bluuebunny/crossref_metadata_2025 huggingface dataset:
Microturbulence studies of pulsed poloidal current drive discharges in the reversed field pinch
Authors: Carmody D. , Pueschel M. J. , Anderson J. K. , Terry P. W.
Published: January 2015

Experimental discharges with pulsed poloidal current drive (PPCD) in the Madison Symmetric Torus reversed field pinch are investigated using a semi-analytic equilibrium model in the gyrokinetic turbulence code Gene. PPCD cases, with plasma currents of 500 kA and 200 kA, exhibit a density-gradient-driven trapped electron mode (TEM) and an ion temperature gradient mode, respectively. Relative to expectations of tokamak core plasmas, the critical gradients for the onset of these instabilities are found to be greater by roughly a factor of the aspect ratio. A significant upshift in the nonlinear TEM transport threshold, previously found for tokamaks, is confirmed in nonlinear reversed field pinch simulations and is roughly three times the threshold for linear instability. The simulated heat fluxes can be brought in agreement with measured diffusivities by introducing a small, resonant magnetic perturbation, thus modeling the residual fluctuations from tearing modes. These fluctuations significantly enhance transport.
Improving p-type doping efficiency in Al0.83Ga0.17N alloy substituted by nanoscale (AlN)5/(GaN)1 superlattice with MgGa-ON δ-codoping: Role of O-atom in GaN monolayer
Authors: Zhong Hong-xia , Shi Jun-jie , Zhang Min , Jiang Xin-he , Huang Pu , Ding Yi-min
Published: January 2015

We calculate Mg-acceptor activation energy EA and investigate the influence of O-atom, occupied the Mg nearest-neighbor, on EA in nanoscale (AlN)5/(GaN)1 superlattice (SL), a substitution for Al0.83Ga0.17N disorder alloy, using first-principles calculations. We find that the N-atom bonded with Ga-atom is more easily substituted by O-atom and nMgGa-ON (n = 1-3) complexes are favorable and stable in the SL. The O-atom plays a dominant role in reducing EA. The shorter the Mg-O bond is, the smaller the EA is. The Mg-acceptor activation energy can be reduced significantly by nMgGa-ON δ-codoping. Our calculated EA for 2MgGa-ON is 0.21 eV, and can be further reduced to 0.13 eV for 3MgGa-ON, which results in a high hole concentration in the order of 1020 cm−3 at room temperature in (AlN)5/(GaN)1 SL. Our results prove that nMgGa-ON (n = 2,3) δ-codoping in AlN/GaN SL with ultrathin GaN-layer is an effective way to improve p-type doping efficiency in Al-rich AlGaN.
Resonant frequency of the silicon micro-structure of MEMS vector hydrophone in fluid-structure interaction
Authors: Zhang Guojun , Zhao Peng , Zhang Wendong
Published: January 2015

The MEMS vector hydrophone developed by the North University of China has advantages of high Signal to Noise Ratio, ease of array integration, etc. However, the resonance frequency of the MEMS device in the liquid is different from that in the air due to the fluid-structure interaction (FSI). Based on the theory of Fluid-Solid Coupling, a generalized distributed mass attached on the micro-structure has been found, which results in the resonance frequency of the microstructure in the liquid being lower than that in the air. Then, an FSI simulation was conducted by ANSYS software. Finally, the hydrophone was measured by using a shaking table and a vector hydrophone calibration system respectively. Results show that, due to the FSI, the resonance frequency of the MEMS devices of the bionic vector hydrophone in the liquid declines approximately 30% compared to the case in the air.
Efficient and broadband Terahertz plasmonic absorbers using highly doped Si as the plasmonic material
Authors: Zhang Yusheng , Han Zhanghua
Published: January 2015

The property of highly doped Si as the plasmonic material in the THz regime is analyzed, based on which the design of efficient and broadband Terahertz plasmonic absorbers is proposed and the performance of these absorbers is numerically investigated. Numerical results from the reflection spectra demonstrate that these structures exhibit high absorption in the terahertz frequencies with large bandwidth and high tunability. It is also shown that the same level of absorptivity and bandwidth can be achieved when the top layer of highly dopes Si stripes are replaced with regular metal materials e.g. copper, highly facilitating the fabrication and practical use of the proposed structure in real Terahertz applications.
Reduction of the interfacial trap density of indium-oxide thin film transistors by incorporation of hafnium and annealing process
Authors: Lin Meng-Fang , Gao Xu , Mitoma Nobuhiko , Kizu Takio , Ou-Yang Wei , Aikawa Shinya , Nabatame Toshihide , Tsukagoshi Kazuhito
Published: January 2015

The stable operation of transistors under a positive bias stress (PBS) is achieved using Hf incorporated into InOx-based thin films processed at relatively low temperatures (150 to 250 °C). The mobilities of the Hf-InOx thin-film transistors (TFTs) are higher than 8 cm2/Vs. The TFTs not only have negligible degradation in the mobility and a small shift in the threshold voltage under PBS for 60 h, but they are also thermally stable at 85 °C in air, without the need for a passivation layer. The Hf-InOx TFT can be stable even annealed at 150 °C for positive bias temperature stability (PBTS). A higher stability is achieved by annealing the TFTs at 250 °C, originating from a reduction in the trap density at the Hf-InOx/gate insulator interface. The knowledge obtained here will aid in the realization of stable TFTs processed at low temperatures.
Winter diet of introduced red deer (Cervus elaphus) in woodland vegetation in Grampians National Park, western Victoria
Authors: Roberts Cathryn , Westbrooke Martin , Florentine Singarayer , Cook Simon
Published: January 2015

