bluuebunny/crossref_metadata_2025 huggingface dataset:
The Whitaker Classification of Craniosynostosis Outcomes: An Assessment of Interrater Reliability
Authors: Wes Ari M. , Naran Sanjay , Sun James , Mazzaferro Daniel , Xu Wen , Nguyen Phuong , Whitaker Linton A. , Bartlett Scott P. , Taylor Jesse A.
Published: June 2017

Background:

The Whitaker classification is a simple and widely used system for describing aesthetic outcomes after craniosynostosis surgery. The purpose of this study is to evaluate its interrater reliability for patients who have undergone fronto-orbital surgery.

Methods:

A retrospective review of patients with craniosynostosis who underwent surgical intervention at a tertiary referral center was conducted. Inclusion criteria were as follows: single-suture craniosynostosis, surgical intervention before age 2 years, and photographs taken before revisions between 5 and 20 years of age. Thirteen craniofacial surgeons independently reviewed the subjects’ photographs and assigned Whitaker classifications. Interrater reliability was assessed with the Cohen kappa statistic.

Results:

Twenty-nine subjects were included. Average ages at surgery and at the time of postoperative photography were 0.8 year and 12.8 years, respectively. The κ value for all 13 raters was 0.1567 (p < 0.0001), indicating “slight agreement.” Pairwise comparisons demonstrated κ values ranging from 0.0384 to 0.5492. The average rating for the set of 29 photographs differed significantly across the 13 raters (p = 0.0020) and ranged from 1.79 ± 0.68 to 2.79 ± 0.77. Finally, we found that average Whitaker classification did not differ significantly between subjects who subsequently underwent cranioplasty and/or fronto-orbital advancement and those who did not (subsequent procedures, 2.45 ± 0.55; no subsequent procedures, 1.88 ± 0.78; p = 0.1087).

Conclusions:

The Whitaker classification exhibits low interrater reliability and does not predict future treatment. It may benefit craniofacial surgeons to create new evaluation tools with greater precision, to improve the quality of patient care and craniofacial outcomes research.
Changes in Electroconvulsive Therapy Practice in the Last 12 Years in Hungary
Authors: Asztalos Márton , Ungvari Gabor S. , Gazdag Gábor
Published: June 2017

Background

Electroconvulsive therapy (ECT) was rarely used in Hungary in 2002, and the majority of patients receiving ECT were diagnosed with schizophrenia. This study aimed to explore the use of ECT in Hungary in 2014.

Methods

Two semi-structured questionnaires were sent to all acute adult psychiatric units in Hungary. The first questionnaire contained items concerning ECT use, and the second explored the reasons for not using ECT.

Results

Fifty-eight acute psychiatric inpatient units were identified, and 54 replied. Although 27 indicated that they used ECT, only 22 actually performed ECT in 2014. Thirty-one units did not offer ECT at all. In 2014, 174 patients received ECT in Hungary, constituting 0.59% of all inpatients treated in the departments where it was offered, equating to 0.176 patients/10,000 population. The indication for ECT shifted from schizophrenia in 2002 (55.6%) to mood disorders in 2014 (58.5%), but the absolute number of ECT-treated patients with mood disorders (110 vs 102) did not change. Reasons for not using ECT included the lack of an ECT machine, unavailability of an anesthesiologist, lack of finances, and lack of experienced staff.

Conclusions

In view of the high frequency of depression and suicide in Hungary, it is very likely that a significant minority of patients who would benefit from ECT cannot access it, which constitutes a violation of their right to the best possible treatment. The main reasons for the inadequate ECT service are the underfinanced hospital system and a lack of necessary knowledge.
Distal Radius Microstructure and Finite Element Bone Strain Are Related to Site-Specific Mechanical Loading and Areal Bone Mineral Density in Premenopausal Women
Authors: Mancuso Megan E. , Johnson Joshua E. , Ahmed Sabahat S. , Butler Tiffiny A. , Troy Karen L.
Published: June 2017

While weight-bearing and resistive exercise modestly increases aBMD, the precise relationship between physical activity and bone microstructure, and strain in humans is not known. Previously, we established a voluntary upper-extremity loading model that assigns a person’s target force based on their subject-specific, continuum FE-estimated radius bone strain. Here, our purpose was to quantify the inter-individual variability in radius microstructure and FE-estimated strain explained by site-specific mechanical loading history, and to determine whether variability in strain is captured by aBMD, a clinically relevant measure of bone density and fracture risk. Seventy-two women aged 21-40 were included in this cross-sectional analysis. High resolution peripheral quantitative computed tomography (HRpQCT) was used to measure macro- and micro-structure in the distal radius. Mean energy equivalent strain in the distal radius was calculated from continuum finite element models generated from clinical resolution CT images of the forearm. Areal BMD was used in a nonlinear regression model to predict FE strain. Hierarchical linear regression models were used to assess the predictive capability of intrinsic (age, height) and modifiable (body mass, grip strength, physical activity) predictors. Fifty-one percent of the variability in FE bone strain was explained by its relationship with aBMD, with higher density predicting lower strains. Age and height explained up to 31.6% of the variance in microstructural parameters. Body mass explained 9.1% and 10.0% of the variance in aBMD and bone strain, respectively, with higher body mass indicative of greater density. Overall, results suggest that meaningful differences in bone structure and strain can be predicted by subject characteristics.

