bluuebunny/crossref_metadata_2025 huggingface dataset:
Fundamental limits on the accuracy of demographic inference based on the sample frequency spectrum
Authors: Terhorst Jonathan , Song Yun S.
Published: June 2015

Significance

Numerous empirical studies in population genetics have used a summary statistic called the sample frequency spectrum (SFS), which summarizes the information in a sample of DNA sequences. Despite their popularity, the accuracy of inference methods based on the SFS is difficult to characterize theoretically, and it is currently unknown how the estimation accuracy improves as more sites in the genome are used. Here, we establish information theoretic limits on the accuracy of all estimators that use the SFS to infer population size histories. We study the rate of convergence to the true answer as the amount of data increases, and obtain the surprising result that it is exponentially worse than known convergence rates for many classical estimation problems in statistics.
Children with autism spectrum disorder show reduced adaptation to number
Authors: Turi Marco , Burr David C. , Igliozzi Roberta , Aagten-Murphy David , Muratori Filippo , Pellicano Elizabeth
Published: June 2015

Significance

It has long been known that perception is atypical in autism. The mechanisms underlying these atypicalities, however, are far from being well understood. Here, we test the integrity of one candidate mechanism, adaptation, in children with and without autism by assessing their susceptibility to number adaptation. We show that adaptation to numerosity is significantly attenuated in children with autism, with the size of their aftereffects only one-third of those of typical children. These results extend existing findings of reduced adaptation to high-level social stimuli and critically suggest that atypicalities in adaptive mechanisms may be pervasive in autism, at least at higher levels. These results fit well with recent Bayesian theories of autism, which propose fundamental problems with prediction.
Tenebrionid secretions and a fungal benzoquinone oxidoreductase form competing components of an arms race between a host and pathogen
Authors: Pedrini Nicolás , Ortiz-Urquiza Almudena , Huarte-Bonnet Carla , Fan Yanhua , Juárez M. Patricia , Keyhani Nemat O.
Published: June 2015

Significance

Although entomopathogenic fungi and their invertebrate hosts share a >300 million year co-evolutionary history, little is known concerning the biochemical and genetic basis of insect defensive tactics and the countermeasures evolved and evolving by the pathogen to thwart these defenses. Our results provide a molecular mechanism to help explain why some insects are more resistant to broad host-range entomopathogenic fungi. We identify beetle cuticular secretions and a fungal detoxifying enzyme as components of an arms race between insects and the fungal pathogen, suggesting an evolving role for the quinone reductase enzyme as a specific virulence factor for host quinone detoxification. As races have winners and losers, this paper captures a snapshot where the host is leading the race.
Pre-TCR ligand binding impacts thymocyte development before αβTCR expression
Authors: Mallis Robert J. , Bai Ke , Arthanari Haribabu , Hussey Rebecca E. , Handley Maris , Li Zhenhai , Chingozha Loice , Duke-Cohan Jonathan S. , Lu Hang , Wang Jia-Huai , Zhu Cheng , Wagner Gerhard , Reinherz Ellis L.
Published: June 2015

Significance

The thymus generates the repertoire of disease-fighting T lymphocytes, affording lifelong host protection against infectious organisms and other pathogens. To achieve this goal, a microinductive environment converts precursors into millions of distinct functional T cells. Because each T lineage cell displays a clone-specific T-cell receptor (TCR) that is generated through stochastic (i.e., haphazard) recombination events, the specificities of thymocytes must be interrogated, and those expressing useless or harmful TCRs are removed before their exit from the thymus. Here, we show that repertoire selection begins at a stage preceding the one currently identified. The pre–T-cell receptor, previously thought to operate autonomously, has robust ligand binding behavior to initiate the first stage of this process.
Mechanochemical tuning of myosin-I by the N-terminal region
Authors: Greenberg Michael J. , Lin Tianming , Shuman Henry , Ostap E. Michael
Published: June 2015

Significance

Myosin molecular motors generate forces in the cell and act as mechanosensors, adjusting their power outputs in response to mechanical loads. Little is known about the structural elements involved in myosin mechanosensing. Our results identify the N-terminal region (NTR) of the myosin-I protein as having an important role in tuning mechanochemistry. Appending the NTR from a highly tension-sensitive myosin (Myo1b) onto a less tension-sensitive motor (Myo1c) changes the identity of the primary force-sensitive transition of Myo1c, making it sensitive to forces <2 pN. Moreover, we show that the NTR stabilizes the post–power-stroke conformation. These results identify the NTR as an important structural element in myosin force sensing and suggest a mechanism for generating diversity of function among myosin isoforms.
Broadband surface-wave transformation cloak
Authors: Xu Su , Xu Hongyi , Gao Hanhong , Jiang Yuyu , Yu Faxin , Joannopoulos John D. , Soljačić Marin , Chen Hongsheng , Sun Handong , Zhang Baile
Published: June 2015

