bluuebunny/crossref_metadata_2025 huggingface dataset:
Fault diagnosis scheme for open‐circuit faults in switched reluctance motor drives using fast Fourier transform algorithm with bus current detection
Authors: Gan Chun , Wu Jianhua , Yang Shiyou , Hu Yihua , Cao Wenping , Si Jikai
Published: August 2015

Reliability of power converters is of crucial importance in switched reluctance motor drives used for safety‐critical applications. Open‐circuit faults in power converters will cause the motor to run in unbalanced states, and if left untreated, they will lead to damage to the motor and power modules, and even cause a catastrophic failure of the whole drive system. This study is focused on using a single current sensor to detect open‐circuit faults accurately. An asymmetrical half‐bridge converter is considered in this study and the faults of single‐phase open and two‐phase open are analysed. Three different bus positions are defined. On the basis of a fast Fourier transform algorithm with Blackman window interpolation, the bus current spectrums before and after open‐circuit faults are analysed in details. Their fault characteristics are extracted accurately by the normalisations of the phase fundamental frequency component and double phase fundamental frequency component, and the fault characteristics of the three bus detection schemes are also compared. The open‐circuit faults can be located by finding the relationship between the bus current and rotor position. The effectiveness of the proposed diagnosis method is validated by the simulation results and experimental tests.
Ant colony optimisation of decision tree and contingency table models for the discovery of gene–gene interactions
Authors: Sapin Emmanuel , Keedwell Ed , Frayling Tim
Published: August 2015

In this study, ant colony optimisation (ACO) algorithm is used to derive near‐optimal interactions between a number of single nucleotide polymorphisms (SNPs). This approach is used to discover small numbers of SNPs that are combined into a decision tree or contingency table model. The ACO algorithm is shown to be very robust as it is proven to be able to find results that are discriminatory from a statistical perspective with logical interactions, decision tree and contingency table models for various numbers of SNPs considered in the interaction. A large number of the SNPs discovered here have been already identified in large genome‐wide association studies to be related to type II diabetes in the literature, lending additional confidence to the results.
Simple evaluation of squared weight
Authors: Fair I.J. , Carle E.R.
Published: August 2015

Squared weight is an excellent metric on which to base codeword selection in DC‐free multimode coding. It has, however, been considered too complex to implement in practice. In this Letter, the authors present a simple approach to evaluate this metric that enables it to be implemented in high‐speed digital logic.
Invertibility of retarded response functions for Laplace transformable potentials: Application to one-body reduced density matrix functional theory
Authors: Giesbertz K. J. H.
Published: August 2015

A theorem for the invertibility of arbitrary response functions is presented under the following conditions: the time dependence of the potentials should be Laplace transformable and the initial state should be a ground state, though it might be degenerate. This theorem provides a rigorous foundation for all density-functional-like theories in the time-dependent linear response regime. Especially for time-dependent one-body reduced density matrix (1RDM) functional theory, this is an important step forward, since a solid foundation has currently been lacking. The theorem is equally valid for static response functions in the non-degenerate case, so can be used to characterize the uniqueness of the potential in the ground state version of the corresponding density-functional-like theory. Such a classification of the uniqueness of the non-local potential in ground state 1RDM functional theory has been lacking for decades. With the aid of presented invertibility theorem presented here, a complete classification of the non-uniqueness of the non-local potential in 1RDM functional theory can be given for the first time.
Matrix geometries and fuzzy spaces as finite spectral triples
Authors: Barrett John W.
Published: August 2015

A class of real spectral triples that are similar in structure to a Riemannian manifold but have a finite-dimensional Hilbert space is defined and investigated, determining a general form for the Dirac operator. Examples include fuzzy spaces defined as real spectral triples. Fuzzy 2-spheres are investigated in detail, and it is shown that the fuzzy analogues correspond to two spinor fields on the commutative sphere. In some cases, it is necessary to add a mass mixing matrix to the commutative Dirac operator to get a precise agreement for the eigenvalues.
Hollow vortices and minimal surfaces
Authors: Traizet Martin
Published: August 2015

We consider an overdetermined elliptic problem known as the hollow vortex problem. We prove that the solutions to this problem are in 1:1 correspondence with minimal graphs bounded by horizontal symmetry lines. We use this correspondence to give various examples of domains with hollow vortices.
On the Einstein-Weyl and conformal self-duality equations
Authors: Dunajski M. , Ferapontov E. V. , Kruglikov B.
Published: August 2015

The equations governing anti-self-dual and Einstein-Weyl conformal geometries can be regarded as “master dispersionless systems” in four and three dimensions, respectively. Their integrability by twistor methods has been established by Penrose and Hitchin. In this note, we present, in specially adapted coordinate systems, explicit forms of the corresponding equations and their Lax pairs. In particular, we demonstrate that any Lorentzian Einstein-Weyl structure is locally given by a solution to the Manakov-Santini system, and we find a system of two coupled third-order scalar partial differential equations for a general anti-self-dual conformal structure in neutral signature.
Observing the semiconducting band-gap alignment of MoS2 layers of different atomic thicknesses using a MoS2/SiO2/Si heterojunction tunnel diode
Authors: Nishiguchi Katsuhiko , Castellanos-Gomez Andres , Yamaguchi Hiroshi , Fujiwara Akira , van der Zant Herre S. J. , Steele Gary A.
Published: August 2015

