bluuebunny/crossref_metadata_2025 huggingface dataset:
Design of high‐efficiency non‐insulated step‐up converters
Authors: Schirone Luigi , Macellari Michele
Published: March 2015

The design techniques of high‐efficiency non‐insulated step‐up converters were upgraded on the basis of a comprehensive model of power losses, also including several feeble effects whose contribution, although overshadowed at large power by conduction and switching losses, is relevant in the low‐power regime and at the maximum power point. The thorough loss analysis was used as a basis to design state‐of‐art high‐boost‐ratio three levels neutral‐point‐clamped dc–dc converters, whose experimental efficiency showed an outstanding agreement with theoretical predictions in a wide range of operating conditions.
A protection strategy for micro‐grids based on positive‐sequence component
Authors: Mirsaeidi Sohrab , Mat Said Dalila , Mustafa Mohammad Wazir , Hafiz Habibuddin Mohammad
Published: March 2015

In recent years, the concept of micro‐grid has appeared as an appropriate way for the integration of distributed energy resources (DERs) in the distribution networks. However, micro‐grids have encountered a number of challenges from control and protection aspects. One of the main issues relevant to the protection of micro‐grids is to develop a suitable protection technique which is effective in both grid‐connected and stand‐alone operation modes. This study presents a micro‐grid protection scheme based on positive‐sequence component using phasor measurement units and designed microprocessor‐based relays (MBRs) along with a digital communication system. The proposed scheme has the ability to protect radial and looped micro‐grids against different types of faults with the capability of single‐phase tripping. Furthermore, since the MBRs are capable of updating their pickup values (upstream and downstream equivalent positive‐sequence impedances of each line) after the first change in the micro‐grid configuration (such as transferring from grid‐connected to islanded mode and or disconnection of a line, bus or DER either in grid‐connected mode or in islanded mode), they can protect micro‐grid lines and buses against subsequent faults. Finally, in order to verify the effectiveness of the suggested scheme and the designed MBR, several simulations have been undertaken using DIgSILENT PowerFactory and MATLAB software packages.
Doping effect on the evolution of the pairing symmetry in n-type superconductor near antiferromagnetic phase boundary
Authors: Charikova T. B. , Shelushinina N. G. , Harus G. I. , Neverov V. N. , Petukhov D. S. , Petukhova O. E. , Ivanov A. A.
Published: March 2015

We present the investigation results of the in-plane ρ(T) resistivity tensor at the temperature range 0.4–40 K in magnetic fields up to 90 kOe (H || c, J || ab) for electron-doped Nd2−xCexCuO4+δ with different degree of disorder near antiferromagnetic-superconducting phase boundary. We have experimentally found that for optimally doped compound both the upper critical field slope and the critical temperature decrease with increasing of the disorder parameter (d-wave pairing) while in the case of the underdoped system the critical temperature remains constant and dHc2/dT increases with increasing of the disorder (s-wave pairing). These features suggest a possible implementation of the complex mixture state as the s + id pairing.
Anomalous fast ion losses at high β on the tokamak fusion test reactor
Authors: Fredrickson E. D. , Bell M. G. , Budny R. V. , Darrow D. S. , White R.
Published: March 2015

This paper describes experiments carried out on the Tokamak Fusion Test Reactor (TFTR) [R. J. Hawryluk et al., Plasma Phys. Controlled Fusion 33, 1509 (1991)] to investigate the dependence of β-limiting disruption characteristics on toroidal field strength. The hard disruptions found at the β-limit in high field plasmas were not found at low field, even for β's 50% higher than the empirical β-limit of βn ≈ 2 at high field. Comparisons of experimentally measured β's to TRANSP simulations suggest anomalous loss of up to half of the beam fast ions in the highest β, low field shots. The anomalous transport responsible for the fast ion losses may at the same time broaden the pressure profile. Toroidal Alfvén eigenmodes, fishbone instabilities, and Geodesic Acoustic Modes are investigated as possible causes of the enhanced losses. Here, we present the first observations of high frequency fishbones [F. Zonca et al., Nucl. Fusion 49, 085009 (2009)] on TFTR. The interpretation of Axi-symmetric Beam-driven Modes as Geodesic Acoustic Modes and their possible correlation with transport barrier formation are also presented.
Three-dimensional topological insulator based on a strained HgTe film
Authors: Kozlov D. A. , Kvon Z. D. , Savchenko M. L. , Weiss D. , Mikhailov N. N. , Dvoretskii S. A.
Published: March 2015

We investigated electron and hole transport in a three-dimensional topological insulator based on a high-mobility (up to 4 × 105 cm2/V·s) 80-nm-thick strained mercury telluride film. The presence of the gate electrode made it possible to shift the position of the Fermi energy from the valence band through the bulk gap to the conduction band. Specific features observed in classical and quantum transport allowed us to disentangle the contributions to the conductivity by bulk holes, bulk electrons, and the Dirac electrons on the surfaces of the film.
Diffusion-limited kinetics of the antiferromagnetic to ferrimagnetic λ-transition in Fe1−xS
Authors: Herbert F. William , Krishnamoorthy Aravind , Yildiz Bilge , Van Vliet Krystyn J.
Published: March 2015