Significance

Guiding surface electromagnetic waves around disorder without disturbing the wave amplitude or phase is in great demand for modern photonic and plasmonic devices. In this work, we introduce a class of cloaks capable of remarkable broadband surface electromagnetic waves guidance around ultrasharp corners and bumps with no perceptible changes in amplitude and phase. This work provides strong support for the application of transformation optics to plasmonic circuits and could pave the way for high-performance, large-scale integrated photonic circuits.
Predicting visual acuity from the structure of visual cortex
Authors: Srinivasan Shyam , Carlo C. Nikoosh , Stevens Charles F.
Published: June 2015

Significance

In 1980, a group of researchers published a study claiming that the number of neurons under a square millimeter of visual cortex is 2.5 times higher in primates than nonprimates. This claim has been debated ever since. We replicated their study using modern stereology techniques and confirmed the original conclusion. What would be the advantage of this extra surface density in the visual cortex? The extra density allows primates to have 2.5 times more neurons and computational power in their visual cortex. As a result, their visual acuity is better than their nonprimate mammalian relatives.
GGEMS-Brachy: GPU GEant4-based Monte Carlo simulation for brachytherapy applications
Authors: Lemaréchal Yannick , Bert Julien , Falconnet Claire , Després Philippe , Valeri Antoine , Schick Ulrike , Pradier Olivier , Garcia Marie-Paule , Boussion Nicolas , Visvikis Dimitris
Published: June 2015

In brachytherapy, plans are routinely calculated using the AAPM TG43 formalism which considers the patient as a simple water object. An accurate modeling of the physical processes considering patient heterogeneity using Monte Carlo simulation (MCS) methods is currently too time-consuming and computationally demanding to be routinely used. In this work we implemented and evaluated an accurate and fast MCS on Graphics Processing Units (GPU) for brachytherapy low dose rate (LDR) applications. A previously proposed Geant4 based MCS framework implemented on GPU (GGEMS) was extended to include a hybrid GPU navigator, allowing navigation within voxelized patient specific images and analytically modeled 125I seeds used in LDR brachytherapy. In addition, dose scoring based on track length estimator including uncertainty calculations was incorporated. The implemented GGEMS-brachy platform was validated using a comparison with Geant4 simulations and reference datasets. Finally, a comparative dosimetry study based on the current clinical standard (TG43) and the proposed platform was performed on twelve prostate cancer patients undergoing LDR brachytherapy. Considering patient 3D CT volumes of 400  × 250  × 65 voxels and an average of 58 implanted seeds, the mean patient dosimetry study run time for a 2% dose uncertainty was 9.35 s (≈500 ms 10−6 simulated particles) and 2.5 s when using one and four GPUs, respectively. The performance of the proposed GGEMS-brachy platform allows envisaging the use of Monte Carlo simulation based dosimetry studies in brachytherapy compatible with clinical practice. Although the proposed platform was evaluated for prostate cancer, it is equally applicable to other LDR brachytherapy clinical applications. Future extensions will allow its application in high dose rate brachytherapy applications.
Unimodularity of invariant random subgroups
Authors: Biringer Ian , Tamuz Omer
Published: June 2015

An invariant random subgroup

H
≤
G

H \leq G

is a random closed subgroup whose law is invariant to conjugation by all elements of

G
G

. When

G
G

is locally compact and second countable, we show that for every invariant random subgroup

H
≤
G

H \leq G

there almost surely exists an invariant measure on

G

/

H

G/H

. Equivalently, the modular function of

H
H

is almost surely equal to the modular function of

G
G

, restricted to

H
H

.