Although red deer (Cervus elaphus) have the potential to play a major role in influencing the structure and composition of vegetation, little is known about the dietary preferences of red deer in Australia. In the Grampians National Park, Victoria, where there is a large, established red deer population, there has been concern over the condition of woodlands, with lack of perennial seedling recruitment observed. We estimated the diets of 12 red deer using macroscopic sorting techniques. We examined rumen contents of seven male and five female red deer from four woodland Ecological Vegetation Classes, which indicate that they act as intermediate feeders. A wide variety of plants were ingested, with evergreen tree species, small trees and woody shrubs making up a large proportion of the diet, along with grasses. This study found that red deer show significantly different dietary intake due to sex, with females consuming a diet much higher in grasses, while males consume more trees and shrubs. These findings have implications for the management of red deer populations within the park and broader implications for their effects on Australian ecosystems.
Ethylene is involved in high air humidity promoted stomatal opening of tomato (Lycopersicon esculentum) leaves
Authors: Arve Louise E. , Torre Sissel
Published: January 2015

High relative air humidity (RH) promotes stomatal opening in tomato leaves. This study examined the role of the plant hormones abscisic acid (ABA) and ethylene in high RH induced stomatal opening. Plants were grown in high (90%) and moderate (60%) RH or transferred from moderate to high RH. ABA levels were only slightly, but significantly decreased during darkness by increasing RH. However, a significantly higher ethylene evolution was found in high RH compared with moderate RH. Ethephon increased conductance and stomatal aperture in moderate RH. Treatment with amino-ethoxyvinylglycine (AVG) suppressed stomatal opening when plants were transferred from moderate to high RH. Similarly, blocking the ethylene receptor or using an ethylene-insensitive mutant (NR) reduced the response to high RH. These results demonstrate that both ethylene production and sensitivity play a role in high RH-induced stomatal opening in tomato leaves. The increased conductance found when plants were transferred to high RH could be counteracted by exogenous ABA spray. The ABA deficient mutant ‘Flacca’ produced high levels of ethylene irrespective of the RH and the difference in water loss and conductance between high and moderate grown ‘Flacca’ plants was attenuated compared with WT. The results indicate that both ABA and ethylene play a role in air humidity control of stomatal movement in tomato.
Access to medication and pharmacy services for resettled refugees: a systematic review
Authors: Bellamy Kim , Ostini Remo , Martini Nataly , Kairuz Therese
Published: January 2015

The difficulties that resettled refugees experience in accessing primary health-care services have been widely documented. In most developed countries, pharmacists are often the first health-care professional contacted by consumers; however, the ability of refugees to access community pharmacies and medication may be limited. This review systematically reviewed the literature and synthesised findings of research that explored barriers and/or facilitators of access to medication and pharmacy services for resettled refugees. This review adhered to guidelines for systematic reviews by PRISMA (preferred reporting items for systematic reviews and meta-analyses). Databases were searched during March 2014 and included Scopus, ProQuest Sociological Abstracts, PubMed, Embase and APAIS Health. The Australian and International grey literature was also explored. Nine studies met the quality and inclusion criteria. The research reported in seven of the nine studies was conducted in the US, one was conducted in Australia and the other in the UK. The majority of studies focussed on South-east Asian refugees. Themes identified across the studies included language and the use of interpreters; navigating the Western health-care system; culture and illness beliefs; medication non-adherence; use of traditional medicine; and family, peer and community support. There is a significant paucity of published research exploring barriers to medication and pharmacy services among resettled refugees. This systematic review highlights the need for appropriate interpreting and translation services, as well as pharmacy staff demonstrating effective cross-cultural communication skills.
Identifying strains that contribute to complex diseases through the study of microbial inheritance
Authors: Faith Jeremiah J. , Colombel Jean-Frédéric , Gordon Jeffrey I.
Published: January 2015

It has been 35 y since Carl Woese reported in PNAS how sequencing ribosomal RNA genes could be used to distinguish the three domains of life on Earth. During the past decade, 16S rDNA sequencing has enabled the now frequent enumeration of bacterial communities that populate the bodies of humans representing different ages, cultural traditions, and health states. A challenge going forward is to quantify the contributions of community members to wellness, disease risk, and disease pathogenesis. Here, we explore a theoretical framework for studies of the inheritance of bacterial strains and discuss the advantages and disadvantages of various study designs for assessing the contribution of strains to complex diseases.
Effects of Celiprolol and Bisoprolol on Blood Pressure, Vascular Stiffness, and Baroreflex Sensitivity
Authors: Eguchi Kazuo , Hoshide Satoshi , Kario Kazuomi
Published: January 2015

BACKGROUND

We tested the hypothesis that celiprolol and bisoprolol have differential effects on blood pressure (BP), flow-mediated dilation (FMD), and vascular stiffness.

METHODS

We analyzed 102 hypertensives (mean age: 59±14 years) who were being treated other than beta-blockers. They were randomized to receive add-on treatment with either celiprolol 100–200mg (C group) or bisoprolol 2.5–5mg (B group), and followed up for 3 months. In addition to clinic, home, and ambulatory BP monitoring, the FMD, radial augmentation index (AI), brachial–ankle pulse wave velocity (baPWV), urine albumin-to-creatinine ratio, and baroreflex sensitivity (BRS) were measured at baseline and at the end of the study.