Fe1−xS (0.08 ≤ x ≤ 0.11) exhibits a simultaneous magneto-structural “λ-transition” at approximately 200 °C. Time-dependent magnetization measurements demonstrate the λ-transition can be accurately modeled by a stretched exponential function, consistent with a nucleation-free, continuous reordering of the vacancy-bearing sublattice. The experimental result is supported by kinetic Monte Carlo simulations that confirm the activation energy for the transition to be 1.1 ± 0.1 eV—representing the iron vacancy migration energy in ordered Fe1−xS. A mechanistic understanding of the λ-transition enables potential functional uses of Fe1−xS such as thermally activated magnetic memory, switches, or storage.
The kinetics of the changes in charge carrier concentration with doping, for lead telluride-based alloys with transition metal impurities
Authors: Skipetrov E. P. , Knotko A. V. , Slynko E. I. , Slynko V. E.
Published: March 2015

A study of the crystal structure, phase and elemental composition, and galvanomagnetic properties of transition metal (Sc, Ti, Cr, V and Fe) doped alloys, based on lead telluride and synthesized using the Bridgman method. We determined the distribution of solid solution components along the length of single-crystal ingots. It is found that the increase in the impurity leads to the appearance of regions enriched with impurity content and microscopic inclusions of compounds similar in structure to the known compounds of impurity atoms with tellurium. We found a p-n inversion of conductivity type, metal-dielectric and dielectric-metal transitions, and pinning of the Fermi level by deep impurity levels, with increasing impurity content. We compare the kinetics of changes in the concentration of free charge carriers and the Fermi energy with doping, varying matrix composition, and type of impurity. A general model for reorganizing the electron structure of the studied alloys with doping, is proposed.
Short-time transport properties of bidisperse suspensions and porous media: A Stokesian dynamics study
Authors: Wang Mu , Brady John F.
Published: March 2015

We present a comprehensive computational study of the short-time transport properties of bidisperse hard-sphere colloidal suspensions and the corresponding porous media. Our study covers bidisperse particle size ratios up to 4 and total volume fractions up to and beyond the monodisperse hard-sphere close packing limit. The many-body hydrodynamic interactions are computed using conventional Stokesian Dynamics (SD) via a Monte-Carlo approach. We address suspension properties including the short-time translational and rotational self-diffusivities, the instantaneous sedimentation velocity, the wavenumber-dependent partial hydrodynamic functions, and the high-frequency shear and bulk viscosities and porous media properties including the permeability and the translational and rotational hindered diffusivities. We carefully compare the SD computations with existing theoretical and numerical results. For suspensions, we also explore the range of validity of various approximation schemes, notably the pairwise additive approximations with the Percus-Yevick structural input. We critically assess the strengths and weaknesses of the SD algorithm for various transport properties. For very dense systems, we discuss in detail the interplay between the hydrodynamic interactions and the structures due to the presence of a second species of a different size.
Ferro- and antiferro-magnetism in (Np, Pu)BC
Authors: Klimczuk T. , Shick A. B. , Kozub A. L. , Griveau J.-C. , Colineau E. , Falmbigl M. , Wastin F. , Rogl P.
Published: March 2015

Two new transuranium metal boron carbides, NpBC and PuBC, have been synthesized. Rietveld refinements of powder XRD patterns of {Np,Pu}BC confirmed in both cases isotypism with the structure type of UBC. Temperature dependent magnetic susceptibility data reveal antiferromagnetic ordering for PuBC below TN = 44 K, whereas ferromagnetic ordering was found for NpBC below TC = 61 K. Heat capacity measurements prove the bulk character of the observed magnetic transition for both compounds. The total energy electronic band structure calculations support formation of the ferromagnetic ground state for NpBC and the antiferromagnetic ground state for PuBC.
Dependence of the saturable absorption of graphene upon excitation photon energy
Authors: Zhang Fang , Han Shuo , Liu Yanqing , Wang Zhengping , Xu Xinguang
Published: March 2015

Using an optical parametric oscillation laser as the excitation source, the dependence of the saturable absorption of multiple-layer graphene upon photon energy is investigated and, in all cases, the saturation intensity is lower for lower excitation photon energy. This result experimentally proves the hourglass shape of the energy band of graphene, which is a well-known theoretical deduction from first principles. The modulation depth increases from 1.5% to 5.1% when the layer number increases from a monolayer to 5–7 layers and, at the same time, the saturation intensity decreases with increasing number of layers. The results demonstrate that, as a saturable absorber of a pulsed laser, graphene can more easily achieve optical modulation in the low energy region, i.e., the infrared waveband.
Surface effects on the mechanical elongation of AuCu nanowires: De-alloying and the formation of mixed suspended atomic chains
Authors: Lagos M. J. , Autreto P. A. S. , Bettini J. , Sato F. , Dantas S. O. , Galvao D. S. , Ugarte D.
Published: March 2015

We report here an atomistic study of the mechanical deformation of AuxCu(1−x) atomic-size wires (nanowires (NWs)) by means of high resolution transmission electron microscopy experiments. Molecular dynamics simulations were also carried out in order to obtain deeper insights on the dynamical properties of stretched NWs. The mechanical properties are significantly dependent on the chemical composition that evolves in time at the junction; some structures exhibit a remarkable de-alloying behavior. Also, our results represent the first experimental realization of mixed linear atomic chains (LACs) among transition and noble metals; in particular, surface energies induce chemical gradients on NW surfaces that can be exploited to control the relative LAC compositions (different number of gold and copper atoms). The implications of these results for nanocatalysis and spin transport of one-atom-thick metal wires are addressed.
Magnetism and electronic structures of novel layered CaFeAs2 and Ca0.75(Pr/La)0.25FeAs2
Authors: Huang Yi-Na , Yu Xiang-Long , Liu Da-Yong , Zou Liang-Jian
Published: March 2015

