bluuebunny/crossref_metadata_2025 huggingface dataset:
The Centiloid Project: Standardizing quantitative amyloid plaque estimation by PET
Authors: Klunk William E. , Koeppe Robert A. , Price Julie C. , Benzinger Tammie L. , Devous Michael D. , Jagust William J. , Johnson Keith A. , Mathis Chester A. , Minhas Davneet , Pontecorvo Michael J. , Rowe Christopher C. , Skovronsky Daniel M. , Mintun Mark A.
Published: October 2014

Although amyloid imaging with PiB‐PET ([C‐11]Pittsburgh Compound‐B positron emission tomography), and now with F‐18‐labeled tracers, has produced remarkably consistent qualitative findings across a large number of centers, there has been considerable variability in the exact numbers reported as quantitative outcome measures of tracer retention. In some cases this is as trivial as the choice of units, in some cases it is scanner dependent, and of course, different tracers yield different numbers. Our working group was formed to standardize quantitative amyloid imaging measures by scaling the outcome of each particular analysis method or tracer to a 0 to 100 scale, anchored by young controls (≤45 years) and typical Alzheimer's disease patients. The units of this scale have been named “Centiloids.” Basically, we describe a “standard” method of analyzing PiB PET data and then a method for scaling any “nonstandard” method of PiB PET analysis (or any other tracer) to the Centiloid scale.
Pestalotiopsis revisited
Authors: Maharachchikumbura S.S.N. , Hyde K.D. , Groenewald J.Z. , Xu J. , Crous P.W.
Published: October 2014

Species of Pestalotiopsis occur commonly as plant pathogens, and represent a fungal group known to produce a wide range of chemically novel, diverse metabolites. In the present study, we investigated 91 Pestalotiopsis isolates from the CBS-KNAW Fungal Biodiversity Centre
(CBS) culture collection. The phylogeny of the Amphisphaeriaceae was constructed based on analysis of 28S nrRNA gene (LSU) sequence data, and taxonomic changes are proposed to reflect more natural groupings. We combined morphological and DNA data, and segregated two novel genera from
Pestalotiopsis, namely Neopestalotiopsis and Pseudopestalotiopsis. The three genera are easily distinguishable on the basis of their conidiogenous cells and colour of their median conidial cells. We coupled morphological and combined sequence data of internal transcribed
spacer (ITS), partial β-tubulin (TUB) and partial translation elongation factor 1-alpha (TEF) gene regions, which revealed 30 clades in Neopestalotiopsis and 43 clades in Pestalotiopsis. Based on these data, 11 new species are introduced in Neopestalotiopsis,
24 in Pestalotiopsis, and two in Pseudopestalotiopsis. Several new combinations are proposed to emend monophyly of Neopestalotiopsis, Pestalotiopsis and Pseudopestalotiopsis.
GRace: A MATLAB-Based Application for Fitting the Discrimination-Association Model
Authors: Stefanutti Luca , Vianello Michelangelo , Anselmi Pasquale , Robusto Egidio
Published: October 2014

The Implicit Association Test (IAT) is a computerized two-choice discrimination task in which stimuli have to be categorized as belonging to target categories or attribute categories by pressing, as quickly and accurately as possible, one of two response keys. The discrimination association model has been recently proposed for the analysis of reaction time and accuracy of an individual respondent to the IAT. The model disentangles the influences of three qualitatively different components on the responses to the IAT: stimuli discrimination, automatic association, and termination criterion. The article presents General Race (GRace), a MATLAB-based application for fitting the discrimination association model to IAT data. GRace has been developed for Windows as a standalone application. It is user-friendly and does not require any programming experience. The use of GRace is illustrated on the data of a Coca Cola-Pepsi Cola IAT, and the results of the analysis are interpreted and discussed.
Quantitative Oxygen Extraction Fraction from 7-Tesla MRI Phase: Reproducibility and Application in Multiple Sclerosis
Authors: Fan Audrey P , Govindarajan Sindhuja T , Kinkel R Philip , Madigan Nancy K , Nielsen A Scott , Benner Thomas , Tinelli Emanuele , Rosen Bruce R , Adalsteinsson Elfar , Mainero Caterina
Published: October 2014

Quantitative oxygen extraction fraction (OEF) in cortical veins was studied in patients with multiple sclerosis (MS) and healthy subjects via magnetic resonance imaging (MRI) phase images at 7 Tesla (7 T). Flow-compensated, three-dimensional gradient-echo scans were acquired for absolute OEF quantification in 23 patients with MS and 14 age-matched controls. In patients, we collected T2∗-weighted images for characterization of white matter, deep gray matter, and cortical lesions, and also assessed cognitive function. Variability of OEF across readers and scan sessions was evaluated in a subset of volunteers. OEF was averaged from 2 to 3 pial veins in the sensorimotor, parietal, and prefrontal cortical regions for each subject (total of ∼10 vessels). We observed good reproducibility of mean OEF, with intraobserver coefficient of variation (COV)=2.1%, interobserver COV=5.2%, and scan—rescan COV=5.9%. Patients exhibited a 3.4% reduction in cortical OEF relative to controls ( P=0.0025), which was not different across brain regions. Although oxygenation did not relate with measures of structural tissue damage, mean OEF correlated with a global measure of information processing speed. These findings suggest that cortical OEF from 7-T MRI phase is a reproducible metabolic biomarker that may be sensitive to different pathologic processes than structural MRI in patients with MS.
CoCuAl layered double hydroxides – efficient solid catalysts for the preparation of industrially important fatty epoxides
Authors: Sankaranarayanan Sivashunmugam , Sharma Ankita , Srinivasan Kannan
Published: October 2014

