bluuebunny/crossref_metadata_2025 huggingface dataset:
Modeling laser-induced periodic surface structures: Finite-difference time-domain feedback simulations
Authors: Skolski J. Z. P. , Römer G. R. B. E. , Vincenc Obona J. , Huis in 't Veld A. J.
Published: March 2014

A model predicting the formation of laser-induced periodic surface structures (LIPSSs) is presented. That is, the finite-difference time domain method is used to study the interaction of electromagnetic fields with rough surfaces. In this approach, the rough surface is modified by “ablation after each laser pulse,” according to the absorbed energy profile, in order to account for inter-pulse feedback mechanisms. LIPSSs with a periodicity significantly smaller than the laser wavelength are found to “grow” either parallel or orthogonal to the laser polarization. The change in orientation and periodicity follow from the model. LIPSSs with a periodicity larger than the wavelength of the laser radiation and complex superimposed LIPSS patterns are also predicted by the model.
Damping mechanism of terahertz plasmons in graphene on heavily doped substrate
Authors: Satou A. , Koseki Y. , Ryzhii V. , Vyurkov V. , Otsuji T.
Published: March 2014

Coupling of plasmons in graphene at terahertz frequencies with surface plasmons in a heavily doped substrate is studied theoretically. We reveal that a huge scattering rate may completely damp out the plasmons, so that proper choices of material and geometrical parameters are essential to suppress the coupling effect and to obtain the minimum damping rate in graphene. Even with the doping concentration 1019−1020 cm-3 and the thickness of the dielectric layer between graphene and the substrate 100 nm, which are typical values in real graphene samples with a heavily doped substrate, the increase in the damping rate is not negligible in comparison with the acoustic-phonon-limited damping rate. Dependence of the damping rate on wavenumber, thicknesses of graphene-to-substrate and gate-to-graphene separation, substrate doping concentration, and dielectric constants of surrounding materials are investigated. It is shown that the damping rate can be much reduced by the gate screening, which suppresses the field spread of the graphene plasmons into the substrate.
Surface potential at a ferroelectric grain due to asymmetric screening of depolarization fields
Authors: Genenko Yuri A. , Hirsch Ofer , Erhart Paul
Published: March 2014

Nonlinear screening of electric depolarization fields, generated by a stripe domain structure in a ferroelectric grain of a polycrystalline material, is studied within a semiconductor model of ferroelectrics. It is shown that the maximum strength of local depolarization fields is rather determined by the electronic band gap than by the spontaneous polarization magnitude. Furthermore, field screening due to electronic band bending and due to presence of intrinsic defects leads to asymmetric space charge regions near the grain boundary, which produce an effective dipole layer at the surface of the grain. This results in the formation of a potential difference between the grain surface and its interior of the order of 1 V, which can be of either sign depending on defect transition levels and concentrations. Exemplary acceptor doping of BaTiO3 is shown to allow tuning of the said surface potential in the region between 0.1 and 1.3 V.
Periodic ordering of clusters and stripes in a two-dimensional lattice model. I. Ground state, mean-field phase diagram and structure of the disordered phases
Authors: Pȩkalski J. , Ciach A. , Almarza N. G.
Published: March 2014

The short-range attraction and long-range repulsion between nanoparticles or macromolecules can lead to spontaneous pattern formation on solid surfaces, fluid interfaces, or membranes. In order to study the self-assembly in such systems we consider a triangular lattice model with nearest-neighbor attraction and third-neighbor repulsion. At the ground state of the model (T = 0) the lattice is empty for small values of the chemical potential μ, and fully occupied for large μ. For intermediate values of μ periodically distributed clusters, bubbles, or stripes appear if the repulsion is sufficiently strong. At the phase coexistences between the vacuum and the ordered cluster phases and between the cluster and the lamellar (stripe) phases the entropy per site does not vanish. As a consequence of this ground state degeneracy, disordered fluid phases consisting of clusters or stripes are stable, and the surface tension vanishes. For T > 0 we construct the phase diagram in the mean-field approximation and calculate the correlation function in the self-consistent Brazovskii-type field theory.
Orthogonally twisted planar concentric split ring resonators towards strong near field coupled terahertz metamaterials
Authors: Chowdhury Dibakar Roy , O'Hara John F. , Taylor Antoinette J. , Azad Abul K.
Published: March 2014

We present strongly coupled planar terahertz metamaterials in which the metamolecule design comprised two concentric split ring resonators (SRRs) with their capacitive gaps oriented orthogonally in order to establish strong near field coupling. Experimental results clearly demonstrate huge splitting in the fundamental inductive-capacitive resonance when the incident terahertz polarization couples to the metamolecule system through the outer SRR. However, the strengths of split resonances are too weak to detect experimentally when the meta-molecule system is excited through the inner SRR. Such strongly coupled metamolecules can enable additional dispersion tuning and polarization control in metamaterials.
Silicene-based DNA nucleobase sensing
Authors: Sadeghi Hatef , Bailey S. , Lambert Colin J.
Published: March 2014