RESULTS

Compared to the baseline values, home and 24-hour BP were significantly lowered in the third month in both groups (all Ps < 0.05). Pulse rate (PR) and baPWV were reduced (P < 0.001), and BRS was increased significantly only in the B group (P = 0.02). Radial AI was unchanged in the C group but was significantly increased in the B group (P < 0.001). Central BP was significantly reduced in the C group (P = 0.003) but was unchanged in the B group. FMD was significantly increased in both groups (both P < 0.01).

CONCLUSION

Bisoprolol achieved the greater reduction of PR and improved BRS and vascular stiffness, whereas, celiprolol reduced the central BP level. In treated hypertensive patients, add-on use of celiprolol may be favorable in uncomplicated stage of hypertension. On the other hand, bisoprolol may be useful in hypertensives with cardiac or vascular diseases who have advanced atherosclerotic changes and sympathetic nervous system activation.
ENViz: a Cytoscape App for integrated statistical analysis and visualization of sample-matched data with multiple data types
Authors: Steinfeld Israel , Navon Roy , Creech Michael L. , Yakhini Zohar , Tsalenko Anya
Published: January 2015

Summary: ENViz (Enrichment Analysis and Visualization) is a Cytoscape app that performs joint enrichment analysis of two types of sample matched datasets in the context of systematic annotations. Such datasets may be gene expression or any other high-throughput data collected in the same set of samples. The enrichment analysis is done in the context of pathway information, gene ontology or any custom annotation of the data. The results of the analysis consist of significant associations between profiled elements of one of the datasets to the annotation terms (e.g. miR-19 was associated to the cell-cycle process in breast cancer samples). The results of the enrichment analysis are visualized as an interactive Cytoscape network.

Availability and implementation: ENViz is publically available in the Cytoscape App Store (http://apps.cytoscape.org/apps/enviz). For additional information please visit the tool website: http://www.agilent.com/labs/research/compbio/enviz/

Contact:  israel_steinfeld@agilent.com
Shifted Hamming distance: a fast and accurate SIMD-friendly filter to accelerate alignment verification in read mapping
Authors: Xin Hongyi , Greth John , Emmons John , Pekhimenko Gennady , Kingsford Carl , Alkan Can , Mutlu Onur
Published: January 2015

Motivation: Calculating the edit-distance (i.e. minimum number of insertions, deletions and substitutions) between short DNA sequences is the primary task performed by seed-and-extend based mappers, which compare billions of sequences. In practice, only sequence pairs with a small edit-distance provide useful scientific data. However, the majority of sequence pairs analyzed by seed-and-extend based mappers differ by significantly more errors than what is typically allowed. Such error-abundant sequence pairs needlessly waste resources and severely hinder the performance of read mappers. Therefore, it is crucial to develop a fast and accurate filter that can rapidly and efficiently detect error-abundant string pairs and remove them from consideration before more computationally expensive methods are used.

Results: We present a simple and efficient algorithm, Shifted Hamming Distance (SHD), which accelerates the alignment verification procedure in read mapping, by quickly filtering out error-abundant sequence pairs using bit-parallel and SIMD-parallel operations. SHD only filters string pairs that contain more errors than a user-defined threshold, making it fully comprehensive. It also maintains high accuracy with moderate error threshold (up to 5% of the string length) while achieving a 3-fold speedup over the best previous algorithm (Gene Myers’s bit-vector algorithm). SHD is compatible with all mappers that perform sequence alignment for verification.

Availability and implementation: We provide an implementation of SHD in C with Intel SSE instructions at: https://github.com/CMU-SAFARI/SHD.

Contact: hxin@cmu.edu, calkan@cs.bilkent.edu.tr or onur@cmu.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Experimental myositis inducible with transfer of dendritic cells presenting a skeletal muscle C protein-derived CD8 epitope peptide
Authors: Okiyama Naoko , Hasegawa Hisanori , Oida Takatoku , Hirata Shinya , Yokozeki Hiroo , Fujimoto Manabu , Miyasaka Nobuyuki , Kohsaka Hitoshi
Published: January 2015

It is suggested that polymyositis, an autoimmune inflammatory myopathy, is mediated by autoaggressive CD8 T cells. Skeletal muscle C protein is a self-antigen that induces C protein-induced myositis, a murine model of polymyositis. To establish a new murine model of myositis inducible with a single CD8 T-cell epitope peptide that derives from the C protein, three internet-based prediction systems were employed to identify 24 candidate peptides of the immunogenic fragment of the C protein and bind theoretically to major histocompatibility complex class I molecules of C57BL/6 (B6) mice. RMA-S cell assay revealed that a HILIYSDV peptide, amino acid position 399–406 of the C protein, had the highest affinity to the H2-Kb molecules. Transfer of mature bone marrow-derived dendritic cells pulsed with HILIYSDV induced myositis in naive B6 mice. This myositis was suppressed by anti-CD8-depleting antibodies but not by anti-CD4-depleting antibodies. Because this myositis model is mediated by CD8 T cells independently of CD4 T cells, it should be a useful tool to investigate pathology of polymyositis and develop therapies targeting CD8 T cells.
Association between sHLA-G and HLA-G 14-bp deletion/insertion polymorphism in Crohn’s disease
Authors: Zidi Inès , Ben Yahia Hamza , Bortolotti Daria , Mouelhi Leila , Laaribi Ahmed Baligh , Ayadi Shema , Zidi Nour , Houissa Fatma , Debbech Radhouane , Boudabous Abdellatif , Najjar Taoufik , Di Luca Dario , Rizzo Roberta
Published: January 2015

