bluuebunny/crossref_metadata_2025 huggingface dataset:
Bayesian Peak Picking for NMR Spectra
Authors: Cheng Yichen , Gao Xin , Liang Faming
Published: November 2013

Protein structure determination is a very important topic in structural genomics, which helps people to understand varieties of biological functions such as protein-protein interactions, protein–DNA interactions and so on. Nowadays, nuclear magnetic resonance (NMR) has often been used to determine the three-dimensional structures of protein in vivo. This study aims to automate the peak picking step, the most important and tricky step in NMR structure determination. We propose to model the NMR spectrum by a mixture of bivariate Gaussian densities and use the stochastic approximation Monte Carlo algorithm as the computational tool to solve the problem. Under the Bayesian framework, the peak picking problem is casted as a variable selection problem. The proposed method can automatically distinguish true peaks from false ones without preprocessing the data. To the best of our knowledge, this is the first effort in the literature that tackles the peak picking problem for NMR spectrum data using Bayesian method.
Organizational Change Strategies within Healthcare
Authors: Steinke Claudia , Dastmalchian Ali , Blyton Paul , Hasselback Paul
Published: November 2013

This study explores ways in which healthcare organizations can improve their organizational fitness for change using Beer and Nohria's framework of Theory E (concentrating on the economic value of change) and Theory O (concentrating on the organization's long-term capabilities for change). Data were collected from senior leaders/medical directors from health regions in Alberta. The results show that even though there is a tendency for reliance on Theory E change strategies, the respondents demonstrated other preferred approaches to change.
A Survey of how Occupational Therapy Fieldwork Influences Future Professional Preference
Authors: Chiang Hsin-Yu (Ariel) , Liu Chien-Hsiuo , Chen Yi , Wang Shin-Han , Lin Wei-Shan , Su Fan-Ya , Su Chia-Ting , Pan Chien-Hsuan , Wang Chieh-An
Published: November 2013

Objective/Background

Although fieldwork experience plays an important role in an occupational therapy (OT) student's choice of future area of practice, studies on the influences of fieldwork on the preference of practice areas remain limited. The goal of the study was to further understand how OT students choose their future areas of practice. Methods: A questionnaire, “The preferred future practice areas of occupational therapy students”, was created by systematic review of the relevant literature and collection of opinions from occupational therapists, students, and faculty. In total, 152 OT students undergoing their Level II fieldwork participated in the survey. Reliability tests, factor analysis tests, and discrimination analysis were carried out.

Results

The questionnaire demonstrated good to moderate reliability and validity. The factorial analysis indicated that the most influential factors for the preference of future practice areas of senior occupational therapy students are as follows: fieldwork experiences with clinical supervisors, fieldwork experiences with peers, social factors, college courses, and pressure from future work. The discrimination analysis revealed that social factors and college courses are the best factors for discriminating the variable “Choosing physical dysfunction, paediatric, or psychiatric OT as the most preferred future practice area.”

Conclusion

The choice of future area of practice is proved to be influenced by the experience in fieldwork for OT students. The psychometric properties of the questionnaire used in this study are supported, and it is recommended for use in future studies.
Le voile intégral: analyse juridique d’un objet religieux
Authors: Koussens David , Bernatchez Stéphane , Robert Marie-Pierre
Published: November 2013

Cet article analyse la qualification juridique du voile intégral porté par les femmes usagères des services publics canadiens. Questionnant les modalités par lesquelles l’État se saisit de l’objet « voile intégral » dans différentes sociétés occidentales, l’article postule que la traduction juridique de ce vêtement comme « objet religieux » est nécessaire à une pleine garantie de la liberté de conscience et de religion par les tribunaux. Empruntant au droit constitutionnel et à la théorie du droit, l’article analyse ensuite le traitement juridique de cet objet religieux à partir du cadre d’analyse formulé par la Cour suprême du Canada dans l’affaire NS.
Stability of internal gravity wave beams to three-dimensional modulations
Authors: Kataoka T. , Akylas T. R.
Published: November 2013

The linear stability of uniform, plane internal wave beams with locally confined spatial profile, in a stratified fluid of constant buoyancy frequency, is discussed. The associated eigenvalue problem is solved asymptotically, assuming perturbations of long wavelength relative to the beam width. In this limit, instability is found only for oblique disturbances which vary in the along-beam and the horizontal transverse directions. The mechanism of instability is a first-harmonic–mean resonant interaction between the underlying wave beam and three-dimensional perturbations that comprise a time-harmonic component, with the beam frequency, and a mean flow. Progressive beams which transport energy in one direction, in particular, are unstable if the beam steepness exceeds a certain threshold value, whereas purely standing beams are unstable even at infinitesimal steepness. A distinguishing feature of this three-dimensional modulational instability is the generation of circulating horizontal mean flows at large distances from the vicinity of the beam.
On the persistence of memory: do initial conditions impact vortex formation?
Authors: Kriegseis Jochen , Kinzel Matthias , Rival David E.
Published: November 2013