We use this result to construct invariant measures on orbit equivalence relations of measure preserving actions. Additionally, we prove a mass transport principle for discrete or compact invariant random subgroups.
Eastern Baltic cod in distress: biological changes and challenges for stock assessment
Authors: Eero Margit , Hjelm Joakim , Behrens Jane , Buchmann Kurt , Cardinale Massimiliano , Casini Michele , Gasyukov Pavel , Holmgren Noél , Horbowy Jan , Hüssy Karin , Kirkegaard Eskild , Kornilovs Georgs , Krumme Uwe , Köster Friedrich W. , Oeberst Rainer , Plikshs Maris , Radtke Krzysztof , Raid Tiit , Schmidt Jörn , Tomczak Maciej T. , Vinther Morten , Zimmermann Christopher , Storr-Paulsen Marie
Published: June 2015

The eastern Baltic (EB) cod (Gadus morhua) stock was depleted and overexploited for decades until the mid-2000s, when fishing mortality rapidly declined and biomass started to increase, as shown by stock assessments. These positive developments were partly assigned to effective management measures, and the EB cod was considered one of the most successful stock recoveries in recent times. In contrast to this optimistic view, the analytical stock assessment failed in 2014, leaving the present stock status unclear. Deteriorated quality of some basic input data for stock assessment in combination with changes in environmental and ecological conditions has led to an unusual situation for cod in the Baltic Sea, which poses new challenges for stock assessment and management advice. A number of adverse developments such as low nutritional condition and disappearance of larger individuals indicate that the stock is in distress. In this study, we (i) summarize the knowledge of recent changes in cod biology and ecosystem conditions, (ii) describe the subsequent challenges for stock assessment, and (iii) highlight the key questions where answers are urgently needed to understand the present stock status and provide scientifically solid support for cod management in the Baltic Sea.
Coercive Process and Intimate Partner Violence in Committed Relationships
Authors: Slep Amy M. Smith , Heyman Richard E. , Lorber Michael F.
Published: June 2015

This chapter proposes a unifying explanation to two questions: Why do people persist in exhibiting angry, coercive escalating behaviors toward family members despite the unpleasant and destructive qualities of the behavior and despite the fact that such behaviors typically violate personal and societal norms about how to treat loved ones? How are some people able to deescalate out of angry conflict in a way that strengthens, rather than corrodes, their relationships? It posits an integrative model of the mechanisms that control dyadic anger escalation and deescalation in couples’ conflict and examines evidence from studies that have tested it. It reviews the extant literature pertinent to coercion in couples’ interactions and intimate partner violence and discusses the results of a study intended to test and extend the coercion model in couples.
Coercion and Public Health
Authors: Biglan Anthony
Published: June 2015

This book looks at the evidence of the effects of coercion on multiple psychological, behavioral, and health problems. It discusses these effects in the context of families, schools, communities, neighborhoods, and work sites. Then it provides the encouraging notion that treatment and prevention of coercion can exist within a public health framework. The chapter describes how public health principles can bolster existing knowledge about treatment and prevention to further expand efforts already in place to help reduce the prevalence of coercion. The chapter contains clearly defined steps to challenge researchers and policymakers to bring about the changes that can improve the emotional health of the nation as dramatically as the tobacco control movement affected smoking in this country.
Mind and Body
Authors: Harmer Adam
Published: June 2015

This chapter discusses Gottfried Wilhelm Leibniz’s philosophical reflections on mind and body. It first considers Leibniz’s distinction between substance and aggregate, referring to the former as a being that must have true unity (what he calls unum per se) and to the latter as simply a collection of other beings. It then outlines Leibniz’s extension of the term “substance” to monads and other things such as animals and living beings. It also examines Leibniz’s views about the union of mind and body, whether mind and body interact, and how interaction is related to union. More specifically, the chapter asks whether mind and body together constitute an unum per se and analyzes Leibniz’s account of the per se unity of mind-body composites. In addition, the chapter explores the problem of soul-body union as opposed to mind-body union and concludes by discussing Leibniz’s explanation of soul-body interaction using a system of pre-established harmony.
An Empirical Justification for the Use of Draft Lottery Numbers as a Random Treatment in Political Science Research
Authors: Berinsky Adam J. , Chatfield Sara
Published: June 2015