The magnetic and electronic properties of the parent material CaFeAs2 of new superconductors are investigated using first-principles calculations. We predict that the ground state of CaFeAs2 is a spin-density-wave (SDW)-type striped antiferromagnet driven by Fermi surface nesting. The magnetic moment around each Fe atom is about 2.1 μB. We also present electronic and magnetic structures of electron-doped phase Ca0.75(Pr/La)0.25FeAs2, the SDW order was suppressed by La/Pr substitution. The As in arsenic layers is negative monovalent and acts as blocking layers enhancing two-dimensional character by increasing the spacing distance between the FeAs layers. This favors strong antiferromagnetic fluctuations mediated pairing, implying higher Tc in Ca0.75(Pr/La)0.25FeAs2 than Ca0.75(Pr/La)0.25Fe2As2.
Perpendicular magnetic anisotropy of Mn4N films fabricated by reactive sputtering method
Authors: Kabara Kazuki , Tsunoda Masakiyo
Published: March 2015

Manganese nitride films were fabricated on MgO substrates by changing N2 flow ratio into Ar gas (PN2) during reactive sputtering deposition of the films, and their crystal structures and magnetic properties were investigated. Single phased ε-Mn4N films were obtained when PN2 was 5%–9%, and the tetragonal lattice distortion was identified in all the Mn4N films (the lattice constant ratio, c/a = 0.99). Perpendicular magnetic anisotropy was observed in all the specimens. The Mn4N film, fabricated with PN2 = 8%, has a low saturation magnetization (Ms = 110 emu/cc) and relatively high magnetic anisotropic energy (Ku = 8.8 × 105 erg/cc). Both Ms and Ku of the films drastically changed with mixing other phases (α-Mn, β-Mn, η-Mn3N2, and possibly γ-Mn) by varying PN2.
Resistive states created in superconducting NbTiN filaments by an electrical current pulse
Authors: Harrabi K.
Published: March 2015

We have observed as a function of the time the appearance of the voltage caused by a larger-than-critical (I > Ic) step-pulse of current in narrow NbTiN strips at 4.2 K. Different current intensities produced either phase-slip centres characterized by a voltage saturating with the time, or ever expanding hot spots. These dissipative structures occur after a measurable delay time, whose dependence upon the ratio I/Ic can be analysed through a Ginzburg-Landau theory to yield a unique adjustable time constant.
Influence of the nanoparticles agglomeration state in the quantum-confinement effects: Experimental evidences
Authors: Lorite I. , Romero J. J. , Fernandez J. F.
Published: March 2015

The agglomeration state facilitates particle-particle interaction which produces important effects in the phonon confinement effects at the nanoscale. A partial phonon transmission between close nanoparticles yields a lower momentum conservation relaxation than in a single isolated nanoparticle. It means a larger red shift and broadening of the Raman modes than the expected ones for Raman quantum confinement effects. This particle-particle interaction can drive to error when Raman responses are used to estimate the size of the nanoscaled materials. In this work different corrections are suggested to overtake this source of error.
MinD-like ATPase FlhG effects location and number of bacterial flagella during C-ring assembly
Authors: Schuhmacher Jan S. , Rossmann Florian , Dempwolff Felix , Knauer Carina , Altegoer Florian , Steinchen Wieland , Dörrich Anja K. , Klingl Andreas , Stephan Milena , Linne Uwe , Thormann Kai M. , Bange Gert
Published: March 2015

Significance

Flagella are bacterial organelles of locomotion. The number and location of flagella (flagellation pattern) are species specific and represent one of the earliest taxonomic criteria in microbiology. During each round of cell division, bacteria reproduce their flagellation pattern. FlhG is essential to a variety of flagellation patterns (e.g., polar, lateral) by yet-unknown mechanisms. We show that FlhG is an MinD-like ATPase that interacts with the flagellar C-ring proteins FliM/FliY in a nucleotide-independent manner. FlhG activates FliM/FliY to assemble with the C-ring protein FliG. FlhG-driven assembly of the FliM/FliY/FliG complex is strongly enhanced by ATP and lipids. We identify an underappreciated structural diversity of flagellar building blocks that contribute to formation of different flagellation patterns.
Relative and absolute structure of phomolide C
Authors: Ito Atsushi , Maeda Hyato , Tonouchi Akio , Hashimoto Masaru
Published: March 2015

Phomolide C (1) was isolated from a fungus Diaporthe sp. being found at Shirakami mountainous area. Although only the planar structure of 1 has been known, our detailed NMR spectroscopic analysis and ECD studies revealed its both relative and absolute configuration.
SimSeq: a nonparametric approach to simulation of RNA-sequence datasets
Authors: Benidt Sam , Nettleton Dan
Published: February 2015

Motivation: RNA sequencing analysis methods are often derived by relying on hypothetical parametric models for read counts that are not likely to be precisely satisfied in practice. Methods are often tested by analyzing data that have been simulated according to the assumed model. This testing strategy can result in an overly optimistic view of the performance of an RNA-seq analysis method.

Results: We develop a data-based simulation algorithm for RNA-seq data. The vector of read counts simulated for a given experimental unit has a joint distribution that closely matches the distribution of a source RNA-seq dataset provided by the user. We conduct simulation experiments based on the negative binomial distribution and our proposed nonparametric simulation algorithm. We compare performance between the two simulation experiments over a small subset of statistical methods for RNA-seq analysis available in the literature. We use as a benchmark the ability of a method to control the false discovery rate. Not surprisingly, methods based on parametric modeling assumptions seem to perform better with respect to false discovery rate control when data are simulated from parametric models rather than using our more realistic nonparametric simulation strategy.