We propose a DNA sequencing scheme based on silicene nanopores. Using first principles theory, we compute the electrical properties of such pores in the absence and presence of nucleobases. Within a two-terminal geometry, we analyze the current-voltage relation in the presence of nucleobases with various orientations. We demonstrate that when nucleobases pass through a pore, even after sampling over many orientations, changes in the electrical properties of the ribbon can be used to discriminate between bases.
Plasticity mechanisms in ultrafine grained freestanding aluminum thin films revealed by in-situ transmission electron microscopy nanomechanical testing
Authors: Idrissi Hosni , Kobler Aaron , Amin-Ahmadi Behnam , Coulombier Michael , Galceran Montserrat , Raskin Jean-Pierre , Godet Stéphane , Kübel Christian , Pardoen Thomas , Schryvers Dominique
Published: March 2014

In-situ bright field transmission electron microscopy (TEM) nanomechanical tensile testing and in-situ automated crystallographic orientation mapping in TEM were combined to unravel the elementary mechanisms controlling the plasticity of ultrafine grained Aluminum freestanding thin films. The characterizations demonstrate that deformation proceeds with a transition from grain rotation to intragranular dislocation glide and starvation plasticity mechanism at about 1% deformation. The grain rotation is not affected by the character of the grain boundaries. No grain growth or twinning is detected.
Axis-switching of a micro-jet
Authors: Cabaleiro Juan Martin , Aider Jean-Luc
Published: March 2014

In this study, it is shown that free microjets can undergo complex transitions similar to large-scale free jets despite relatively low Reynolds numbers. Using an original experimental method allowing for the 3D reconstruction of the instantaneous spatial organization of the microjet, the axis-switching of a micro-jet is observed for the first time. This is the first experimental evidence of such complex phenomena for free micro-jets. Combining these experimental results with Direct Numerical Simulations it is shown that the mechanism responsible for the axis-switching is the deformation of a micro-vortex ring due to induction by the corner vortices, as it occurs in large scale non-circular jets.
Janus particle microshuttle: 1D directional self-propulsion modulated by AC electrical field
Authors: Chen Jiliang , Zhang Hongyan , Zheng Xu , Cui Haihang
Published: March 2014

A catalytic Janus particle is capable of gaining energy from the surrounding fuel solution to drive itself to move continuously, which has an important impact in different fields, especially the field of micro-systems. However, the randomness of self-propulsion at the microscale restricts its use in practice. Achieving a directed self-propelled movement would greatly promote the application of the Janus particle. We proved experimentally that an AC electric field was an effective way to suppress Brownian motion and control the direction of self-propelled movement. The self-propulsion and dielectrophoretic response of a 2μm Janus particle were observed and the related basic data were collected. Interdigital electrodes, 20 μm in width, were energized in pulsed style to modulate the self-propulsion, which resulted in a shuttle-style motion in which a single Janus particle moved to and fro inside the strip electrode. The change of direction depends on its unique position: the catalyst side is always pointed outward and the orientation angle relative to the electrode is about 60°. Numerical simulation also proved that this position is reasonable. The present study could be beneficial with regard to self-propulsion and AC electrokinetics of the Janus particle.
Fabrication of polyimide sacrificial layers with inclined sidewalls based on reactive ion etching
Authors: Chen Yuanjing , Mao Haiyang , Tan Qiulin , Xue Chenyang , Ou Wen , Liu Jin , Chen Dapeng
Published: March 2014

Polyimide is used as a sacrificial material because of its low stress, its removable ability and its compatibility with standard micromachining processes. In this work, polyimide structures with inclined sidewalls are fabricated with a reactive ion etching process, where SiO2 is used as the hard-mask material. The structures can be further used as sacrificial layers in micro-electro-mechanical systems infrared (IR) sensors to support IR absorbers, to realize the thermal connections between the absorbers and the thermopiles, and to scale down the size of the sensors. As a result, IR sensors with low-residual-stress absorption, high structural stability, low heat loss and small dimensions can be achieved.
Characteristics of radio-frequency atmospheric pressure dielectric-barrier discharge with dielectric electrodes
Authors: Hussain S. , Qazi H. I. A. , Badar M. A.
Published: March 2014

An experimental investigation to characterize the properties and highlight the benefits of atmospheric pressure radio-frequency dielectric-barrier discharge (rf DBD) with dielectric electrodes fabricated by anodizing aluminium substrate is presented. The current-voltage characteristics and millisecond images are used to distinguish the α and γ modes. This atmospheric rf DBD is observed to retain the discharge volume without constriction in γ mode. Optical emission spectroscopy demonstrates that the large discharge current leads to more abundant reactive species in this plasma source.
Inductance due to spin current
Authors: Chen Wei
Published: March 2014

The inductance of spintronic devices that transport charge neutral spin currents is discussed. It is known that in a media that contains charge neutral spins, a time-varying electric field induces a spin current. We show that since the spin current itself produces an electric field, this implies existence of inductance and electromotive force when the spin current changes with time. The relations between the electromotive force and the corresponding flux, which is a vector calculated by the cross product of electric field and the trajectory of the device, are clarified. The relativistic origin generally renders an extremely small inductance, which indicates the advantage of spin current in building low inductance devices. The same argument also explains the inductance due to electric dipole current and applies to physical dipoles consist of polarized bound charges.
Government policy change and evolution of regional innovation systems in China: evidence from strategic emerging industries in Shenzhen
Authors: Yang Chun
Published: March 2014