The aim of this study was to evaluate the association between the HLA-G 14-bp deletion/insertion (Del/Ins) polymorphism and soluble (s) HLA-G production in patients with Crohn’s disease (CD). We analyzed also the sHLA-G molecules by ELISA and western blot in plasma samples. Among unselected patients, the 14-bp Del/Ins polymorphism was not significantly associated with increased CD risk neither for alleles (P = 0.371) nor for genotypes (P = 0.625). However, a significant association was reported between the 14-bp Del/Ins polymorphism and CD, in particular in young-onset CD patients for alleles [P = 0.020, odds ratio (OR) = 2.438, 95% confidence interval (CI): 1.13–5.25] but not with adult-onset CD patients. A significant association was reported concerning the genotype Ins/Ins for young-onset CD patients (P = 0.029, OR = 3.257, 95% CI: 1.08–9.77). We observed also a significant increase in sHLA-G measured by ELISA in CD patients compared to controls (P = 0.002). The 14-bp Del/Del and 14-bp Del/Ins genotypes are the high HLA-G producers. Among sHLA-Gpositive patients, 43% of subjects present dimers of HLA-G. The presence of dimers seems to be related to the advanced stages of the disease. The 14-bp Del/Ins polymorphism is associated with an increased risk of CD particularly in young-onset CD patients and controls sHLA-G plasma levels. Dimers of sHLA-G are frequent in advanced disease stages. The above findings indicate that the genetic 14-bp Del/Ins polymorphism in exon 8 of the HLA-G gene is associated with the risk of CD and suggest a role for sHLA-G as a prognostic marker for progressive disease.
New plasmid-mediated aminoglycoside 6′-N-acetyltransferase, AAC(6′)-Ian, and ESBL, TLA-3, from a Serratia marcescens clinical isolate
Authors: Jin Wanchun , Wachino Jun-ichi , Kimura Kouji , Yamada Keiko , Arakawa Yoshichika
Published: January 2015

Objectives

Enterobacteriaceae clinical isolates showing amikacin resistance (MIC 64 to >256 mg/L) in the absence of 16S rRNA methyltransferase (MTase) genes were found. The aim of this study was to clarify the molecular mechanisms underlying amikacin resistance in Enterobacteriaceae clinical isolates that do not produce 16S rRNA MTases.

Methods

PCR was performed to detect already-known amikacin resistance determinants. Cloning experiments and sequence analyses were performed to characterize unknown amikacin resistance determinants. Transfer of amikacin resistance determinants was performed by conjugation and transformation. The complete nucleotide sequence of the plasmids was determined by next-generation sequencing technology. Amikacin resistance enzymes were purified with a column chromatography system. The enzymatic function of the purified protein was investigated by thin-layer chromatography (TLC) and HPLC.

Results

Among the 14 isolates, 9 were found to carry already-known amikacin resistance determinants such as aac(6′)-Ia and aac(6′)-Ib. Genetic analyses revealed the presence of a new amikacin acetyltransferase gene, named aac(6′)-Ian, located on a 169 829 bp transferable plasmid (p11663) of the Serratia marcescens strain NUBL-11663, one of the five strains negative for known aac(6′) genes by PCR. Plasmid p11663 also carried a novel ESBL gene, named blaTLA-3. HPLC and TLC analyses demonstrated that AAC(6′)-Ian catalysed the transfer of an acetyl group from acetyl coenzyme A onto an amine at the 6′-position of various aminoglycosides.

Conclusions

We identified aac(6′)-Ian as a novel amikacin resistance determinant together with a new ESBL gene, blaTLA-3, on a transferable plasmid of a S. marcescens clinical isolate.
A NuSTAR observation of the fast symbiotic nova V745 Sco in outburst
Authors: Orio M. , Rana V. , Page K. L. , Sokoloski J. , Harrison F.
Published: January 2015

The fast recurrent nova V745 Sco was observed in the 3–79 keV X-rays band with NuSTAR 10 d after the optical discovery. The measured X-ray emission is consistent with a collisionally ionized optically thin plasma at temperature of about 2.7 keV. A prominent iron line observed at 6.7 keV does not require enhanced iron in the ejecta. We attribute the X-ray flux to shocked circumstellar material. No X-ray emission was observed at energies above 20 keV, and the flux in the 3–20 keV range was about 1.6 × 10−11 erg cm−2 s−1. The emission measure indicates an average electron density of the order of 107 cm−2. The X-ray flux in the 0.3–10 keV band almost simultaneously measured with Swift was about 40 times larger, mainly due to the luminous central supersoft source emitting at energy below 1 keV. The fact that the NuSTAR spectrum cannot be fitted with a power law, and the lack of hard X-ray emission, allow us to rule out Comptonized gamma-rays, and to place an upper limit of the order of 10−11 erg cm−2 s−1 on the gamma-ray flux of the nova on the tenth day of the outburst.
The ultraluminous X-ray source NuSTAR J095551+6940.8: a magnetar in a high-mass X-ray binary
Authors: Ekşi K. Y. , Andaç İ. C. , Çıkıntoğlu S. , Gençali A. A. , Güngör C. , Öztekin F.
Published: January 2015

