardnerella vaginalis is an important component of the human vaginal microflora. It is proposed to play a key role in the pathogenesis of bacterial vaginosis (BV), the most common vaginal condition. Here we describe the development, validation and comparative analysis of a novel molecular approach capable of G. vaginalis identification, quantification and subtyping in noncultured vaginal specimens. Using two quantitative PCR (qPCR) assays, we analysed G. vaginalis bacterial loads and clade distribution in 60 clinical vaginal-swab samples. A very high pathogen prevalence was revealed by species-specific qPCR not only among BV patients (100 %), but also in healthy women (97 %), although the G. vaginalis concentration was significantly lower in non-BV samples. G. vaginalis clades identified in vaginal specimens by subtyping multiplex qPCR, which targets four clade-specific genetic markers, had frequencies of 53 % for clade 1, 25 % for clade 2, 32 % for clade 3 and 83 % for clade 4. Multiple clades were found in 70 % of samples. Single G. vaginalis clades were represented by clade 1 and clade 4 in 28 % of specimens. A positive association with BV was shown for clade 1 and clade 3, while clade 2 was positively associated with intermediate vaginal microflora, but not with BV. Clade 4 demonstrated no correlation with the disorder. The presence of multiple clades had a high positive association with BV, whereas G. vaginalis identified as a single clade was negatively linked with the condition. Polyclonal G. vaginalis infection may be a risk factor for BV.
Discovery of recurrent structural variants in nasopharyngeal carcinoma
Authors: Valouev Anton , Weng Ziming , Sweeney Robert T. , Varma Sushama , Le Quynh-Thu , Kong Christina , Sidow Arend , West Robert B.
Published: November 2013

We present the discovery of genes recurrently involved in structural variation in nasopharyngeal carcinoma (NPC) and the identification of a novel type of somatic structural variant. We identified the variants with high complexity mate-pair libraries and a novel computational algorithm specifically designed for tumor-normal comparisons, SMASH. SMASH combines signals from split reads and mate-pair discordance to detect somatic structural variants. We demonstrate a >90% validation rate and a breakpoint reconstruction accuracy of 3 bp by Sanger sequencing. Our approach identified three in-frame gene fusions (YAP1-MAML2,PTPLB-RSRC1, andSP3-PTK2) that had strong levels of expression in corresponding NPC tissues. We found two cases of a novel type of structural variant, which we call “coupled inversion,” one of which produced theYAP1-MAML2fusion. To investigate whether the identified fusion genes are recurrent, we performed fluorescent in situ hybridization (FISH) to screen 196 independent NPC cases. We observed recurrent rearrangements ofMAML2(three cases),PTK2(six cases), andSP3(two cases), corresponding to a combined rate of structural variation recurrence of 6% among tested NPC tissues.