An investigation into redistribution of vorticity for rapidly accelerating plates with varying kinematics and initial conditions has been performed. Both three-dimensional particle tracking velocimetry and direct force measurements were applied simultaneously. The effective velocity of the feeding shear layer has been identified as the appropriate characteristic velocity rather than the commonly used plunge or free stream velocity. Based on this new normalization for circulation, it has been demonstrated that the existence of initial boundary-layer vorticity on the plunging plate – at least in the near-midplane region – does not contribute to the eventual vortex formation process. In accordance with the literature, however, the tip vortex positioning relative to the plate surface has been identified as an important contributor in the overall force production, particularly once the plate acceleration has ceased.
Temporal discounting in major depressive disorder
Authors: Pulcu E. , Trotter P. D. , Thomas E. J. , McFarquhar M. , Juhasz G. , Sahakian B. J. , Deakin J. F. W. , Zahn R. , Anderson I. M. , Elliott R.
Published: November 2013

Background

Major depressive disorder (MDD) is associated with abnormalities in financial reward processing. Previous research suggests that patients with MDD show reduced sensitivity to frequency of financial rewards. However, there is a lack of conclusive evidence from studies investigating the evaluation of financial rewards over time, an important aspect of reward processing that influences the way people plan long-term investments. Beck's cognitive model posits that patients with MDD hold a negative view of the future that may influence the amount of resources patients are willing to invest into their future selves.

Method

We administered a delay discounting task to 82 participants: 29 healthy controls, 29 unmedicated participants with fully remitted MDD (rMDD) and 24 participants with current MDD (11 on medication).

Results

Patients with current MDD, relative to remitted patients and healthy subjects, discounted large-sized future rewards at a significantly higher rate and were insensitive to changes in reward size from medium to large. There was a main effect of clinical group on discounting rates for large-sized rewards, and discounting rates for large-sized rewards correlated with severity of depressive symptoms, particularly hopelessness.

Conclusions

Higher discounting of delayed rewards in MDD seems to be state dependent and may be a reflection of depressive symptoms, specifically hopelessness. Discounting distant rewards at a higher rate means that patients are more likely to choose immediate financial options. Such impairments related to long-term investment planning may be important for understanding value-based decision making in MDD, and contribute to ongoing functional impairment.
Imperfect but true competition: innovation and profitability in Portuguese banking during the golden age (1950–1973)
Authors: Amaral Luciano
Published: November 2013

The institutional environment of Portuguese banking during the golden age years of economic growth (1950–73) has been criticised in many instances, at the time and in recent literature. Direct observers of the period as well as historians have stressed two main aspects of that environment: excessive protection of existing banks, allowing them to obtain high rents, which represented a disincentive for them to compete and innovate; excessive concentration of their activity on short-term commercial paper, thus preventing them from contributing to finance growth. There seems to be a contradiction here, however, with the high growth rates of the years 1950 to 1973. The apparent contradiction is not limited to Portugal, in fact, as rapid growth in many economies in that period occurred within a framework of heavily regulated financial systems. This is the ‘financial paradox’ of the golden age. Portugal is an interesting case in the international perspective. As in the rest of the western world, legislation repressed banking quite tightly, but banks circumvented the law and competed with each other. The signs of competition were visible mostly in two dimensions: the growth of time deposits and geographical expansion.
Monetary policy, asset prices and financial institutions
Authors: Booth Philip
Published: November 2013

The operation of monetary policy is likely to affect securities markets and asset values. This is of relevance to actuaries who work in or advise non-bank financial institutions such as pension funds and insurance companies. This paper examines different theories of monetary policy and the relationship between monetary policy and asset prices. It is found that central bank models have, at least until recently, tended to sideline consideration of the transmission of monetary policy through asset markets but that, with the implementation of quantitative easing, it is a subject that cannot be ignored. Many monetary schools, in fact, suggest that asset markets can be significantly affected by changes to monetary policy and those schools have lessons for important aspects of actuarial theory and practice.
Loss of iron triggers PINK1/Parkin‐independent mitophagy
Authors: Allen George F G , Toth Rachel , James John , Ganley Ian G
Published: November 2013

In this study, we develop a simple assay to identify mitophagy inducers on the basis of the use of fluorescently tagged mitochondria that undergo a colour change on lysosomal delivery. Using this assay, we identify iron chelators as a family of compounds that generate a strong mitophagy response. Iron chelation‐induced mitophagy requires that cells undergo glycolysis, but does not require PINK1 stabilization or Parkin activation, and occurs in primary human fibroblasts as well as those isolated from a Parkinson's patient with Parkin mutations. Thus, we have identified and characterized a mitophagy pathway, the induction of which could prove beneficial as a potential therapy for several neurodegenerative diseases in which mitochondrial clearance is advantageous.
A dual conformation of the post-decarboxylation intermediate is associated with distinct enzyme states in mycobacterial KGD (α-ketoglutarate decarboxylase)
Authors: Wagner Tristan , Barilone Nathalie , Alzari Pedro M. , Bellinzoni Marco
Published: November 2013