We demonstrate a tunnel diode composed of a vertical MoS2/SiO2/Si heterostructure. A MoS2 flake consisting four areas of different thicknesses functions as a gate terminal of a silicon field-effect transistor. A thin gate oxide allows tunneling current to flow between the n-type MoS2 layers and p-type Si channel. The tunneling-current characteristics show multiple negative differential resistance features, which we interpret as an indication of different conduction-band alignments of the MoS2 layers of different thicknesses. The presented tunnel device can be also used as a hybrid-heterostructure device combining the advantages of two-dimensional materials with those of silicon transistors.
On the origin of multi-component bulk metallic glasses: Atomic size mismatches and de-mixing
Authors: Zhang Kai , Dice Bradley , Liu Yanhui , Schroers Jan , Shattuck Mark D. , O’Hern Corey S.
Published: August 2015

The likelihood that an undercooled liquid vitrifies or crystallizes depends on the cooling rate R. The critical cooling rate Rc, below which the liquid crystallizes upon cooling, characterizes the glass-forming ability (GFA) of the system. While pure metals are typically poor glass formers with Rc>1012K/s, specific multi-component alloys can form bulk metallic glasses (BMGs) even at cooling rates below R∼1K/s. Conventional wisdom asserts that metal alloys with three or more components are better glass formers (with smaller Rc) than binary alloys. However, there is currently no theoretical framework that provides quantitative predictions for Rc for multi-component alloys. In this manuscript, we perform simulations of ternary hard-sphere systems, which have been shown to be accurate models for the glass-forming ability of BMGs, to understand the roles of geometric frustration and demixing in determining Rc. Specifically, we compress ternary hard sphere mixtures into jammed packings and measure the critical compression rate, below which the system crystallizes, as a function of the diameter ratios σB/σA and σC/σA and number fractions xA, xB, and xC. We find two distinct regimes for the GFA in parameter space for ternary hard spheres. When the diameter ratios are close to 1, such that the largest (A) and smallest (C) species are well-mixed, the GFA of ternary systems is no better than that of the optimal binary glass former. However, when σC/σA ≲ 0.8 is below the demixing threshold for binary systems, adding a third component B with σC < σB < σA increases the GFA of the system by preventing demixing of A and C. Analysis of the available data from experimental studies indicates that most ternary BMGs are below the binary demixing threshold with σC/σA < 0.8.
Pattern manipulation via on-chip phase modulation between orbital angular momentum beams
Authors: Li Huanlu , Strain Michael J. , Meriggi Laura , Chen Lifeng , Zhu Jiangbo , Cicek Kenan , Wang Jianwei , Cai Xinlun , Sorel Marc , Thompson Mark G. , Yu Siyuan
Published: August 2015

An integrated approach to thermal modulation of relative phase between two optical vortices with opposite chirality has been demonstrated on a silicon-on-insulator substrate. The device consists of a silicon-integrated optical vortex emitter and a phase controlled 3 dB coupler. The relative phase between two optical vortices can be actively modulated on chip by applying a voltage on the integrated heater. The phase shift is shown to be linearly proportional to applied electrical power, and the rotation angle of the interference pattern is observed to be inversely proportional to topological charge. This scheme can be used in lab-on-chip, communications and sensing applications. It can be intentionally implemented with other modulation elements to achieve more complicated applications.
Detection of spin torque magnetization dynamics through low frequency noise
Authors: Cascales Juan Pedro , Herranz David , Ebels Ursula , Katine Jordan A. , Aliev Farkhad G.
Published: August 2015

We present a comparative study of high frequency dynamics and low frequency noise in elliptical magnetic tunnel junctions with lateral dimensions under 100 nm presenting current-switching phenomena. The analysis of the high frequency oscillation modes with respect to the current reveals the onset of a steady-state precession regime for negative bias currents above J=107A/cm2, when the magnetic field is applied along the easy axis of magnetization. By the study of low frequency noise for the same samples, we demonstrate the direct link between changes in the oscillation modes with the applied current and the normalised low frequency (1/f) noise as a function of the bias current. These findings prove that low frequency noise studies could be a simple and powerful technique to investigate spin-torque based magnetization dynamics.
Ge-on-Si photodiode with black silicon boosted responsivity
Authors: Steglich M. , Oehme M. , Käsebier T. , Zilk M. , Kostecki K. , Kley E.-B. , Schulze J. , Tünnermann A.
Published: August 2015

Normal-incidence Ge-on-Si photodiodes with 300 nm thick intrinsic Ge absorber layer and black silicon light-trapping are fabricated and analyzed with regard to their responsivity. Compared to a standard Ge-on-Si photodiode without black silicon, the black silicon device exhibits a 3-times increased responsivity of 0.34 A/W at 1550 nm. By that, the problematic bandwidth-responsivity trade-off in ultrafast Ge-on-Si detectors can be widely overcome. The black silicon light-trapping structure can be applied to the device rear during back-end processing.
Electronic structure and magnetic properties of zigzag blue phosphorene nanoribbons
Authors: Hu Tao , Hong Jisang
Published: August 2015