The mid-2000s witnessed a paradigm shift of technological innovation in China, characterized by a policy change from expectation of technological spillover from transnational corporations to an emphasis on indigenous innovation and domestic firms. Notably, seven strategic emerging industries (SEIs) have been designated by the central government to foster technological upgrading in the wake of the 2008 global financial crisis. While increasing attention has been paid to these policy changes, the practice of developing SEIs and subsequent impacts on innovation dynamisms remain understudied. Drawing upon an institutional evolution perspective on the regional innovation systems (RIS) approach, I examine how foreign-invested and domestic firms have adjusted their innovation strategies in the changing institutional environment, through examining the light-emitting diode (LED) industry, one of the state-designated SEIs in Shenzhen. This study was conducted primarily from on-site field investigation, firm-level surveys, and in-depth interviews during the period of 2008 and early 2013. It sheds light on the adaptation of the local state, reflected by the Shenzhen municipal government's recent abolishment of the LED industry development plan after four years of implementation. I urge more studies to examine other SEIs designated by various governments in different cities and regions in China to better understand policy change and effects on national innovation systems and RISs in the contemporary global economy.
Detecting burrows and trapping for mulgaras (Dasycercus cristicauda and D. blythi) can be difficult
Authors: Thompson Graham G. , Thompson Scott A.
Published: March 2014

Mulgaras (Dasycercus cristicauda and D. blythi) are protected by state and commonwealth environmental statutes; as a consequence, land developers and mining companies have an obligation to avoid, mitigate or minimise impacts on these species when they occur in their area of operation (i.e. to implement trapping and translocation programs). Here we assess the effectiveness of searching and trapping programs for mulgaras in four case studies and provide management recommendations to improve outcomes for these species.
GRIP1 interlinks N-cadherin and AMPA receptors at vesicles to promote combined cargo transport into dendrites
Authors: Heisler Frank F. , Lee Han Kyu , Gromova Kira V. , Pechmann Yvonne , Schurek Beate , Ruschkies Laura , Schroeder Markus , Schweizer Michaela , Kneussel Matthias
Published: March 2014

Significance

Synapses form and change in response to neuronal activity, and they dynamically exchange transmembrane proteins over time. Most synaptic proteins are synthesized in the cell body and undergo long-distance vesicular transport powered by molecular motors along microtubules. Here we show that two synaptic key proteins (GluA2 and N-cadherin) are simultaneously delivered within distinct transport vesicles through motor proteins. Our data suggest that multidomain cargo adaptors tether synaptic proteins destined for the same subcellular compartment. We propose that vesicular presorting is an alternative mechanism to efficiently supply synapses.
Field-evolved resistance by western corn rootworm to multipleBacillus thuringiensistoxins in transgenic maize
Authors: Gassmann Aaron J. , Petzold-Maxwell Jennifer L. , Clifton Eric H. , Dunbar Mike W. , Hoffmann Amanda M. , Ingber David A. , Keweshan Ryan S.
Published: March 2014

Significance

Crops genetically engineered to produce insecticidal toxins derived from the bacteriumBacillus thuringiensis(Bt) kill pest insects and reduce the use of conventional insecticides. However, the evolution of Bt resistance can diminishes these benefits. The western corn rootworm is a serious pest of maize and is managed with Bt maize. Beginning in 2009, western corn rootworm with resistance to maize producing the Bt toxin Cry3Bb1 imposed severe injury to Cry3Bb1 maize in Iowa. We show that cross-resistance exists between Cry3Bb1 maize and mCry3A maize and is associated with severe injury to Bt maize in farmers’ fields. These results illustrate that Bt crops producing less than a high dose of toxin against target pests may select for resistance rapidly; consequently, current approaches for managing Bt resistance should be reexamined.
Attributing awareness to oneself and to others
Authors: Kelly Yin T. , Webb Taylor W. , Meier Jeffrey D. , Arcaro Michael J. , Graziano Michael S. A.
Published: March 2014

Significance

What is the relationship between your own private awareness of events and the awareness that you intuitively attribute to the people around you? In this study, a region of the human cerebral cortex was active when people attributed sensory awareness to someone else. Furthermore, when that region of cortex was temporarily disrupted, the person’s own sensory awareness was disrupted. The findings suggest a fundamental connection between private awareness and social cognition.
Cellular, Pharmacological, and Biophysical Evaluation of Explanted Lungs from a Patient with Sickle Cell Disease and Severe Pulmonary Arterial Hypertension
Authors: Rogers Natasha M. , Yao Mingyi , Sembrat John , George M. Patricia , Knupp Heather , Ross Mark , Sharifi‐Sanjani Maryam , Milosevic Jadranka , Croix Claudette St. , Rajkumar Revathi , Frid Maria C. , Hunter Kendall S. , Mazzaro Luciano , Novelli Enrico M. , Stenmark Kurt R. , Gladwin Mark T. , Ahmad Ferhaan , Champion Hunter C. , Isenberg Jeffrey S.
Published: March 2014