α-Ketoacid dehydrogenases are large multi-enzyme machineries that orchestrate the oxidative decarboxylation of α-ketoacids with the concomitant production of acyl-CoA and NADH. The first reaction, catalysed by α-ketoacid decarboxylases (E1 enzymes), needs a thiamine diphosphate cofactor and represents the overall rate-limiting step. Although the catalytic cycles of E1 from the pyruvate dehydrogenase (E1p) and branched-chain α-ketoacid dehydrogenase (E1b) complexes have been elucidated, little structural information is available on E1o, the first component of the α-ketoglutarate dehydrogenase complex, despite the central role of this complex at the branching point between the TCA (tricarboxylic acid) cycle and glutamate metabolism. In the present study, we provide structural evidence that MsKGD, the E1o (α-ketoglutarate decarboxylase) from Mycobacterium smegmatis, shows two conformations of the post-decarboxylation intermediate, each one associated with a distinct enzyme state. We also provide an overall picture of the catalytic cycle, reconstructed by either crystallographic snapshots or modelling. The results of the present study show that the conformational change leading the enzyme from the initial (early) to the late state, although not required for decarboxylation, plays an essential role in catalysis and possibly in the regulation of mycobacterial E1o.
Molecular dynamics simulation of self-rotation effects on ultra-precision polishing of single-crystal copper
Authors: Yang Yihan , Zhao Hongwei , Zhang Lin , Shao Mingkun , Liu Hongda , Huang Hu
Published: November 2013

Understanding the behaviors of the material removal mechanism of ultra-precision polishing process has been a critical issue of generating well-formed surface. In order to make clear the abrasive self-rotation effects on material removal at the atomic level, a three-dimensional molecular dynamics (MD) model is conducted to study the mechanics of ultra-precision polishing on single-crystal copper with a diamond abrasive and the effects of abrasive self-rotation velocity and direction. Morse potential energy function and EAM potential energy function are applied to model the copper/diamond and copper/copper interactions, respectively. The simulation results show that the deformation mechanism of single-crystal copper is due to the formation and movement of dislocations in the specimen. In addition, with the increasing of abrasive self-rotation velocity, the deformation mechanism falls from cutting to plowing regimes. The abrasive self-rotation velocity and direction have effects on the morphology and quality of the specimen surface, distribution and evolution of defects under the surface of the specimen. Also, the interatomic force between abrasive and specimen is studied to account for the effects of different polishing conditions.
Low-temperature reversible giant magnetocaloric effect in the HoCuAl compound
Authors: Wang L. C. , Dong Q. Y. , Mo Z. J. , Xu Z. Y. , Hu F. X. , Sun J. R. , Shen B. G.
Published: November 2013

Magnetic properties and magnetocaloric effect (MCE) of the HoCuAl compound is investigated. The compound is found to be ferromagnetic and undergoes a second-order phase transition from ferromagnetic (FM)-to-paramagnetic (PM) state around Curie temperature TC = 11.2 K. A giant MCE is observed and no magnetic hysteresis loss is found. The maximum values of magnetic entropy change (ΔS) are found to be −17.5 J/kg K and −30.6 J/kg K with a refrigerant capacity (RC) value of 178 and 486 J/kg for the field changes of 0–20 kOe and 0–50 kOe, respectively. The large ΔS as well as no hysteresis loss imply HoCuAl a promising candidate for low temperature magnetic refrigerant.
A new method for comparing rankings through complex networks: Model and analysis of competitiveness of major European soccer leagues
Authors: Criado Regino , García Esther , Pedroche Francisco , Romance Miguel
Published: November 2013

In this paper, we show a new technique to analyze families of rankings. In particular, we focus on sports rankings and, more precisely, on soccer leagues. We consider that two teams compete when they change their relative positions in consecutive rankings. This allows to define a graph by linking teams that compete. We show how to use some structural properties of this competitivity graph to measure to what extend the teams in a league compete. These structural properties are the mean degree, the mean strength, and the clustering coefficient. We give a generalization of the Kendall's correlation coefficient to more than two rankings. We also show how to make a dynamic analysis of a league and how to compare different leagues. We apply this technique to analyze the four major European soccer leagues: Bundesliga, Italian Lega, Spanish Liga, and Premier League. We compare our results with the classical analysis of sport ranking based on measures of competitive balance.
Optimization of a counter-rotating wind turbine using the blade element and momentum theory
Authors: Hwang Byeongho , Lee Seungmin , Lee Soogab
Published: November 2013

A counter-rotating wind turbine has a front rotor and a rear rotor which rotate in opposite directions on the same axis. Compared to a single rotor, the flow field of the counter-rotating wind turbine is complicated due to the interactions between the front rotor and the rear rotor. The wake induced by the front rotor works on the inflow of the rear rotor and is essentially an unsteady flow state. In order to estimate the performance of a counter-rotating wind turbine, it is necessary to consider more variables than the case of a single-rotor wind turbine and to prepare an estimation system capable of performing delicate predictions. For the optimization of a counter-rotating wind turbine, the pitch angles, radius ratios, and rotation speeds of two rotors are chosen as the design values and variations of the power coefficients and thrust coefficients can be observed in this study. The torque balance of the two rotors due to the kinematic coupling of the generator is considered. Modeling by means of the blade element and momentum theory for the optimization of a counter-rotating wind turbine is developed to predict the front rotor flow and the wake flow generated by the front rotor. The wake flow is then applied for the inflow of the rear rotor. A vehicle test is carried out to validate the prediction. The optimized solution is found using a multi-island genetic algorithm.
CO dissociation on iron nanoparticles: Size and geometry effects
Authors: Melander Marko , Latsa Ville , Laasonen Kari
Published: November 2013

