bluuebunny/crossref_metadata_2025 huggingface dataset:
901 nm Lithographic vertical‐cavity surface‐emitting laser with stable single‐lobed beam pattern
Authors: Li M. , Yang X. , Zhang Y. , Zhao G. , Beadsworth J. , Eifert L. , Tucker F. , Deppe D.G.
Published: October 2015

Data are presented on 901 nm lithographic vertical‐cavity surface‐emitting lasers (VCSELs) demonstrating high efficiency for small VCSEL sizes, and stable beam patterns. Power conversion efficiency >40% is obtained for VCSELs ranging in size from 6 to 2 µm diameter. The 2 µm diameter VCSELs produce output powers in excess of 6.5 mW, and produce single‐lobed far‐field radiation patterns over the full range of operation.
Cost–benefit analysis of battery storage in medium‐voltage distribution networks
Authors: Mateo Carlos , Reneses Javier , Rodriguez‐Calvo Andrea , Frías Pablo , Sánchez Álvaro
Published: October 2015

The increasing deployment of non‐dispatchable generation in electric systems where generation and demand must be balanced at all times has led to a renewed interest in technologies for energy storage. This study presents a cost–benefit analysis of energy storage for peak demand reduction in medium‐voltage distribution networks. In particular, the installation of batteries in secondary substations is studied for three realistic large‐scale networks representing urban, semi‐urban and rural distribution areas. On the one hand, savings in energy costs derived from storing energy at low‐priced hours and selling it at peak hours are considered. On the other hand, savings in network reinforcement due to the peak shaving are evaluated. Network reinforcement requirements are assessed using reference network models, large‐scale network‐planning tools often used by distribution regulators to establish the allowed distribution costs. Additionally, sensitivity to different demand growth ratios and battery capacities is analysed. The final objective is to determine the target cost for batteries to be profitable from the point of view of distribution. Results show that significant savings can be obtained, especially in urban and semi‐urban areas.
Design of a uniplanar printed triple band‐rejected ultra‐wideband antenna using particle swarm optimisation and the firefly algorithm
Authors: Mohammed Husham J. , Abdullah Abdulkareem S. , Ali Ramzy S. , Abd‐Alhameed Raed A. , Abdulraheem Yasir I. , Noras James M.
Published: October 2015

A compact planar monopole antenna is proposed for ultra‐wideband applications. The antenna has a microstrip line feed and band‐rejected characteristics and consists of a ring patch and a partial ground plane with a defective ground structure of rectangular shape. An annular strip is etched above the radiating element and two slots, one C‐shaped and one arc‐shaped, are embedded in the radiating patch. The proposed antenna has been optimised using bio‐inspired algorithms such as the particle swarm optimisation and the firefly algorithm, based on a new software algorithm (Antenna Optimizer). Multi‐objective optimisation achieves rejection bands at 3.3–3.7 GHz for Worldwide Interoperability for Microwave Access, 5.15–5.825 GHz for the 802.11a wireless local area network system or HIPERLAN/2, and 7.25–7.745 GHz for C‐band satellite communication systems. Validated results show wideband performance from 2.7 to 10.6 GHz with S11 < −10 dB. The antenna has compact dimensions of 28 × 30 mm2. The radiation pattern is comparatively stable across the operating band with a relatively stable gain except in the notched bands.
Comparison of two kinds of Ka‐band circular polarisers for use in a gyro‐travelling wave amplifier
Authors: Tikhov Yuri
Published: October 2015

This study presents a rigorous theoretical and experimental comparison of two kinds of rectangular waveguide polarisers for use in Ka‐band gyro‐travelling wave amplifier. It is shown how overall field distribution inside of polariser structures having different kinds of corrugation affects the resulting performances. To the best of the authors’ knowledge, this is the first theoretical estimation of the breakdown power (in watts) of sine‐corrugated polariser in competition with conventional polariser having rectangular shaped corrugation. This study also discusses the general practice of smooth structuring in microwave and millimetre‐wave component design.
High-resolution setup for measuring wavelength sensitivity of photoyellowing of translucent materials
Authors: Vaskuri Anna , Kärhä Petri , Heikkilä Anu , Ikonen Erkki
Published: October 2015

Polystyrene and many other materials turn yellow when exposed to ultraviolet (UV) radiation. All photodegradation mechanisms including photoyellowing are functions of the exposure wavelength, which can be described with an action spectrum. In this work, a new high-resolution transmittance measurement setup based on lasers has been developed for measuring color changes, such as the photoyellowing of translucent materials aged with a spectrograph. The measurement setup includes 14 power-stabilized laser lines between 325 nm and 933 nm wavelengths, of which one at a time is directed on to the aged sample. The power transmitted through the sample is measured with a silicon detector utilizing an integrating sphere. The sample is mounted on a high-resolution XY translation stage. Measurement at various locations aged with different wavelengths of exposure radiation gives the transmittance data required for acquiring the action spectrum. The combination of a UV spectrograph and the new high-resolution transmittance measurement setup enables a novel method for studying the UV-induced ageing of translucent materials with a spectral resolution of 3–8 nm, limited by the adjustable spectral bandwidth range of the spectrograph. These achievements form a significant improvement over earlier methods.
Effect of mobile ions on the electric field needed to orient charged diblock copolymer thin films
Authors: Dehghan Ashkan , Schick M. , Shi An-Chang
Published: October 2015