Pulmonary hypertension is recognized as a leading cause of morbidity and mortality in patients with sickle cell disease (SCD). We now report benchtop phenotyping from the explanted lungs of the first successful lung transplant in SCD. Pulmonary artery smooth muscle cells (PASMCs) cultured from the explanted lungs were analyzed for proliferate capacity, superoxide (O2•–) production, and changes in key pulmonary arterial hypertension (PAH)–associated molecules and compared with non‐PAH PASMCs. Upregulation of several pathologic processes persisted in culture in SCD lung PASMCs in spite of cell passage. SCD lung PASMCs showed growth factor– and serum‐independent proliferation, upregulation of matrix genes, and increased O2•– production compared with control cells. Histologic analysis of SCD‐associated PAH arteries demonstrated increased and ectopically located extracellular matrix deposition and degradation of elastin fibers. Biomechanical analysis of these vessels confirmed increased arterial stiffening and loss of elasticity. Functional analysis of distal fifth‐order pulmonary arteries from these lungs demonstrated increased vasoconstriction to an α1‐adrenergic receptor agonist and concurrent loss of both endothelial‐dependent and endothelial‐independent vasodilation compared with normal pulmonary arteries. This is the first study to evaluate the molecular, cellular, functional, and mechanical changes in end‐stage SCD‐associated PAH.
Clinical Characterization and Survival of Patients with Borderline Elevation in Pulmonary Artery Pressure
Authors: Heresi Gustavo A. , Minai Omar A. , Tonelli Adriano R. , Hammel Jeffrey P. , Farha Samar , Parambil Joseph G. , Dweik Raed A.
Published: March 2014

Normal resting mean pulmonary artery pressure (PAP) is 8–20 mmHg. Pulmonary hypertension is defined as mean PAP of ≥25 mmHg. Borderline PAP levels of 21–24 mmHg are of unclear significance. We sought to determine the clinical characteristics and survival of subjects with mean PAP of 21–24 mmHg. We examined 1,491 patients enrolled in the Cleveland Clinic Pulmonary Hypertension Registry between February 1990 and May 2012 with baseline right heart catheterization. The relationship between PAP and all‐cause mortality was assessed by Cox models and a tree‐based analysis. Sixty‐three patients had borderline PAP (underlying conditions: 12 left heart disease, 20 respiratory disease, 17 connective‐tissue disease, 4 others, and 10 none). We then compared 3 groups: borderline PAP without heart or lung disease (n = 31), normal PAP without heart or lung disease (n = 51), and category 1 pulmonary arterial hypertension (PAH; n = 387). Borderline‐PAP patients had levels of hemodynamic and functional compromise between those for normal‐PAP patients and those for patients with PAH. Borderline PAP was associated with increased mortality compared to normal PAP (hazard ratio: 4.03 [95% confidence interval: 0.78–20.80], P = 0.099). A tree‐based analysis demonstrated almost identical cut points in mean PAP (≤20, 21–26, and ≥27 mmHg) associated with differential survival (P < 0.001). Connective‐tissue disease and an elevated transpulmonary gradient were predictors of worse survival in the borderline‐PAP population. Borderline PAP elevation is associated with decreased survival, particularly in the context of connective‐tissue disease and an elevated transpulmonary gradient.
Acute Respiratory Failure Mimicking Acute Respiratory Distress Syndrome Due to Parenchymal Infiltration by Metastatic Melanoma
Authors: Kapnadak Siddhartha G. , Abt David , Risbano Michael G.
Published: March 2014

Malignant melanoma is the most aggressive form of skin cancer and carries a predisposition for metastasis to many different organs. Pulmonary dissemination is common, most often presenting as multiple discrete pulmonary nodules. While a variety of other intrathoracic patterns can occur, diffuse parenchymal infiltration causing acute respiratory failure is an extremely rare manifestation of metastatic disease. We present a case of an otherwise healthy man who developed rapidly progressive respiratory failure mimicking acute respiratory distress syndrome due to melanomatous infiltration of the lung parenchyma and airways.
A condensed proof of the differential Grothendieck–Riemann–Roch theorem
Authors: Ho Man-Ho
Published: March 2014

We give a direct proof that the Freed–Lott differential analytic index is well defined and a condensed proof of the differential Grothendieck–Riemann–Roch theorem. As a byproduct we also obtain a direct proof that the

R

/

Z

\mathbb {R}/\mathbb {Z}

analytic index is well defined and a condensed proof of the

R

/

Z

\mathbb {R}/\mathbb {Z}

Grothendieck–Riemann–Roch theorem.
Making use of Johan Hjort's “unknown” legacy: reconstruction of a 150-year coastal time-series on northeast Arctic cod (Gadus morhua) liver data reveals long-term trends in energy allocation patterns
Authors: Kjesbu Olav Sigurd , Opdal Anders Frugård , Korsbrekke Knut , Devine Jennifer A. , Skjæraasen Jon Egil
Published: March 2014

Hidden within the seminal 1914 publication by Johan Hjort, we find what is probably one of the first comprehensive teleost time-series ever published. The series is liver size and fat content of northeast Arctic (NEA) cod measured during the traditional winter fishery in Lofoten, Northern Norway, in 1880–1912 and 1883–1913, respectively. The data were collected well before the advent of the great industrialized fisheries in the 1930s. The raw data used by Hjort originate from annual reports of the Lofoten fishery, initiated by Member of Parliament and pioneer fishery inspector of Northern Norway, Ketil Motzfeldt, in 1859. Based on these reports and following various calibration exercises, we present robust estimates of the hepatosomatic index (HSI) from 1859 to 2012 (except 1863), i.e. over 153 years—extending Hjort's analysis both backwards (1859–1879) and forwards (1913–present). This series of bulk HSI contained five major periods: 1859–1880, 1881–1919, 1920–1974, 1975–2003, and 2004–2012; the highest HSI was recorded 1920–1974, whereas the lowest was from the most recent period. Despite variability, total length was a significant predictor of HSI, 1932–2012. A weak but significant relationship existed with both total-stock biomass and ocean temperature, as well as with the North Atlantic Oscillation winter index under a 1-year lag. The present exceptionally long HSI series will give an excellent opportunity for further research on the “quality of the cod” in a historic perspective.
Role of B-1 cells in the immune response against an antigen encapsulated into phosphatidylcholine-containing liposomes
Authors: Cruz-Leal Yoelys , Machado Yoan , López-Requena Alejandro , Canet Liem , Laborde Rady , Alvares Anuska Marcelino , Lucatelli Laurindo María F. , Santo Tomas Julio F. , Alonso María E. , Álvarez Carlos , Mortara Renato A. , Popi Ana F. , Mariano Mario , Pérez Rolando , Lanio María E.
Published: March 2014