The reactivity of 0.5-1.4 nm iron nanoparticles and corresponding bulk surfaces has been systematically studied using density functional theory. The study includes both ideally symmetric and more realistic rugged nanoparticles. The activation energies for CO dissociation vary between 1.1 and 2.1 eV. An increasing particle size and roughness result in lower activation energies. For a single particle, variations as large as 0.9 eV occur indicating the importance of local particle morphology. Depending on the nanoparticle size, geometry, and CO dissociation pathway the reaction rates span five orders of magnitude at conditions relevant for gas-phase chemical vapor deposition synthesis of carbon nanotubes. Studies on the smallest particles and bulk surfaces show that these systems cannot be used as reliable models for catalysis on larger iron nanoparticles. It has also been demonstrated that predictive d-band and linear-energy relationships cannot be used to explain the reactivity of iron for CO dissociation as reaction mechanisms vary from one particle to another. The changes in reaction mechanisms can be rationalized by the varying Fe-Fe bond lengths in different particles leading to changes in back-bonding between the iron surface and CO. CO dissociation on nano-sized iron seems to be more complex than that seen on more conventional non-magnetic noble metal particles.
Mechanism of ion permeation through a model channel: Roles of energetic and entropic contributions
Authors: Sumikama Takashi , Saito Shinji , Ohmine Iwao
Published: November 2013

Mechanism of ion permeation through an anion-doped carbon nanotube (ANT), a model of ion channel, is investigated. Using this model system, many trajectory calculations are performed to obtain the potential energy profile, in addition to the free energy profile, that enables to separate the energy and the entropic contributions, along the ion permeation. It is found that the mechanism of the transport is governed by the interplay between the energetic and the entropic forces. The rate of the ion permeation can be controlled by changing the balance between these contributions with altering, for example, the charge and/or the length of ANT, which increases the rate of the ion permeation by nearly two orders of magnitude. The dominant free energy barrier at the entrance of ANT is found to be caused by the entropy bottleneck due to the narrow phase space for the exchange of a water molecule and an incoming ion.
Spin transport and magnetoresistance in Thue-Morse graphene superlattice with two ferromagnetic graphene electrodes
Authors: Liu Haiyan , Zhang Hongmei , Liu De , Kong Xiaojun
Published: November 2013

We investigate theoretically the spin-dependent transport and tunnel magnetoresistance in a system consisting of two ferromagnetic graphene (FG) electrodes separated by the Thue-Morse graphene superlattice (TMGSL) or periodic graphene superlattice (PGSL). Using transfer matrix methods, the spin-dependent conductance, tunnel magnetoresistance, and spin polarization of current of the FG/TMGSL/FG junctions are numerically calculated and compared with those of the FG/PGSL/FG junctions. The results indicate that all the physical quantities considered here show typical quasiperiodic oscillations as the electrostatic barrier height increases. Furthermore, the conductances, spin polarization of the current for the parallel configuration of magnetization, and tunnel magnetoresistance monotonically increase or decrease with increasing exchange splitting energy. Interestingly, compared to the FG/PGSL/FG junctions, all the physical quantities, considered here, of the FG/TMGSL/FG junctions can exhibit a more marked growth stage effect, along with stronger and more irregular oscillations with increasing electrostatic barrier height.
Magnetic effect on hopping rate of electrons in organic semiconductors
Authors: Zhao Junqing , Wang Ting , Zhang Meisheng , Zhang Ningyu , Pang Yantao , Li Luyan , Ji Yanju , Zhuang Shidong , Mao Jinhua , Wang Huilin
Published: November 2013

Considering effects of molecular vibration (ω0), hyperfine interaction (J), spin energy split, spin flip, and spin entanglement (η) of electron with nucleus on the hopping rate of electrons in organic semiconductors, we establish a model to calculate organic magnetoresistance (OMAR) within magnetic field B of 1 T. The results show that the effect of spin energy split is minimal, ω0 influences the gradient of OMAR to B in high field, J influences the OMAR in low field, the spin flip shows impact mainly in low field, η affects OMAR throughout the considered magnetic field and turns the high-field OMAR from positive to negative value.
Nurse-led supportive care management: a 6-month review of the role of a nurse practitioner in a chemotherapy unit
Authors: Cox Keith , Karikios Deme , Roydhouse Jessica K. , White Kate
Published: November 2013