We examine the behavior of lamellar phases of charged/neutral diblock copolymer thin films containing mobile ions in the presence of an external electric field. We employ self-consistent field theory and focus on the aligning effect of the electric field on the lamellae. Of particular interest are the effects of the mobile ions on the critical field, the value required to reorient the lamellae from the parallel configuration favored by the surface interaction to the perpendicular orientation favored by the field. We find that the critical field depends strongly on whether the neutral or charged species is favored by the substrates. In the case in which the neutral species is favored, the addition of charges decreases the critical electric field significantly. The effect is greater when the mobile ions are confined to the charged lamellae. In contrast, when the charged species is favored by the substrate, the addition of mobile ions stabilizes the parallel configuration and thus results in an increase in the critical electric field. The presence of ions in the system introduces a new mixed phase in addition to those reported previously.
Stability of In-Ga-Zn-O metal-semiconductor field-effect-transistors under bias, illumination, and temperature stress
Authors: Dang Giang T. , Kawaharamura Toshiyuki , Furuta Mamoru , Saxena Saurabh , Allen Martin W.
Published: October 2015

The stability of metal-semiconductor field-effect-transistors (MESFETs) with silver oxide Schottky gates on In-Ga-Zn-O (IGZO) channels, grown by mist chemical-vapor-deposition, was examined under different combinations of positive and negative bias, illumination, and temperature stress. These devices were remarkably stable, even under the most severe condition of negative-bias-illumination-temperature-stress (NBITS), where the threshold voltage shift after 10 h NBITS was only +0.12 V and was mainly attributed to a decrease in the carrier density of the channel. The stability of these IGZO MESFETs is associated with the use of a conducting Schottky gate that significantly reduces charge trapping at the gate-channel interface.
Versatile magnetometer assembly for characterizing magnetic properties of nanoparticles
Authors: Araujo J. F. D. F. , Bruno A. C. , Louro S. R. W.
Published: October 2015

We constructed a versatile magnetometer assembly for characterizing iron oxide nanoparticles. The magnetometer can be operated at room temperature or inside a cryocooler at temperatures as low as 6 K. The magnetometer’s sensor can be easily exchanged and different detection electronics can be used. We tested the assembly with a non-cryogenic commercial Hall sensor and a benchtop multimeter in a four-wire resistance measurement scheme. A magnetic moment sensitivity of 8.5 × 10−8 Am2 was obtained with this configuration. To illustrate the capability of the assembly, we synthesized iron oxide nanoparticles coated with different amounts of a triblock copolymer, Pluronic F-127, and characterized their magnetic properties. We determined that the polymer coating does not affect the magnetization of the particles at room temperature and demonstrates that it is possible to estimate the average size of coating layers from measurements of the magnetic field of the sample.
Brightness measurement of an electron impact gas ion source for proton beam writing applications
Authors: Liu N. , Xu X. , Pang R. , Santhana Raman P. , Khursheed A. , van Kan J. A.
Published: October 2015

We are developing a high brightness nano-aperture electron impact gas ion source, which can create ion beams from a miniature ionization chamber with relatively small virtual source sizes, typically around 100 nm. A prototype source of this kind was designed and successively micro-fabricated using integrated circuit technology. Experiments to measure source brightness were performed inside a field emission scanning electron microscope. The total output current was measured to be between 200 and 300 pA. The highest estimated reduced brightness was found to be comparable to the injecting focused electron beam reduced brightness. This translates into an ion reduced brightness that is significantly better than that of conventional radio frequency ion sources, currently used in single-ended MeV accelerators.
Kinetics study of the evolution of oxygen-related defects in mono-crystalline silicon subjected to electron-irradiation and thermal treatment
Authors: Quemener V. , Raeissi B. , Herklotz F. , Murin L. I. , Monakhov E. V. , Svensson B. G.
Published: October 2015

The diffusion and dissociation mechanisms governing the evolution of oxygen and vacancy-oxygen defects in Czochralski-grown Si samples have been studied. The samples were irradiated at (i) room temperature or (ii) elevated temperature (350 °C) by MeV electrons and then isothermally annealed at 8 different temperatures in the range of 300 °C to 500 °C. The evolution of the concentrations of oxygen complexes (On, n ≤ 3) and mono-vacancy-oxygen defects (VOn, n ≤ 4) have been followed by infrared absorption measurements of local vibrational modes originating from the individual defects. The experimental kinetics data have been compared with simulation results based on the theory for diffusion limited reactions, assuming a model where sequential build-up of the VOn defects is a key ingredient. A close quantitative agreement is obtained for both sets of samples despite quite different initial conditions prior to the annealing, which adds evidence to the validity of the model. Values for the diffusivity and dissociation rates of VOn (n ≤ 4) and On (n ≤ 3) have been deduced and in general, the mobility and stability of VOn decrease and increase with n, respectively. For all the defects, partial dissociation appears as a prevailing process during diffusion, while full dissociation of VOn is limited by an energy barrier identical to that of interstitial oxygen (Oi) diffusion (∼2.55 eV). The oxygen dimer and trimer are fast diffusers but slower than substitutional oxygen, i.e., VO; VO is found to be the most mobile species, whilst Oi is the slowest one with a difference in diffusivity of up to 7 orders of magnitude in the studied temperature range.
Electronic transition above room temperature in CaMn7O12 films
Authors: Huon A. , Lang A. C. , Saldana-Greco D. , Lim J. S. , Moon E. J. , Rappe A. M. , Taheri M. L. , May S. J.
Published: October 2015