The recent detection of pulsations from the ultraluminous X-ray source (ULX) NuSTAR J095551+6940.8 in M82 by Bachetti et al. indicates that the object is an accreting neutron star in a high-mass X-ray binary (HMXB) system. The super-Eddington luminosity of the object implies that the magnetic field is sufficiently strong to suppress the scattering cross-section unless its beam is viewed at a favourable angle. We show that the torque equilibrium condition for the pulsar indicates that the dipole magnetic field of the neutron star is 6.7 × 1013 G, two orders of magnitude higher than that estimated by Bachetti et al., and further point to the possibility that even stronger magnetic fields could well be in the higher multipoles. This supports the recent view that magnetars descent from HMXBs if the magnetic field decays an order of magnitude during the process of transition.
An ultraluminous nascent millisecond pulsar
Authors: Kluźniak Włodek , Lasota Jean-Pierre
Published: January 2015

If the ultraluminous source (ULX) M82 X-2 sustains its measured spin-up value of $\dot{\nu }= 10^{-10}\,{\rm s^{-2}}$, it will become a millisecond pulsar in less than 105 yr. The observed (isotropic) luminosity of 1040 erg s−1 also supports the notion that the neutron star will spin up to a millisecond period upon accreting about 0.1 Mȯ – the reported hard X-ray luminosity of this ULX, together with the spin-up value, implies torques consistent with the accretion disc extending down to the vicinity of the stellar surface, as expected for low values of the stellar dipole magnetic field (B ≲ 109 G). This suggests a new channel of millisecond pulsar formation – in high-mass X-ray binaries – and may have implications for studies of gravitational waves, and possibly for the formation of low-mass black holes through accretion-induced collapse.
Spectroscopy of the Type Ia supernova 2011fe past 1000 d
Authors: Taubenberger S. , Elias-Rosa N. , Kerzendorf W. E. , Hachinger S. , Spyromilio J. , Fransson C. , Kromer M. , Ruiter A. J. , Seitenzahl I. R. , Benetti S. , Cappellaro E. , Pastorello A. , Turatto M. , Marchetti A.
Published: January 2015

In this Letter we present an optical spectrum of SN 2011fe taken 1034 d after the explosion, several hundred days later than any other spectrum of a Type Ia supernova (disregarding light-echo spectra and Local Group remnants). The spectrum is still dominated by broad emission features, with no trace of a light echo or interaction of the supernova ejecta with surrounding interstellar material. Comparing this extremely late spectrum to an earlier one taken 331 d after the explosion, we find that the most prominent feature at 331 d – [Fe iii] emission around 4700 Å – has entirely faded away, suggesting a significant change in the ionization state. Instead, [Fe ii] lines are probably responsible for most of the emission at 1034 d. An emission feature at 6300–6400 Å has newly developed at 1034 d, which we tentatively identify with Fe i λ6359, [Fe i] λλ6231, 6394 or [O i] λλ6300, 6364. Interestingly, the features in the 1034 d spectrum seem to be collectively redshifted, a phenomenon that we currently have no convincing explanation for. We discuss the implications of our findings for explosion models, but conclude that sophisticated spectral modelling is required for any firm statement.
Methanoculleus taiwanensis sp. nov., a methanogen isolated from deep marine sediment at the deformation front area near Taiwan
Authors: Weng Chieh-Yin , Chen Sheng-Chung , Lai Mei-Chin , Wu Sue-Yao , Lin Saulwood , Yang Tsanyao F. , Chen Po-Chun
Published: January 2015

A mesophilic, hydrogenotrophic methanogen, strain CYW4T, was isolated from deep-sea sediment obtained by the Ocean Researcher I cruiser, ORI-961, in 2011. The sediment was from the deformation front area offshore of south-western Taiwan. Here, seismic reflections indicated that methane hydrates were abundant. The methanogenic substrates utilized by strain CYW4Twere formate and H2/CO2, but not acetate, secondary alcohols, methylamines, methanol and ethanol. Cells of strain CYW4Twere non-motile, irregular cocci and 0.6–1.5 µm in diameter. The S-layer protein had anMrof 112 000. The optimum growth conditions were at 37 °C, pH 8.1 and 0.08 M NaCl. Growth of the strain was stimulated by acetate. The G+C content of the chromosomal DNA of strain CYW4Twas 61 mol%. Phylogenetic analysis revealed that strain CYW4Twas most closely related toMethanoculleus marisnigriJR1T(96.82 % 16S rRNA gene sequence similarity). Based on the morphological, phenotypic and phylogenetic characteristics presented here, it is evident that strain CYW4Trepresents a novel species of the genusMethanoculleus, and the nameMethanoculleus taiwanensissp. nov. is proposed. The type strain is CYW4T( = BCRC AR10043T = NBRC 110782T). The optical density of cultures of strain CYW4Tdropped abruptly upon entering the stationary growth phase. During this time numerous particles of approximately 50 nm in diameter were observed on and around the cells. This suggests that strain CYW4Tharbours a lytic virus that is induced in the stationary phase, which is of interest because only a few lytic viruses have been reported in methanogens.
Reconciling timber extraction with biodiversity conservation in tropical forests using reduced‐impact logging
Authors: Bicknell Jake E. , Struebig Matthew J. , Davies Zoe G.
Published: January 2015

Over 20% of the world's tropical forests have been selectively logged, and large expanses are allocated for future timber extraction. Reduced‐impact logging (RIL) is being promoted as best practice forestry that increases sustainability and lowersCO2emissions from logging, by reducing collateral damage associated with timber extraction.RILis also expected to minimize the impacts of selective logging on biodiversity, although this is yet to be thoroughly tested.