Objectives This case study evaluates the oncology nurse practitioner (NP) role in a chemotherapy unit. Background The NP works in the cancer centre of a major metropolitan public hospital. The NP role was established in the chemotherapy unit in 2007. The NP reviews all patients that have an unscheduled presentation to the unit, with symptoms relating either to their disease or treatment. Methods All unscheduled occasions of service provided by the NP in the chemotherapy unit over 6 months were recorded. Data were collected on patient demographic characteristics, medical problems and reason for presentation. Data on duration of care, interventions and outcomes administered by the NP were captured. Results There were 87 occasions of service (72 patients) during the study period. Nausea, vomiting or dehydration were the most common presenting problems and most presenting problems were moderate or severe (n = 73, 84%). The median time to review for the NP was 5 min and nearly all consultations (n = 83, 96%) took 30 min or less. Following NP consultation, most occasions of service did not require subsequent hospital admission (n = 52, 60%), medical advice (n = 61, 70%) or medical review (n = 75, 86%). Conclusions The NP is a valuable asset to a busy department, increasing access to timely and appropriate healthcare for patients on chemotherapy. What is known about the topic? Models of care for oncology NP roles are being developed in Australia, but few published reports and descriptions of the work of oncology NP exist. What does this paper add? This paper presents a description and evaluation of occasions of service for an oncology NP in a chemotherapy unit and the impact of the NP’s role on the hospital and clinical workload. What are the implications for practitioners? This paper can inform the development of other oncology NP roles in Australian chemotherapy units, and highlights potential areas of evaluation for new NP roles in cancer care.
Azobenzene-Functionalised Core Cross-Linked Star Polymers and their Host–Guest Interactions
Authors: Tan Shereen , Wong Edgar H. H. , Fu Qiang , Ren Jing M. , Sulistio Adrian , Ladewig Katharina , Blencowe Anton , Qiao Greg G.
Published: November 2013

Water-soluble poly(2-hydroxyethyl acrylate) (PHEA)-based core cross-linked star polymers were efficiently synthesised with high macroinitiator-to-star-conversion (>95 %) in a one-pot system via single electron transfer-living radical polymerisation. The star polymers display excellent water solubility and the pendant hydroxyl groups provide a platform for facile post-functionalisation with various molecules. In demonstrating this, a photo-isomerisable molecule, 4-(phenylazo)benzoic acid was conjugated onto the preformed stars through partial esterification of the available hydroxyl groups (5–20 %). The azobenzene functionalised stars were subsequently employed to form reversible inclusion complexes with α-cyclodextrin.
Preventing maternal and early childhood obesity: the fetal flaw in Australian perinatal care
Authors: Miller Margaret , Hearn Lydia , van der Pligt Paige , Wilcox Jane , Campbell Karen J.
Published: November 2013

Almost half of Australian women of child-bearing age are overweight or obese, with a rate of 30–50% reported in early pregnancy. Maternal adiposity is a costly challenge for Australian obstetric care, with associated serious maternal and neonatal complications. Excess gestational weight gain is an important predictor of offspring adiposity into adulthood and higher maternal weight later in life. Current public health and perinatal care approaches in Australia do not adequately address excess perinatal maternal weight or gestational weight gain. This paper argues that the failure of primary health-care providers to offer systematic advice and support regarding women’s weight and related lifestyle behaviours in child-bearing years is an outstanding ‘missed opportunity’ for prevention of inter-generational overweight and obesity. Barriers to action could be addressed through greater attention to: clinical guidelines for maternal weight management for the perinatal period, training and support of maternal health-care providers to develop skills and confidence in raising weight issues with women, a variety of weight management programs provided by state maternal health services, and clear referral pathways to them. Attention is also required to service systems that clearly define roles in maternal weight management and ensure consistency and continuity of support across the perinatal period.
Response of eastern pygmy possums, Cercartetus nanus, to selective logging in New South Wales: home range, habitat selection and den use
Authors: Law Bradley , Chidel Mark , Britton Alf , Brassil Traecey
Published: November 2013

Context Selective logging of native forests creates a mosaic of disturbance histories; however, little is known about how different taxa respond to such a mosaic. Aims We followed adaptive-management principles to test logging and burning impacts on eastern pygmy possums, Cercartetus nanus (Geoffroy and Desmarest, 1817), by undertaking a large-scale field experiment that coincided with harvesting. We predicted that home range would increase after logging because of a reduction in resources (food and/or dens) and because hollows suitable for denning would decrease, resulting in greater use of unlogged patches and alternate dens. Methods We radio-tracked C. nanus in a before-and-after logging experiment to investigate home range, habitat selection and den use. We tracked 50 possums, some individuals for a maximum of 8 months, within control, recently logged and regrowth (5 years since logging) sites. Key results Home ranges were variable (0.04–19.5 ha), with males having significantly larger home ranges. We were unable to detect a difference in home-range size between controls and the first year after logging and burning, or regrowth 5 years after logging. Home ranges comprised a mosaic of disturbed and undisturbed areas, and possums did not avoid logged habitat in their home ranges, indicating that logging did not significantly influence habitat selection. We suggest that possums were not sensitive to selective logging and burning because nectar-producing plants are adapted to fire disturbance and because a variety of den sites were used, most commonly in tree hollows and fallen logs, which were commonly left as logging residue. Indeed, possums frequently denned in logged patches, both recently after logging (63% of dens) and in regrowth 5 years after logging (76% of dens). Counts of fallen hollow logs at each site indicated that their density was not reduced by logging, with regrowth sites having the greatest abundance of logs (260 ha–1). Conclusions The mosaic of disturbance created by selective logging operations did not negatively affect home range or den selection of C. nanus. Implications Ecologically sustainable logging practices that include a range of mitigation measures to protect biodiversity can be compatible with the management of threatened species. Assessment of the effectiveness of these methods often will rely on scientific research.
Geographic variation in the diet of the powerful owl (Ninox strenua) at a local scale
Authors: Bilney Rohan J.
Published: November 2013