Over the past several years, there has been growing use of the draft lottery instrument to study political attitudes and behaviors (see, e.g., Bergan 2009; Erikson and Stoker 2011; Henderson 2012; Davenport 2015). Draft lotteries, held in the United States from 1969 to 1972, provide a potentially powerful design; in theory, they should provide true randomization for the “treatment” of military service or behavioral reactions to the threat of such service. However, the first draft lottery conducted in 1969 was not conducted in a random manner, giving those citizens born in the fourth quarter of the year disproportionately higher chances of being drafted. In this note, we describe the randomization failure and discuss how this failure could in theory compromise the use of draft lottery numbers as an instrumental variable. We then use American National Election Studies data to provide support for the conclusion that individuals most affected by the randomization failure (those born in the fourth quarter of the year) largely do not look statistically distinct from those born at other times of the year. With some caveats, researchers should be able to treat the 1969 draft numbers as if they were assigned at random. We also discuss broader lessons to draw from this example, both for scholars interested in using the draft lottery as an instrumental variable, and for researchers leveraging other instruments with randomization failures. Specifically, we suggest that scholars should pay particular attention to the sources of randomization failure, sample attrition, treatment and dependent variable selection, and possible failure of the exclusion restriction, and we outline ways in which these problems may apply to the draft lottery instrument and other natural experiments.
Back to Gondwanaland: can ancient vicariance explain (some) Indian Ocean disjunct plant distributions?
Authors: Pirie Michael D. , Litsios Glenn , Bellstedt Dirk U. , Salamin Nicolas , Kissling Jonathan
Published: June 2015

Oceans, or other wide expanses of inhospitable environment, interrupt present day distributions of many plant groups. Using molecular dating techniques, generally incorporating fossil evidence, we can estimate when such distributions originated. Numerous dating analyses have recently precipitated a paradigm shift in the general explanations for the phenomenon, away from older geological causes, such as continental drift, in favour of more recent, long-distance dispersal (LDD). For example, the ‘Gondwanan vicariance’ scenario has been dismissed in various studies of Indian Ocean disjunct distributions. We used the gentian tribe Exaceae to reassess this scenario using molecular dating with minimum (fossil), maximum (geological), secondary (from wider analyses) and hypothesis-driven age constraints. Our results indicate that ancient vicariance cannot be ruled out as an explanation for the early origins of Exaceae across Africa, Madagascar and the Indian subcontinent unless a strong assumption is made about the maximum age of Gentianales. However, both the Gondwanan scenario and the available evidence suggest that there were also several, more recent, intercontinental dispersals during the diversification of the group.
Properties of neuronal facilitation that improve target tracking in natural pursuit simulations
Authors: Bagheri Zahra M. , Wiederman Steven D. , Cazzolato Benjamin S. , Grainger Steven , O'Carroll David C.
Published: June 2015

Although flying insects have limited visual acuity (approx. 1°) and relatively small brains, many species pursue tiny targets against cluttered backgrounds with high success. Our previous computational model, inspired by electrophysiological recordings from insect ‘small target motion detector’ (STMD) neurons, did not account for several key properties described from the biological system. These include the recent observations of response ‘facilitation’ (a slow build-up of response to targets that move on long, continuous trajectories) and ‘selective attention’, a competitive mechanism that selects one target from alternatives. Here, we present an elaborated STMD-inspired model, implemented in a closed loop target-tracking system that uses an active saccadic gaze fixation strategy inspired by insect pursuit. We test this system against heavily cluttered natural scenes. Inclusion of facilitation not only substantially improves success for even short-duration pursuits, but it also enhances the ability to ‘attend’ to one target in the presence of distracters. Our model predicts optimal facilitation parameters that are static in space and dynamic in time, changing with respect to the amount of background clutter and the intended purpose of the pursuit. Our results provide insights into insect neurophysiology and show the potential of this algorithm for implementation in artificial visual systems and robotic applications.
Barrientosiimonas endolithica sp. nov., isolated from pebbles, reclassification of the only species of the genus Tamlicoccus, Tamlicoccus marinus Lee 2013, as Barrientosiimonas marina comb. nov. and emended description of the genus Barrientosiimonas
Authors: Parag B. , Sasikala Ch. , Ramana Ch. V.
Published: June 2015