We investigated the electronic structure and magnetism of zigzag blue phosphorene nanoribbons (ZBPNRs) using first principles density functional theory calculations by changing the widths of ZBPNRs from 1.5 to 5 nm. In addition, the effect of H and O passivation was explored as well. The ZBPNRs displayed intra-edge antiferromagnetic ground state with a semiconducting band gap of ∼0.35 eV; and this was insensitive to the edge structure relaxation effect. However, the edge magnetism of ZBPNRs disappeared with H-passivation. Moreover, the band gap of H-passivated ZBPNRs was greatly enhanced because the calculated band gap was ∼1.77 eV, and this was almost the same as that of two-dimensional blue phosphorene layer. For O-passivated ZBPNRs, we also found an intra-edge antiferromagnetic state. Besides, both unpassivated and O-passivated ZBPNRs preserved almost the same band gap. We predict that the electronic band structure and magnetic properties can be controlled by means of passivation. Moreover, the edge magnetism can be also modulated by the strain. Nonetheless, the intrinsic physical properties are size independent. This feature can be an advantage for device applications because it may not be necessary to precisely control the width of the nanoribbon.
Cl-doping of Te-rich CdTe: Complex formation, self-compensation and self-purification from first principles
Authors: Lindström A. , Klintenberg M. , Sanyal B. , Mirbt S.
Published: August 2015

The coexistence in Te-rich CdTe of substitutional Cl-dopants, ClTe, which act as donors, and Cd vacancies, VCd−1, which act as electron traps, was studied from first principles utilising the HSE06 hybrid functional. We find ClTe to preferably bind to VCd−1 and to form an acceptor complex, (ClTe–VCd)−1. The complex has a (0,-1) charge transfer level close to the valence band and shows no trap state (deep level) in the band gap. During the complex formation, the defect state of VCd−1 is annihilated and leaves the Cl-doped CdTe bandgap without any trap states (self-purification). We calculate Cl-doped CdTe to be semi-insulating with a Fermi energy close to midgap. We calculate the formation energy of the complex to be sufficiently low to allow for spontanous defect formation upon Cl-doping (self-compensation). In addition, we quantitatively analyse the geometries, DOS, binding energies and formation energies of the (ClTe–VCd) complexes.
Model of care for a changing healthcare system: are there foundational pillars for design?
Authors: Booker Catriona , Turbutt Adam , Fox Robyn
Published: August 2015

Currently, healthcare organisations are being challenged to provide optimal clinical services within budget limitations while simultaneously being confronted by aging consumers and labour and skill shortages. Within this dynamic and changing environment, the ability to remain responsive to patient needs while managing these issues poses further challenges. Development or review of the model of care (MOC) may provide a possible solution to support efficiencies in service provision. Although MOC are not readily understood or appreciated as an efficiency strategy, they can be more easily explained by considering several recurring pillars when developing or redesigning an MOC. Generic and recurring foundational pillars include integrated care models, team functioning and communication, leadership, change management and lean thinking. These foundational pillars should be incorporated into the development and application of MOC in order to achieve desired outcomes. However, sustainability requires continuous review to enable improvement and must be integrated into routine business. Moreover, successful review of MOC requires collaboration and commitment by all stakeholders. Leaders are critical to motivating clinicians and stakeholders in the review process. Further, it is imperative that leaders engage stakeholders to commit to support the agreed strategies designed to provide efficient and comprehensive healthcare services. Redesign of MOC can significantly improve patient care by applying the agreed strategies. In the current healthcare environment, these strategies can favourably affect healthcare expenditure and, at the same time, improve the quality of interprofessional health services. What is known about the topic? Clarity concerning ‘model of care’ (MOC) terminology, how the healthcare professional interprets the framework and the implications for practice are not well understood. There is significant literature postulating the value of speciality MOC, but there is minimal literature that identifies the common foundational pillars that can be used in any review or development of MOC. What does this paper add? Extensive review of MOC literature and the resultant synthesis of these data have been undertaken to appreciate the essential components that support best patient outcomes. This paper proffers the value of five critical and consistent foundational pillars that should be incorporated into the development or revision of all MOC in order to support efficiencies and improvement of the patient experience. What are the implications for practitioners? Inclusion of these five foundational pillars into the development or revision of MOC will potentially generate increased staff satisfaction, synergistic team processes and improved flexibility and responsiveness to service demand. In addition, positive effects on healthcare expenditure and enhanced quality of interdisciplinary healthcare services should be realised.
State of origin: Australian states use widely different resources for hospital management of hip fracture, but achieve similar outcomes
Authors: Ireland Anthony W. , Kelly Patrick J. , Cumming Robert G.
Published: August 2015