We undertake the most comprehensive study to date to investigate the biodiversity impacts ofRILacross multiple taxonomic groups. We quantified birds, bats and large mammal assemblage structures, using a before‐after control‐impact (BACI) design across 20 sample sites over a 5‐year period. Faunal surveys utilized point counts, mist nets and line transects and yielded >250 species. We examined assemblage responses to logging, as well as partitions of feeding guild and strata (understorey vs. canopy), and then tested for relationships with logging intensity to assess the primary determinants of community composition.

Community analysis revealed little effect ofRILon overall assemblages, as structure and composition were similar before and after logging, and between logging and control sites. Variation in bird assemblages was explained by natural rates of change over time, and not logging intensity. However, when partitioned by feeding guild and strata, the frugivorous and canopy bird ensembles changed as a result ofRIL, although the latter was also associated with change over time. Bats exhibited variable changes post‐logging that were not related to logging, whereas large mammals showed no change at all.

Indicator species analysis and correlations with logging intensities revealed that some species exhibited idiosyncratic responses toRIL, whilst abundance change of most others was associated with time.

Synthesis and applications. Our study demonstrates the relatively benign effect of reduced‐impact logging (RIL) on birds, bats and large mammals in a neotropical forest context, and therefore, we propose that forest managers should improve timber extraction techniques more widely. IfRILis extensively adopted, forestry concessions could represent sizeable and important additions to the global conservation estate – over 4 million km2.
Curriculum‐Based Measurement of Oral Reading fluency (CBM‐R): An objective orientated evaluation study
Authors: Grima‐Farrell Christine
Published: January 2015

The knowledge and practices associated with improved outcomes for readers have yielded converging evidence about practices associated with improved reading outcomes for primary students. This considerable intervention knowledge can be beneficial for English teachers working with struggling secondary readers. Fluency is one critical element that becomes increasingly important for many older students with reading difficulties as they strive to read large quantities of text written at challenging levels, with sufficient speed, accuracy and understanding to keep up with class content and demands. This objective‐orientated evaluation study examined the effects of Curriculum‐Based Measurement of Oral Reading (CBM‐R), a prevention‐orientated approach designed to identify readers at risk of not achieving adequate outcomes, on 94 second‐grade students from a primary school in New South Wales, Australia. Results indicate that teachers found CBM‐R to be a reliable and easily implemented prevention‐orientated system, which has the capacity to raise awareness of fluency abilities to guide differentiated practice and reduce the risk of failure in English.
An individualised curriculum to teach numeracy skills to children with autism: programme description and pilot data
Authors: Tzanakaki Pagona , Grindle Corinna Fay , Saville Maria , Hastings Richard Patrick , Hughes John Carl , Huxley Kathleen
Published: January 2015

Teaching mathematics to children with autism is an area with limited research evidence. In this study we developed a teaching manual based on Maths Recovery, a numeracy programme designed for typically developing children. Six children with autism participated in the study and received daily numeracy teaching over a 20‐week period. Our aims were to explore whether Maths Recovery can be used as a numeracy curriculum for children with autism and to evaluate the progress the children make after a period of intensive teaching. Using a pre‐test post‐test design we found that the adapted Maths Recovery numeracy curriculum was successfully incorporated within each child's individualised teaching programme, and that all six children improved their mathematical ability over the course of the intervention. Our data show promising results and support the rationale for larger evaluation studies.
Story Links: working with parents of pupils at risk of exclusion
Authors: Waters Trisha
Published: January 2015

This paper presents the results of the evaluation of the 20‐month Story Links project delivered by the University of Chichester in collaboration with the Centre for Therapeutic Storywriting and funded by the Esmée Fairbairn Foundation and the Training and Development Agency for Schools (TDA). Story Links is a ten‐week intervention that involves pupils at risk of exclusion and with poor literacy, along with teachers and parents, in co‐creating stories that address the pupils' emotional and behavioural issues. These stories are then used to develop the pupils' reading skills. The theoretical background draws on Bowlby's concept of attachment and research that highlights the relationship between parental involvement and academic achievement. Analysis of the co‐created stories showed a high correlation between the story metaphor and the child's presenting of emotional issues as identified by the parents and professionals. The findings also showed a significant increase in parental involvement in their child's learning and improvement in both pupils' behaviour and pupils' attitudes to learning.
A method for analysing replicated point patterns in ecology
Authors: Bagchi Robert , Illian Janine B.
Published: January 2015

Many ecological questions could gain insight from linking variation in spatial structure to explanatory variables. Although methods that make these links have been developed in the statistical literature, they have been used rarely in ecology.

We present an approach that considers point patterns from different sources (e.g. multiple plots or species) as replicates of the spatial processes of interest. Using an integrated two‐step procedure, the method uses a linear mixed‐effects modelling framework to explain variation in the spatial structure of the replicated patterns with categorical and continuous predictors.

Inferences on the strength of the relationships between the predictors and spatial structure are made on the basis of a semi‐parametric bootstrap procedure that accounts for the dependency among spatial scales and, if required, among replicates.

We illustrate the approach with three simulated examples. These demonstrate that replicated analyses can increase the performance of spatial point pattern analyses, allow analysis of sparse patterns (e.g. rare species) and help identify the drivers of variation among spatial point patterns.