A scalable catalytic process for industrially important fatty epoxides is achieved by epoxidation of unsaturated fatty acid derivatives over recyclable CoCuAl-LDHs.
Systematic methodology for the development of biocatalytic hydrogen-borrowing cascades: application to the synthesis of chiral α-substituted carboxylic acids from α-substituted α,β-unsaturated aldehydes
Authors: Knaus Tanja , Mutti Francesco G. , Humphreys Luke D. , Turner Nicholas J. , Scrutton Nigel S.
Published: October 2014

The development of hydrogen-borrowing biocatalytic cascades is presented and applied to the synthesis of diverse α-chiral substituted carboxylic acids.
General and efficient synthesis of benzoxazol-2(3H)-ones: evolution of their anti-cancer and anti-mycobacterial activities
Authors: Indrasena Reddy K. , Aruna C. , Sudhakar Babu K. , Vijayakumar V. , Manisha M. , Padma Sridevi J. , Yogeeswari P. , Sriram D.
Published: October 2014

A novel class of benzo[d]oxazol-2(3H)-one derivatives has been synthesized and their in vitro cytotoxicity against human pancreatic adenocarcinoma and human non-small cell lung carcinoma cancer cell lines was evaluated.
Graphene–hemin hybrid nanosheets as a label-free colorimetric platform for DNA and small molecule assays
Authors: Hu Cui , Xi Qiang , Ge Jia , Luo Feng-Yan , Tang Li-Juan , Jiang Jian-Hui , Yu Ru-Qin
Published: October 2014

A novel colorimetric platform has been developed for detecting DNA and small molecules based on a graphene–hemin hybrid nanosheet in a homogenous solution.
A covalently anchored 2,4,6-triallyloxy-1,3,5-triazine Pd(ii) complex over a modified surface of SBA-15: catalytic application in hydrogenation reaction
Authors: Sharma Priti , Singh A. P.
Published: October 2014

Highly efficient and reusable SBA-15–TAT–Pd(ii) has been synthesized by anchoring a 2,4,6-triallyloxy-1,3,5-triazine (TAT) complex over the organo-functionalized surface of SBA-15.
Suzuki–Miyaura coupling of phosphinoyl-α-allenic alcohols with arylboronic acids catalyzed by a palladium complex “on water”: an efficient method to generate phosphinoyl 1,3-butadienes and derivatives
Authors: Liu Teng , Dong Jie , Cao Shu-Jun , Guo Li-Cheng , Wu Lei
Published: October 2014

We report here the first palladium-catalyzed Suzuki–Miyaura couplings of phosphinoyl-α-allenic alcohols with arylboronic acids “on water” without phase-transfer catalysts or additives.
Implementation of 5E inquiry incorporated with analogy learning approach to enhance conceptual understanding of chemical reaction rate for grade 11 students
Authors: Supasorn Saksri , Promarak Vinich
Published: October 2014

The main purpose of this study was to enhance student understanding of the scientific concepts of chemical reaction rate. Forty-four grade 11 students were the target group. The treatment tools were seven learning plans of 5E inquiry incorporated with an analogy learning approach during 15 hours of class time. In each learning plan, the students (1) addressed a scientific question regarding chemical reaction rate, (2) explored evidence to answer the question by carrying out a corresponding experiment, (3) drew explanations from collected evidence to answer the question, (4) elaborated their understanding by studying the given analogy and the target, and (5) evaluated their conceptual understandings by creating their own analogy and identifying similarities and differences of their analogies and the targets. The data collecting tool was a conceptual test of chemical reaction rate, consisting of 30 two-tier three-choice questions. The normalized learning gain for the whole conceptual test was at the medium gain level (0.64). The dependent samplest-test analysis indicated that the post-conceptual test score (mean 45.32, SD 6.46) was statistically higher than the pre-test score (mean 19.70, SD 3.10), but was statistically lower than the retention test score (mean 48.03, SD 9.04) at the significance level of 0.05. In the pre-conceptual test, the percentages of students in the good-, alternative-, and misconception categories were 13.69, 38.45, and 47.86, respectively. In the post-conceptual test, the percentages of students in these categories were 64.72, 24.6, and 10.63, respectively. This finding indicates that this implementation was an effective means to enhance and retain students' conceptual understanding of chemical reaction rate.
Polymer conformations in polymer nanocomposites containing spherical nanoparticles
Authors: Karatrantos Argyrios , Clarke Nigel , Composto Russell J. , Winey Karen I.
Published: October 2014

We investigate the effect of various spherical nanoparticles on chain dimensions in polymer melts for high nanoparticle loading which is larger than the percolation threshold, using molecular dynamics simulations.
Highly selective Fe3+ sensing and proton conduction in a water-stable sulfonate–carboxylate Tb–organic-framework
Authors: Dong Xi-Yan , Wang Rui , Wang Jun-Zhe , Zang Shuang-Quan , Mak Thomas C. W.
Published: October 2014