Highlights

Areal bone mineral density (aBMD) explains 51% of the variability in bone strain.

Adult bone loading predicts greater cortical porosity and trabecular density.

Greater body mass predicts greater aBMD and lower bone strain.
Saccharomyces cerevisiaestrain YH166: a novel wild yeast for the production of tropical fruit sensory attributes in fermented beverages
Authors: Osburn Kara , Caputo Robert , Miller Justin , Bochman Matthew L.
Published: June 2017

All ales are fermented by various strains ofSaccharomyces cerevisiae.However, recent whole-genome sequencing has revealed that most commercially available ale yeasts are highly related and represent a small fraction of the genetic diversity found amongS. cerevisiaeisolates as a whole. This lack of diversity limits the phenotypic variations between these strains, which translates into a limited number of sensory compounds created during fermentation. Here, we characterized a collection of wildS. cerevisiae,S. kudriavzevii, andS. paradoxusstrains for their ability to ferment wort into beer. Although many isolates performed well,S. cerevisiaestrain YH166 was the most promising, displaying excellent fermentation kinetics and attenuation, as well as a tropical fruit sensory profile. Use of this strain in multiple styles of beer suggested that it is broadly applicable in the brewing industry. Thus, YH166 is a novel ale strain that can be used to lend fruity esters to beer and should pair well with citrusy hops in hop-forward ales.
Controlling complex microbial communities: a network-based approach
Authors: Angulo Marco Tulio , Moog Claude H. , Liu Yang-Yu
Published: June 2017

Microbes comprise nearly half of all biomass on Earth. Almost every habitat on Earth is teeming with microbes, from hydrothermal vents to the human gastrointestinal tract. Those microbes form complex communities and play critical roles in maintaining the integrity of their environment or the well-being of their hosts. Controlling microbial communities can help us restore natural ecosystems and maintain healthy human microbiota. Yet, our ability to precisely manipulate microbial communities has been fundamentally impeded by the lack of a systematic framework to control them. Here we fill this gap by developing a control framework based on the new notion of structural accessibility. This framework allows identifying minimal sets of “driver species” through which we can achieve feasible control of the entire microbial community. We numerically validate our control framework on large microbial communities, and then we demonstrate its application for controlling the gut microbiota of gnotobiotic mice infected withClostridium difficileand the core microbiota of the sea spongeIrcinia oros.
Collaborations between CpG sites in DNA methylation
Authors: Song You , Ren Honglei , Lei Jinzhi
Published: June 2017

DNA methylation patterns have profound impacts on genome stability, gene expression, and development. The molecular base of DNA methylation patterns has long been focused at single CpG sites level. Here, we construct a kinetic model of DNA methylation with collaborations between CpG sites, from which a correlation function was established based on experimental data. The function consists of three parts that suggest three possible sources of the correlation: movement of enzymes along DNA, collaboration between DNA methylation and nucleosome modification, and global enzyme concentrations within a cell. Moreover, the collaboration strength between DNA methylation and nucleosome modification is universal for mouse early embryo cells. The obtained correlation function provide insightful understanding for the mechanisms of inheritance of DNA methylation patterns.
Conserved lipid and small molecule modulation of COQ8 reveals regulation of the ancient UbiB family
Authors: Reidenbach Andrew G. , Kemmerer Zachary A. , Aydin Deniz , Jochem Adam , McDevitt Molly T. , Hutchins Paul D. , Wilkerson Emily M. , Stark Jaime L. , Stefely Jonathan A. , Johnson Isabel E. , Bingman Craig A. , Markley John L. , Coon Joshua J. , Peraro Matteo Dal , Pagliarini David J.
Published: June 2017

Human COQ8A (ADCK3) andSaccharomyces cerevisiaeCoq8p (collectively COQ8) are UbiB family proteins essential for mitochondrial coenzyme Q (CoQ) biosynthesis. However, the biochemical activity of COQ8 and its direct role in CoQ production remain unclear, in part due to lack of known endogenous regulators of COQ8 function and of effective small molecules for probing its activityin vivo. Here we demonstrate that COQ8 possesses evolutionarily conserved ATPase activity that is activated by binding to membranes containing cardiolipin and by phenolic compounds that resemble CoQ pathway intermediates. We further create an analog-sensitive version of Coq8p and reveal that acute chemical inhibition of its endogenous activity in yeast is sufficient to cause respiratory deficiency concomitant with CoQ depletion. Collectively, this work defines lipid and small molecule modulators of an ancient family of atypical kinase-like proteins and establishes a chemical genetic system for further exploring the mechanistic role of COQ8 in CoQ biosynthesis.
Variation and inheritance of theXanthomonasgene cluster required for activation of XA21-mediated immunity
Authors: Liu Furong , McDonald Megan , Schwessinger Benjamin , Joe Anna , Pruitt Rory , Erickson Teresa , Zhao Xiuxiang , Stewart Valley , Ronald Pamela C.
Published: June 2017