The paucity of ecological studies that utilize replicated point pattern analysis may be due partly to a lack of familiarity with the methods. By highlighting the options available, we hope to encourage greater use of these methods by ecologists in the future.
Phylogeny of split‐footed lacewings (Neuroptera, Nymphidae), with descriptions of new Cretaceous fossil species from China
Authors: Shi Chaofan , Winterton Shaun L. , Ren Dong
Published: January 2015

A phylogeny of the lacewing family Nymphidae based on morphology and DNA sequences is presented including representatives of all living genera and selected fossil genera. Widely distributed Jurassic and Cretaceous genera gave rise to recent taxa now restricted to Australasia. Two previously defined clades (i.e. Nymphinae and Myiodactylinae) were recovered and reflect the diverging adult and larval morphology of members of these two subfamilies. From Chinese Cretaceous deposits, a new genus (Spilonymphes gen. nov.) is described with one new species, as well as new species described in the genera Baissoleon Makarkin and Sialium Westwood.
EngageUC: Developing an Efficient and Ethical Approach to Biobanking Research at the University of California
Authors: Garrett Sarah B. , Koenig Barbara A. , Brown Arleen , Hult Jen R. , Boyd Elizabeth A. , Dry Sarah , Dohan Daniel ,   in collaboration with UC BRAID
Published: January 2015

Biorepositories, or biobanks, provide researchers with access to biological samples and associated data in support of translational research. Efficient operation and ethical stewardship of biobanks involves coordinated efforts among multiple stakeholders including researchers who manage and use the repository, institutional officials charged with its oversight, and patients and volunteers who contribute samples and data. As advancements in translational research increasingly involve more data derived from larger numbers of diverse samples, the size and governance challenges facing biorepositories have grown. We describe an approach to developing efficient and ethical biobank governance that includes all major stakeholders. This model provides a pathway for addressing the technical and ethical challenges that must be resolved to ensure biorepositories continue to support translational research.
Sympathoadrenal neural crest cells: The known, unknown and forgotten?
Authors: Lumb Rachael , Schwarz Quenten
Published: January 2015

Neural crest cells (NCCs) are highly migratory progenitor cells that give rise to a vast array of differentiated cell types. One of their key derivatives is the autonomic nervous system (ANS) that is comprised in part from chromaffin cells of the adrenal medulla and organ of Zuckerkandl, the sympathetic chain and additional prevertebral ganglia such as the celiac ganglia, suprarenal ganglia and mesenteric ganglia. In this review we discuss recent advances toward our understanding of how the NCC precursors of the ANS migrate to their target regions, how they are instructed to differentiate into the correct cell types, and the morphogenetic signals controlling their development. Many of these processes remain enigmatic to developmental biologists worldwide. Taking advantage of lineage tracing mouse models one of our own aims is to address the morphogenetic events underpinning the formation of the ANS and to identify the molecular mechanisms that help to segregate a mixed population of NCCs into pathways specific for the sympathetic ganglia, sensory ganglia or adrenal medulla.
Predation pressure in Ugandan cotton fields measured by a sentinel prey method
Authors: Howe Andy G. , Nachman Gösta , Lövei Gábor L.
Published: January 2015

Pest suppression by natural enemies is an important ecosystem service, which is a valuable resource to poor smallholders in developing countries. Diverse natural enemy assemblages of arthropod predators and parasitoids are documented in various regions in Africa, but our knowledge of their impact on herbivores in agroecosystems remains limited. We conducted experiments in cotton, Gossypium hirsutum L. (Malvaceae), under typical local agronomic practices in Uganda to assess levels of predation pressure ascribed to natural enemies. We measured predation rates on artificial caterpillars made of plasticine glued to cotton plants. Predation pressure on cotton fields varied between 1.96 and 4.1% per day, but was not significantly influenced by cotton treatments (insecticide/no insecticide, monocropping/intercropping with Phaseolus spp.). Predation pressure in non‐crop habitats adjacent to cotton fields was up to 12× higher than in the fields. Marks left on the artificial caterpillars revealed that arthropods and birds were largely accountable for predation in cotton fields, whereas arthropods and small mammals were dominant in non‐cultivated habitats.
Early‐life stress induces anxiety‐like behaviors and activity imbalances in the medial prefrontal cortex and amygdala in adult rats
Authors: Ishikawa Junko , Nishimura Ryoichi , Ishikawa Akinori
Published: January 2015

Early‐life stress increases the prevalence of psychiatric diseases associated with emotional dysregulation. Emotional regulation requires the inhibitory influence of the medial prefrontal cortex (mPFC) on amygdalar activity, and dysfunction of this system is believed to induce anxiety. Because mPFC and amygdala have dense reciprocal connections and projections between them continue to develop until adolescence, early‐life stress may impair the function of this circuit and cause emotional dysregulation. We examined the effects of stress during circuit development on anxiety‐like behaviors, neural activities in the mPFC and amygdala, and impulse transmission in the mPFC–amygdala circuit in adult rats. Early‐life stress, unpredictable stress twice a day for 12 days following early weaning, increased anxiety‐like behaviors in the open‐field and elevated plus‐maze tests. In the open‐field test, stress altered Fos expression in the mPFC and amygdala. Compared to non‐stressed rats, which were exposed to neither unpredictable stress nor early weaning, stressed rats exhibited decreased Fos expression in the right superficial layers of the infralimbic cortex and increased Fos expression in the right basolateral amygdala and both sides of the central amygdala. Electrophysiological analysis revealed that excitatory latencies of mPFC neurons to amygdalar stimulation in stressed rats were significantly longer than control rats in the right, but not left, hemisphere. Stress had no effect on excitatory latencies of amygdalar neurons to mPFC stimulation in the mPFC–amygdala circuits in the both hemisphere. These data suggest that early‐life stress impairs the mPFC–amygdala circuit development, resulting in imbalanced mPFC and amygdala activities and anxiety‐like behaviors.
Nickel acts as an adjuvant during cobalt sensitization
Authors: Bonefeld Charlotte Menné , Nielsen Morten Milek , Vennegaard Marie T. , Johansen Jeanne Duus , Geisler Carsten , Thyssen Jacob P.
Published: January 2015