Objective Hospital management of hip fracture varies widely with regard to length of stay, delivery of post-surgical care and costs. The present study compares the association between hospital utilisation and costs and patient outcomes in the six Australian states. Methods The present study was a retrospective cohort study of linked administrative databases for 2530 Australian veterans and war widows aged ≥65 years, hospitalised for hip fracture in 2008–09. Department of Veterans’ Affairs datasets for hospital episodes, residential aged care admissions and date of death were linked. Patient characteristics, hospital utilisation and process data, rates of mortality and residential care placement and delivery of community services were compared for patients from each of the states. Results There were no significant differences in fracture incidence, patient demographics or fracture type among the states. Adjusted total mean length of hospital stay ranged from 24.7 days (95% confidence interval (CI) 22.3–27.5 days) to 35.0 days (95% CI 32.6–37.6 days; P < 0.001) and adjusted total hospital cost ranged between A$24 792 (95% CI A$22 191–A$27 700) and A$35 494 (95% CI A$32 853–A$38 343; P < 0.001). Rates of referral to rehabilitation ranged from 31.7% to 50.4% (P = 0.003). At 1 year, there were no significant differences between states for key outcome determinants of mortality (P = 0.71) or for the proportion of patients who retained their independent living status (P = 0.66). Conclusion Hospital resources for management of hip fracture differ substantially among the Australian states. Key medium-term patient outcomes do not show significant differences. A potential for substantial cost-efficiencies without increased risk to patient welfare is suggested. What is known about this topic? Hospital resources deployed in the initial management of hip fracture differ widely between countries, regions and individual hospitals. Patient outcomes also vary widely, but are inconsistently associated with resource outlays. What does this paper add? The paper describes the different resource outlays for management of hip fracture in six Australian jurisdictions and the absence of equivalent differences in medium-term patient outcomes. What are the implications for practitioners? Efficiencies in hospital management of hip fracture may be achievable without negative consequences for patients. The elements of models of care should be examined for their contribution to early and later patient outcomes.
Convergent synthesis of 4,5-branched inner-core oligosaccharides of lipopoly- and lipooligosaccharides
Authors: Yi Ruiqin , Narimoto Hirofumi , Nozoe Miku , Ichiyanagi Tsuyoshi
Published: August 2015

The convergent synthesis of branched inner-core oligosaccharides of lipopoly- and lipooligosaccharide with a 3-deoxy-d-manno-oct-2-ulosonic acid (Kdo) disaccharide acceptor was achieved. The l-glycero-d-manno-heptopyranose (Hep) units for the branched core oligosaccharide Galβ(1-4)Glcβ(1-4)Hep and Hepα(1-3)Hep were prepared from the corresponding Hep building blocks. To obtain 4,5-branched core oligosaccharide structures, the common acceptor Kdoα(2-4)Kdo was glycosylated with the Hep units.
MiT/TFE transcription factors are activated during mitophagy downstream of Parkin and Atg5
Authors: Nezich Catherine L. , Wang Chunxin , Fogel Adam I. , Youle Richard J.
Published: August 2015

The kinase PINK1 and ubiquitin ligase Parkin can regulate the selective elimination of damaged mitochondria through autophagy (mitophagy). Because of the demand on lysosomal function by mitophagy, we investigated a role for the transcription factor EB (TFEB), a master regulator of lysosomal biogenesis, in this process. We show that during mitophagy TFEB translocates to the nucleus and displays transcriptional activity in a PINK1- and Parkin-dependent manner. MITF and TFE3, homologues of TFEB belonging to the same microphthalmia/transcription factor E (MiT/TFE) family, are similarly regulated during mitophagy. Unlike TFEB translocation after starvation-induced mammalian target of rapamycin complex 1 inhibition, Parkin-mediated TFEB relocalization required Atg9A and Atg5 activity. However, constitutively active Rag guanosine triphosphatases prevented TFEB translocation during mitophagy, suggesting cross talk between these two MiT/TFE activation pathways. Analysis of clustered regularly interspaced short palindromic repeats–generated TFEB/MITF/TFE3/TFEC single, double, and triple knockout cell lines revealed that these proteins partly facilitate Parkin-mediated mitochondrial clearance. These results illuminate a pathway leading to MiT/TFE transcription factor activation, distinct from starvation-induced autophagy, which occurs during mitophagy.
A developmental biologist’s “outside-the-cell” thinking
Authors: Sherwood David R.
Published: August 2015

A major gap in our understanding of cell biology is how cells generate and interact with their surrounding extracellular matrix. Studying this problem during development has been particularly fruitful. Recent work on the basement membrane in developmental systems is transforming our view of this matrix from one of a static support structure to that of a dynamic scaffold that is regularly remodeled to actively shape tissues and direct cell behaviors.
Jan van Deursen: From knockout pioneer to antiaging innovator
Authors: Powell Kendall
Published: August 2015

van Deursen’s career visits both sides of the cancer–senescence coin.
Temperature Affects Aggressiveness and Fungicide Sensitivity of Four Pythium spp. that Cause Soybean and Corn Damping Off in Iowa
Authors: Matthiesen R. L. , Ahmad A. A. , Robertson A. E.
Published: August 2015

Damping off of soybean and corn, caused by Pythium spp., is favored by cool temperatures and wet soil conditions and is primarily managed using fungicide seed treatments. The goal of this research was to determine the effect of temperature on aggressiveness and fungicide sensitivity of Pythium spp. recovered from soybean and corn in Iowa. A total of 21 isolates of four of the most prevalent Pythium spp. in Iowa were screened. Seed and seedling assays were used to quantify the aggressiveness of P. lutarium, P. oopapillum, P. sylvaticum, and P. torulosum on soybean and corn at 13, 18, and 23°C. Isolates recovered from soybean or corn were equally pathogenic on both hosts. P. torulosum was more aggressive at 13°C compared with 18 and 23°C. Conversely, P. sylvaticum was more aggressive at 18 and 23°C than at 13°C. A plate assay was used to assess fungicide sensitivity to seven fungicides that are commonly used as seed treatments, and EC50 values at each of the three temperatures were determined and compared. EC50 values for P. torulosum were higher for all fungicides tested at 13°C, compared with 18 or 23°C, whereas EC50 values for P. sylvaticum were higher for all fungicides at 18 and 23°C compared with 13°C. These data contribute to our understanding of the effect of soil temperature on the risk of soybean and corn damping off, which may aid in the development of more effective management practices.
Spring Barley Resistance and Tolerance to the Cereal Cyst Nematode Heterodera avenae
Authors: Marshall Juliet M., , Smiley Richard W.
Published: August 2015