B-1 lymphocytes comprise a unique subset of B cells that differ phenotypically, ontogenetically and functionally from conventional B-2 cells. A frequent specificity of the antibody repertoire of peritoneal B-1 cells is phosphatidylcholine. Liposomes containing phosphatidylcholine have been studied as adjuvants and their interaction with dendritic cells and macrophages has been demonstrated. However, the role of B-1 cells in the adjuvanticity of liposomes composed of phosphatidylcholine has not been explored. In the present work, we studied the contribution of B-1 cells to the humoral response against ovalbumin (OVA) encapsulated into dipalmitoylphosphatidylcholine (DPPC) and cholesterol-containing liposomes. BALB/X-linked immunodeficient (xid) mice, which are deficient in B-1 cells, showed quantitative and qualitative differences in the anti-OVA antibody response compared with wild-type animals after immunization with these liposomes. The OVA-specific immune response was significantly increased in the BALB/xid mice when reconstituted with B-1 cells from naive BALB/c mice. Our results indicate the internalization of DPPC-containing liposomes by these cells and their migration from the peritoneal cavity to the spleen. Phosphatidylcholine significantly contributed to the immunogenicity of liposomes, as DPPC-containing liposomes more effectively stimulated the anti-OVA response compared with vesicles composed of dipalmitoylphosphatidylglycerol. In conclusion, we present evidence for a cognate interaction between B-1 cells and phosphatidylcholine liposomes, modulating the immune response to encapsulated antigens. This provides a novel targeting approach to assess the role of B-1 cells in humoral immunity.
A Potent Antimicrobial Peptide Derived from the Protein LsGRP1 of Lilium
Authors: Lin Chia-Hua , Chang Min-Wei , Chen Chao-Ying
Published: March 2014

LsGRP1 is a defense-related gene differentially expressed in lily leaves in response to pathogen attack. The difficulty in the expression of LsGRP1 in Escherichia coli suggested the presence of antimicrobial activity in LsGRP1. To evaluate the antimicrobial trait of LsGRP1, three LsGRP1-derived peptides were chemically synthesized; namely LsGRP1N (N-terminal region without the signal peptide), LsGRP1G (glycine-rich region), and LsGRP1C (C-terminal cysteine-rich region). LsGRP1C was proposed to be a potential antimicrobial agent according to its broad-spectrum and effective antimicrobial activity. LsGRP1C displayed inhibition effects on bacterial and fungal growth, possibly by altering the integrity of the cell membrane, as indicated by scanning electron microscopy and SYTOX Green staining assays. Additionally, LsGRP1C induced programmed cell death-like phenomenon in the tested fungal species as indicated by 2′,7′-dichlorodihydrofluorescein diacetate and 4′,6′-diamidino-2-phenylindole assays. Further immunofluorescence staining showed that LsGRP1C was located at the fungal cell surface. According to these observations, we concluded that LsGRP1C originated from the plant defense-related protein LsGRP1 would play a role as an antimicrobial peptide and have a potential for practical use.
A note on the genus name Rhodococcus Zopf 1891 and its homonyms
Authors: Tindall B. J.
Published: March 2014

The genus nameRhodococcusZopf 1891 was created to accommodate two species of red pigment (lipochrome)-producing bacteria. However, the genus nameRhodococcusHansgirg 1884 had already been applied to an algal taxon. The wording of the 1975 and subsequent revisions of the Code dealing with bacteria/prokaryotes is such that the nameRhodococcusZopf 1891 isillegitimate, despite the fact that it was included on the Approved Lists of Bacterial Names. Further research using databases of scientific names of organisms indicate the status of the nameRhodococcusZopf 1891 needs to be carefully considered.
What ever happened to Thermomicrobium fosteri Phillips and Perry 1976?
Authors: Tindall B. J.
Published: March 2014

Thermomicrobium fosteri

Phillips and Perry 1976 was included on the Approved List of Bacterial Names with the type strain designated ATCC 29033. However, this strain is no longer directly listed in the ATCC online catalogue and the only reference to ATCC 29033 is under ATCC 35268, a strain of

Thermoleophilum minutum

Zarilla and Perry 1986. There currently appears to be no formal documentation in the pages of the International Journal of Systematic and Evolutionary Microbiology with regards either the current status of the name

Thermomicrobium fosteri

Phillips and Perry 1976 or its type strain ATCC 29033.
Pigeon circoviruses display patterns of recombination, genomic secondary structure and selection similar to those of beak and feather disease viruses
Authors: Stenzel Tomasz , Piasecki Tomasz , Chrząstek Klaudia , Julian Laurel , Muhire Brejnev M. , Golden Michael , Martin Darren P. , Varsani Arvind
Published: March 2014