Metal allergy is the most frequent form of contact allergy with nickel and cobalt being the main culprits. Typically, exposure comes from metal‐alloys where nickel and cobalt co‐exist. Importantly, very little is known about how co‐exposure to nickel and cobalt affects the immune system. We investigated these effects by using a recently developed mouse model. Mice were epicutaneously sensitized with i) nickel alone, ii) nickel in the presence of cobalt, iii) cobalt alone, or iv) cobalt in the presence of nickel, and then followed by challenge with either nickel or cobalt alone. We found that sensitization with nickel alone induced more local inflammation than cobalt alone as measured by increased ear‐swelling. Furthermore, the presence of nickel during sensitization to cobalt led to a stronger challenge response to cobalt as seen by increased ear‐swelling and increased B and T cell responses in the draining lymph nodes compared to mice sensitized with cobalt alone. In contrast, the presence of cobalt during nickel sensitization only induced an increased CD8+ T cell proliferation during challenge to nickel. Thus, the presence of nickel during cobalt sensitization potentiated the challenge response against cobalt more than the presence of cobalt during sensitization to nickel affected the challenge response against nickel. Taken together, our study demonstrates that sensitization with a mixture of nickel and cobalt leads to an increased immune response to both nickel and cobalt, especially to cobalt, and furthermore that the adjuvant effect appears to correlate with the inflammatory properties of the allergen..
The role of vegetation–microclimate feedback in promoting shrub encroachment in the northern Chihuahuan desert
Authors: He Yufei , D'Odorico Paolo , De Wekker Stephan F.J.
Published: January 2015

Many arid and semi‐arid landscapes around the world are affected by a shift from grassland to shrubland vegetation, presumably induced by climate warming, increasing atmospheric CO2 concentrations, and/or changing land use. This major change in vegetation cover is likely sustained by positive feedbacks with the physical environment. Recent research has focused on a feedback with microclimate, whereby cold intolerant shrubs increase the minimum nocturnal temperatures in their surroundings. Despite the rich literature on the impact of land cover change on local climate conditions, changes in microclimate resulting from shrub expansion into desert grasslands have remained poorly investigated. It is unclear to what extent such a feedback can affect the maximum extent of shrub expansion and the configuration of a stable encroachment front. Here, we focus on the case of the northern Chihuahuan desert, where creosotebush (Larrea tridentata) has been replacing grasslands over the past 100–150 years. We use a process‐based coupled atmosphere‐vegetation model to investigate the role of this feedback in sustaining shrub encroachment in the region. Simulations indicate that the feedback allows juvenile shrubs to establish in the grassland during average years and, once established, reduce their vulnerability to freeze‐induced mortality by creating a warmer microclimate. Such a feedback is crucial in extreme cold winters as it may reduce shrub mortality. We identify the existence of a critical zone in the surroundings of the encroachment front, in which vegetation dynamics are bistable: in this zone, vegetation can be stable both as grassland and as shrubland. The existence of these alternative stable states explains why in most cases the shift from grass to shrub cover is found to be abrupt and often difficult to revert.
The linkages between photosynthesis, productivity, growth and biomass in lowland Amazonian forests
Authors: Malhi Yadvinder , Doughty Christopher E. , Goldsmith Gregory R. , Metcalfe Daniel B. , Girardin Cécile A. J. , Marthews Toby R. , del Aguila‐Pasquel Jhon , Aragão Luiz E. O. C. , Araujo‐Murakami Alejandro , Brando Paulo , da Costa Antonio C. L. , Silva‐Espejo Javier E. , Farfán Amézquita Filio , Galbraith David R. , Quesada Carlos A. , Rocha Wanderley , Salinas‐Revilla Norma , Silvério Divino , Meir Patrick , Phillips Oliver L.
Published: January 2015

Understanding the relationship between photosynthesis, net primary productivity and growth in forest ecosystems is key to understanding how these ecosystems will respond to global anthropogenic change, yet the linkages among these components are rarely explored in detail. We provide the first comprehensive description of the productivity, respiration and carbon allocation of contrasting lowland Amazonian forests spanning gradients in seasonal water deficit and soil fertility. Using the largest data set assembled to date, ten sites in three countries all studied with a standardized methodology, we find that (i) gross primary productivity (GPP) has a simple relationship with seasonal water deficit, but that (ii) site‐to‐site variations in GPP have little power in explaining site‐to‐site spatial variations in net primary productivity (NPP) or growth because of concomitant changes in carbon use efficiency (CUE), and conversely, the woody growth rate of a tropical forest is a very poor proxy for its productivity. Moreover, (iii) spatial patterns of biomass are much more driven by patterns of residence times (i.e. tree mortality rates) than by spatial variation in productivity or tree growth. Current theory and models of tropical forest carbon cycling under projected scenarios of global atmospheric change can benefit from advancing beyond a focus on GPP. By improving our understanding of poorly understood processes such as CUE, NPP allocation and biomass turnover times, we can provide more complete and mechanistic approaches to linking climate and tropical forest carbon cycling.