Availability and implementation: The nonparametric simulation algorithm developed in this article is implemented in the R package SimSeq, which is freely available under the GNU General Public License (version 2 or later) from the Comprehensive R Archive Network (http://cran.rproject.org/).

Contact:  sgbenidt@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
An exploration of the properties of the CORE problem list subset and how it facilitates the implementation of SNOMED CT
Authors: Fung Kin Wah , Xu Julia
Published: February 2015

Objective Systematized Nomenclature of Medicine Clinical Terms (SNOMED CT) is the emergent international health terminology standard for encoding clinical information in electronic health records. The CORE Problem List Subset was created to facilitate the terminology’s implementation. This study evaluates the CORE Subset’s coverage and examines its growth pattern as source datasets are being incorporated.

Methods Coverage of frequently used terms and the corresponding usage of the covered terms were assessed by “leave-one-out” analysis of the eight datasets constituting the current CORE Subset. The growth pattern was studied using a retrospective experiment, growing the Subset one dataset at a time and examining the relationship between the size of the starting subset and the coverage of frequently used terms in the incoming dataset. Linear regression was used to model that relationship.

Results On average, the CORE Subset covered 80.3% of the frequently used terms of the left-out dataset, and the covered terms accounted for 83.7% of term usage. There was a significant positive correlation between the CORE Subset’s size and the coverage of the frequently used terms in an incoming dataset. This implies that the CORE Subset will grow at a progressively slower pace as it gets bigger.

Conclusion The CORE Problem List Subset is a useful resource for the implementation of Systematized Nomenclature of Medicine Clinical Terms in electronic health records. It offers good coverage of frequently used terms, which account for a high proportion of term usage. If future datasets are incorporated into the CORE Subset, it is likely that its size will remain small and manageable.
Concepts and Sources of Meaning
Authors: Breitbart William S. , Poppito Shannon R.
Published: March 2015

This chapter provides instructions for conducting the first session of meaning-centered group psychotherapy. The reader is instructed to introduce facilitators and group members to one another, introduce patients to a general overview of the intervention (including treatment goals, structured weekly topics, and logistics), become familiar with each patient’s story of illness, introduce patients to the first session topic of Viktor Frankl’s work and foundations of meaning, and share definitions of meaning and conduct the “meaningful moments” experiential exercise.
Historical Sources of Meaning
Authors: Breitbart William S. , Poppito Shannon R.
Published: March 2015

This chapter provides instructions for conducting the third session of meaning-centered group psychotherapy. The reader is instructed to introduce and explore the topic of ‘Historical Sources of Meaning’ and the guiding theme ‘Life as a Legacy’ to the group. Facilitators should provide members with the chance to describe their personal understanding of ‘legacy’ on their own terms before the leaders explore the concept of ‘legacy’ in historical context (e.g., past, present, future legacy). By the end of Session 3, group members will have a solid understanding of the legacy that has been given to them via past familial upbringing, family values, meaningful relationships, and memories that have shaped their lives.
Attitudinal Sources of Meaning
Authors: Breitbart William S. , Poppito Shannon R.
Published: March 2015

This chapter provides instructions for conducting the fifth session of meaning-centered group psychotherapy. The reader is instructed to explore the topic of ‘Attitudinal Sources of Meaning’ and the guiding theme ‘Encountering Life’s Limitations.’ Leaders will pick up where they left off from Session 4 by continuing to explore the concept of ‘legacy’ in historical context (e.g., past, present, future dimensions) in light of confronting the ultimate limitation of death and the lasting legacy they will leave. By the end of Session 5, group members will have a solid understanding of ‘attitudinal sources of meaning’ based on the core theme that our last vestige of human freedom is to choose our attitude toward suffering and life’s limitations. Group members will come to understand that life presents us with many circumstances that may be opportunities or limitations, and while we often don’t have control over what life gives us, we always have the freedom to choose how we respond to and the attitude we take toward what life gives us, good or bad.
Creative Sources of Meaning
Authors: Breitbart William S. , Poppito Shannon R.
Published: March 2015

This chapter provides instructions for conducting the sixth session of meaning-centered group psychotherapy. The reader is instructed to introduce and explore the topic of ‘Creative Sources of Meaning’ and the guiding theme ‘Creativity, Courage, and Responsibility.’ By the end of Session 6, group members will have a solid understanding of the significance of the creative sources of meaning (creativity, courage, and responsibility) as important resources for meaning in their lives.
Experiential Sources of Meaning
Authors: Breitbart William S. , Poppito Shannon R.
Published: March 2015

This chapter provides instructions for conducting the seventh session of meaning-centered group psychotherapy. The reader is instructed to introduce and explore the topic of ‘Experiential Sources of Meaning’ by way of the guiding theme ‘Connecting with Life.’ By the end of Session 7, group members will have a solid understanding of the significance of connecting with life through experiential sources of meaning—particularly through the experiential sources of love, beauty, and humor.
Monitoring Obstetric Anesthesia Safety across Hospitals through Multilevel Modeling
Authors: Guglielminotti Jean , Li Guohua
Published: February 2015

AbstractAbstract

In an analysis of nearly 500,000 labor and delivery records from 144 hospitals in New York, multilevel modeling substantially improved the reliability in the estimated rates of obstetric anesthesia-related adverse events across hospitals compared with the traditional risk-adjustment method.