We report on the electronic phase transition in CaMn7O12 quadruple perovskite films synthesized by oxide molecular beam epitaxy on SrLaAlO4 and La0.3Sr0.7Al0.65Ta0.35O3 substrates. We use x-ray diffraction and transmission electron microscopy to confirm that the CaMn7O12 phase has been realized. Temperature dependent resistivity measurements reveal a signature of a charge ordering phase transition at ≈425 K, consistent with bulk CaMn7O12. The transition temperature is found to be relatively invariant to changes in the cation stoichiometry. Density functional theory calculations reveal the changes in atomic and electronic structure induced by the charge ordering transition.
Identification of donor deactivation centers in heavily As-doped Si using time-of-flight medium-energy ion scattering spectroscopy
Authors: Min Won Ja , Park Kyungsu , Yu Kyu-Sang , Joo Sungjung , Kim Yong-Sung , Moon Dae Won
Published: October 2015

Electrically-inactive arsenic (As) complexes in silicon are investigated using time-of-flight medium-energy ion scattering spectroscopy. In heavily As-doped Si, the As atoms that are segregated in the Si interface region just below the SiO2 are found to be in interstitial forms (Asi), while the As atoms in the bulk Si region are found to be in the substitutional form (AsSi). Despite the substitutional form of As, most of the As are found to be electrically inactive in the bulk region, and we identify the As to be in the form of a 〈111〉-oriented AsSi-Si-vacancy (AsSi-VSi) complex. The Asi atoms in the interface Si region are found to exist together with Si-interstitial atoms (Sii), suggesting that the Asi atoms in the interface Si region accompany the Sii atoms.
Site-controlled quantum dots coupled to a photonic crystal molecule
Authors: Rigal B. , Jarlov C. , Gallo P. , Dwir B. , Rudra A. , Calic M. , Kapon E.
Published: October 2015

Two site-controlled quantum dots (QDs) were integrated in a photonic crystal molecule (PCM) formed by L3 nanocavities. A statistical analysis of the coupled cavity modes demonstrated the formation of bonding and anti-bonding delocalized PCM states. Excitonic transitions belonging to each QD were identified by scanning micro-photoluminescence spectroscopy. Co-polarization of the QDs photoluminescence with the coupled cavity modes provides evidence for the simultaneous coupling of two spatially separated QDs to the same PCM mode.
Electrical properties of pseudo-single-crystalline germanium thin-film-transistors fabricated on glass substrates
Authors: Kasahara K. , Nagatomi Y. , Yamamoto K. , Higashi H. , Nakano M. , Yamada S. , Wang D. , Nakashima H. , Hamaya K.
Published: October 2015

By developing a low-temperature (≤300 °C) fabrication process for the gate-stack structure on Ge(111), we study electrical properties of thin film transistors (TFTs) consisting of (111)-oriented pseudo-single-crystalline-germanium (PSC-Ge) channels on glass. Although the Hall mobility (μHall) of p-type PSC-Ge layers reaches 210 cm2/V s and the gate-stack/Ge interface has low trap density, we observe field-effect-mobility (μFE) fluctuation in the p-channel TFTs from 8.2 to 71 cm2/V s, depending on the thickness of the PSC-Ge layer. Considering the μFE fluctuation and low Ion/Ioff ratio in the p-TFTs, we infer the presence of defective Ge layers near the surface of the glass substrate. This study reveals that it is quite important for the high-performance p-Ge TFTs to improve the quality of the Ge layer near the surface of the glass substrate or to choose other materials with better Ge/substrate interface qualities.
High-performance short-wavelength infrared photodetectors based on type-II InAs/InAs1-xSbx/AlAs1−xSbx superlattices
Authors: Haddadi A. , Suo X. V. , Adhikary S. , Dianat P. , Chevallier R. , Hoang A. M. , Razeghi M.
Published: October 2015

A high-performance short-wavelength infrared n-i-p photodiode based on InAs/InAs1−xSbx/AlAs1−xSbx type-II superlattices on GaSb substrate has been demonstrated. The device is designed to have a 50% cut-off wavelength of ∼1.8 μm at 300 K. The photodetector exhibited a room-temperature (300 K) peak responsivity of 0.47 A/W at 1.6 μm, corresponding to a quantum efficiency of 37% at zero bias under front-side illumination, without any anti-reflection coating. With an R × A of 285 Ω cm2 and a dark current density of 9.6 × 10−5 A/cm2 under −50 mV applied bias at 300 K, the photodiode exhibited a specific detectivity of 6.45 × 1010 cm Hz1/2/W. At 200 K, the photodiode exhibited a dark current density of 1.3 × 10−8 A/cm2 and a quantum efficiency of 36%, resulting in a detectivity of 5.66 × 1012 cm Hz1/2/W.
A mechatronic power boosting design for piezoelectric generators
Authors: Liu Haili , Liang Junrui , Ge Cong
Published: October 2015