Heterodera avenae is a cereal cyst nematode that reduces wheat yields in the Pacific Northwest of the United States. Barley is also susceptible but there were no previous reports of resistance or tolerance to H. avenae in the United States. Spring barley cultivars were assayed in H. avenae-infested fields over 2 years. Cultivars were planted in plots treated or not treated with aldicarb. Forty-five cultivars were evaluated for the market classes of two- and six-row feed barley cultivars and two- and six-row malt barley cultivars. One two-row feed barley (‘Lenetah’) was ranked as resistant and four were tolerant or very tolerant. In total, 1 two-row malt barley (‘Odyssey’) was very resistant and 10 were tolerant or very tolerant. Two six-row feed and two six-row malt barley cultivars were tolerant or very tolerant but none were resistant. Seven feed barley cultivars were ranked as having a balance of at least moderate resistance plus moderate tolerance: ‘Champion’, Lenetah, ‘Xena’, ‘Idagold II’, ‘Transit’, ‘Millennium’, and ‘Goldeneye’. This is the first report of resistance and tolerance of barley in H. avenae-infested fields in the Pacific Northwest. Barley productivity can be improved by planting resistant plus tolerant cultivars or by using highly resistant and highly tolerant cultivars as parents in barley improvement programs.
Microscopic Aspects of Silicon-Mediated Rice Resistance to Leaf Scald
Authors: Araujo Leonardo , Paschoalino Rayane Silva , Rodrigues Fabrício Ávila
Published: August 2015

This study investigated the effect of silicon (Si) on the potentiation of rice resistance against leaf scald at the microscopic level. Rice plants (‘Primavera’) were grown in a nutrient solution containing 0 (−Si) or 2 mM (+Si) Si. The foliar Si concentration of the +Si plants (3.6 dag/kg) increased in comparison with the −Si plants (0.3 dag/kg). An X-ray microanalysis revealed that the leaf tissue of +Si plants infected with Microdochium oryzae had higher peaks and deposition of insoluble Si than that of −Si plants. The high foliar Si concentration for the +Si plants reduced the expansion of leaf scald lesions. Scanning electron microscopy revealed that fungal hyphae and appressorium-like structures of M. oryzae were more abundant in the leaf surface of −Si plants relative to +Si plants. At both histopathological and ultrastructural levels, fungal hyphae grew abundantly into the leaf tissue of −Si plants. By contrast, rice cell walls were rarely degraded and fungal hyphae were often surrounded by amorphous granular material in the leaf tissue of +Si plants. Conidiophores emerged from stomata 36 h after fungal penetration, and conidia were noticed inside the leaf tissue of the −Si plants in great abundance. The collective results of the present study showed a high concentration and deposition of Si and a considerable deposition of phenolic-like compounds in the leaf tissue of +Si plants. These results indicate that the potentiation of the phenylpropanoid pathway in these plants supplied with Si was favorable for the increase in rice resistance to leaf scald.
Borrelia yangtzensis sp. nov., a rodent-associated species in Asia, is related to Borrelia valaisiana
Authors: Margos Gabriele , Chu Chen-Yi , Takano Ai , Jiang Bao-Gui , Liu Wei , Kurtenbach Klaus , Masuzawa Toshiyuki , Fingerle Volker , Cao Wu-Chun , Kawabata Hiroki
Published: August 2015

Twenty-nine isolates of Lyme borreliosis (LB) group spirochaetes collected from ticks and rodents in China and Japan were included in a multilocus sequence analysis (MLSA). Using a different typing system, three of these strains had previously been identified as being divergent from other LB spirochaete species and the name ‘Borrelia yangtze’ sp. nov. was proposed. The data presented here confirm that the genetic distance, calculated using sequences of MLSA housekeeping genes, to other known LB group spirochaete species was < 95 % and toBorrelia valaisianawas 96.67 % (which represents the most closely related species within the group of LB spirochaetes). This and the fact that these strains are ecologically distinct fromB. valaisiana(rodent-transmitted vs bird-transmitted) provide strong support for the validation of the proposed species status. We suggest the nameBorrelia yangtzensissp. nov. The type strain is Okinawa-CW62T( = DSM 24625T = JCM 17189T).
Actinoplanes tropicalis sp. nov. and Actinoplanes cibodasensis sp. nov., isolated from leaf litter
Authors: Nurkanto Arif , Lisdiyanti Puspita , Hamada Moriyuki , Ratnakomala Shanti , Shibata Chiyo , Tamura Tomohiko
Published: August 2015