A new 3D porous terbium–organic framework has been assembled by Tb3+ ions and a sulfonate-carboxylate linker disodium-2,2′-disulfonate-4,4′-oxydibenzoic acid for Fe3+ sensing and proton conduction.
Origin of the increased open circuit voltage in PbS–CdS core–shell quantum dot solar cells
Authors: Speirs M. J. , Balazs D. M. , Fang H.-H. , Lai L.-H. , Protesescu L. , Kovalenko M. V. , Loi M. A.
Published: October 2014

The physics of PbS–CdS core–shell QDs is investigated, to enlighten the origin of the enhanced VOC in solar cells.
Carborane–β-cyclodextrin complexes as a supramolecular connector for bioactive surfaces
Authors: Neirynck P. , Schimer J. , Jonkheijm P. , Milroy L.-G. , Cigler P. , Brunsveld L.
Published: October 2014

The supramolecular carborane–β-cyclodextrin system allows for effective monovalent immobilization of biologically active peptides resulting in efficient cell adhesion and spreading.
Fabrication and characterisation of spin coated oxidised PMMA to provide a robust surface for on-chip assays
Authors: Rowinska M. , Kelleher S. M. , Soberon F. , Ricco A. J. , Daniels S.
Published: October 2014

Smooth, thin PMMA layers have been oxidised using two methods on various surfaces. The longevity of activation and ability of the films to bind and retain biomolecules has been investigated.
Eukaryotic elongation factor 2 kinase regulates the cold stress response by slowing translation elongation
Authors: Knight John R. P. , Bastide Amandine , Roobol Anne , Roobol Jo , Jackson Thomas J. , Utami Wahyu , Barrett David A. , Smales C. Mark , Willis Anne E.
Published: October 2014

Cells respond to external stress conditions by controlling gene expression, a process which occurs rapidly via post-transcriptional regulation at the level of protein synthesis. Global control of translation is mediated by modification of translation factors to allow reprogramming of the translatome and synthesis of specific proteins that are required for stress protection or initiation of apoptosis. In the present study, we have investigated how global protein synthesis rates are regulated upon mild cooling. We demonstrate that although there are changes to the factors that control initiation, including phosphorylation of eukaryotic translation initiation factor 2 (eIF2) on the α-subunit, the reduction in the global translation rate is mediated by regulation of elongation via phosphorylation of eukaryotic elongation factor 2 (eEF2) by its specific kinase, eEF2K (eukaryotic elongation factor 2 kinase). The AMP/ATP ratio increases following cooling, consistent with a reduction in metabolic rates, giving rise to activation of AMPK (5′-AMP-activated protein kinase), which is upstream of eEF2K. However, our data show that the major trigger for activation of eEF2K upon mild cooling is the release of Ca2+ ions from the endoplasmic reticulum (ER) and, importantly, that it is possible to restore protein synthesis rates in cooled cells by inhibition of this pathway at multiple points. As cooling has both therapeutic and industrial applications, our data provide important new insights into how the cellular responses to this stress are regulated, opening up new possibilities to modulate these responses for medical or industrial use at physiological or cooler temperatures.
Protein intrinsic disorder in Arabidopsis NAC transcription factors: transcriptional activation by ANAC013 and ANAC046 and their interactions with RCD1
Authors: O’Shea Charlotte , Kryger Mikael , Stender Emil G. P. , Kragelund Birthe B. , Willemoës Martin , Skriver Karen
Published: October 2014

Protein ID (intrinsic disorder) plays a significant, yet relatively unexplored role in transcription factors (TFs). In the present paper, analysis of the transcription regulatory domains (TRDs) of six phylogenetically representative, plant-specific NAC [no apical meristem, ATAF (Arabidopsis transcription activation factor), cup-shaped cotyledon] TFs shows that the domains are present in similar average pre-molten or molten globule-like states, but have different patterns of order/disorder and MoRFs (molecular recognition features). ANAC046 (Arabidopsis NAC 046) was selected for further studies because of its simple MoRF pattern and its ability to interact with RCD1 (radical-induced cell death 1). Experiments in yeast and thermodynamic characterization suggest that its single MoRF region is sufficient for both transcriptional activation and interaction with RCD1. The remainder of the large regulatory domain is unlikely to contribute to the interaction, since the domain and truncations thereof have similar affinities for RCD1, which are also similar for ANAC013–RCD1 interactions. However, different enthalpic and entropic contributions to binding were revealed for ANAC046 and ANAC013, suggestive of differences in binding mechanisms. Although substitution of both hydrophobic and acidic residues of the ANAC046 MoRF region abolished binding, substitution of other residues, even with α-helix-breaking proline, was less disruptive. Together, the biophysical analyses suggest that RCD1–ANAC046 complex formation does not involve folding-upon-binding, but rather fuzziness or an unknown structure in ANAC046. We suggest that the ANAC046 regulatory domain functions as an entropic chain with a terminal hot spot interacting with RCD1. RCD1, a cellular hub, may be able to interact with many different TFs by exploiting their ID-based flexibility, as demonstrated for its interactions with ANAC046 and ANAC013.
Successes and failures of Hubbard-corrected density functional theory: The case of Mg doped LiCoO2
Authors: Santana Juan A. , Kim Jeongnim , Kent P. R. C. , Reboredo Fernando A.
Published: October 2014