Strain JC268T was isolated from pebbles collected from a dam located in Lalitpur, Uttar Pradesh, India. Cells of strain JC268T were coccoid, appeared in pairs/triads/tetrads or short chains and were Gram-stain-positive, non-spore-forming, non-motile and obligately aerobic. Strain JC268T was catalase- and oxidase-positive and utilized citrate for growth. The genomic DNA G+C content of strain JC268T was 65.3 mol%. The cell-wall peptidoglycan contained l-lysine–l-serine–d-aspartic acid as interpeptide bridge with the type A4α. The major menaquinone was MK-8(H4). Major (>10 %) fatty acids were iso-C16 : 0, iso-C16 : 1H and anteiso-C17 : 1ω9c. Diphosphatidylglycerol, phosphoglycolipid, phosphatidylinositol, glycolipid, four unidentified lipids, an amino lipid and phospholipid were the polar lipids of strain JC268T. EzTaxon-e blast search of 16S rRNA gene sequences showed that strain JC268T has highest similarity to Barrientosiimonas humi 39T (98.65 %) and Tamlicoccus marinus MSW-24T (97.8 %) of the family Dermacoccaceae. Genome reassociation (based on DNA–DNA hybridization) of strain JC268T with Barrientosiimonas humi CGMCC 4.6864T ( = 39T) and T. marinus KCTC 19485T ( = MSW-24T) yielded values of 32.5 ± 2 % and 27.3 ± 2 %, respectively. Based on the data from phylogenetic and polyphasic taxonomic analyses, strain JC268T represents a novel species of the genus Barrientosiimonas for which the name Barrientosiimonas endolithica sp. nov., is proposed. The type strain of Barrientosiimonas endolithica is JC268T ( = KCTC 29672T = NBRC 110608T). Our data suggest that T. marinus should be reclassified within the genus Barrientosiimonas. Thus, a reclassification is proposed for T. marinus, the type and only species of the genus Tamlicoccus, as Barrientosiimonas marina comb. nov., which implies the emendation of the description of the genus Barrientosiimonas.
Participative decision-making and job satisfaction for teachers in the UAE
Authors: Al Nuaimi Samira , Chowdhury Hossan , Eleftheriou Konstantinos , Katsioloudes Marios I.
Published: June 2015

Purpose

– Knowledge of teachers’ participative decision making (PDM) and job satisfaction (JS) is important, as teachers comprise most of a school’s staff. The purpose of this paper is to examine the effect of teacher gender, nationality and school type on teachers’ PDM and JS in Abu Dhabi’s schools and to determine whether there any significant differences in PDM and teachers’ JS among teachers of different genders, school types and nationalities.

Design/methodology/approach

– A questionnaire was used to collect data for the study by measuring each responding teacher’s involvement in making school decisions in both the instructional and managerial domains and JS. The questionnaire was distributed among teachers in 28 different schools around the Emirate of Abu Dhabi.

Findings

– The primary results demonstrated that teachers’ PDM differs by teacher gender, nationality and school type, whereas teacher’s JS differs by teacher gender and nationality, with school type having in general no significant effect on teacher JS.

Originality/value

– This study contributes to literature on the UAE educational field, educational leadership and school management.
Single‐cell genomics of uncultivated deep‐branching magnetotactic bacteria reveals a conserved set of magnetosome genes
Authors: Kolinko Sebastian , Richter Michael , Glöckner Frank‐Oliver , Brachmann Andreas , Schüler Dirk
Published: June 2015

While magnetosome biosynthesis within the magnetotactic Proteobacteria is increasingly well understood, much less is known about the genetic control within deep‐branching phyla, which have a unique ultrastructure and biosynthesize up to several hundreds of bullet‐shaped magnetite magnetosomes arranged in multiple bundles of chains, but have no cultured representatives. Recent metagenomic analysis identified magnetosome genes in the genus ‘Candidatus Magnetobacterium’ homologous to those in Proteobacteria. However, metagenomic analysis has been limited to highly abundant members of the community, and therefore only little is known about the magnetosome biosynthesis, ecophysiology and metabolic capacity in deep‐branching MTB. Here we report the analysis of single‐cell derived draft genomes of three deep‐branching uncultivated MTB. Single‐cell sorting followed by whole genome amplification generated draft genomes of Candidatus Magnetobacterium bavaricum and Candidatus Magnetoovum chiemensis CS‐04 of the Nitrospirae phylum. Furthermore, we present the first, nearly complete draft genome of a magnetotactic representative from the candidate phylum Omnitrophica, tentatively named Candidatus Omnitrophus magneticus SKK‐01. Besides key metabolic features consistent with a common chemolithoautotrophic lifestyle, we identified numerous, partly novel genes most likely involved in magnetosome biosynthesis of bullet‐shaped magnetosomes and their arrangement in multiple bundles of chains.
Comparative genomics and mutagenesis analyses of choline metabolism in the marine Roseobacter clade
Authors: Lidbury Ian , Kimberley George , Scanlan David J. , Murrell J. Colin , Chen Yin
Published: June 2015