Two actinomycete strains, designated LIPI11-2-Ac034T and LIPI11-2-Ac042T, were isolated from leaf litter collected from Cibodas Botanical Garden, West Java, Indonesia. Phylogenetic analysis based on 16S rRNA gene sequences suggested that both isolates belong to the genus Actinoplanes. These isolates were closely related to Actinoplanes ferrugineus and Actinoplanes durhamensis with similarity values of 98.2 % and 97.7 % respectively, for strain LIPI11-2-Ac034T, and 99.0 % and 97.4–97.7 % respectively for strain LIPI11-2-Ac042T. Both isolates grew well on ISP 7 medium with brown soluble pigment production. Spores were motile and sporangia were irregular. The isolates contained meso-diaminopimelic acid in cell-wall hydrolysates, and mannose, glucose and galactose in whole-cell hydrolysates. The predominant menaquinone of strain LIPI11-2-Ac034T was MK-9(H4) while that of strain LIPI11-2-Ac042T was MK-9(H6). The major cellular fatty acids were iso-C16 : 0, iso-C15 : 0 and anteiso-C15 : 0 for strain LIPI11-2-Ac034T, and iso-C16 : 0, anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0 for strain LIPI11-2-Ac042T. Phosphatidylethanolamine was detected as the diagnostic polar lipid. The DNA G+C contents of strains LIPI11-2-Ac034T and LIPI11-2-Ac042T were 71.5 and 70.7 mol%, respectively. Based on the differential phenotypic characteristics and the results of DNA–DNA hybridization and phylogenetic analysis, it is proposed that strains LIPI11-2-Ac034T and LIPI11-2-Ac042T represent two novel species of the genus Actinoplanes, for which the names Actinoplanes tropicalis sp. nov. (type strain LIPI11-2-Ac034T = InaCC A459T = NBRC 110973T) and Actinoplanes cibodasensis sp. nov. (type strain LIPI11-2-Ac042T = InaCC A458T = NBRC 110974T) are proposed.
Micromonospora oryzae sp. nov., isolated from roots of upland rice
Authors: Kittiwongwattana Chokchai , Thanaboripat Dusanee , Laosinwattana Chamroon , Koohakan Prommart , Parinthawong Nonglak , Thawai Chitti
Published: August 2015

An actinomycete strain, designated CP2R9-1T, was isolated from root internal tissues of upland rice (Oryza sativa). Based on a polyphasic approach, strain CP2R9-1T was characterized as a member of the genus Micromonospora. meso-Diaminopimelic acid and 3-OH-diaminopimelic acid were present in the cell-wall peptidoglycan. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides, two unidentified phospholipids and four unidentified polar lipids. Predominant menaquinones were MK-9(H4), MK-9(H6) and MK-10(H4). Whole-cell sugars consisted of ribose, xylose, arabinose and glucose. Phylogenetic analysis of the nearly complete 16S rRNA gene sequence suggested that strain CP2R9-1T was closely related to Micromonospora haikouensis 232617T (99.32 % similarity), Micromonospora carbonacea DSM 43168T (99.18 %) and Micromonospora krabiensis MA-2T (99.16 %). Strain CP2R9-1T was distinct from its closest relatives based on low levels of DNA–DNA relatedness (21.3 ± 0.1–41.7 ± 0.7 %) and phenotypic differences. The results presented in this study showed that strain CP2R9-1T represents a novel species of the genus Micromonospora, for which the name Micromonospora oryzae sp. nov. is proposed. The type strain is CP2R9-1T ( = BCC 67266T = NBRC 110007T).
Halarchaeum grantii sp. nov., a moderately acidophilic haloarchaeon isolated from a commercial salt sample
Authors: Shimane Yasuhiro , Minegishi Hiroaki , Echigo Akinobu , Kamekura Masahiro , Itoh Takashi , Ohkuma Moriya , Tsubouchi Taishi , Usui Keiko , Maruyama Tadashi , Usami Ron , Hatada Yuji
Published: August 2015

Three moderately acidophilic, halophilic archaeal strains, MH1-243-3T, MH1-243-5 and MH1-243-6, were isolated from a commercial salt sample made from seawater in Okinawa, Japan. Cells of the three strains were pleomorphic and stained Gram-negative. Colonies of the strains were orange–red-pigmented. Strain MH1-243-3T was able to grow at 15–27 % (w/v) NaCl (optimum 24 °C), at pH 4.5–6.5 (pH 5.5) and at 35–50 °C (45 °C). Strains MH1-243-5 and MH1-243-6 grew within slightly different ranges (shown in text). The 16S rRNA gene sequences of the three strains were identical, and the closest phylogenetic relative was Halarchaeum salinum MH1-34-1T with 97.0 % similarity. The rpoB′ gene sequences of the three strains were also identical, and the closest phylogenetic relative was Halarchaeum acidiphilum JCM 16109T with 92.0 % similarity. The DNA G+C content of MH1-243-3T, MH1-243-5 and MH1-243-6 was 65.2 mol%. The levels of DNA–DNA relatedness amongst the three strains were 84.1–99.8 %, while that between MH1-243-3T and H. salinum MH1-34-1T was 30.6 % and 31.6 % (reciprocally), and those between MH1-243-3T and type strains of other species in the genus Halarchaeum were 42.3–29.4 %. Based on the phenotypic, genotypic and phylogenetic analyses, it is proposed that the isolates should represent a novel species of the genus Halarchaeum, for which the name Halarchaeum grantii sp. nov. is proposed. The type strain is MH1-243-3T ( = JCM 19585T = KCTC 4142T), isolated from commercial sea salt produced in Okinawa, Japan. MH1-243-5 ( = JCM 19586) and MH1-243-6 ( = JCM 18422) are additional strains of the species.
Rapid Isolation of Nuclei from Cells In Vitro
Authors: Nabbi Arash , Riabowol Karl
Published: August 2015