We have evaluated the successes and failures of the Hubbard-corrected density functional theory approach to study Mg doping of LiCoO2. We computed the effect of the U parameter on the energetic, geometric, and electronic properties of two possible doping mechanisms: (1) substitution of Mg onto a Co (or Li) site with an associated impurity state and (2) formation of impurity-state-free complexes of substitutional Mg and point defects in LiCoO2. We find that formation of impurity states results in changes on the valency of Co in LiCoO2. Variation of the Co U shifts the energy of the impurity state, resulting in energetic, geometric, and electronic properties that depend significantly on the specific value of U. In contrast, the properties of the impurity-state-free complexes are insensitive to U. These results identify reasons for the strong dependence on the doping properties on the chosen value of U and for the overall difficulty of achieving agreement with the experimentally known energetic and electronic properties of doped transition metal oxides such as LiCoO2.
Dynamics and control of DNA sequence amplification
Authors: Marimuthu Karthikeyan , Chakrabarti Raj
Published: October 2014

DNA amplification is the process of replication of a specified DNA sequence in vitro through time-dependent manipulation of its external environment. A theoretical framework for determination of the optimal dynamic operating conditions of DNA amplification reactions, for any specified amplification objective, is presented based on first-principles biophysical modeling and control theory. Amplification of DNA is formulated as a problem in control theory with optimal solutions that can differ considerably from strategies typically used in practice. Using the Polymerase Chain Reaction as an example, sequence-dependent biophysical models for DNA amplification are cast as control systems, wherein the dynamics of the reaction are controlled by a manipulated input variable. Using these control systems, we demonstrate that there exists an optimal temperature cycling strategy for geometric amplification of any DNA sequence and formulate optimal control problems that can be used to derive the optimal temperature profile. Strategies for the optimal synthesis of the DNA amplification control trajectory are proposed. Analogous methods can be used to formulate control problems for more advanced amplification objectives corresponding to the design of new types of DNA amplification reactions.
Quasi-particle energy spectra in local reduced density matrix functional theory
Authors: Lathiotakis Nektarios N. , Helbig Nicole , Rubio Angel , Gidopoulos Nikitas I.
Published: October 2014

Recently, we introduced [N. N. Lathiotakis, N. Helbig, A. Rubio, and N. I. Gidopoulos, Phys. Rev. A 90, 032511 (2014)] local reduced density matrix functional theory (local RDMFT), a theoretical scheme capable of incorporating static correlation effects in Kohn-Sham equations. Here, we apply local RDMFT to molecular systems of relatively large size, as a demonstration of its computational efficiency and its accuracy in predicting single-electron properties from the eigenvalue spectrum of the single-particle Hamiltonian with a local effective potential. We present encouraging results on the photoelectron spectrum of molecular systems and the relative stability of C20 isotopes. In addition, we propose a modelling of the fractional occupancies as functions of the orbital energies that further improves the efficiency of the method useful in applications to large systems and solids.
Effect of carboxylic acid of periodic mesoporous organosilicas on the fructose-to-5-hydroxymethylfurfural conversion in dimethylsulfoxide systems
Authors: Dutta Saikat , Kao Hsien-Ming , Wu Kevin C.-W.
Published: October 2014

This manuscript presents the preparation and catalytic application of highly ordered benzene bridged periodic mesoporous organosilicas (PMOs) functionalized with carboxylic acid (–COOH) group at varied density. The COOH-functionalized PMOs were synthesized by one-step condensation of 1,4-bis (triethoxysilyl) benzene and carboxylic group containing organosilane carboxyethylsilanetriol sodium salt using Brij-76 as the template. The obtained materials were characterized by a mean of methods including powder X-ray diffraction, nitrogen adsorption-desorption, scanning- and transmission electron microscopy, and 13C solid-state nuclear magnetic resonance measurements. The potentials of the obtained PMO materials with ordered mesopores were examined as solid catalysts for the chemical conversion of fructose to 5-hydroxymethylfurfural (HMF) in an organic solvent. The results showed that COOH-functionalized PMO with 10% COOH loading exhibited best results for the fructose to HMF conversion and selectivity. The high surface area, the adequate density acid functional group, and the strength of the PMO materials contributing to a promising catalytic ability were observed.
Properties of a soft-core model of methanol: An integral equation theory and computer simulation study
Authors: Huš Matej , Munaò Gianmarco , Urbic Tomaz
Published: October 2014

Thermodynamic and structural properties of a coarse-grained model of methanol are examined by Monte Carlo simulations and reference interaction site model (RISM) integral equation theory. Methanol particles are described as dimers formed from an apolar Lennard-Jones sphere, mimicking the methyl group, and a sphere with a core-softened potential as the hydroxyl group. Different closure approximations of the RISM theory are compared and discussed. The liquid structure of methanol is investigated by calculating site-site radial distribution functions and static structure factors for a wide range of temperatures and densities. Results obtained show a good agreement between RISM and Monte Carlo simulations. The phase behavior of methanol is investigated by employing different thermodynamic routes for the calculation of the RISM free energy, drawing gas-liquid coexistence curves that match the simulation data. Preliminary indications for a putative second critical point between two different liquid phases of methanol are also discussed.
Critical boron-doping levels for generation of dislocations in synthetic diamond
Authors: Alegre M. P. , Araújo D. , Fiori A. , Pinero J. C. , Lloret F. , Villar M. P. , Achatz P. , Chicot G. , Bustarret E. , Jomard F.
Published: October 2014