This study reports the diet of the powerful owl (Ninox strenua) in East Gippsland, from a dataset of 2009 vertebrate prey items collected from 53 sites. Mammals dominated the diet at all sites, but birds were also consumed regularly. The greater glider (Petauroides volans) was the dominant dietary item across the region in terms of both frequency of consumption and biomass contribution. There was geographical dietary variation between coastal and foothill forest sites, with the sugar glider (Petaurus breviceps) and birds consumed more frequently in foothill forests, whereas the common ringtail possum (Pseudocheirus peregrinus) was frequently consumed only in coastal forests. Typically, a higher percentage of powerful owl diet comprised birds closer to cleared land. The dietary reliance upon hollow-dependent mammals in foothill forests (averaging >70%) is of conservation concern, especially when non-hollow-dependent prey are rare. Forest management activities, especially logging, that reduce densities of hollow-bearing trees in the landscape are therefore likely to decrease the long-term carrying capacity of the landscape for the powerful owl.
It takes two to tango: knowledge mobilization and ignorance mobilization in science research and innovation
Authors: Gaudet Joanne
Published: November 2013

The main goal of this paper is to propose a dynamic mapping for knowledge and ignorance mobilization in science research and innovation. An underlying argument is that ‘knowledge mobilization’ science policy agendas in countries such as Canada and the United Kingdom fail to capture a critical element of science and innovation: ignorance mobilization. The latter draws attention to dynamics upstream of knowledge in science research and innovation. Although perhaps less visible, there is ample evidence that researchers value, actively produce, and thereby mobilize ignorance. For example, scientists and policymakers routinely mobilize knowledge gaps (cf. ignorance) in the process of establishing and securing research funding to argue the relevance of a scientific paper or a presentation, and to launch new research projects. Ignorance here is non-pejorative and by and large points to the borders and the limits of scientific knowing – what is known to be unknown. In addition, processes leading to the intentional or unintentional consideration or bracketing out of what is known to be unknown are intertwined with, yet remain distinct from, knowledge mobilization dynamics. The concepts of knowledge mobilization and of ignorance mobilization, respectively, are understood to be the use of knowledge or ignorance towards the achievement of goals. The value of this paper lies in its conceptualization of the mobilization of knowledge as related to the mobilization of ignorance within a complex, dynamic and symbiotic relationship in science research and innovation: it takes two to tango.
MetaboNetworks, an interactive Matlab-based toolbox for creating, customizing and exploring sub-networks from KEGG
Authors: Posma Joram M. , Robinette Steven L. , Holmes Elaine , Nicholson Jeremy K.
Published: November 2013

Summary: MetaboNetworks is a tool to create custom sub-networks in Matlab using main reaction pairs as defined by the Kyoto Encyclopaedia of Genes and Genomes and can be used to explore transgenomic interactions, for example mammalian and bacterial associations. It calculates the shortest path between a set of metabolites (e.g. biomarkers from a metabonomic study) and plots the connectivity between metabolites as links in a network graph. The resulting graph can be edited and explored interactively. Furthermore, nodes and edges in the graph are linked to the Kyoto Encyclopaedia of Genes and Genomes compound and reaction pair web pages.

Availability and implementation: MetaboNetworks is available from http://www.mathworks.com/matlabcentral/fileexchange/42684.

Contact:  jmp111@ic.ac.uk or j.nicholson@imperial.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
NCS: incorporating positioning data to quantify nucleosome stability in yeast
Authors: Chiang Jung-Hsien , Lin Chan-Hsien
Published: November 2013

Motivation: With the spreading technique of mass sequencing, nucleosome positions and scores for their intensity have become available through several previous studies in yeast, but relatively few studies have specifically aimed to determine the score of nucleosome stability. Based on mass sequencing data, we proposed a nucleosome center score (NCS) for quantifying nucleosome stability by measuring shifts of the nucleosome center, and then mapping NCS scores to nucleosome positions in Brogaard et al.’s study.

Results: We demonstrated the efficiency of NCS by known preference of A/T-based tracts for nucleosome formation, and showed that central nucleosomal DNA is more sensitive to A/T-based tracts than outer regions, which corresponds to the central histone tetramer-dominated region. We also found significant flanking preference around nucleosomal DNA for A/T-based dinucleotides, suggesting that neighboring sequences could affect nucleosome stability. Finally, the difference between results of NCS and Brogaard et al.’s scores was addressed and discussed.

Contacts:  jchiang@mail.ncku.edu.tw

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Diagnostic Guide for Gummy Stem Blight and Black Rot on Cucurbits
Authors: Keinath Anthony P.
Published: November 2013

Gummy stem blight and black rot affect all commonly cultivated cucurbits, including melon, watermelon, cucumber, pumpkin, and squash. Symptoms may be found on all vegetative and reproductive parts of plants, although there is variation in susceptibility among species and horticultural types. Characteristic symptoms include foliar blight, crown and stem cankers, and fruit rot. The pathogen, Didymella bryoniae, can be identified from its fruiting bodies of pycnidia and pseudothecia on diseased tissue and in culture.