Background:

The rate of anesthesia-related adverse events (ARAEs) is recommended for monitoring patient safety across hospitals. To ensure comparability, it is adjusted for patients’ characteristics with logistic models (i.e., risk adjustment). The rate adjusted for patient-level characteristics and hospital affiliation through multilevel modeling is suggested as a better metric. This study aims to assess a multilevel model-based rate of ARAEs.

Methods:

Data were obtained from the State Inpatient Database for New York 2008–2011. Discharge records for labor and delivery and ARAEs were identified with International Classification of Diseases, Ninth Revision, Clinical Modification codes. The rate of ARAEs for each hospital during 2008–2009 was calculated using both the multilevel and the logistic modeling approaches. Performance of the two methods was assessed with (1) interhospital variability measured by the SD of the rates; (2) reclassification of hospitals; and (3) prediction of hospital performance in 2010–2011. Rankability of each hospital was assessed with the multilevel model.

Results:

The study involved 466,442 discharge records in 2008–2009 from 144 hospitals. The overall observed rate of ARAEs in 2008–2009 was 4.62 per 1,000 discharges [95% CI, 4.43 to 4.82]. Compared with risk adjustment, multilevel modeling decreased SD of ARAE rates from 4.7 to 1.3 across hospitals, reduced the proportion of hospitals classified as good performers from 18% to 10%, and performed similarly well in predicting future ARAE rates. Twenty-six hospitals (18%) were nonrankable due to inadequate reliability.

Conclusion:

The multilevel modeling approach could be used as an alternative to risk adjustment in monitoring obstetric anesthesia safety across hospitals.
Prediction of Movement to Surgical Stimulation by the Pupillary Dilatation Reflex Amplitude Evoked by a Standardized Noxious Test
Authors: Guglielminotti Jean , Grillot Nicolas , Paule Marine , Mentré France , Servin Fréderique , Montravers Philippe , Longrois Dan
Published: February 2015

AbstractAbstract

Seventy-six women scheduled for an operative procedure requiring cervical dilation were anesthetized with a target propofol effect-site concentration of 4 μg/ml with a randomly assigned remifentanil effect-site concentration of 0, 1, 3, or 5 ng/ml. Pupillary dilatation reflex amplitude in response to a standardized noxious test predicted movement response on cervical dilation as accurately as the estimated remifentanil effect-site concentration.

Background:

Individual assessment of the amplitude of a physiologic reflex evoked by a standardized noxious test (SNT) before surgical stimulation has been suggested to predict movement upon the forthcoming surgical stimulation. This study aimed to compare the ability of pupillary dilatation reflex amplitude (PDRA) evoked by an SNT and estimated remifentanil effect-site concentration (Ce) to predict movement upon surgical stimulation.

Methods:

Eighty female patients were anesthetized for vacuum aspiration with propofol (Ce 4 μg/ml) and remifentanil. Remifentanil Ce was randomized to 0, 1, 3, or 5 ng/ml. SNT was a 60-mA, 5-s, 100-Hz tetanus applied on median nerve before cervix dilatation. PDRA was calculated as the difference in pupillary diameter after and before SNT. Movement upon cervix dilatation was recorded by an independent observer. Ability of PDRA and estimated remifentanil Ce to discriminate movers from non-movers during cervix dilatation was measured as the area under the receiver operating characteristics curve.

Results:

Twenty-one of the 76 patients analyzed moved during cervix dilatation. Mean PDRA (±1 SD) evoked by SNT was 2.0 ± 1.2 mm in movers and 0.6 ± 0.7 in non-movers (P < 0.0001). Remifentanil Ce was 0.2 ± 0.4 ng/ml in movers and 3.0 ± 1.7 in non-movers (P < 0.0001). Area under the receiver operating characteristics curve for PDRA was 0.90 (95% CI, 0.83 to 0.96) and for remifentanil Ce 0.94 (0.89 to 0.98), without any significant difference between the two areas.

Conclusions:

PDRA evoked by an SNT is as accurate as the estimated remifentanil Ce to predict movement upon cervix dilatation. PDRA could be valuable when estimated opioid Ce is not available or reliable.
A Patient-centered Approach to Evaluate the Information Needs of Women With Ductal Carcinoma In Situ
Authors: Lo Andrea C. , Olson Robert , Feldman-Stewart Deb , Truong Pauline T. , Aquino-Parsons Christina , Bottorff Joan L. , Carolan Hannah
Published: February 2015

Objective:

To evaluate the information needs of ductal carcinoma in situ (DCIS) patients.

Methods:

Four focus groups involving 24 previously treated DCIS patients were conducted to develop a comprehensive list of questions they felt were important to have answered at the time of diagnosis. Using a survey, a separate group of patients treated for DCIS then rated the importance of having each of these questions addressed before treatment decision making. Response options were “essential,” “desired,” “not important,” “no opinion,” and “avoid.” For each essential/desired question, respondents specified how addressing it would help them: “understand,” “decide,” “plan,” “not sure,” or “other.”

Results:

Focus group participants generated 117 questions used in the survey. Fifty-seven patients completed the survey (55% response rate). Respondents rated a median of 66 questions as essential. The most commonly cited reason for rating a question essential was to “understand,” followed by to “decide.” The top questions women deemed essential to help them understand were disease specific, whereas the top questions deemed essential to help women decide were predominantly treatment specific, pertaining to available options, recurrence and survival outcomes, and timelines to decide and start treatment.