Choline is ubiquitous in marine eukaryotes and appears to be widely distributed in surface marine waters; however, its metabolism by marine bacteria is poorly understood. Here, using comparative genomics and molecular genetic approaches, we reveal that the capacity for choline catabolism is widespread in marine heterotrophs of the marine Roseobacter clade (MRC). Using the model bacterium Ruegeria pomeroyi, we confirm that the betA, betB and betC genes, encoding choline dehydrogenase, betaine aldehyde dehydrogenase and choline sulfatase, respectively, are involved in choline metabolism. The betT gene, encoding an organic solute transporter, was essential for the rapid uptake of choline but not glycine betaine (GBT). Growth of choline and GBT as a sole carbon source resulted in the re‐mineralization of these nitrogen‐rich compounds into ammonium. Oxidation of the methyl groups from choline requires formyltetrahydrofolate synthetase encoded by fhs in R. pomeroyi, deletion of which resulted in incomplete degradation of GBT. We demonstrate that this was due to an imbalance in the supply of reducing equivalents required for choline catabolism, which can be alleviated by the addition of formate. Together, our results demonstrate that choline metabolism is ubiquitous in the MRC and reveal the role of Fhs in methyl group oxidation in R. pomeroyi.
Coccinellid interactions mediated by vegetation heterogeneity
Authors: Amaral Dany S.S.L. , Venzon Madelaine , Perez André L. , Schmidt Jason M. , Harwood James D.
Published: June 2015

Environmental heterogeneity can have profound effects on agroecosystem function and it is important for improving ecosystem services such as biological control. Promoting system diversity via non‐crop plants is one method for increasing habitat heterogeneity within farmscapes. Non‐crop plants provide access to refuges and alternative food resources provide multiple benefits to enhance populations of arthropod predators. In this study, we examined the effects of small‐scale spatial structure on life‐stage specific interactions between the native coccinellid, Hippodamia convergensGuérin‐Méneville, and the exotic Harmonia axyridis (Pallas) (both Coleoptera: Coccinellidae), which overlap in spatial distribution in many crop systems. Squash [Cucurbita pepo L. (Cucurbitaceae)] and non‐crop mugwort [Artemisia vulgaris L. (Asteraceae)] plants with and without aphids were used as a model of spatial heterogeneity in micro‐ and mesocosm experiments. In response to factorial treatment combinations, we evaluated oviposition behavior, egg predation, larval survival, and larval predator‐prey and predator‐predator interactions. Adult H. convergens displayed higher foraging activity on aphids when exposed to complex habitats containing a non‐crop plant. In the presence of the exotic coccinellid, H. convergens preferred to deposit eggs on the non‐crop plant. Furthermore, a combination of spatial heterogeneity and prey availability reduced larval intraguild predation and cannibalism, and improved reproductive output of H. convergens by reducing intra‐ and interspecific egg predation. Our results provide evidence that life‐stage‐specific intraguild interactions are mediated by access to non‐crop plants. Thus, the introduction or maintenance of non‐crop plants has the potential to enhance coexistence of multiple natural enemies and improve top‐down control of pests.
Molecular mechanism of PdxR – a transcriptional activator involved in the regulation of vitamin B6 biosynthesis in the probiotic bacterium Bacillus clausii
Authors: Tramonti Angela , Fiascarelli Alessio , Milano Teresa , di Salvo Martino L. , Nogués Isabel , Pascarella Stefano , Contestabile Roberto
Published: June 2015

Pyridoxal 5′‐phosphate (PLP), the well‐known active form of vitamin B6, is an essential enzyme cofactor involved in a large number of metabolic processes. PLP levels need to be finely tuned in response to cell requirements; however, little is known about the regulation of PLP biosynthesis and recycling pathways. The transcriptional regulator PdxR activates transcription of the pdxST genes encoding PLP synthase. It is characterized by an N‐terminal helix‐turn‐helix motif that binds DNA and an effector‐binding C‐terminal domain homologous to PLP‐dependent enzymes. Although it is known that PLP acts as an anti‐activator, the mechanism of action of PdxR is unknown. In the present study, we analyzed the biochemical and DNA‐binding properties of PdxR from the probiotic Bacillus clausii. Spectroscopic measurements showed that PLP is the only B6 vitamer that acts as an effector molecule of PdxR. Binding of PLP to PdxR determines a protein conformational change, as detected by gel filtration chromatography and limited proteolysis experiments. We showed that two direct repeats and one inverted repeat are present in the DNA promoter region and PdxR is able to bind DNA fragments containing any combination of two of them. However, when PLP binds to PdxR, it modifies the DNA‐binding properties of the protein, making it selective for inverted repeats. A molecular mechanism is proposed in which the two different DNA binding modalities of PdxR determined by the presence or absence of PLP are responsible for the control of pdxST transcription.
Intraspecific trait variation across scales: implications for understanding global change responses
Authors: Moran Emily V. , Hartig Florian , Bell David M.
Published: June 2015