The rice XA21-mediated immune response is activated upon recognition of the RaxX peptide produced by the bacteriumXanthomonas oryzaepv.oryzae(Xoo). The 60 residue RaxX precursor is posttranslationally modified to form a sulfated tyrosine peptide that shares sequence and functional similarity with the plant sulfated tyrosine (PSY) peptide hormones. The five kbraxX-raxSTABgene cluster ofXooencodes RaxX, the RaxST tyrosylprotein sulfotransferase, and the RaxA and RaxB components of a predicted type one secretion system. The identified the completeraxX-raxSTABgene cluster is present only inXanthomonasspp., in five distinct lineages in addition toX. oryzae. The phylogenetic distribution of theraxX-raxSTABgene cluster is consistent with the occurrence of multiple lateral transfer events duringXanthomonasspeciation. RaxX variants representing each of the five lineages, and threeXooRaxX variants, fail to activate the XA21-mediated immune response yet retain peptide hormone activity. These RaxX variants contain a restricted set of missense mutations, consistent with the hypothesis that selection acts to maintain peptide hormone-like function. These observations are also consistent with the hypothesis that the XA21 receptor evolved specifically to recognizeXooRaxX.
K-mer clustering algorithm using a MapReduce framework: application to the parallelization of the Inchworm module of Trinity
Authors: Kim Chang Sik , Winn Martyn D. , Sachdeva Vipin , Jordan Kirk E.
Published: June 2017

Background

De novotranscriptome assembly is an important technique for understanding gene expression in non-model organisms. Many de novo assemblers using the de Bruijn graph of a set of the RNA sequences rely on in-memory representation of this graph. However, current methods analyse the complete set of read-derived k-mer sequence at once, resulting in the need for computer hardware with large shared memory.

Results

We introduce a novel approach that clusters k-mers as the first step. The clusters correspond to small sets of gene products, which can be processed quickly to give candidate transcripts. We implement the clustering step using the MapReduce approach for parallelising the analysis of large datasets, which enables the use of compute clusters. The computational task is distributed across the compute system, and no specialised hardware is required. Using this approach, we have re-implemented the Inchworm module from the widely used Trinity pipeline, and tested the method in the context of the full Trinity pipeline. Validation tests on a range of real datasets show large reductions in the runtime and per-node memory requirements, when making use of a compute cluster.

Conclusions

Our study shows that MapReduce-based clustering has great potential for distributing challenging sequencing problems, without loss of accuracy. Although we have focussed on the Trinity package, we propose that such clustering is a useful initial step for other assembly pipelines.
Assessing tACS-induced phosphene perception using closed-loop Bayesian optimization
Authors: Lorenz Romy , Simmons Laura E. , Monti Ricardo P. , Arthur Joy L. , Limal Severin , Laakso Ilkka , Leech Robert , Violante Ines
Published: June 2017

Transcranial alternating current stimulation (tACS) can evoke illusory flash-like visual percepts known asphosphenes. The perception of phosphenes represents a major experimental challenge when studying tACS-induced effects on cognitive performance. Besides growing concerns that retinal phosphenes themselves could potentially have neuromodulatory effects, the perception of phosphenes may also modify the alertness of participants. Past research has shown that stimulation intensity, frequency and electrode montage affect phosphene perception. However, to date, the effect of an additional tACS parameter on phosphene perception has been completely overlooked: the relative phase difference between stimulation electrodes. This is a crucial and timely topic given the confounding nature of phosphene perception and the increasing number of studies reporting changes in cognitive function following tACS phase manipulations. However, studying phosphene perception for different frequencies and phases simultaneously is not tractable using standard approaches, as the physiologically plausible range of parameters results in a combinatorial explosion of experimental conditions, yielding impracticable experiment durations. To overcome this limitation, here we applied a Bayesian optimization approach to efficiently sample an exhaustive tACS parameter space. Moreover, unlike conventional methodology, which involves subjects judging the perceived phosphene intensity on a rating scale, our study leveraged the strength of human perception by having the optimization driven based on a subject’s relative judgement. Applying Bayesian optimization for two different montages, we found that phosphene perception was affected by differences in the relative phase between cortical electrodes. The results were replicated in a second study involving new participants and validated using computational modelling. In summary, our results have important implications for the experimental design and conclusions drawn from future tACS studies investigating the effects of phase on cognition.
Pump−probe experiments at the TEMPO beamline using the low-α operation mode of Synchrotron SOLEIL
Authors: Silly Mathieu G. , Ferté Tom , Tordeux Marie Agnes , Pierucci Debora , Beaulieu Nathan , Chauvet Christian , Pressacco Federico , Sirotti Fausto , Popescu Horia , Lopez-Flores Victor , Tortarolo Marina , Sacchi Maurizio , Jaouen Nicolas , Hollander Philippe , Ricaud Jean Paul , Bergeard Nicolas , Boeglin Christine , Tudu Bharati , Delaunay Renaud , Luning Jan , Malinowski Gregory , Hehn Michel , Baumier Cédric , Fortuna Franck , Krizmancic Damjan , Stebel Luigi , Sergo Rudi , Cautero Giuseppe
Published: June 2017