This protocol presents a rapid, efficient, and practical (REAP) method to separate nuclei from cultured cells in vitro with as little damage and contamination as possible. The REAP procedure is performed at low temperature and takes <2 min, which minimizes protein degradation, protein modification, and diffusion of soluble proteins out of the nuclear compartment while maintaining the integrity of protein complexes. A mild detergent, NP-40, is used together with mild mechanical shearing to disrupt the plasma membrane, leaving the nuclear membrane intact. The REAP method can be used with various cell lines grown in vitro and requires minimal optimization. The isolated nuclei are suitable for numerous downstream applications (e.g., western blotting, 2D gel electrophoresis, and immunoprecipitation). If desired, aliquots of whole-cell lysate and the cytoplasmic fraction can be saved for comparison.
Isolation of Pure Nuclei Using a Sucrose Method
Authors: Nabbi Arash , Riabowol Karl
Published: August 2015

This protocol describes a modified version of a widely used method to isolate nuclei from tissue culture cells. It involves mechanical homogenization of cells in isotonic sucrose, followed by velocity centrifugation of nuclei through a denser layer of sucrose. This method, which yields highly pure and intact nuclei, can be optimized for use in various types of tissues and cells. Limitations of the method, alternative options for homogenization, and recommendations for the use of detergents are discussed.
Deep Mutational Scanning: Library Construction, Functional Selection, and High-Throughput Sequencing
Authors: Starita Lea M. , Fields Stanley
Published: August 2015

Deep mutational scanning is a highly parallel method that uses high-throughput sequencing to track changes in >105 protein variants before and after selection to measure the effects of mutations on protein function. Here we outline the stages of a deep mutational scanning experiment, focusing on the construction of libraries of protein sequence variants and the preparation of Illumina sequencing libraries.
Deep Mutational Scanning: Calculating Enrichment Scores for Protein Variants from DNA Sequencing Output Files
Authors: Starita Lea M. , Fields Stanley
Published: August 2015

During a deep mutational scanning experiment, a collection of variants of a given protein is subjected to high-throughput sequencing before and after selection. The variants that perform well during selection will increase in abundance, whereas those that perform poorly will decrease. Generating a sequence–function map of a protein from a deep mutational scan requires the calculation and comparison of the enrichment scores for each protein variant, based on the results of high-throughput DNA sequencing output files. Here we describe the use of the software program Enrich, which was written specifically for the data analysis phase of a deep mutational scanning experiment.
Removal of rRNA from Deproteinized, Phenol-Extracted Total RNA by Hybrid Selection
Authors: Nilsen Timothy W.
Published: August 2015

In this protocol, rRNAs are selectively removed from a total RNA sample by hybridizing the rRNAs to complementary biotinylated oligodeoxynucleotides that can be affinity-purified using streptavidin beads, leaving all other RNAs behind. Although commercially available kits can be used to perform this procedure, they are expensive. We recommend that investigators order species-specific oligodeoxynucleotides for their own applications. There are well-established secondary structure predictions for all rRNAs.
Monitoring the Localization of MAP1LC3B by Indirect Immunofluorescence
Authors: Ktistakis Nicholas T.
Published: August 2015

The autophagy protein MAP1LC3B (microtubule-associated proteins 1A/1B light chain 3B, hereafter referred to as LC3B), which is one of several mammalian homologs of yeast Atg8, is one of the most popular markers for autophagosome formation because its distribution changes from cytosolic/diffuse to punctate upon the induction of autophagy. In many settings, plasmids encoding fluorescently tagged LC3B are introduced into cells, and the subsequent autophagy response is monitored. However, for a variety of reasons, it would be desirable also to have a protocol to monitor the localization of endogenous LC3B under various conditions. This protocol provides such a methodology for the staining of endogenous LC3B by indirect immunofluorescence, such that autophagy responses can be monitored in mammalian cells.
Just for us?
Authors: Braun Artur
Published: August 2015

It is a regrettable decision by Karlsruhe Institute of Technology that ANKA, the Angströmquelle Karlsruhe, is terminating its external synchrotron user support program. ANKA has an excellent performance review grading sheet and has been a valuable source and resource to international users for over a decade. There is concern among users that ANKA's decision could become an example for other synchrotrons as well.
Negative expectancies measured with the Substance Use Beliefs Questionnaire can differentiate controls from those in treatment for alcohol dependence
Authors: Kouimtsidis Christos , Stahl Daniel , West Robert , Drummond Colin
Published: August 2015

Purpose

– The purpose of this paper is to test the discriminative validity of the Substance Use Beliefs Questionnaire (SUBQ) with alcohol dependent users, by assessing if the new tool can successfully differentiate between two extreme groups.

Design/methodology/approach

– The criterion used to select the two extreme groups was participation or not in treatment for alcohol dependence. Score of the Severity of Alcohol Dependence Questionnaire (SADQ) was used as a secondary confirmation criterion of extreme difference.