It was shown that the piezoelectric power generation can be boosted by using the synchronized switch power conditioning circuits. This letter reports a self-powered and self-sensing mechatronic design in substitute of the auxiliary electronics towards a compact and universal synchronized switch solution. The design criteria are derived based on the conceptual waveforms and a two-degree-of-freedom analytical model. Experimental result shows that, compared to the standard bridge rectifier interface, the mechatronic design leads to an extra 111% increase of generated power from the prototyped piezoelectric generator under the same deflection magnitude excitation. The proposed design has introduced a valuable physical insight of electromechanical synergy towards the improvement of piezoelectric power generation.
Room temperature concurrent formation of ultra-dense arrays of ferroelectric domain walls
Authors: Mtebwa Mahamudu , Feigl Ludwig , Yudin Petr , McGilly Leo J. , Shapovalov Konstantin , Tagantsev Alexander K. , Setter Nava
Published: October 2015

Properties of ferroelectric domain walls are attractive for future nano- and optoelectronics. An important element is the potential to electrically erase/rewrite domain walls inside working devices. Dense domain wall patterns, formed upon cooling through the ferroelectric phase transition, were demonstrated. However, room temperature domain wall writing is done with a cantilever tip, one domain stripe at a time, and reduction of the inter-wall distance is limited by the tip diameter. Here, we show, at room temperature, controlled formation of arrays of domain walls with sub-tip-diameter spacing (i.e., inter-wall distance down to ≈10 nm). Each array contains 100–200 concurrently formed walls. Array rewriting is confirmed. The method is demonstrated in several materials. Dense domain pattern formation through a continuous electrode, practical for potential device applications, is also demonstrated. A quantitative theory of the phenomenon is provided.
Role of polarizer-tilting-angle in zero-field spin-transfer nano-oscillators with perpendicular anisotropy
Authors: Gonzalez-Fuentes C. , Gallardo R. A. , Landeros P.
Published: October 2015

An analytical model for studying the stability of a single domain ferromagnetic layer under the influence of a spin-polarized current is presented. The theory is applied to bias-field-free nano-oscillators with perpendicular anisotropy, which allows to obtain a polarizer-angle vs. current phase diagram that describes the stability of magnetic states. Explicit formulae for the critical current densities unveil the influence of the relative orientation between free and polarizer layers, allowing the emergence of precessional steady-states, and also the possibility to reduce the magnitude of the threshold current density to produce microwave oscillations. It is shown that oscillating steady-states arise in a broad angular region, and the dependence of their boundaries is fully specified by the model. The reliability of the analytical results has been corroborated by comparison to numerical calculations. Such structures are currently under intense research because of remarkable properties offering new prospects for microwave applications in communication technologies.
Modulation of hole-injection in GaInN-light emitting triodes and its effect on carrier recombination behavior
Authors: Hwang Sunyong , Kim Dong Yeong , Park Jun Hyuk , Ryu Han-Youl , Kim Jong Kyu
Published: October 2015

The effects of the hole injection modulated by using a three-terminal GaInN-based light emitter, light-emitting triode (LET), on carrier recombination behavior and efficiency droop are investigated. It was found that the lateral electric field created by applying voltage bias between the two anodes effectively reduces efficiency droop as well as dynamic conductance of LETs. Detailed analyses of LETs under various operation conditions by APSYS simulations reveal that the asymmetry in carrier transport between electrons and holes is alleviated by promoted injection of hot holes over the potential barrier, increasing the hole concentration as well as the radiative recombination rate in the multiple quantum well active region.
Gorillas in Our Midst: Sustained Inattentional Blindness for Dynamic Events
Authors: Simons Daniel J , Chabris Christopher F
Published: October 2015

With each eye fixation, we experience a richly detailed visual world. Yet recent work on visual integration and change direction reveals that we are surprisingly unaware of the details of our environment from one view to the next: we often do not detect large changes to objects and scenes (‘change blindness’). Furthermore, without attention, we may not even perceive objects (‘inattentional blindness’). Taken together, these findings suggest that we perceive and remember only those objects and details that receive focused attention. In this paper, we briefly review and discuss evidence for these cognitive forms of ‘blindness’. We then present a new study that builds on classic studies of divided visual attention to examine inattentional blindness for complex objects and events in dynamic scenes. Our results suggest that the likelihood of noticing an unexpected object depends on the similarity of that object to other objects in the display and on how difficult the priming monitoring task is. Interestingly, spatial proximity of the critical unattended object to attended locations does not appear to affect detection, suggesting that observers attend to objects and events, not spatial positions. We discuss the implications of these results for visual representations and awareness of our visual environment.
Fooling the Eyes: Trompe L'Oeil and Reverse Perspective
Authors: Wade Nicholas J , Hughes Patrick
Published: October 2015

Trompe l'oeil pictures have been produced for hundreds of years. They attempt to create the impression of a surface that has different three-dimensional structure to the work; successful examples of trompe l'oeil typically constrain the observer's viewpoint and require use of a single eye. The works of Patrick Hughes are in relief but are painted to appear like conventional flat pictures; those parts that protrude from the picture plane are pictorially distant, or in reverse perspective. Movements of the observer result in fluid distortions of the pictorial image. These distortions occur with binocular observation and over a wide range of viewing distances.
90Y-daclizumab, an anti-CD25 monoclonal antibody, provided responses in 50% of patients with relapsed Hodgkin’s lymphoma
Authors: Janik John E. , Morris John C. , O’Mahony Deirdre , Pittaluga Stefania , Jaffe Elaine S. , Redon Christophe E. , Bonner William M. , Brechbiel Martin W. , Paik Chang H. , Whatley Millie , Chen Clara , Lee Jae-Ho , Fleisher Thomas A. , Brown Maggie , White Jeffrey D. , Stewart Donn M. , Fioravanti Suzanne , Lee Cathryn C. , Goldman Carolyn K. , Bryant Bonita R. , Junghans Richard P. , Carrasquillo Jorge A. , Worthy Tat’Yana , Corcoran Erin , Conlon Kevin C. , Waldmann Thomas A.
Published: October 2015