The SOLEIL synchrotron radiation source is regularly operated in special filling modes dedicated to pump–probe experiments. Among others, the low-α mode operation is characterized by shorter pulse duration and represents the natural bridge between 50 ps synchrotron pulses and femtosecond experiments. Here, the capabilities in low-α mode of the experimental set-ups developed at the TEMPO beamline to perform pump–probe experiments with soft X-rays based on photoelectron or photon detection are presented. A 282 kHz repetition-rate femtosecond laser is synchronized with the synchrotron radiation time structure to induce fast electronic and/or magnetic excitations. Detection is performed using a two-dimensional space resolution plus time resolution detector based on microchannel plates equipped with a delay line. Results of time-resolved photoelectron spectroscopy, circular dichroism and magnetic scattering experiments are reported, and their respective advantages and limitations in the framework of high-time-resolution pump–probe experiments compared and discussed.
The impact of acquisitions on inventory performance
Authors: Hameri Ari-Pekka , Weiss Lawrence A.
Published: June 2017

Purpose

The purpose of this paper is to examine the relationship between acquisitions and inventory performance. Specifically, it analyzes the inventory performance (inventory level) of acquirers and their targets pre- and post-acquisition.

Design/methodology/approach

Using several business databases, a sample of 270 horizontal acquisitions by US firms between 1996 and 2004 is subject to multivariate analysis. Various robustness tests are applied to validate the results.

Findings

Three main results are found. First, the acquirer’s inventory performance is normally better than its target’s prior to the acquisition, consistent with acquirers taking over less efficient firms rather than cherry picking the more efficient ones. Second, inventory performance improves over time in the post-acquisition period in those cases where the acquirer is more efficient than the target. Third, inventory performance deteriorates over time in the post-acquisition period in those cases where the acquirer is less efficient than the target. The results are consistent with acquisitions being associated with both efficiency gains and efficiency losses due to (in)efficiency transfers from acquirers to targets.

Practical implications

From the management point of view, the study delivers the strongest message to companies that have substantial inventories and for whom efficient inventory management is vital to overall performance. Managers who are unaware of the potential consequences of acquisitions on inventory performance destroy value.

Originality/value

This research complements past research by showing that in spite of their synergetic potential, reducing inventory receives only limited attention in acquisitions.
Corporate political strategies: a contemporary literature review
Authors: Gorostidi-Martinez Haritz , Zhao Xiaokang
Published: June 2017

Purpose

By reviewing the overall concept of corporate political strategy (CPS), the purpose of this paper is to display a contemporary summary of issues of the diverse global CPSs. This study additionally aims to provide relevant corporate political behavioral concepts that surround a firm’s political actions when entering specific politico-economic markets as well as future work recommendations. This paper further provides a contemporary bibliographic analysis on CPS.

Design/methodology/approach

Through a systematic ISI Web of KnowledgeTMAll Databases literature review on “CPS,” the research was refined in relation to articles from “all year time-span,” “social science,” and “business economic” areas. After relevant papers were retrieved, sorted, and analyzed, a final bibliographic analysis on CPS was performed using HistCite reference graph maker.

Findings

Results of this research provide a table with a conceptual summary of different CPS types, approaches to political strategy, participation levels, assessment of the political environments, research implications, as well as other related CPS factors.

Research limitations/implications

There is still a lack of empirical research on how specific firm CPSs can help overcome the effect of foreignness within different host countries. This study provides an overview and list of CPSs that companies use when entering a particular politico-economic context as well as inner CPS research streams.

Originality/value

This contemporary conceptual taxonomy on CPS provides researchers as well as practitioners with insights into the global CPS evolution, in addition to a current picture of CPS within different contexts.
Dynamic linkages among developed, emerging and frontier capital markets of Asia-Pacific region
Authors: Thomas Nisha Mary , Kashiramka Smita , Yadav Surendra S.
Published: June 2017

Purpose

The purpose of this paper is to investigate the long-run equilibrium relationship between developed, emerging and frontier markets of the Asia-Pacific region during January 2000 to June 2016.

Design/methodology/approach

Zivot and Andrews’ unit root test is used to examine the existence of unit root in index series in the presence of a structural break. Gregory and Hansen’s test of cointegration is employed to examine the stable long-run relationship between the indices under study.

Findings

The results suggest that the emerging markets of China and Thailand and the frontier markets of Sri Lanka and Pakistan are fairly segmented from most of the markets in the Asia-Pacific region. Hence, these markets provide good diversification opportunities to global investors. Bidirectional cointegration analysis indicates that emerging and frontier markets influence developed markets. Hence, it can be inferred that the de facto position that only bigger markets influence small markets no longer holds true in the current environment.