Defects induced by boron doping in diamond layers were studied by transmission electron microscopy. The existence of a critical boron doping level above which defects are generated is reported. This level is found to be dependent on the CH4/H2 molar ratios and on growth directions. The critical boron concentration lied in the 6.5–17.0 × 1020at/cm3 range in the ⟨111⟩ direction and at 3.2 × 1021 at/cm3 for the ⟨001⟩ one. Strain related effects induced by the doping are shown not to be responsible. From the location of dislocations and their Burger vectors, a model is proposed, together with their generation mechanism.
Working Culture: The Agency and Employment Experiences of Nonunionized Workers in the Surfboard Industry
Authors: Warren Andrew
Published: October 2014

This paper examines the agency of nonunionized workers employed in the surfboard industry. Informing a labor geography approach with cultural economy theory, the paper contributes to the progression of labor geographies beyond the confines of unionized labor–management relations. Using ethnographic methods with 135 workers across thirty-five workshops and three hubs of production (O'ahu, Hawai'i, southern California, and east coast Australia) I reveal how cultural values and logics powerfully shape labor relations in the surfboard industry. Under labor-intensive systems of craft-based, customized production, workers handle most aspects of business themselves: taking orders, designing, making, and exchanging finished products. Workers use deliberate, targeted actions to create agency and achieve stable, well-paid jobs anchored in vibrant surfing locations. Over the last decade, however, standardization, international competition, and managerial ambitions to upscale for export have instigated pervasive shifts to automated, capital-intensive production. Computer automation is transforming the scope, scale, and conditions of work. Human skills have been replicated, work hours have declined, and wages have stagnated. Against an increasingly precarious employment backdrop, workers' strategies to achieve positive change remain perceptible. But workers' agency is now being hampered by the laid-back, subcultural values pertaining to commercial production and workplace relations.
When Regions Collide: In What Sense a New ‘Regional Problem’?
Authors: Harrison John , Growe Anna
Published: October 2014

Going beyond the territorial/relational divide in regional studies requires researchers to do more than examine the extent to which territoriality and relationality are complementary alternatives. The variety of networked regional spaces means it is intellectually unsustainable to simply relate a single networked regional space to territory–scale without first considering how networked regional spaces interact. Illustrated through the experience of Germany, our paper demonstrates that interaction between different networked regional spaces (eg, city-regions and cross-border regions) is resulting in new networked regional imaginaries (eg, cross-border metropolitan regions). Its overall aim is to show that the production of entirely new networked spaces can assist in overcoming the contradictions present in one configuration of regions, but this only serves to create a new ‘regional problem’ requiring ever more complex configurations of regions.
Criminal Neighbourhoods: Does the Density of Prior Offenders in an Area Encourage others to Commit Crime?
Authors: Livingston Mark , Galster George , Kearns Ade , Bannister Jon
Published: October 2014

Using crime data over a period of a decade for Glasgow, this paper explores whether the density of prior offenders in a neighbourhoods has an influence on the propensity of others to (re)commence offending. The study shows that the number of ‘newly active’ offenders in a neighbourhood in the current quarter is positively associated with the density of prior offenders for both violent and property crime from the previous two years. In the case of newly active property offenders, the relationship with active prior offenders is apparent only when prior offender counts exceed the median. The paper postulates that intraneighbourhood social mechanisms may be at work to create these effects. The results suggest that policies which concentrate offenders in particular neighbourhoods may increase the number of newly active offenders, and point to evidence of a threshold at which these effects take place.
Sampling through time and phylodynamic inference with coalescent and birth–death models
Authors: Volz Erik M. , Frost Simon D. W.
Published: October 2014

Many population genetic models have been developed for the purpose of inferring population size and growth rates from random samples of genetic data. We examine two popular approaches to this problem, the coalescent and the birth–death-sampling model (BDM), in the context of estimating population size and birth rates in a population growing exponentially according to the birth–death branching process. For sequences sampled at a single time, we found the coalescent and the BDM gave virtually indistinguishable results in terms of the growth rates and fraction of the population sampled, even when sampling from a small population. For sequences sampled at multiple time points, we find that the birth–death model estimators are subject to large bias if the sampling process is misspecified. Since BDMs incorporate a model of the sampling process, we show how much of the statistical power of BDMs arises from the sequence of sample times and not from the genealogical tree. This motivates the development of a new coalescent estimator, which is augmented with a model of the known sampling process and is potentially more precise than the coalescent that does not use sample time information.
An efficient and unbiased method for sensitivity analysis of stochastic reaction networks
Authors: Gupta Ankit , Khammash Mustafa
Published: October 2014