Significance

Despite advances, a significant proportion of patients with Hodgkin’s lymphoma (HL) will not respond or will relapse. We demonstrated that up to seven infusions of90Y-daclizumab, an anti-CD25–directed monoclonal antibody, provided responses in 50% of patients with relapsed HL. The daclizumab was directed primarily not at tumor cells themselves but toward nonmalignant T cells rosetting around the Reed–Sternberg cells.90Y provided strong β emissions that killed antigen-nonexpressing tumor cells at a distance by a crossfire effect. Furthermore, the strong β irradiation killed normal cells in the tumor microenvironment that nurture the malignant cells in the lymphomatous mass. Therefore90Y-daclizumab infusions provide meaningful therapy for select HL patients.
Retracted: Interaction of Thermus thermophilus ArsC enzyme and gold nanoparticles naked-eye assays speciation between As(III) and As(V)
Authors: Politi Jane , Spadavecchia Jolanda , Fiorentino Gabriella , Antonucci Immacolata , Casale Sandra , De Stefano Luca
Published: October 2015

The thermophilic bacterium Thermus thermophilus HB27 encodes chromosomal arsenate reductase (TtArsC), the enzyme responsible for resistance to the harmful effects of arsenic. We report on adsorption of TtArsC onto gold nanoparticles for naked-eye monitoring of biomolecular interaction between the enzyme and arsenic species. Synthesis of hybrid biological–metallic nanoparticles has been characterized by transmission electron microscopy (TEM), ultraviolet-visible (UV–vis), dynamic light scattering (DLS) and phase modulated infrared reflection absorption (PM-IRRAS) spectroscopies. Molecular interactions have been monitored by UV–vis and Fourier transform-surface plasmon resonance (FT-SPR). Due to the nanoparticles’ aggregation on exposure to metal salts, pentavalent and trivalent arsenic solutions can be clearly distinguished by naked-eye assay, even at 85 μM concentration. Moreover, the assay shows partial selectivity against other heavy metals.
Bans vs. Fees: Disposable Carryout Bag Policies and Bag Usage
Authors: Taylor Rebecca L. , Villas‐Boas Sofia B.
Published: October 2015

Using observational data on consumer carryout bag usage, we measure the effects of disposable bag policies on disposable and reusable bag demand. Our results show that plastic bag bans coupled with paper bag fees decrease total disposable bag demand but lead to significant increases in paper bag consumption. We compare our results to a study on bag fees and find that both policies lead to similar increases in reusable bag usage. However, the success of bans versus fees in discouraging disposable bag usage is contingent upon the types and prices of bags that stores choose to sell in lieu of disposable plastic.
Morphology and molecular phylogeny of Pleuronema orientale spec. nov. and Pleuronema paucisaetosum spec. nov. (Ciliophora, Scuticociliata) from Hangzhou Bay, China
Authors: Pan Hongbo , Hu Juxiang , Warren Alan , Wang Liqing , Jiang Jiamei , Hao Ruijuan
Published: October 2015

Two novel species, Pleuronema orientale spec. nov. and Pleuronema paucisaetosum spec. nov., isolated from coastal waters of Hangzhou Bay, China, were investigated with standard methods. Pleuronema orientale is characterized as follows: size in vivo 95–135 × 50–85 μm; usually one spherical macronucleus; 12–15 prolonged caudal cilia; two or three preoral kineties and 42–50 somatic kineties; membranelle 1 (M1) about 20 % of the anterior fragment of membranelle 2 (M2a) in length, consisting of three longitudinal rows of kinetosomes; posterior end of M2a hook-like; membranelle 3 (M3) three-rowed. Pleuronema paucisaetosum is characterized as follows: size in vivo about 55–85 × 25–55 μm; four or five preoral kineties and 21–23 somatic kineties; posterior end of M2a hook-like; M3 three-rowed. The small-subunit rRNA gene was sequenced for both species. Phylogenetic analyses revealed that P. orientale is most closely related to Pleuronema puytoraci and that P. paucisaetosum is sister to Pleuronema grolierei and Pleuronema setigerum (GenBank accession no. JX310015). With the inclusion of the two new sequences, the monophyly of the genus Pleuronema is not supported.
Chitinophaga dinghuensis sp. nov., isolated from soil
Authors: Lv Ying-ying , Wang Jia , You Jia , Qiu Li-hong
Published: October 2015