Recognition of the importance of intraspecific variation in ecological processes has been growing, but empirical studies and models of global change have only begun to address this issue in detail. This review discusses sources and patterns of intraspecific trait variation and their consequences for understanding how ecological processes and patterns will respond to global change. We examine how current ecological models and theories incorporate intraspecific variation, review existing data sources that could help parameterize models that account for intraspecific variation in global change predictions, and discuss new data that may be needed. We provide guidelines on when it is most important to consider intraspecific variation, such as when trait variation is heritable or when nonlinear relationships are involved. We also highlight benefits and limitations of different model types and argue that many common modeling approaches such as matrix population models or global dynamic vegetation models can allow a stronger consideration of intraspecific trait variation if the necessary data are available. We recommend that existing data need to be made more accessible, though in some cases, new experiments are needed to disentangle causes of variation.
Dynamic regulation of CD24 expression and release of CD24‐containing microvesicles in immature B cells in response to CD24 engagement
Authors: Ayre D. Craig , Elstner Marcus , Smith Nicole C. , Moores Emily S. , Hogan Andrew M. , Christian Sherri L.
Published: June 2015

The glycophosphatidylinositol‐anchored cell surface receptor CD24 (also called heat‐stable antigen) promotes the apoptosis of progenitor and precursor B‐lymphocytes. However, the immediate proximal events that occur after engagement of CD24 in B cells are not precisely understood. Using a bioinformatics analysis of mouse (Mus musculus) gene expression data from the Immunological Genome Project, we found that known vesicle trafficking and cellular organization genes have similar expression patterns to CD24 during B‐cell development in the bone marrow. We therefore hypothesized that CD24 regulates vesicle trafficking. We first validated that antibody‐mediated engagement of CD24 induces apoptosis in the mouse WEHI‐231 cell line and mouse primary bone marrow‐derived B cells. We next found that CD24 surface protein expression is rapidly and dynamically regulated in both WEHI‐231 cells and primary immature B cells in response to engagement of CD24. The change in surface expression was not mediated by classical endocytosis or exocytosis. However, we found that CD24‐bearing plasma membrane‐derived extracellular microvesicles were released in response to CD24 engagement. Furthermore, in response to CD24 engagement we observed a clear exchange of CD24 between different populations of B cells. Hence, we show that engagement of CD24 in immature B cells results in a dynamic regulation of surface CD24 protein and a redistribution of CD24 within the population.
Diffusion Dynamics and Creative Destruction in a Simple Classical Model
Authors: Haas David
Published: June 2015

The article explores the impact of the diffusion of new methods of production on output and employment growth and income distribution within a Classical one‐sector framework. Disequilibrium paths are studied analytically and in terms of simulations. Diffusion by differential growth affects aggregate dynamics through several channels. The analysis reveals the non‐steady nature of economic change and shows that the adaptation pattern depends both on the innovation's factor‐saving bias and on the extent of the bias, which determines the strength of the selection pressure on non‐innovators. The typology of different cases developed shows various aspects of Schumpeter's concept of creative destruction.
Growth on glucose decreases cAMP‐CRP activity while paradoxically increasing intracellular cAMP in the light‐organ symbiont Vibrio fischeri
Authors: Colton Deanna M. , Stoudenmire Julie L. , Stabb Eric V.
Published: June 2015