Accepted for publication 27 August 2013. Published 24 October 2013.
Evaluation of Foliar Fungicide Sprays for the Control of Boxwood Blight, Caused by the Fungus Cylindrocladium buxicola
Authors: Henricot B. , Wedgwood E.
Published: November 2013

Cylindrocladium buxicola causes a damaging blight disease on boxwood which has spread rapidly throughout Europe since introduction of the pathogen in England in the mid 1990s. The pathogen has also been recently identified in the USA and British Columbia. The disease is difficult to control using cultural methods and information about chemical control is lacking. To address this, preventative and curative foliar fungicide sprays previously shown in laboratory tests to have efficacy were evaluated over two autumn/winter seasons in the UK. Results from the first autumn/winter season showed that the premix product Opponent (epoxiconazole + kresoxim-methyl + pyraclostrobin) was the best treatment when applied preventatively 3 days before inoculation. In the second autumn/winter season, curative treatment of diseased plants was best achieved with a weekly program of fungicides starting 3 days before inoculation and alternating with two or three products including Bravo (chlorothalonil), Signum (boscalid + pyraclostrobin), and Octave (prochloraz). The only fungicide tested and available to amateur growers in the UK, Fungus Clear (penconazole), was found to give moderate control of boxwood blight.

Accepted for publication 7 August 2012. Published 24 October 2013.
Microvirga vignae sp. nov., a root nodule symbiotic bacterium isolated from cowpea grown in semi-arid Brazil
Authors: Radl Viviane , Simões-Araújo Jean Luiz , Leite Jakson , Passos Samuel Ribeiro , Martins Lindete Míria Vieira , Xavier Gustavo Ribeiro , Rumjanek Norma Gouvêa , Baldani José Ivo , Zilli Jerri Edson
Published: November 2013

16S rRNA gene sequence analysis of eight strains (BR 3299T, BR 3296, BR 10192, BR 10193, BR 10194, BR 10195, BR 10196 and BR 10197) isolated from nodules of cowpea collected from a semi-arid region of Brazil showed 97 % similarity to sequences of recently described rhizobial species of the genus

Microvirga

. Phylogenetic analyses of four housekeeping genes (gyrB, recA, dnaK and rpoB), DNA–DNA relatedness and AFLP further indicated that these strains belong to a novel species within the genus

Microvirga

. Our data support the hypothesis that genes related to nitrogen fixation were obtained via horizontal gene transfer, as sequences of nifH genes were very similar to those found in members of the genera

Rhizobium

and

Mesorhizobium

, which are not immediate relatives of the genus

Microvirga

, as shown by 16S rRNA gene sequence analysis. Phenotypic traits, such as host range and carbon utilization, differentiate the novel strains from the most closely related species,

Microvirga lotononidis

,

Microvirga zambiensis

and

Microvirga lupini

. Therefore, these symbiotic nitrogen-fixing bacteria are proposed to be representatives of a novel species, for which the name Microvirga vignae sp. nov. is suggested. The type strain is BR3299T ( = HAMBI 3457T).
Structural basis for targeting the chromatin repressor Sfmbt to Polycomb response elements
Authors: Alfieri Claudio , Gambetta Maria Cristina , Matos Raquel , Glatt Sebastian , Sehr Peter , Fraterman Sven , Wilm Matthias , Müller Jürg , Müller Christoph W.
Published: November 2013

Polycomb group (PcG) protein complexes repress developmental regulator genes by modifying their chromatin. How different PcG proteins assemble into complexes and are recruited to their target genes is poorly understood. Here, we report the crystal structure of the core of the Drosophila PcG protein complex Pleiohomeotic (Pho)-repressive complex (PhoRC), which contains the Polycomb response element (PRE)-binding protein Pho and Sfmbt. The spacer region of Pho, separated from the DNA-binding domain by a long flexible linker, forms a tight complex with the four malignant brain tumor (4MBT) domain of Sfmbt. The highly conserved spacer region of the human Pho ortholog YY1 binds three of the four human 4MBT domain proteins in an analogous manner but with lower affinity. Comparison of the Drosophila Pho:Sfmbt and human YY1:MBTD1 complex structures provides a molecular explanation for the lower affinity of YY1 for human 4MBT domain proteins. Structure-guided mutations that disrupt the interaction between Pho and Sfmbt abolish formation of a ternary Sfmbt:Pho:DNA complex in vitro and repression of developmental regulator genes in Drosophila. PRE tethering of Sfmbt by Pho is therefore essential for Polycomb repression in Drosophila. Our results support a model where DNA tethering of Sfmbt by Pho and multivalent interactions of Sfmbt with histone modifications and other PcG proteins create a hub for PcG protein complex assembly at PREs.
Preparation of Microsomes to Study Ca2+ Channels
Authors: Bezprozvanny Ilya
Published: November 2013

Native cerebellar microsomes are used to study the properties of native cerebellar inositol(1,4,5)-trisphosphate receptor 1 (InsP3R1) and ryanodine receptor 1 (RyanR1) Ca2+ release channels. Additionally, microsomes prepared from Sf9 cells infected with InsP3R- or RyanR-expressing recombinant baculoviruses can be used to compare properties of different InsP3R and RyanR isoforms and to perform structure–function studies of both types of receptors. This protocol describes how to prepare ER microsomes from native cerebellar tissue or Sf9 cells infected with InsP3R- or RyanR-expressing recombinant baculoviruses for planar lipid bilayer (also called black lipid membranes or BLM) experiments. Prepared material is aliquoted and can be stored at −80°C freezer for many months before BLM experiments.
Tracking Individual Intracellular Proteins Using Quantum Dots
Authors: Courty Sébastien , Dahan Maxime
Published: November 2013