A Gram-reaction-negative, aerobic, non-motile bacterial strain, DHOC24T, was isolated from the forest soil of Dinghushan Biosphere Reserve, Guangdong Province, PR China. Strain DHOC24T underwent a shape change during the course of culture from long filamentous cells (10–30 × 0.4–0.5 μm) at 2 days to coccobacilli (0.5–1.0 × 0.7–1.0 μm) at 15 days after inoculation. It grew optimally at 28–33 °C and pH 6.5–7.5. The major quinone of strainDHOC24T was MK-7, the main fatty acids were iso-C15 : 0, C16 : 1ω5c and iso-C17 : 0 3-OH and the DNA G+C content was 43.1 mol%. On the basis of 16S rRNA gene sequence analysis, the strain was found to be affiliated with members of the genus Chitinophaga, but was clearly separated from established species of the genus. Strain DHOC24T was most closely related to Chitinophaga jiangningensis JN53T (98.3 % 16S rRNA gene sequence similarity) and Chitinophaga terrae KP01T (97.9 %). DNA–DNA hybridization study showed relatively low relatedness values (32.1 %) of strain DHOC24T with C. jiangningensis JN53T. The phenotypic, chemotaxonomic and phylogenetic data showed that strain DHOC24T represents a novel species of the genus Chitinophaga, for which the name Chitinophaga dinghuensis sp. nov. is proposed. The type strain is DHOC24T ( = CGMCC 1.12995T = DSM 29821T).
Shetti, a simple tool to parse, manipulate and search large datasets of sequences
Authors: Sobhy Haitham
Published: October 2015

Parsing and manipulating long and/or multiple protein or gene sequences can be a challenging process for experimental biologists and microbiologists lacking prior knowledge of bioinformatics and programming. Here we present a simple, easy, user-friendly and versatile tool to parse, manipulate and search within large datasets of long and multiple protein or gene sequences. The Shetti tool can be used to search for a sequence, species, protein/gene or pattern/motif. Moreover, it can also be used to construct a universal consensus or molecular signatures for proteins based on their physical characteristics. Shetti is an efficient and fast tool that can deal with large sets of long sequences efficiently. Shetti parses UniProt Knowledgebase and NCBI GenBank flat files and visualizes them as a table.
Capturing phenotypes for precision medicine
Authors: Robinson Peter N. , Mungall Christopher J. , Haendel Melissa
Published: October 2015

Deep phenotyping followed by integrated computational analysis of genotype and phenotype is becoming ever more important for many areas of genomic diagnostics and translational research. The overwhelming majority of clinical descriptions in the medical literature are available only as natural language text, meaning that searching, analysis, and integration of medically relevant information in databases such as PubMed is challenging. The new journal Cold Spring Harbor Molecular Case Studies will require authors to select Human Phenotype Ontology terms for research papers that will be displayed alongside the manuscript, thereby providing a foundation for ontology-based indexing and searching of articles that contain descriptions of phenotypic abnormalities—an important step toward improving the ability of researchers and clinicians to get biomedical information that is critical for clinical care or translational research.
Whole-genome sequencing of a malignant granular cell tumor with metabolic response to pazopanib
Authors: Wei Lei , Liu Song , Conroy Jeffrey , Wang Jianmin , Papanicolau-Sengos Antonios , Glenn Sean T. , Murakami Mitsuko , Liu Lu , Hu Qiang , Conroy Jacob , Miles Kiersten Marie , Nowak David E. , Liu Biao , Qin Maochun , Bshara Wiam , Omilian Angela R. , Head Karen , Bianchi Michael , Burgher Blake , Darlak Christopher , Kane John , Merzianu Mihai , Cheney Richard , Fabiano Andrew , Salerno Kilian , Talati Chetasi , Khushalani Nikhil I. , Trump Donald L. , Johnson Candace S. , Morrison Carl D.
Published: October 2015

Granular cell tumors are an uncommon soft tissue neoplasm. Malignant granular cell tumors comprise <2% of all granular cell tumors, are associated with aggressive behavior and poor clinical outcome, and are poorly understood in terms of tumor etiology and systematic treatment. Because of its rarity, the genetic basis of malignant granular cell tumor remains unknown. We performed whole-genome sequencing of one malignant granular cell tumor with metabolic response to pazopanib. This tumor exhibited a very low mutation rate and an overall stable genome with local complex rearrangements. The mutation signature was dominated by C>T transitions, particularly when immediately preceded by a 5′ G. A loss-of-function mutation was detected in a newly recognized tumor suppressor candidate, BRD7. No mutations were found in known targets of pazopanib. However, we identified a receptor tyrosine kinase pathway mutation in GFRA2 that warrants further evaluation. To the best of our knowledge, this is only the second reported case of a malignant granular cell tumor exhibiting a response to pazopanib, and the first whole-genome sequencing of this uncommon tumor type. The findings provide insight into the genetic basis of malignant granular cell tumors and identify potential targets for further investigation.
Metabolomics: an emerging but powerful tool for precision medicine
Authors: Clish Clary B.
Published: October 2015

Metabolomics, which is defined as the comprehensive analysis of metabolites in a biological specimen, is an emerging technology that holds promise to inform the practice of precision medicine. Historically, small numbers of metabolites have been used to diagnose complex metabolic diseases as well as monogenic disorders such as inborn errors of metabolism. Current metabolomic technologies go well beyond the scope of standard clinical chemistry techniques and are capable of precise analyses of hundreds to thousands of metabolites. Consequently, metabolomics affords detailed characterization of metabolic phenotypes and can enable precision medicine at a number of levels, including the characterization of metabolic derangements that underlie disease, discovery of new therapeutic targets, and discovery of biomarkers that may be used to either diagnose disease or monitor activity of therapeutics.
Distribution rules of systematic absences on the Conway topograph and their application to powder auto-indexing: erratum
Authors: Oishi-Tomiyasu Ryoko
Published: October 2015