Conclusions:

DCIS patients want a large number of questions answered, mostly for understanding, and also for deciding and planning. A core set of questions that most patients consider essential for decision making has been formulated and may be used in the clinical setting and in research to develop educational resources and decision-making tools specific to DCIS.
Blastomonas aquatica sp. nov., a bacteriochlorophyll-containing bacterium isolated from lake water
Authors: Xiao Na , Liu Yongqin , Liu Xiaobo , Gu Zhengquan , Jiao Nianzhi , Liu Hongcan , Zhou Yuguang , Shen Liang
Published: February 2015

Yellow or orange-to-brown pigmented, ovoid or rod-shaped, Gram-negative staining, aerobic strains PE 4-5T and N5-10 m-1 were isolated from brackish water in Lake Peng Co and fresh to brackish water in Lake Namtso on the Tibetan Plateau, China. Bacteriochlorophyll a was produced by the isolates. The predominant cellular fatty acids were C16 : 1, C17 : 1 and C18 : 1 unsaturated fatty acids, C17 : 1ω6c (55.3 %), C17 : 1ω8c (13.0 %) and C18 : 1ω7c (10.4 %) for PE 4-5T and C18 : 1ω7c (54.7 %) and C16 : 1ω7c (18.0 %) for N5-10 m-1. The polar lipid profiles of strains PE 4-5T and N5-10 m-1 were composed of diphosphatidylglycerol, phosphatidylcholine (not detected in N5-10 m-1), phosphatidyldimethylethanolamine, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, sphingoglycolipid and an unknown phospholipid. The predominant respiratory quinone was ubiquinone Q10 and the DNA G+C content was 66.0 mol% for both strains. The16S rRNA gene sequence of strain PE 4-5T shared 99.0 % similarity with that of N5-10 m-1, and 97.56 % similarity with those of

Blastomonas natatoria

LMG 17322T and

Blastomonas ursincola

DSM 9006T, respectively. The DNA–DNA hybridization relatedness between strains PE 4-5T and N5-10 m-1 was 79.0±1.0 %, but below 70 % with the type strains in the genus

Blastomonas

. Based on the variability of phylogenetic and phenotypic characteristics, the isolates should be classified as representatives of a novel species of the genus

Blastomonas

; the name Blastomonas aquatica sp. nov. is proposed. The type strain is PE 4-5T ( = JCM 30179T = CGMCC 1.12851T).
Planctomicrobium piriforme gen. nov., sp. nov., a stalked planctomycete from a littoral wetland of a boreal lake
Authors: Kulichevskaya Irina S. , Ivanova Anastasia A. , Detkova Ekaterina N. , Rijpstra W. Irene C. , Sinninghe Damsté Jaap S. , Dedysh Svetlana N.
Published: February 2015

An aerobic, budding, non-pigmented and rosette-forming bacterium was isolated from a littoral wetland of a boreal lake located in Valaam Island, northern Russia, and designated strain P3T. Ellipsoidal to pear-shaped cells of this bacterium were covered with crateriform pits and possessed stalks suggesting a planctomycete morphotype. 16S rRNA gene sequence analysis confirmed that strain P3T was a member of the order

Planctomycetales

and belonged to a phylogenetic lineage defined by the genus

Planctomyces

, with 89 and 86 % sequence similarity to

Planctomyces brasiliensis

and

Planctomyces maris

, respectively. Strain P3T was a mildly acidophilic, mesophilic organism capable of growth at pH values between pH 4.2 and 7.1 (with an optimum at pH 6.0–6.5) and at temperatures between 10 and 30 °C (optimum at 20–28 °C). Most sugars, a number of polysaccharides and several organic acids were the preferred growth substrates. Compared with

Planctomyces brasiliensis

and

Planctomyces maris

, which require NaCl for growth, strain P3T was salt-sensitive and did not develop at NaCl concentrations above 0.5 % (w/v). The major fatty acids were C16 : 0 and C16 : 1ω7c; the cells also contained significant amounts of C18 : 1ω7c and C18 : 0. The major intact polar lipids were diacylglycerol-O-(N,N,N-trimethyl)homoserine (DGTS) lipids; the major neutral lipids were long-chain 1,(ω-1)-diols and C31 : 9 hydrocarbon. The quinone was MK-6, and the G+C content of the DNA was 59.0 mol%. Strain P3T differed from

Planctomyces brasiliensis

and

Planctomyces maris

by cell morphology, substrate utilization pattern and a number of physiological characteristics. Based on these data, the novel isolate should be considered as representing a novel genus and species of planctomycetes, for which the name Planctomicrobium piriforme gen. nov., sp. nov., is proposed. The type strain is P3T ( = DSM 26348T = VKM B-2887T).
Chelativorans intermedius sp. nov. and proposal to reclassify Thermovum composti as Chelativorans composti comb. nov.
Authors: Kämpfer P. , Arun A. B. , Busse H.-J. , Zhang Zhen-Li , Young Chiu-Chung , Glaeser S. P.
Published: February 2015

Two Gram-stain-negative, non-endospore-forming, rod-shaped bacteria, strains CC-MHSW-5T and A1392, were isolated from water of coastal hot springs located in Taiwan and China, respectively, and investigated for their taxonomic position. The two strains shared identical 16S rRNA gene sequences, a DNA-DNA hybridization value >80 % and similar genomic DNA G+C contents (64.3 and 64.6 mol%), but showed different genomic fingerprint patterns generated by BOX-PCR and three random amplification polymorphic DNA PCRs. The strains shared highest 16S rRNA gene sequence similarities with the type strains of

Chelativorans multitrophicus

(96.7 and 96.1 %),

Thermovum composti

(96.2 and 96.1 %) and

Chelativorans oligotrophicus

(96.1 and 95.8 %). Phylogenetic trees (based on 16S rRNA and recA gene sequence comparisons) showed a distinct clustering of both strains with the type strains of species of the genus