We consider the problem of estimating parameter sensitivity for Markovian models of reaction networks. Sensitivity values measure the responsiveness of an output with respect to the model parameters. They help in analysing the network, understanding its robustness properties and identifying the important reactions for a specific output. Sensitivity values are commonly estimated using methods that perform finite-difference computations along with Monte Carlo simulations of the reaction dynamics. These methods are computationally efficient and easy to implement, but they produce a biased estimate which can be unreliable for certain applications. Moreover, the size of the bias is generally unknown and hence the accuracy of these methods cannot be easily determined. There also exist unbiased schemes for sensitivity estimation but these schemes can be computationally infeasible, even for very simple networks. Our goal in this paper is to present a new method for sensitivity estimation, which combines the computational efficiency of finite-difference methods with the accuracy of unbiased schemes. Our method is easy to implement and it relies on an exact representation of parameter sensitivity that we recently proved elsewhere. Through examples, we demonstrate that the proposed method can outperform the existing methods, both biased and unbiased, in many situations.
Comparative brain transcriptomic analyses of scouting across distinct behavioural and ecological contexts in honeybees
Authors: Liang Zhengzheng S. , Mattila Heather R. , Rodriguez-Zas Sandra L. , Southey Bruce R. , Seeley Thomas D. , Robinson Gene E.
Published: October 2014

Individual differences in behaviour are often consistent across time and contexts, but it is not clear whether such consistency is reflected at the molecular level. We explored this issue by studying scouting in honeybees in two different behavioural and ecological contexts: finding new sources of floral food resources and finding a new nest site. Brain gene expression profiles in food-source and nest-site scouts showed a significant overlap, despite large expression differences associated with the two different contexts. Class prediction and ‘leave-one-out’ cross-validation analyses revealed that a bee's role as a scout in either context could be predicted with 92.5% success using 89 genes at minimum. We also found that genes related to four neurotransmitter systems were part of a shared brain molecular signature in both types of scouts, and the two types of scouts were more similar for genes related to glutamate and GABA than catecholamine or acetylcholine signalling. These results indicate that consistent behavioural tendencies across different ecological contexts involve a mixture of similarities and differences in brain gene expression.
Introducing lesson study in promoting a new mathematics curriculum in Irish post-primary schools
Authors: Brosnan Anne
Published: October 2014

Purpose

– The purpose of this paper is to investigate and review how the practices of Lesson Study fare in enhancing the professional capabilities of mathematics teachers when introduced as part of a pilot project in reforming the post-primary mathematics curriculum in Ireland.

Design/methodology/approach

– Totally, 250 mathematics teachers teaching Junior and Senior Cycle mathematics in 24 post-primary schools constitute the population of this study. The schools which participated are representative of the range of all post-primary schools in Ireland.

Findings

– Lesson Study has an important role to play in the continuing professional development of teachers in the 24 post-primary schools and beyond in Ireland. An investigation of the maths teachers’ engagement with Lesson Study reveals some considerable initial resistance. Reasons for this resistance are examined and the lessons learned from the steps taken to deal with this are reviewed. Lesson Study is an innovation that teachers need to understand deeply and to practice regularly through mutual support if they are to avail of it fruitfully. Accordingly, further approaches need to be explored, not least the important role of school leadership, to adapt Lesson Study more fully and more productively to the professional cultures of teaching in Ireland.

Originality/value

– An analytic and evaluative account of the challenges and complexities involved in introducing Lesson Study to post-primary schools in Ireland is presented for the first time.
Exploring illness beliefs about diabetes among individuals with type 2 diabetes
Authors: Lakshmi Rema , Ganesan Palanisamy , Mohan Anjana Ranjit , Balasubramanyam Muthuswamy , Mohan Viswanathan
Published: October 2014

Purpose

– The purpose of this paper is to explore illness beliefs among adults with type 2 diabetes (T2DM), studied in a clinical setting in the Indian context. Diabetes management lies primarily in the hands of the patient, which signifies the need for understanding the various dimensions of individuals’ illness beliefs. While past research from abroad has stressed the need for understanding the patient’s perspective in effective illness management, the lack of studies in the Indian context calls for further research in this area.

Design/methodology/approach

– Drawing on the Self-Regulation Model (Leventhal et al., 1980), semi-structured interviews were carried out to understand the beliefs about diabetes among individuals diagnosed to have T2DM. In total, 70 individuals with T2DM were included, taking into account the disease duration, urban-rural, age and gender distinctions. The data were analyzed using content analysis method.

Findings

– The results of the analysis revealed numerous sub-themes related to the perceived consequences of diabetes, control or cure issues, timeline and emotional issues as experienced by the subjects.

Research limitations/implications

– Carrying out a triangulated research with the various stakeholders, namely, diabetologists, general practitioners and other support staff like dieticians could add more value to this exploratory study.

Originality/value

– There is a dearth of research work that explores the illness beliefs that patients’ hold about diabetes, as discussed in the Indian context. It is expected that the insight provided by the study can help the government bodies, healthcare organizations and practitioners design and develop interventions from a patient-centric view. Additionally, such a patient-centric approach will enable individuals to achieve their treatment goals.
Root responses of grassland species to spatial heterogeneity of plant–soil feedback
Authors: Hendriks Marloes , Visser Eric J. W. , Visschers Isabella G. S. , Aarts Bart H. J. , de Caluwe Hannie , Smit‐Tiekstra Annemiek E. , van der Putten Wim H. , de Kroon Hans , Mommer Liesje
Published: October 2014

Plant roots selectively forage for soil nutrients when these are heterogeneously distributed. In turn, effects of plant roots on biotic and abiotic conditions in the soil, which result in so‐called plant–soil feedback can be heterogeneously distributed as well, but it is unknown how this heterogeneity affects root distribution, nutrient uptake and plant biomass production. Here, we investigate plant root distribution patterns as influenced by spatial heterogeneity of plant–soil feedback in soil and quantify consequences for plant nitrogen uptake and biomass production.