Practical implications

The findings of this study will provide valuable inputs to global investors for creating an optimal investment portfolio.

Originality/value

This study does a comprehensive examination of market integration in the Asia-Pacific region. It also contributes to the thin body of work done on frontier markets. Unlike past studies, this paper analyzes the bidirectional cointegration relationship to examine if the notion that only bigger markets influence smaller markets holds true or not. Finally, this study employs advanced techniques of unit root test and cointegration test that consider structural breaks in the models.
Italian craft beer revolution: do spatial factors matter?
Authors: Esposti Roberto , Fastigi Matteo , Viganò Elena
Published: June 2017

Purpose

The purpose of this paper is to investigate the emergence of microbreweries in Italy over the last 20 years (period 1993-2014) and assess its main determinants.

Design/methodology/approach

The recent intense growth is expressed by the increasing number of entries in the sector actually accompanied, in most recent years, by an increasing number of exits. The paper proposes a quantitative assessment of this entry-exit dynamics through a sequence of econometric models known as survival models.

Findings

Together with two other orders of possible determinants (idiosyncratic characteristics and the exogenous evolution of the beer market), the paper assesses the role played by specific geographical and local factors within these dynamics. Estimation results show that, whereas market force and individual features unquestionably affect entry and exit choices, geographical and local factors are of limited relevance, especially for the recent entry dynamics.

Originality/value

Although the literature on the so-called craft beer revolution is already vast and increasing, the novel contribution of the paper concerns the specificity (if any) of the Italian case and the role of spatial factors in this respect. This investigation is performed adopting an advanced quantitative approach and this attempt is also quite original within this literature.
Linear geophysical inversion via the discrete cosine pseudo‐inverse: application to potential fields
Authors: Fernández‐Martínez J.L. , Fernández‐Muñiz Z. , Pallero J.L.G. , Bonvalot S.
Published: June 2017

In this paper, we present a methodology to perform geophysical inversion of large‐scale linear systems via a covariance‐free orthogonal transformation: the discrete cosine transform. The methodology consists of compressing the matrix of the linear system as a digital image and using the interesting properties of orthogonal transformations to define an approximation of the Moore–Penrose pseudo‐inverse. This methodology is also highly scalable since the model reduction achieved by these techniques increases with the number of parameters of the linear system involved due to the high correlation needed for these parameters to accomplish very detailed forward predictions and allows for a very fast computation of the inverse problem solution. We show the application of this methodology to a simple synthetic two‐dimensional gravimetric problem for different dimensionalities and different levels of white Gaussian noise and to a synthetic linear system whose system matrix has been generated via geostatistical simulation to produce a random field with a given spatial correlation. The numerical results show that the discrete cosine transform pseudo‐inverse outperforms the classical least‐squares techniques, mainly in the presence of noise, since the solutions that are obtained are more stable and fit the observed data with the lowest root‐mean‐square error. Besides, we show that model reduction is a very effective way of parameter regularisation when the conditioning of the reduced discrete cosine transform matrix is taken into account. We finally show its application to the inversion of a real gravity profile in the Atacama Desert (north Chile) obtaining very successful results in this non‐linear inverse problem. The methodology presented here has a general character and can be applied to solve any linear and non‐linear inverse problems (through linearisation) arising in technology and, particularly, in geophysics, independently of the geophysical model discretisation and dimensionality. Nevertheless, the results shown in this paper are better in the case of ill‐conditioned inverse problems for which the matrix compression is more efficient. In that sense, a natural extension of this methodology would be its application to the set of normal equations.
Partial diel migration: A facultative migration underpinned by long‐term inter‐individual variation
Authors: Harrison Philip M. , Gutowsky Lee F. G. , Martins Eduardo G. , Patterson David A. , Cooke Steven J. , Power Michael
Published: June 2017

The variations in migration that comprise partial diel migrations, putatively occur entirely as a consequence of behavioural flexibility. However, seasonal partial migrations are increasingly recognised to be mediated by a combination of reversible plasticity in response to environmental variation and individual variation due to genetic and environmental effects.

Here, we test the hypothesis that while partial diel migration heterogeneity occurs primarily due to short‐term within‐individual flexibility in behaviour, long‐term individual differences in migratory behaviour also underpin this migration variation.

Specifically, we use a hierarchical behavioural reaction norm approach to partition within‐ and among‐individual variation in depth use and diel plasticity in depth use, across short‐ and long‐term time‐scales, in a group of 47 burbot (Lota lota) tagged with depth‐sensing acoustic telemetry transmitters.

We found that within‐individual variation at the among‐dates‐within‐seasons and among‐seasons scale, explained the dominant proportion of phenotypic variation. However, individuals also repeatedly differed in their expression of migration behaviour over the 2 year study duration.

These results reveal that diel migration variation occurs primarily due to short‐term within‐individual flexibility in depth use and diel migration behaviour. However, repeatable individual differences also played a key role in mediating partial diel migration.