Chelativorans

and

T. composti

Nis3T. The quinone systems of strains CC-MHSW-5T and Nis3T contained ubiquinone Q-10 as the major component. The major polyamine in both strains was sym-homospermidine. Putrescine, spermidine and, for strain CC-MHSW-5T, spermine were found in minor concentrations. Their polar lipid profiles consisted of phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and diphosphatidylglycerol. The fatty acid profile contained major amounts of C18 : 1ω7c and C19 : 0 cyclo ω8c. On the basis of these results, the two strains are considered to represent a novel species of the genus

Chelativorans

, for which the name Chelativorans intermedius sp. nov. is proposed. The type strain is CC-MHSW-5T ( = CCM 8543T = LMG 28482T = DSM 29391T = CIP 110825T). Based on both genotypic and phenotypic characters, it is proposed that

T. composti

be reclassified within the genus

Chelativorans

as Chelativorans composti comb. nov.
O
leiagrimonas soli gen. nov., sp. nov., a genome-sequenced gammaproteobacterium isolated from an oilfield
Authors: Fang Tingting , Wang Hui , Huang Yong , Zhou Haiyan , Dong Peiyan
Published: February 2015

A yellow-pigmented strain, designated strain 3.5XT, was isolated from oil-contaminated saline soil in Gudao, Shandong Province, China, and was characterized taxonomically. The results showed that the isolate was a Gram-stain-negative, aerobic, motile, rod-shaped cell with a polar flagellum. Phylogenetic analysis of 16S rRNA gene sequences revealed the strain belonged to the family

Xanthomonadaceae

in the class

Gammaproteobacteria

and represented an independent taxon separated from other genera. The closest relative of strain 3.5XT was

Fulvimonas soli

DSM 14263T (94 % similarity). The genomic DNA G+C content was 67 mol% by thermal denaturation and 66.3 mol% from genome sequences. The cells mainly consisted of branched fatty acids, with iso-C17 : 0, iso-C15 : 0, iso-C17 : 1ω9c and/or C16 : 010-methyl and iso-C11 : 0 as the major fatty acids. The main polar lipids were phosphatidylmonomethylethanolamine, diphosphatidylglycerol and phosphatidylethanolamine. In addition, ubiquinone Q-8 was the major component of the quinone system and the polyamine pattern contained the major compound spermidine plus minor amounts of putrescine and spermine. On the basis of phenotypic, genotypic and phylogenetic distinctiveness, it is proposed that the isolate represents a novel species in a novel genus, namely Oleiagrimonas soli gen. nov., sp. nov. The type strain is 3.5XT ( = NBRC 110685T = KCTC 42351T = CPCC 100614T).
Analysis of the history and spread of HIV-1 in Uganda using phylodynamics
Authors: Yebra Gonzalo , Ragonnet-Cronin Manon , Ssemwanga Deogratius , Parry Chris M. , Logue Christopher H. , Cane Patricia A. , Kaleebu Pontiano , Brown Andrew J. Leigh
Published: February 2015

HIV prevalence has decreased in Uganda since the 1990s, but remains substantial within high-risk groups. Here, we reconstruct the history and spread of HIV subtypes A1 and D in Uganda and explore the transmission dynamics in high-risk populations. We analysed HIV pol sequences from female sex workers in Kampala (n = 42), Lake Victoria fisher-folk (n = 46) and a rural clinical cohort (n = 74), together with publicly available sequences from adjacent regions in Uganda (n = 412) and newly generated sequences from samples taken in Kampala in 1986 (n = 12). Of the sequences from the three Ugandan populations, 60 (37.1 %) were classified as subtype D, 54 (33.3 %) as subtype A1, 31 (19.1 %) as A1/D recombinants, six (3.7 %) as subtype C, one (0.6 %) as subtype G and 10 (6.2 %) as other recombinants. Among the A1/D recombinants we identified a new candidate circulating recombinant form. Phylodynamic and phylogeographic analyses using BEAST indicated that the Ugandan epidemics originated in 1960 (1950–1968) for subtype A1 and 1973 (1970–1977) for D, in rural south-western Uganda with subsequent spread to Kampala. They also showed extensive interconnection with adjacent countries. The sequence analysis shows both epidemics grew exponentially during the 1970s–1980s and decreased from 1992, which agrees with HIV prevalence reports in Uganda. Inclusion of sequences from the 1980s indicated the origin of both epidemics was more recent than expected and substantially narrowed the confidence intervals in comparison to previous estimates. We identified three transmission clusters and ten pairs, none of them including patients from different populations, suggesting active transmission within a structured transmission network.
A high performing brain-machine interface driven by low-frequency local field potentials alone and together with spikes
Authors: Stavisky Sergey D , Kao Jonathan C , Nuyujukian Paul , Ryu Stephen I , Shenoy Krishna V
Published: February 2015