We conditioned soils by four grassland plant species to obtain ‘own’ and ‘foreign’ soils that differed in biotic conditions similar as is done by the first phase of plant–soil feedback experiments. We used these conditioned soils to create heterogeneous (one patch of own and three patches of foreign soils) or homogeneous substrates where own and foreign soils were mixed. We also included sterilized soil to study the effect of excluding soil biota, such as pathogens, symbionts and decomposers. We supplied 15N as tracer to measure nutrient uptake.

In nonsterile conditions, most plant species produced more biomass in heterogeneous than in homogeneous soil. Root biomass and 15N uptake rates were higher in foreign than own soil patches. These differences between heterogeneous and homogeneous soil disappeared when soil was sterilized, suggesting that the effects in nonsterilized soils were due to species‐specific soil biota that had responded to soil conditioning.

We conclude that plants produce more biomass when own and foreign soils are patchily distributed than when mixed. We show that this enhanced productivity is due to nutrient uptake being overall most efficient when own and foreign soils are spatially separated. We propose that spatial heterogeneity of negative plant–soil feedback in species diverse plant communities may provide a better explanation of overyielding than assuming that plant–soil feedback effects are diluted.
No energetic benefits from sociality in tropical hibernation
Authors: Dausmann Kathrin H. , Glos Julian
Published: October 2014

Mammals generally profit from social thermoregulation, and the primary benefit of sociality during hibernation is thought to be the reduction of metabolic demands during periodic arousals. It has even been postulated that the energetic advantages during hibernation might have been the driver for the evolution of sociality in some mammal species.

As the necessity to show arousals and the concurring energetic costs depend on the temperature regime in the hibernacula, we tested whether this is also a plausible scenario in tropical hibernators such as the Malagasy lemur Cheirogaleus medius, with comparatively high and often fluctuating temperature regimes in their hibernacula.

To this end, we studied group composition and energy budgets (skin temperature patterns, metabolic rate) over three hibernation and activity seasons in a total of 53 free‐ranging C. medius.

Our results show that C. medius mostly occupied tree hollows solitarily during hibernation, contrary to the active season, and that the energetic savings were comparable for individuals hibernating socially in groups or solitarily (both about 74% compared to the resting metabolic rate of the active season). However, in larger groups, hibernation patterns were less regular and synchronized and individual torpor–arousal cycles were more frequently interrupted by euthermic group members than in individuals hibernating solitarily or in pairs.

We conclude that sociality during hibernation is not necessarily driven by energetic demands and might even be energetically disadvantageous in tropical species (at least in larger groups). Other factors, like social coherence or ecological and behavioural constraints, may be of greater influence for the evolution of sociality under tropical conditions.
Public opinion and government policy inBritain: A case of congruence, amplification or dampening?
Authors: Warwick Paul V.
Published: October 2014

This article examines postwar government policy inBritain, as reflected in annual budget speeches. Like previous research, it aims to content‐analyse these speeches to derive estimates of actual, as opposed to intended, government policy stances. Unlike previous research, it also aims to capture and measure the gap between intentions (as represented in electoral manifestos) and actual policy. This gap cannot be assessed from the final output of the Wordscores content analysis programme (in either the original version or theMartin‐Vanberg variation), but it can be teased out of the raw output. This teasing‐out process reveals the gap to be very small: there is no evidence thatBritish governments either moderate or amplify their left‐right stances when in office. This new measurement of government position is then used to cast further light on policy representation inBritain. The findings show that policy positions respond significantly to changes in public opinion as well as to electoral turnover, but do not exhibit or even approach the ideological congruence anticipated by the ‘median mandate’ interpretation of representative democracy.
Does multimarket contact facilitate tacit collusion? Inference on conduct parameters in the airline industry
Authors: Ciliberto Federico , Williams Jonathan W.
Published: October 2014

We provide empirical evidence that multimarket contact facilitates tacit collusion among airlines using a flexible model of oligopolistic behavior, where conduct parameters are modelled as functions of multimarket contact. We find (i) carriers with little multimarket contact do not cooperate in setting fares, whereas carriers serving many markets simultaneously sustain almost perfect coordination; (ii) cross‐price elasticities play a crucial role in determining the impact of multimarket contact on equilibrium fares; (iii) marginal changes in multimarket contact matter only at low or moderate levels of contact; (iv) assuming firms behave as Bertrand‐Nash competitors leads to biased estimates of marginal costs.
Inspection technology, detection, and compliance: evidence from Florida restaurant inspections
Authors: Jin Ginger Zhe , Lee Jungmin
Published: October 2014