Single-molecule detection of quantum dot (QD)-tagged proteins located in the cytoplasm or the nucleus presents a significant challenge in live-cell imaging. First, QDs must enter the cell cytoplasm and reach their molecular target but still preserve cell integrity. Second, the fluorescence of individual QDs must be detected in a noisy environment and distinguished from the autofluorescence of intracellular compartments and organelles. Finally, molecular motion in the cytosol is likely to be three-dimensional, compared to two-dimensional diffusion in the membrane. In this protocol, streptavidin-coated QDs (QD-SAVs) are coupled with biotinylated proteins (ideally in a 1:1 molar ratio) in hypertonic medium. The coupled reaction product (QD-P) is then added to live cells (e.g., mammalian HeLa cells) using a cell-loading technique based on the osmotic lysis of pinocytic vesicles. The osmotic lysis of pinocytic vesicles in hypotonic solution does not alter the viability of cultured cells and does not result in lysosomal enzyme release. By comparison with other internalization techniques, such as microinjection, this method is much simpler and more reproducible because all of the cells are simultaneously loaded under the same conditions. It can provide quantitative information on the movement of intracellular biomolecules, enhancing our understanding of complex biological processes such as signal transduction, cell division, or motility.
Time-Lapse Analysis of Primordium Migration during the Development of the Fish Lateral Line
Authors: Schuster Kevin , Ghysen Alain
Published: November 2013

The lateral line is a mechanosensory system that comprises a set of discrete sense organs called neuromasts, which are arranged in reproducible patterns on the surface of fish and amphibians. The system is used by these animals to extract information from the movements of water around their body, providing them with a sense of “touch-at-a-distance” that is involved in most aspects of fish behavior. Each neuromast has a core of mechanosensory hair cells, each of which is depolarized by water motion in one direction and hyperpolarized by motion in the other direction. Based on the position of their ganglion, two components of the lateral-line system can be distinguished: the anterior lateral-line (ALL) system comprises the neuromasts on the head and has its ganglion just anterior to the otic vesicle, the posterior lateral-line (PLL) system comprises the neuromasts on the body and tail and has its ganglion just posterior to the otic vesicle. The peripheral location of the PLL system makes it accessible and easily visualized by imaging methods. The PLL develops from the migrating primordium and so can be used to examine various aspects of neural development, including the control of long-range, collective cell migration and the mechanisms underlying the establishment of appropriate connectivity. Here we discuss imaging methods for exploring these processes.
Ultrasensitive Imaging in Live Cells Using Fluorescent Quantum Dots
Authors: Courty Sébastien , Dahan Maxime
Published: November 2013

Semiconductor quantum dots (QDs) are fluorescent nanoparticles that can be used for biological imaging. Because of their brightness and photostability, which are far superior to those of organic dyes and fluorescent proteins, they can be detected at the single-particle level over long periods of time using standard fluorescence microscopy techniques. QDs can be conjugated to biomolecules and then used to track the motion of these molecules.
High-resolution thermal imaging with a combination of nano-focus X-ray diffraction and ultra-fast chip calorimetry
Authors: Rosenthal Martin , Doblas David , Hernandez Jaime J. , Odarchenko Yaroslav I. , Burghammer Manfred , Di Cola Emanuela , Spitzer Denis , Antipov A. E. , Aldoshin L. S. , Ivanov Dimitri A.
Published: November 2013

A microelectromechanical-systems-based calorimeter designed for use on a synchrotron nano-focused X-ray beamline is described. This instrument allows quantitative DC and AC calorimetric measurements over a broad range of heating/cooling rates (≤100000 K s−1) and temperature modulation frequencies (≤1 kHz). The calorimeter was used for high-resolution thermal imaging of nanogram-sized samples subjected to X-ray-induced heating. For a 46 ng indium particle, the measured temperature rise reaches ∼0.2 K, and is directly correlated to the X-ray absorption. Thermal imaging can be useful for studies of heterogeneous materials exhibiting physical and/or chemical transformations. Moreover, the technique can be extended to three-dimensional thermal nanotomography.
Influence of co-dopant in the europium reduction in SrAl2O4host
Authors: Rezende Marcos V. dos S. , Montes Paulo J. R. , Soares Felipe M. dos S. , Santos Claudiane dos , Valerio Mário E. G.
Published: November 2013

Xerogels of strontium chlorate and aluminium chlorate doped with europium (un-co-doped) and co-doped with rare earth ions (Ln = Gd, Dy, Er and Y) were prepared using the proteic sol–gel route. Synchrotron radiation was used to investigate the effect of different co-dopants on the Eu3+→ Eu2+reduction process during the synthesis of the samples. Samples were excited at the EuLIII-edge and the XANES regions were analyzed. The results suggest that some of the Eu ions can be stabilized in the divalent state and that it is difficult to completely reduce Eu3+to Eu2+during thermal treatment. The mechanisms of the Eu reduction processes are explained by a proposed model based on the incorporation of charge-compensation defects.