These findings represent a significant advancement of our understanding of the mechanisms generating the important, yet poorly understood phenomena of partial diel migration. Moreover, given the pervasive occurrence of diel migrations across aquatic taxa, these findings indicate that individual differences have an important, yet previously unacknowledged role in structuring the temporal and vertical dynamics of aquatic ecosystems.
Specificity traits consistent with legume‐rhizobia coevolution displayed byEnsifer melilotirhizosphere colonization
Authors: Salas María Eugenia , Lozano Mauricio Javier , López José Luis , Draghi Walter Omar , Serrania Javier , Torres Tejerizo Gonzalo Arturo , Albicoro Francisco Javier , Nilsson Juliet Fernanda , Pistorio Mariano , Del Papa María Florencia , Parisi Gustavo , Becker Anke , Lagares Antonio
Published: June 2017

Rhizobia are α‐ and ß‐proteobacteria that associate with legumes in symbiosis to fix atmospheric nitrogen. The chemical communication between roots and rhizobia begins in the rhizosphere. Using signature‐tagged‐Tn5mutagenesis (STM) we performed a genome‐wide screening forEnsifer melilotigenes that participate in colonizing the rhizospheres of alfalfa and other legumes. The analysis of ca. 6,000 mutants indicated that genes relevant for rhizosphere colonization account for nearly 2% of the rhizobial genome and that most (ca. 80%) are chromosomally located, pointing to the relevance and ancestral origin of the bacterial ability to colonize plant roots. The identified genes were related to metabolic functions, transcription, signal transduction, and motility/chemotaxis among other categories; with several ORFs of yet‐unknown function. Most remarkably, we identified a subset of genes that impacted more severely the colonization of the roots of alfalfa than of pea. Further analyses using other plant species revealed that such early differential phenotype could be extended to other members of the Trifoliae tribe (Trigonella,Trifolium), but not the Fabeae and Phaseoleae tribes. The results suggest that consolidation ofE. melilotiinto its current symbiotic state should have occurred in a rhizobacterium that had already been adapted to rhizospheres of the Trifoliae tribe.
Cascading influence of inorganic nitrogen sources on DOM production, composition, lability and microbial community structure in the open ocean
Authors: Goldberg S. J. , Nelson C. E. , Viviani D. A. , Shulse C. N. , Church M. J.
Published: June 2017

Nitrogen frequently limits oceanic photosynthesis and the availability of inorganic nitrogen sources in the surface oceans is shifting with global change. We evaluated the potential for abrupt increases in inorganic N sources to induce cascading effects on dissolved organic matter (DOM) and microbial communities in the surface ocean. We collected water from 5 m depth in the central North Pacific and amended duplicate 20 liter polycarbonate carboys with nitrate or ammonium, tracking planktonic carbon fixation, DOM production, DOM composition and microbial community structure responses over 1 week relative to controls. Both nitrogen sources stimulated bulk phytoplankton, bacterial and DOM production and enriched Synechococcus and Flavobacteriaceae; ammonium enriched for oligotrophic Actinobacteria OM1 and Gammaproteobacteria KI89A clades while nitrate enriched Gammaproteobacteria SAR86, SAR92 and OM60 clades. DOM resulting from both N enrichments was more labile and stimulated growth of copiotrophic Gammaproteobacteria (Alteromonadaceae and Oceanospirillaceae) and Alphaproteobacteria (Rhodobacteraceae and Hyphomonadaceae) in weeklong dark incubations relative to controls. Our study illustrates how nitrogen pulses may have direct and cascading effects on DOM composition and microbial community dynamics in the open ocean.
Developmental aspects of reading motivation and reading achievement among second grade low achievers and typical readers
Authors: Vaknin‐Nusbaum Vered , Nevo Einat , Brande Sigi , Gambrell Linda
Published: June 2017

This investigation examined developmental aspects of 155 second‐graders' intrinsic reading motivation and reading achievement at the beginning and end of a school year. Reading motivation remained at the same level through the school year, while reading achievement was significantly higher at the end of it than at the beginning. According to word reading skills, low reading achievers (n = 63) and typical readers (n = 92) evinced significant differences in reading motivation. The former scored lower in overall reading motivation and self‐concept as a reader, as well as in reading achievement. Throughout the school year, low reading achievers showed a decline in overall motivation, self‐concept as a reader and literacy outloud, and did not improve in reading comprehension achievement. Reading motivation in typical readers remained high and steady during the school year. Implications of the results are discussed in relation to previous studies.
Using the Past to Construct Territorial Identities in Regional Planning: The Case of Mälardalen, Sweden
Authors: Borges Luciane Aguiar
Published: June 2017

This study examines how the past is used in the construction of regional identity narratives in policy discourses and documents. Despite assumptions that regional identity is based on shared culture, some authors argue that new forms of regional identity have emerged as the consequence of regions’ involvement in wider networks. Identity has been pursued as an asset to regional attractiveness and economic growth and, as such, is shaped by regional development strategies concerning particular social groups. Socially shared representations of the past through history, cultural heritage and collective memory play an important role in this process, since the past is a powerful resource that may be used to construct images of places, legitimizing claims on territories. Document analysis and interviews with planners are used to analyse strategies for regional development in five counties located in the Mälardalen region, Sweden. This study shows that regional strategies are guided by narratives framing regions from an exclusive outside perspective, leaving internal qualities unnoticed. The past is used to structure these narratives and construct identities that serve economic growth rather than the integration of the plural heritages of the region.
Breaking With Neoliberalization by Restricting The Housing Market: Novel Urban Policies and the Case of Hamburg
Authors: Vogelpohl Anne , Buchholz Tino
Published: June 2017