In this article, we show that a small innovation in inspection technology can make substantial differences in inspection outcomes. For restaurant hygiene inspections, the state of Florida has introduced a handheld electronic device, the portable digital assistant (PDA), which reminds inspectors of about 1,000 potential violations that may be checked for. Using inspection records from July 2003 to June 2009, we find that the adoption of PDA led to 11% more detected violations and subsequently, restaurants may have gradually increased their compliance efforts. We also find that PDA use is significantly correlated with a reduction in restaurant‐related foodborne disease outbreaks.
Broad ligament hernia successfully treated by laparoscopy: Case report and review of literature
Authors: Matsunami Masatoshi , Kusanagi Hiroshi , Hayashi Ken , Yamada Shigetoshi , Kano Nobuyasu
Published: October 2014

We report a case of a 36‐year‐old woman with a history of caesarean section who presented with small bowel obstruction. Abdominal multi‐detector CT showed discontinuity of the small bowel near the broad ligament on the left. We made a provisional diagnosis of an internal hernia through a defect in the broad ligament and performed laparoscopic exploration, which revealed a viable ileal loop incarcerated by the broad ligament. Multi‐detector CT may be useful for diagnosing this type of defect preoperatively, whereby open surgery can be avoided.
Late‐type port‐site recurrence of unexpected gallbladder carcinoma 11 years after laparoscopic cholecystectomy
Authors: Tsujita Eiji , Ikeda Yasuharu , Kinjo Nao , Uezu Ippei , Matsuyama Junko , Kawano Hiroyuki , Yamaguchi Shohei , Egashira Akinori , Minami Kazuhito , Yamamoto Manabu , Kumagai Reiko , Taguchi Kenichi , Morita Masaru , Toh Yasushi , Okamura Takeshi
Published: October 2014

A 55‐year‐old man had laparoscopic cholecystectomy for acute cholecystitis and unexpected gallbladder cancer, followed by a liver bed resection and lymph node dissection. Eleven years later, he had a port‐site recurrence of gallbladder cancer requiring resection; at that time, no other site of recurrence was observed. The patient has survived for 20 months without another recurrence. Although a rare finding, clinicians should be alert to the possibility of such a recurrence even 11 years after complete cure of the primary tumor, particularly in patients who have undergone laparoscopic cholecystectomy for unexpected gallbladder cancer.
Couple Narratives and Adult Attachment – Using Conversation Analysis in Assessment
Authors: Gross Carola
Published: October 2014

Observation of unstructured interactional dialogue in a clinical setting using the method of conversation analysis found that couples at assessment interact in ways that show close association with features determined from their adult attachment classification. Two couples were selected from a cohort of research participants seeking couple psychotherapy, both with high scores on the Conflict Tactics Scale (Straus, 1979), but with different attachment status as independently assessed in individual adult attachment interviews. Each couple was videotaped, without interviewer, in 15 minute discussions of their problems. Their conversational strategies identified using Conversation Analysis showed close agreement with those associated with each participant's adult attachment status as independently derived using the Adult Attachment Interview. This study provides a first step in building an evidence base for a joint couple attachment interview, as proposed by Fisher and Crandell (2001).
Depressed resilience of bluefin tuna in the western atlantic and age truncation
Authors: Secor D. H. , Rooker J. R. , Gahagan B. I. , Siskey M. R. , Wingate R. W.
Published: October 2014

Following intense overfishing in the 1970s, the western stock of Atlantic bluefin tuna(Thunnus thynnus)experienced a long period of depressed abundance, which has been attributed to failure of the population to periodically produce large numbers of juveniles, the western stock mixing with the more highly exploited eastern stock (fisheries in the Northeast Atlantic Ocean and Mediterranean Sea), and regime shift in the population's ecosystem resulting in lower replacement rates. To evaluate the presence of relatively strong years of juvenile production, we analyzed age structure from a recent sample of otoliths (ear stones) collected from the western stock (2011–2013, North Carolina, U.S.A., winter fishery). Mixing levels for the recent sample were analyzed using otolith stable isotopes to test whether age structure might be biased through immigration of eastern stock bluefin tuna. Age structure from historical samples collected from United States and Canadian fisheries (1975–1981) was compared with more recent samples (1996–2007) to examine whether demographic changes had occurred to the western stock that might have disrupted juvenile production. Relatively high juvenile production occurred in 2003, 2005, and 2006. Otolith stable isotope analysis showed that these recruitments were mostly of western stock origin. However, these high recruitments were >2‐fold less than historical recruitment. We found substantial age truncation in the sampled fisheries. Half the historical sample was >20 years old (mean age = 20.1 [SD 3.7]; skewness = −0.3), whereas <5% of the recent sample was >20 years old (mean age = 13.4 [SD 3.8]; skewness = 1.3). Loss of age structure is consistent with changes in fishing selectivity and trends in the stock assessment used for management. We propose that fishing, as a forcing variable, brought about a threshold shift in the western stock toward lower biomass and production, a shift that emulates the regime shift hypothesis. An abbreviated reproductive life span compromised resilience by reducing the period over which adults spawn and thereby curtailing the stock's ability to sample year‐to‐year variability in conditions that favor offspring survival (i.e., storage effect). Because recruitment dynamics by the western stock exhibit threshold dynamics, returning it to a higher production state will entail greater reductions in exploitation rates.