Objective. Brain-machine interfaces (BMIs) seek to enable people with movement disabilities to directly control prosthetic systems with their neural activity. Current high performance BMIs are driven by action potentials (spikes), but access to this signal often diminishes as sensors degrade over time. Decoding local field potentials (LFPs) as an alternative or complementary BMI control signal may improve performance when there is a paucity of spike signals. To date only a small handful of LFP decoding methods have been tested online; there remains a need to test different LFP decoding approaches and improve LFP-driven performance. There has also not been a reported demonstration of a hybrid BMI that decodes kinematics from both LFP and spikes. Here we first evaluate a BMI driven by the local motor potential (LMP), a low-pass filtered time-domain LFP amplitude feature. We then combine decoding of both LMP and spikes to implement a hybrid BMI. Approach. Spikes and LFP were recorded from two macaques implanted with multielectrode arrays in primary and premotor cortex while they performed a reaching task. We then evaluated closed-loop BMI control using biomimetic decoders driven by LMP, spikes, or both signals together. Main Results. LMP decoding enabled quick and accurate cursor control which surpassed previously reported LFP BMI performance. Hybrid decoding of both spikes and LMP improved performance when spikes signal quality was mediocre to poor. Significance. These findings show that LMP is an effective BMI control signal which requires minimal power to extract and can substitute for or augment impoverished spikes signals. Use of this signal may lengthen the useful lifespan of BMIs and is therefore an important step towards clinically viable BMIs.
Analog nitrogen sensing inEscherichia colienables high fidelity information processing
Authors: Komorowski M. , Schumacher J. , Behrends V. , Jetka T. , Bennett Mark H. , Ale A. , Filippi S. , Pinney J.W. , Bundy J.G. , Buck M. , Stumpf M.P.H.
Published: February 2015

The molecular reaction networks that coordinate the response of an organism to changing environmental conditions are central for survival and reproduction.Escherchia coliemploys an accurate and flexible signalling system that is capable of processing ambient nitrogen availability rapidly and with high accuracy. Carefully orchestrated post-translational modifications of PII and the glutamine synthetase allowE. colito trace nitrogen availability in a continuous, decidedly non-digital fashion. We measure the dynamic proteomic and metabolomic responses to trace the analog computations, and use an information theoretical framework to characterize the information capacity ofE. coli’s nitrogen sensing network: we find that this system can transmit up to 9bits of information about the nitrogen state. This allows cells to respond rapidly and accurately even to small differences in metabolite concentrations.
Speciation inHeliconiusButterflies: Minimal Contact Followed by Millions of Generations of Hybridisation
Authors: Martin Simon H. , Eriksson Anders , Kozak Krzysztof M. , Manica Andrea , Jiggins Chris D.
Published: March 2015

Documenting the full extent of gene flow during speciation poses a challenge, as species ranges change over time and current rates of hybridisation might not reflect historical trends. Theoretical work has emphasized the potential for speciation in the face of ongoing hybridisation, and the genetic mechanisms that might facilitate this process. However, elucidating how the rate of gene flow between species may have changed over time has proved difficult. Here we use Approximate Bayesian Computation (ABC) to fit a model of speciation between the Neotropical butterfliesHeliconius melpomeneandHeliconius cydno. These species are ecologically divergent, rarely hybridize and display female hybrid sterility. Nevertheless, previous genomic studies suggests pervasive gene flow between them, extending deep into their past, and potentially throughout the speciation process. By modelling the rates of gene flow during early and later stages of speciation, we find that these species have been hybridising for hundreds of thousands of years, but have not done so continuously since their initial divergence. Instead, it appears that gene flow was rare or absent for as long as a million years in the early stages of speciation. Therefore, by dissecting the timing of gene flow between these species, we are able to reject a scenario of purely sympatric speciation in the face of continuous gene flow. We suggest that the period of minimal contact early in speciation may have allowed for the accumulation of genomic changes that later enabled these species to remain distinct despite a dramatic increase in the rate of hybridisation.
Chemical integration of proteins in signaling and development
Authors: Dick Jeffrey M.
Published: March 2015

In developing embryos of eukaryotes, varying concentrations and/or duration of exposure to morphogens induce and repress transcription factors (TFs) in a regular order, thereby acting as signals for cell differentiation. I present a chemical thermodynamic model for the formation and degradation of the morphogen Sonic hedgehog (Shh) and the major TFs involved in dorsal-ventral patterning of the vertebrate neural tube. This two-stage model first considers introduction of Shh into a chemically defined (oxidizing) environment. As the system is driven away from metastable equilibrium, the TFs progressively become more stable than Shh, as indicated by comparison of the calculated overall energies of formation (chemical affinity). In the second stage, a gradual return to metastable equilibrium with Shh drives transitions in the relative stabilities of the TFs that follow the experimental patterns of TF expression. At the intracellular level, the major proteins in the signal transduction network show a metastability progression among reactions of Shh and its cell-surface receptor and the intracellular Gli proteins that act as activators and repressors of transcription. If the endocytosis and degradation of receptor-ligand complexes are coupled to localized protein translation, the consequent thermodynamic constraints may represent a high-level source of specificity that coexists with molecular mechanisms of signal transduction.
Flash Photolysis of Caged IP3 to Trigger Intercellular Ca2+ Waves
Authors: Decrock Elke , De Bock Marijke , Wang Nan , Bol Mélissa , Gadicherla Ashish K. , Leybaert Luc
Published: March 2015

Caged IP3 is an inactive form of the second messenger IP3, consisting of the biologically active molecule linked to a cage group through a photolabile bond. This bond is cleaved by exposure to brief “flashes” of ultraviolet (UV) light, thereby releasing the active IP3 molecule. The protection of caged IP3 against metabolic transformation in combination with a defined time point of fast photoliberation of IP3 provides an efficient way to temporally and spatially control the cytosolic release of IP3 and subsequent increase of cytoplasmic Ca2+. These properties make it an ideal method for kinetic studies and also a well-suited procedure to initiate intercellular Ca2+ waves from a point source of IP3. This protocol describes cell loading with membrane impermeable caged IP3 and the UV flash illumination procedure.