Hamburg currently exemplifies the departure from a straightforward neoliberal urban track. The city's neoliberal path only moved into full swing in the first decade of the 2000s. During this period, urban development was primarily subject to property market mechanisms—with projects being granted to the highest bidder—prompting effects such as rapidly rising rents, deepened social segregation and increased property‐led displacement. Since 2009, however, the city's entrepreneurial urban policy encountered comprehensive resistance movements that eventually led to the rediscovery of a political will for a new housing policy and interventionist policy instruments. This article focuses on the turning point of neoliberal policies and examines the wider scope of the contemporary urban agenda in Hamburg. We first conceptualize potential limits of the neoliberal city in general and then discuss three momentous local policy experiments—the International Building Exhibition, promising ‘improvement without displacement'; the rediscovery of housing regulations through the ‘Social Preservation Statute'; and the ‘Alliance for Housing', aiming to tackle the housing shortage. We discuss these approaches as funding, regulation, and actor‐based approaches to limiting the neoliberal city.
Stochastic Frontier Estimation of Market Power in the Food Industries
Authors: Lopez Rigoberto A. , He Xi , Azzam Azzeddine
Published: June 2017

We use a modified version of the stochastic frontier model to estimate oligopoly markups above the perfectly competitive frontier, separating out deterministic markups from purely stochastic markups. Using data from 42 US food processing industries between 1990 and 2010, empirical results indicate a widespread incidence of oligopoly power, with Lerner indexes averaging approximately 21%. Further, the estimated markups increase with industrial concentration but decrease with price elasticities and imports. Finally, the estimated Lerner indexes are in the range of previous food industry estimates using New Empirical Industrial Organization (NEIO) models.
Intraspecific maternal competition induces summer diapause in insect parasitoids
Authors: Tougeron Kévin , Hraoui George , Le Lann Cécile , van Baaren Joan , Brodeur Jacques
Published: June 2017

Organisms often live in unpredictable environments and have to adopt life history strategies that optimize their fitness under these conditions. According to bet‐hedging theory, individuals can reduce variation in fitness outcomes by investing in different strategies at the same time. For arthropods, facultative summer diapause enables survival during dry and hot periods of the year, and can be triggered by a decrease in resource abundance. However, the effect of resource depletion on diapause induction has never been disentangled from the effect of the perception of the presence of competitors. Using two solitary parasitoid species of cereal aphids as a model system, Aphidius avenae (Haliday) and Aphidius rhopalosiphi (De Stefani‐Perez) (Hymenoptera: Braconidae), we tested whether (i) low absolute host density and/or (ii) high levels of parasitoid females’ competition lead to maternal‐induced summer diapause in parasitoid offspring. Under summer‐like climatic conditions, emerging parasitoid females were (i) reared alone and exposed to different host densities (from 5 to 130 aphids), or (ii) reared together with competing females (from 2 to 20 females) and then exposed individually to 50 aphids. For both parasitoid species, low aphid densities did not induce summer diapause. However, the incidence of summer diapause increased up to a maximum of 11% with increasing levels of competition experienced by female parasitoids. More than 60% of the females produced both diapausing and nondiapausing offspring after being kept at the two highest competition densities. Such a “spreading‐the‐risk” strategy has likely evolved to optimize parasitoid fitness by preventing the following generation from exposure to low populations of suitable hosts and high mortality from superparasitism. These results provide the first experimental evidence of direct maternal competition‐induced diapause in insects, and may change the way we apprehend the evolution of arthropod seasonal ecology, by considering intraspecific competition.
Sexual dimorphism in the alpine butterfliesBoloria palesandBoloria napaea: differences in movement and foraging behavior (Lepidoptera: Nymphalidae)
Authors: Ehl Stefan , Hostert Katharina , Korsch Jana , Gros Patrick , Schmitt Thomas
Published: June 2017