A correction is made to the article by Oishi-Tomiyasu [Acta Cryst. (2013), A69, 603–610].
Malignancies in bullous pemphigoid: A controversial association
Authors: Balestri Riccardo , Magnano Michela , La Placa Michelangelo , Patrizi Annalisa , Angileri Luisa , Tengattini Vera , Bardazzi Federico
Published: October 2015

Bullous pemphigoid (BP) is an autoimmune subepidermal blistering disorder that has been reported to be associated with malignancies. Some authors described several cases of pemphigoid associated with malignancies (PAM); however, the evidence of this correlation still remains controversial. Several theories have been postulated to explain the relationship between malignant neoplasms and BP; the main theory suggests that antibodies directed against tumor‐specific antigens of malignant cells may cross‐react with antigens (like BP antigens) in the basement membrane zone leading to the formation of blisters. We performed an extensive review of the English published work focusing on the epidemiology, the pathogenetic theories and the clinical and histological aspects of the disease. We identified 40 cases of PAM: of these, seven cases were associated with hematological malignancies and 33 with solid tumors. Physicians should be aware of the existence of PAM and we suggest an oncological screening in early‐onset pemphigoid, in patients with a former oncological history, in those with signs and symptoms that could be related to a neoplasm and in BP refractory to common immunosuppressive therapy.
Species: a praxiographic study
Authors: Kirksey Eben
Published: October 2015

Taxonomists, who describe new species, are acutely aware of how political, economic, and ecological forces bring new forms of life into being. Conducting ethnographic research among taxonomic specialists – experts who bring order to categories of animals, plants, fungi, and microbes – I found that they pay careful attention to the ebb and flow of agency in multispecies worlds. Emergent findings from genomics and information technologies are transforming existing categories and bringing new ones into being. This article argues that the concept of species remains a valuable sense‐making tool despite recent attacks from cultural critics.
On reflexivity and the conduct of the self in everyday life: reflections on Bourdieu and Archer
Authors: Akram Sadiya , Hogan Anthony
Published: October 2015

This article provides a critique of the concept of reflexivity in social theory today and argues against the tendency to define agency exclusively in terms of reflexivity. Margaret Archer, in particular, is highlighted as a key proponent of this thesis. Archer argues that late modernity is characterized by reflexivity but, in our view, this position neglects the impact of more enduring aspects of agency, such as the routinization of social life and the role of the taken‐for‐granted. These concepts were pivotal to Bourdieu and Giddens' theorization of everyday life and action and to Foucault's understanding of technologies of the self. We offer Bourdieu's habitus as a more nuanced approach to theorizing agency, and provide an alternative account of reflexivity. Whilst accepting that reflexivity is a core aspect of agency, we argue that it operates to a backdrop of the routinization of social life and operates from within and not outside of habitus. We highlight the role of the breach in reflexivity, suggesting that it opens up a critical window for agents to initiate change. The article suggests caution in over‐ascribing reflexivity to agency, instead arguing that achieving reflexivity and change is a difficult and fraught process, which has emotional and moral consequences. The effect of this is that people often prefer the status quo, rather than to risk change and uncertainty.
Funnel compression suture: a conservative procedure to control postpartum bleeding from the lower uterine segment
Authors: Li GT , Li GR , Li XF , Wu BP
Published: October 2015

Bleeding from the lower uterine segment (LUS) during caesarean section remains a life‐threatening obstetric problem, particularly in women with placenta praevia or partial placenta accreta in the LUS. Various conservative measures for the surgical treatment of postpartum haemorrhage have been studied for decades. In this paper we describe a funnel compression suture to staunch intractable bleeding from LUS for placenta praevia accreta. The suture brings the anterior and posterior walls of the LUS together using absorbable thread and was successful in the overwhelming majority of women. It is an easy, safe and effective conservative surgical treatment to stop severe bleeding of the LUS.
‘The Party Hack, and Tool of the British Government’: T.P. O'Connor, America and Irish Party Resilience at the February 1918 South Armagh By‐Election
Authors: Doherty Erica
Published: October 2015

The common view of Irish electoral politics for the 1916 to 1918 period is one of major decline for the traditional nationalist representatives, the Irish Parliamentary Party (IPP), and the meteoric rise of the newly reconstituted Sinn Féin party; culminating in the latter's overwhelming victory at the December 1918 general election. By examining the February 1918 South Armagh by‐election campaign, this article argues that the Irish Parliamentary Party, which won the contest, was much more resilient than is often acknowledged. Through detailed analysis of election pamphlets, newspaper articles, private correspondence and committee minutes, it considers the significance of the grass‐roots strength of both in the form of their local organisations, the role of the Roman catholic church, and the election strategies of the two parties; in particular Sinn Féin's vilification of the IPP member, T.P. O'Connor, who was in America at the time of the contest.
Parliament and the Reformation of Edward VI
Authors: MacCulloch Diarmaid
Published: October 2015