Pigeon circovirus (PiCV) has a ~2 kb genome circular ssDNA genome. All but one of the known PiCV isolates have been found infecting pigeons in various parts of the world. In this study, we screened 324 swab and tissue samples from Polish pigeons and recovered 30 complete genomes, 16 of which came from birds displaying no obvious pathology. Together with 17 other publicly available PiCV complete genomes sampled throughout the Northern Hemisphere and Australia, we find that PiCV displays a similar degree of genetic diversity to that of the related psittacine-infecting circovirus species, beak and feather disease virus (BFDV). We show that, as is the case with its pathology and epidemiology, PiCV also displays patterns of recombination, genomic secondary structure and natural selection that are generally very similar to those of BFDV. It is likely that breeding facilities play a significant role in the emergence of new recombinant PiCV variants and given that ~50 % of the domestic pigeon population is infected subclinically, all pigeon breeding stocks should be screened routinely for this virus.
Horizontal Transfers and Gene Losses in the phospholipid pathway ofBartonellareveal clues about early ecological niches
Authors: Zhu Qiyun , Kosoy Michael , Olival Kevin J. , Dittmar Katharina
Published: March 2014

Bartonellae are mammalian pathogens vectored by blood-feeding arthropods. Although of increasing medical importance, little is known about their ecological past, and host associations are underexplored. Previous studies suggest an influence of horizontal gene transfers in ecological niche colonization by acquisition of host pathogenicity genes. We here expand these analyses to metabolic pathways of 28Bartonellagenomes, and experimentally explore the distribution of bartonellae in 21 species of blood-feeding arthropods. Across genomes, repeated gene losses and horizontal gains in the phospholipid pathway were found. The evolutionary timing of these patterns suggests functional consequences likely leading to an early intracellular lifestyle for stem bartonellae. Comparative phylogenomic analyses discover three independent lineage-specific reacquisitions of a core metabolic gene - NAD(P)H-dependent glycerol-3-phosphate dehydrogenase (gpsA) - from Gammaproteobacteria and Epsilonproteobacteria. Transferred genes are significantly closely related to invertebrateArsenophonus-, andSerratia-like endosymbionts, and mammalianHelicobacter-like pathogens, supporting a cellular association with arthropods and mammals at the base of extant bartonellae. Our studies suggest that the horizontal re-aquisitions had a key impact on bartonellae lineage specific ecological and functional evolution.
The miR-424(322)/503 cluster orchestrates remodeling of the epithelium in the involuting mammary gland
Authors: Llobet-Navas David , Rodríguez-Barrueco Ruth , Castro Verónica , Ugalde Alejandro P. , Sumazin Pavel , Jacob-Sendler Damian , Demircan Berna , Castillo-Martín Mireia , Putcha Preeti , Marshall Netonia , Villagrasa Patricia , Chan Joseph , Sanchez-Garcia Félix , Pe’er Dana , Rabadán Raul , Iavarone Antonio , Cordón-Cardó Carlos , Califano Andrea , López-Otín Carlos , Ezhkova Elena , Silva Jose M.
Published: March 2014

The mammary gland is a very dynamic organ that undergoes continuous remodeling. The critical regulators of this process are not fully understood. Here we identify the microRNA cluster miR-424(322)/503 as an important regulator of epithelial involution after pregnancy. Through the generation of a knockout mouse model, we found that regression of the secretory acini of the mammary gland was compromised in the absence of miR-424(322)/503. Mechanistically, we show that miR-424(322)/503 orchestrates cell life and death decisions by targeting BCL-2 and IGF1R (insulin growth factor-1 receptor). Furthermore, we demonstrate that the expression of this microRNA cluster is regulated by TGF-β, a well-characterized regulator of mammary involution. Overall, our data suggest a model in which activation of the TGF-β pathway after weaning induces the transcription of miR-424(322)/503, which in turn down-regulates the expression of key genes. Here, we unveil a previously unknown, multilayered regulation of epithelial tissue remodeling coordinated by the microRNA cluster miR-424(322)/503.
Communication and self‐esteem in adults with Down syndrome
Authors: Jackson Claire , Cavenagh Penny , Clibbens John
Published: March 2014

Background

It is estimated that around 50–90% of people with learning disabilities experience difficulties in communicating. Previous research has linked communication difficulties and self‐esteem in other populations, yet this relationship has not previously been investigated for people with Down syndrome.

Aims

To explore the relationship between communication and self‐esteem in adults with Down syndrome. This research also aimed to offer an empowering and inclusive opportunity for adults with learning disabilities to be involved in research.

Methods & Procedures

Recruitment took place via a charity established for people with Down syndrome. Twelve adults with Down syndrome and an adult they nominated were approached. A qualitative methodology was selected to explore communication and self‐esteem. A thematic analysis focused on the qualitative data collected via semi‐structured interviews.

Outcomes & Results

Major themes within the data revealed that a relationship between communication and self‐esteem may exist for adults with Down syndrome.