Findings

– In all, 98 staff and 94 people in treatment for alcohol dependence were recruited. The treatment group scored 30.83 higher than the control on SADQ, 10.76 on positive and 28.98 on negative expectancies. Negative expectancies score had correctly classified 88.5 per cent and positive expectancies score only 66 per cent of the original grouped cases. The area under the Receiver Operating Characteristics (ROC) curve for negative expectancies was 0.94 (very good) with a cut-off point of 43.5 with 89 per cent sensitivity and 92 per cent specificity. The area under the ROC curve for positive expectancies was 0.73 (fair). Due to the shape it was difficult to identify a cut-off point.

Research limitations/implications

– The results support the discriminative validity of the negative expectancies sub scale of the SUBQ between two extreme groups. With only the use of negative expectancies score participants could be classified correctly to those of the control and those of the treatment group.

Originality/value

– SUBQ is the first tool to measure outcome expectancies across substances, facilitating relevant research with poly substance users. Future research needs to explore the discriminative validity of the tool with the other three substance groups (smokers, stimulant and opioids users), involved in the development and validation of the SUBQ.
“Take home” naloxone: what does the evidence base tell us?
Authors: Breedvelt Josefien J. F. , Tracy Derek K. , Dickenson Emily C. , Dean Lucy V.
Published: August 2015

Purpose

– Opiod users are at high risk of suffering from drug overdoses. Naloxone has been used for decades in emergency treatment settings to reverse the symptoms of opioid overdose. Pilot studies and regional programmes have been rolled out to make naloxone more widely available. This review of user/carer administration of naloxone – so-called “take home naloxone” – aims to provide health professionals and interested readers with an up-to-date evidence base, clinical implications and practical concern considerations for such community management. The paper aims to discuss these issues.

Design/methodology/approach

– A review and analysis of the recent literature on naloxone.

Findings

– The evidence base suggests training and education is effective in preparing users for wider naloxone distribution. Furthermore, studies of varying quality indicate that naloxone may prove useful in reducing overdose-related deaths. However, even after implementation ineffective response techniques continued to be used at times and there remained a heistance to call medical services post overdose. Intranasal naloxone may reduce some of the risks associated with intramuscular naloxone. Ethical considerations, including provision of a needle and syringe kit to the community, should be considered. Studies suffered from a lack of follow-up data and methodological difficulties are associated with establishing opioid-related deaths post implementation. Two running trials in the UK might mitigate these concerns.

Research limitations/implications

– Future research is needed to address wider context of an overdose and targeting associated risk factors.

Originality/value

– Clinicians and other professionals will be informed on the most up-to-date evidence base and which areas are improtant to consider when take-home naloxone is introduced in their services.
Dissidents with an innovation cause? Non-institutionalized actors’ online social knowledge sharing, solution-finding tensions and technology management innovation
Authors: de Kervenoael Ronan , Bisson Christophe , Palmer Mark
Published: August 2015

Purpose

– Traditionally, most studies focus on institutionalized management-driven actors to understand technology management innovation. The purpose of this paper is to argue that there is a need for research to study the nature and role of dissident non-institutionalized actors’ (i.e. outsourced web designers and rapid application software developers). The authors propose that through online social knowledge sharing, non-institutionalized actors’ solution-finding tensions enable technology management innovation.

Design/methodology/approach

– A synthesis of the literature and an analysis of the data (21 interviews) provided insights in three areas of solution-finding tensions enabling management innovation. The authors frame the analysis on the peripherally deviant work and the nature of the ways that dissident non-institutionalized actors deviate from their clients (understood as the firm) original contracted objectives.

Findings

– The findings provide insights into the productive role of solution-finding tensions in enabling opportunities for management service innovation. Furthermore, deviant practices that leverage non-institutionalized actors’ online social knowledge to fulfill customers’ requirements are not interpreted negatively, but as a positive willingness to proactively explore alternative paths.

Research limitations/implications

– The findings demonstrate the importance of dissident non-institutionalized actors in technology management innovation. However, this work is based on a single country (USA) and additional research is needed to validate and generalize the findings in other cultural and institutional settings.

Originality/value

– This paper provides new insights into the perceptions of dissident non-institutionalized actors in the practice of IT managerial decision making. The work departs from, but also extends, the previous literature, demonstrating that peripherally deviant work in solution-finding practice creates tensions, enabling management innovation between IT providers and users.
Information disclosure of social media users
Authors: Benson Vladlena , Saridakis George , Tennakoon Hemamaali
Published: August 2015

Purpose

– The purpose of this paper is to bridge the gap in the existing literature by exploring the antecedents of information disclosure of social media users. In particular, the paper investigates the link between information disclosure, control over personal information, user awareness and security notices in the social context, all of which are shown to be different from existing studies in e-commerce environments.

Design/methodology/approach

– The authors collected and analysed data from 514 social network users. The model is estimated using ordinary least squares and robust standard errors are estimated using the Huber-White sandwich estimators.

Findings

– The results show that in social networking contexts, control over personal information is negatively and statistically associated with information disclosure. However, both user awareness and security notices have a positive statistical effect on information disclosure.

Originality/value

– Whilst research on issues of individual information privacy in e-commerce is plentiful, the area of social networking and privacy protection remains under-explored. This paper provides a useful model for analysing information disclosure behaviour on social networks. The authors discuss the practical implications of the findings for actors in social media interactions.