Sexual dimorphism is a widespread phenomenon in Lepidoptera. It is reflected in differences in life history, behavior and morphology. Analyses of differences in behavior are mostly difficult and time‐consuming, especially in high mountain ecosystems. To enhance our knowledge on sexual dimorphisms of alpine butterflies, we performed a mark–release–recapture study on 2 species common in the Alps:Boloria palesandBoloria napaea. We analysed movement and foraging behavior to investigate differences between sexes. Both sexes were mostly sedentary and the movement distances of males and females similar. However, obvious differences in dispersal behavior between the sexes were found in the movement patterns. Three different patterns were distinguished. Most males showed intensive flight activity, but mostly flew only in a limited part of the entire habitat (i.e., their individual home range) searching for females, whereas females were less flight active and flew only to find places for oviposition or feeding. The third pattern, where individuals flew larger distances, was only observed in a small number of males, which always returned to their home range. Nearly all feeding was observed on Asteraceae. However, males preferred the generaLeontodonandCrepis, while females preferredLeontodonandCarduus. Apart from this sexual difference in foraging, individuals of both sexes were found to be more or less specialised on nectar sources. Flight activity was generally greater in males than females. Therefore, we think that sex‐specific requirements in nectar ingredients exist, that is, sugar for the intensive flight activity of males and amino acids for egg production of females.
Seed treatment with selected plant growth‐promoting rhizobacteria increases maize yield in the field
Authors: Breedt G. , Labuschagne N. , Coutinho T.A.
Published: June 2017

Maize, Zea mays is the most important grain crop in South Africa and is a staple food in many African countries. The beneficial effects of plant growth‐promoting rhizobacteria on crop growth and yield have been well documented, but obtaining reproducible results under field conditions is often difficult. In the current study, five selected rhizobacterial strains that showed plant growth‐promoting activities in pilot studies were evaluated for potential enhancement of maize yield under field conditions. The five strains together with a commercial standard were assessed as seed treatments of maize over three seasons in four different soil types. The strains were identified on the basis of 16S rRNA sequencing as Lysinibacillus sphaericus (T19), Paenibacillus alvei (T29), Bacillus safensis (S7) Bacillus pumilus (A26) and Brevundimonas vesicularis (A40). The best yield increases in maize were obtained during the 2011/2012 and 2012/2013 seasons in the Shortlands ecotope with the rhizobacterial strains T19, T29 and S7, resulting in yield increases ranging from 24% to 34%. Strain T19 rendered the most consistent yield increases during the three successive field trials amounting to 33% and 24% in Shortlands ecotope and 12% in Clovalley ecotope, respectively. During 2013/2014 a consortium of three strains, viz. T19, S7 and A26 gave a 32% yield increase in Clovalley ecotope. All the rhizobacterial strains solubilised phosphate in vitro except T19. Strain T29 showed the best nitrogen‐fixing activity in vitro, proliferating on a nitrogen‐free substrate and also producing ammonia. All the strains tested positive for indole acetic acid production. The current study demonstrates the ability of rhizobacterial strains T19, T29, S7 and A26 applied as seed treatments to significantly enhance maize yield in the field, making development and commercialisation of these strains a viable option.
Genetic structure and demographic history of the melon fly Zeugodacus cucurbitae (Coquillet) (Diptera: Tephritidae) in Thailand
Authors: Kunprom Chonticha , Pramual Pairot
Published: June 2017

The melon fly Zeugodacus cucurbitae (Coquillett) (Diptera: Tephritidae) is among the most economically important pests of fruits and fleshy vegetables.

The genetic diversity, genetic structure and demographic history of Z. cucurbitae in Thailand were investigated based on mitochondrial cytochrome c oxidase I (COI) sequences.

Low genetic variation was found in populations of Z. cucurbitae in Thailand, which is consistent with other studies of this species. Demographic history analysis detected a signal of population expansion dating back to 140 000 years ago, which possibly followed increases in host plants after climatic recovery of the penultimate Pleistocene glaciation.

Population genetic structure analysis found that 51% of pairwise comparisons are genetically significantly different. Because populations that contributed markedly to genetic structuring possessed very low haplotype diversity, the effect of genetic drift could be a factor driving population differentiation.

Comparisons of genetic differentiation between flies from different host plant species found no evidence of isolation. However, most haplotypes are unique for each host plant species, indicating that there are some degrees of isolation.
Is the atopic march related to confounding by genetics and early‐life environment? A systematic review of sibship and twin data
Authors: Khan S. J. , Dharmage S. C. , Matheson M. C. , Gurrin L. C.
Published: June 2017

A popular hypothesis known as the atopic march proposes a set of sequential allergy and respiratory disorders in early childhood contributes enormously to the burden of disease in developed countries. Although the concept of the atopic march has been refined and strengthened by many cross‐sectional and longitudinal studies linking eczema as the initial manifestation with progression to hay fever and then asthma, there is yet no definitive proof that the atopic march is the primary causal factor in childhood allergic disease. This debate is mainly related to the controversy around potential confounding of these associations by genetic and environmental factors. Family studies are ideally suited to unravelling the role of these factors. While multiple reviews have synthesized evidence from studies investigating this question, no review to date has explored specific evidence generated by twin and sibling studies to understand the aetiology of atopic march diseases. Our aim was to conduct a systematic review of twin and sibling studies that examine the allergic phenotypes that form the atopic march, to determine whether such analyses of data from these studies attempt to control for the effect confounding by shared factors, and to report estimates of the magnitude of associations between multiple phenotypes. Our review suggests that (1) genetics play a bigger role predisposing eczema to hay fever and eczema to asthma than environmental factors, and (2) the link between eczema and asthma and hay fever is independent of shared early‐life environmental factors.