Conclusions & Implication

This study demonstrated that people with Down syndrome may experience low self‐esteem that may be linked to communication. The clinical implications of this are considered and areas for future research are identified.
Risk factors for spontaneous and provider‐initiated preterm delivery in high and low Human Development Index countries: a secondary analysis of the World Health Organization Multicountry Survey on Maternal and Newborn Health
Authors: Morisaki N , Togoobaatar G , Vogel JP , Souza JP , Rowland Hogue CJ , Jayaratne K , Ota E , Mori R ,   on behalf of the WHO Multicountry Survey on Maternal and Newborn Health Research Network
Published: March 2014

Objective

To evaluate how the effect of maternal complications on preterm birth varies between spontaneous and provider‐initiated births, as well as among different countries.

Design

Secondary analysis of a cross‐sectional study.

Setting

Twenty‐nine countries participating in the World Health Organization Multicountry Survey on Maternal and Newborn Health.

Population

299 878 singleton deliveries of live neonates or fresh stillbirths.

Methods

Countries were categorised into very high, high, medium and low developed countries using the Human Development Index (HDI) of 2012 by the World Bank. We described the prevalence and risk of maternal complications, their effect on outcomes and their variability by country development.

Main outcome measures

Preterm birth, fresh stillbirth and early neonatal death.

Results

The proportion of provider‐initiated births among preterm deliveries increased with development: 19% in low to 40% in very high HDI countries. Among preterm deliveries, the socially disadvantaged were less likely, and the medically high risk were more likely, to have a provider‐initiated delivery. The effects of anaemia [adjusted odds ratio (AOR), 2.03; 95% confidence interval (CI), 1.84; 2.25], chronic hypertension (AOR, 2.28; 95% CI, 1.94; 2.68) and pre‐eclampsia/eclampsia (AOR, 5.03; 95% CI, 4.72; 5.37) on preterm birth were similar among all four HDI subgroups.

Conclusions

The provision of adequate obstetric care, including optimal timing for delivery in high‐risk pregnancies, especially to the socially disadvantaged, could improve pregnancy outcomes. Avoiding preterm delivery in women when maternal complications, such as anaemia or hypertensive disorders, are present is important for countries at various stages of development, but may be more challenging to achieve.
Mode and timing of twin delivery and perinatal outcomes in low‐ and middle‐income countries: a secondary analysis of the WHO Multicountry Survey on Maternal and Newborn Health
Authors: Ganchimeg T , Morisaki N , Vogel JP , Cecatti JG , Barrett J , Jayaratne K , Mittal S , Ortiz‐Panozo E , Souza JP , Crowther C , Ota E , Mori R ,   on behalf of the WHO Multicountry Survey on Maternal and Newborn Health Research Network
Published: March 2014

Objective

To describe the mode and timing of delivery of twin pregnancies at ≥34 weeks of gestation and their association with perinatal outcomes.

Design

Secondary analysis of a cross‐sectional study.

Population

Twin deliveries at ≥34 weeks of gestation from 21 low‐ and middle‐income countries participating in the WHO Multicountry Survey on Maternal and Newborn Health.

Methods

Descriptive analysis and effect estimates using multilevel logistic regression.

Main outcome measures

Stillbirth, perinatal mortality, and neonatal near miss (use of selected life saving interventions at birth).

Results

The average length of gestation at delivery was 37.6 weeks. Of all twin deliveries, 16.8 and 17.6% were delivered by caesarean section before and after the onset of labour, respectively. Prelabour caesarean delivery was associated with older maternal age, higher institutional capacity and wealth of the country. Compared with spontaneous vaginal delivery, lower risks of neonatal near miss (adjusted odds ratio, aOR, 0.63; 95% confidence interval, 95% CI, 0.44–0.94) were found among prelabour caesarean deliveries. A lower risk of early neonatal mortality (aOR 0.12; 95% CI 0.02–0.56) was also observed among prelabour caesarean deliveries with nonvertex presentation of the first twin. The week of gestation with the lowest rate of prospective fetal death varied by fetal presentation: 37 weeks for vertex–vertex; 39 weeks for vertex–nonvertex; and 38 weeks for a nonvertex first twin.

Conclusions

The prelabour caesarean delivery rate among twins varied largely between countries, probably as a result of overuse of caesarean delivery in wealthier countries and limited access to caesarean delivery in low‐income countries. Prelabour delivery may be beneficial when the first twin is nonvertex. International guidelines for optimal twin delivery methods are needed.
Overview of abortion cases with severe maternal outcomes in the WHO Multicountry Survey on Maternal and Newborn Health: a descriptive analysis
Authors: Dragoman M , Sheldon WR , Qureshi Z , Blum J , Winikoff B , Ganatra B ,   on behalf of the WHO Multicountry Survey on Maternal Newborn Health Research Network
Published: March 2014

Objective

To summarise individual and institutional characteristics of abortion‐related severe maternal outcomes reported at health facilities.

Design

Secondary analysis of data from the WHO Multicountry Survey on Maternal and Newborn Health.

Setting

85 health facilities in 23 countries.

Sample

322 women with abortion‐related severe maternal outcomes.

Methods

Frequency distributions and comparisons of differences in characteristics between cases of maternal near miss and death using Fisher's exact tests of association.

Main outcome measures

Individual and institutional characteristics and frequencies of potentially life‐threatening conditions, and interventions provided to women with severe maternal outcomes, maternal near miss, and maternal death.