This article explores the ways in which parliament was used to shape the accelerating protestant reformation undertaken by successive governments under Edward VI. It underlines the significance for constitutional history of Thomas Cromwell's extraordinary promotion of England's parliament to enact the break with Rome and evangelical religious change, and the corresponding use of parliament after Cromwell's fall by conservatives to combat evangelical gains, which at first constituted an obstacle to Protector Somerset's plans. There was a steady deliberate erosion of conservative episcopal votes in the Lords through political manœuvres from 1547; nevertheless, up to late 1549, the weight of conservative opposition in the Lords (without much obvious corresponding traditionalist support in the Commons) dictated crabwise progress in legislation. The convocations of Canterbury and York played a more marginal role in religious change. Somerset's unsuccessful attempt at populist innovation in parliament was, arguably, an important element fuelling the coup against him in autumn 1549. Thereafter, events moved much more rapidly, aided by further compulsory retirements of bishops. Attention is drawn to the frustration felt by some enthusiastic evangelicals at the pace of change dictated by parliament, leading the prominent refugee, Jan Łaski, sarcastically to characterise the Edwardian Reformation in retrospect as ‘parliamentary theology’. From late 1552, divisions between clergy and nobility in the evangelical leadership over plundering of church wealth led to confusion, ill will and the disruption of further progress, even before it was obvious that King Edward was rapidly dying.
Spatially explicit summary statistics for historical population genetic inference
Authors: Alvarado‐Serrano Diego F. , Hickerson Michael J.
Published: October 2015

The integration of population genetics with explicit spatial analyses is crucial to address a range of evolutionary and ecological questions under realistic scenarios. Ignoring space can lead to misleading inferences, yet incorporating spatial realism leads to using complex evolutionary models that necessitate distilling raw genetic data into summary statistics that capture information relevant to the models in question. However, summary statistics derived from traditional population genetic theory overlook the valuable spatial component of genetic variation that is innate in natural systems and can be informative about historical spatio‐demographic processes.

To overcome this limitation, we introduce and evaluate a new set of spatially explicit summary statistics that can be calculated from a wide range of molecular markers and that take advantage of well‐established spatial genetic algorithms to summarize the spatial distribution and autocorrelation of genetic variation. Using spatially explicit demographic simulations of SNP data, we characterize their behaviour under different realistic historical demographic scenarios and assess their relative contribution to accurate model selection and parameter estimation.

We demonstrate that under a wide range of parameter values, alternate demographic histories could be best differentiated by supplementing traditional summary statistics with these new spatial statistics. We identify different subset of statistics, including Euclidean distances in spatial‐PCA space, Monmonier's identification of genetic breaks and spatial correlograms, that greatly improve discrimination of complex species histories and have sizeable potential to estimate associated parameters, although the added power is likely to be dependent on landscape models and sampling configurations.

These results highlight the potential benefits of condensing spatial genetic information into informative summary statistics to substantially improve testing alternative historical demographic models that reflect the complex spatio‐temporal dynamics of species evolutionary histories. This study bridges phylogeography and landscape genetics by paving the way for phylogeographers wanting to incorporate spatial models and data as well as landscape geneticists wanting to incorporate history.
On the Image of the Country and the City
Authors: Brennan Timothy
Published: October 2015

We know from the Grundrisse that Marx felt the division of town and country to be as vital to political economy as the division of classes. From the Manifesto we know that he saw this division as a homological version of the dependency created by capitalism of global South on global North. It was, however, the cultural theorists of twentieth‐century Marxism who internalized this geopolitical imagination and significantly developed it in the form of scales and configurations of spatial meaning contained in the concepts “city” and “country”. The structuralist revolt against history, then, as a bid to arrest historical becoming, must really be seen as a perverse analogue of earlier twentieth century Marxist innovations in the spatialization of time. Thinkers like Ernst Bloch, Henri Lefebvre, and Raymond Williams, although unheralded for this aspect of their work, developed Marx's nascent city/country pairing, exploring the materiality of its metaphor. In geography, it is Neil Smith's Uneven Development that follows in the footsteps of this “classical” motif in literary and cultural theory.
Associated extrarenal vascular diseases may complicate the treatment and outcome of renovascular hypertension
Authors: Peco‐Antić Amira , Stajić Nataša , Krstić Zoran , Bogdanović Radovan , Miloševski‐Lomić Gordana , Đukić Milan , Paripović Dušan
Published: October 2015

Aim

This studied reviewed renovascular hypertension (RVH) due to renal artery stenosis (RAS) in two Serbian paediatric centres from 2001 to 2013.

Methods

The patients' demographic data, underlying syndromes, blood pressure (BP), antihypertensive treatments and outcomes were reviewed.

Results

The incidence of RVH was 1.9 per million children per year during the study period, and there were 25 patients with RAS, aged 10.4 ± 5.2 years. At presentation, their mean blood pressure (BP) standard deviation scores were 6.9 ± 3.4 systolic and 5.2 ± 2.6 diastolic. BP loads on 24‐hour ambulatory BP were 88 ± 14% systolic and 80 ± 29% diastolic. We found that 72% had fibromuscular dysplasia and 28% had underlying syndromes. RAS was unilateral in 64% and bilateral in 28%, and 8% had RAS of a single kidney. Antihypertensive treatment included antihypertensive drugs (100%), percutaneous transluminal angioplasty (92%), renal auto‐transplantation (16%), surgical revascularisation (12%) and nephrectomy (12%). After 4.4 ± 3.6 years of follow‐up, high BP was cured in 40% of the patients and 39.4% of the kidneys and improved in 48% (75.7%), with BP decreases of 20.3 ± 3.7% systolic and 16.3 ± 6.2% diastolic.

Conclusion

Fibromuscular dysplasia was the most common cause of RVH in this study, and hypertension was cured or improved in 88% of the patients.