Results

Most women with abortion‐related severe maternal outcomes (SMOs) were 20–34 years old (65.2%), married or cohabitating (92.3%), parous (84.2%), and presented with abortions resulting from pregnancies at less than 14 weeks of gestation (67.1%). The women who died were younger, more frequently without a partner, and had abortions at ≥14 weeks of gestation, compared with women with maternal near miss (MNM). Curettage was the most common mode of uterine evacuation. The provision of blood products and therapeutic antibiotics were the most common other interventions recorded for all women with abortion‐related SMOs; those who died more frequently had antibiotics, laparotomy, and hysterectomy, compared with women with MNM. Although haemorrhage was the most common cause of abortion‐related SMO, infection (alone and in combination with haemorrhage) was the most common cause of death.

Conclusion

This analysis affirms a number of previously observed characteristics of women with abortion‐related severe morbidity and mortality, despite the fact that facility‐based data on abortion‐related SMO suffers a number of limitations.
A reliable DNA barcode reference library for the identification of the North European shelf fish fauna
Authors: Knebelsberger Thomas , Landi Monica , Neumann Hermann , Kloppmann Matthias , Sell Anne F. , Campbell Patrick D. , Laakmann Silke , Raupach Michael J. , Carvalho Gary R. , Costa Filipe O.
Published: March 2014

Valid fish species identification is an essential step both for fundamental science and fisheries management. The traditional identification is mainly based on external morphological diagnostic characters, leading to inconsistent results in many cases. Here, we provide a sequence reference library based on mitochondrial cytochromecoxidase subunit I (COI) for a valid identification of 93 North Atlantic fish species originating from the North Sea and adjacent waters, including many commercially exploited species. Neighbour‐joining analysis based on K2P genetic distances formed nonoverlapping clusters for all species with a ≥99% bootstrap support each. Identification was successful for 100% of the species as the minimum genetic distance to the nearest neighbour always exceeded the maximum intraspecific distance. A barcoding gap was apparent for the whole data set. Within‐species distances ranged from 0 to 2.35%, while interspecific distances varied between 3.15 and 28.09%. Distances between congeners were on average 51‐fold higher than those within species. The validation of the sequence library by applyingBOLDs barcode index number (BIN) analysis tool and a ranking system demonstrated high taxonomic reliability of theDNAbarcodes for 85% of the investigated fish species. Thus, the sequence library presented here can be confidently used as a benchmark for identification of at least two‐thirds of the typical fish species recorded for the North Sea.
Discovery of a novel long terminal repeat (LTR2i_SS) in Sus Scrofa
Authors: Lim Sim L. , Kortschak R. Daniel , Adelson David L.
Published: March 2014

Long terminal repeat (LTR) retrotransposons are transposable elements flanked by 5′/3′ LTRs. They have a structure similar to endogenous retroviruses, but they lack the envelope (env) gene making them non‐infectious. Long terminal repeats are motif‐rich sequences and can act as bidirectional promoters or enhancers to regulate or inactivate genes by insertion. In this study, we identified a new chimeric LTR subfamily, LTR2i_SS, in the pig genome. This chimeric LTR family appears to be the ancestral form of the previously described LTR2_SS family. LTR2_SS appears to have deleted ~300 bp of un‐annotated, ancestral sequence from LTR2i_SS. We identified no functional provirus sequences for either of these LTR types. LTR2i_SS sequences have been exapted into the untranslated regions of two protein‐coding gene mRNAs. Both of these genes lie within previously mapped pig quantitative trait loci.
Bounds on causal interactions for binary outcomes
Authors: Sjölander A. , Lee W. , Källberg H. , Pawitan Y.
Published: March 2014

A common goal of epidemiologic research is to study how two exposures interact in causing a binary outcome. Causal interaction is defined as the presence of subjects for which the causal effect of one exposure depends on the level of the other exposure. For binary exposures, it has previously been shown that the presence of causal interaction is testable through additive statistical interaction. However, it has also been shown that the magnitude of causal interaction, defined as the proportion of subjects for which there is causal interaction, is generally not identifiable. In this article, we derive bounds on causal interactions, which are applicable to binary outcomes and categorical exposures with arbitrarily many levels. These bounds can be used to assess the magnitude of causal interaction, and serve as an important complement to the statistical test that is frequently employed. The bounds are derived both without and with an assumption about monotone exposure effects. We present an application of the bounds to a study of gene–gene interaction in rheumatoid arthritis.
Meta‐analysis of methylprednisolone pulse therapy for Graves' ophthalmopathy
Authors: Gao Guohong , Dai Jinhui , Qian Yifeng , Ma Fei
Published: March 2014

A meta‐analysis was performed to evaluate the efficacy of methylprednisolone pulse therapy for Graves' ophthalmopathy. Eight studies involving 376 patients were included. A higher effective rate was found for patients treated with intravenous glucocorticoids (IVGC) over oral glucocorticoids (OGC) (risk ratio [RR] = 1.48; 95% confidence interval [CI] = 1.18−1.86). The combined IVGC and orbital radiotherapy (OR) was markedly more effective than OGC+OR (RR = 1.40; 95% CI = 1.11−1.77). IVGC resulted in an obvious reduction of clinical activity score (CAS) compared with OGC, with a weighted mean difference (WMD) of 0.86 (95% CI = 0.53−1.18). The WMD for the reduction of the CAS between IVGC+OR and OGC+OR was 0.66 (95% CI = 0.30−1.02). IVGC is an effective treatment and cause fewer adverse events. Limiting the total cumulative dose of methylprednisolone, careful patient selection and monitoring the condition of patients during treatment are necessary.