Proteobacteria often co‐ordinate responses to carbon sources using CRP and the second messenger cyclic 3′, 5′‐AMP (cAMP), which combine to control transcription of genes during growth on non‐glucose substrates as part of the catabolite‐repression response. Here we show that cAMP‐CRP is active and important in Vibrio fischeri during colonization of its host squid Euprymna scolopes. Moreover, consistent with a classical role in catabolite repression, a cAMP‐CRP‐dependent reporter showed lower activity in cells grown in media amended with glucose rather than glycerol. Surprisingly though, intracellular cAMP levels were higher in glucose‐grown cells. Mutant analyses were consistent with predictions that CyaA was responsible for cAMP generation, that the EIIAGlc component of glucose transport could enhance cAMP production and that the phophodiesterases CpdA and CpdP consumed intracellular and extracellular cAMP respectively. However, the observation of lower cAMP levels in glycerol‐grown cells seemed best explained by changes in cAMP export, via an unknown mechanism. Our data also indicated that cAMP‐CRP activity decreased during growth on glucose independently of crp's native transcriptional regulation or cAMP levels. We speculate that some unknown mechanism, perhaps carbon‐source‐dependent post‐translational modulation of CRP, may help control cAMP‐CRP activity in V. fischeri.
Molecular mechanisms underlying the emergence of bacterial pathogens: an ecological perspective
Authors: Bartoli Claudia , Roux Fabrice , Lamichhane Jay Ram
Published: June 2015

The rapid emergence of new bacterial diseases negatively affects both human health and agricultural productivity. Although the molecular mechanisms underlying these disease emergences are shared between human‐ and plant‐pathogenic bacteria, not much effort has been made to date to understand disease emergences caused by plant‐pathogenic bacteria. In particular, there is a paucity of information in the literature on the role of environmental habitats in which plant‐pathogenic bacteria evolve and on the stress factors to which these microbes are unceasingly exposed. In this microreview, we focus on three molecular mechanisms underlying pathogenicity in bacteria, namely mutations, genomic rearrangements and the acquisition of new DNA sequences through horizontal gene transfer (HGT). We briefly discuss the role of these mechanisms in bacterial disease emergence and elucidate how the environment can influence the occurrence and regulation of these molecular mechanisms by directly impacting disease emergence. The understanding of such molecular evolutionary mechanisms and their environmental drivers will represent an important step towards predicting bacterial disease emergence and developing sustainable management strategies for crops.
B‐1 cells as a source of IgA
Authors: Meyer‐Bahlburg Almut
Published: June 2015

Immunoglobulin A (IgA) is the most abundantly produced immunoglobulin found primarily on mucosal surfaces. The generation of IgA and its involvement in mucosal immune responses have been intensely studied over the past years. IgA can be generated in T cell–dependent and T cell–independent pathways, and it has an important impact on maintaining homeostasis within the mucosal immune system. There is good evidence that B‐1 cells contribute substantially to the production of mucosal IgA and thus play an important role in regulating commensal microbiota. However, whether B‐1 cells produce antigen‐specific or only nonspecific IgA remains to be determined. This review will discuss what is currently known about IgA production by B‐1 cells and the functional relevance of B‐1 cell–derived IgA both in vitro and in vivo.
A population‐based study of animal component sensitization, asthma, and rhinitis in schoolchildren
Authors: Bjerg Anders , Winberg Anna , Berthold Malin , Mattsson Lars , Borres Magnus P. , Rönmark Eva
Published: June 2015

Background

Animal sensitization is a major determinant of asthma in children. Component‐resolved studies of unselected pediatric populations are lacking. The aim was to describe sensitization to animal components and the association with asthma and rhinitis in animal‐sensitized schoolchildren.

Methods

A random sample of 696 children (11–12 years) from a Swedish population‐based cohort was tested for sensitization to cat, dog, and horse dander using ImmunoCAP. Sera from animal‐sensitized children were further analyzed by microarray including three allergen components from cat, four from dog, and two from horse. The parents completed an expanded ISAAC questionnaire.

Results

Of 259 animal‐sensitized children (≥0.1 kUA/l), 51% were sensitized to all three, 23% to two, and 25% to one species. Current asthma and asthma symptoms following contact with cats were associated with co‐sensitization to Fel d 1 and Fel d 4. This association was seen already at moderate‐level sensitization (1–15 ISU) to Fel d 4, at which level most children were sensitized to Fel d 1, as well. In dog‐sensitized children, the majority was sensitized to more than one dog component, and co‐sensitization to Can f 5 and Can f 1/f 2 conferred the greatest risk for asthma. Sensitization to the highly cross‐reactive serum albumins was uncommon and not associated with asthma.

Conclusions

Among schoolchildren in northern Sweden, where mite allergy is uncommon, furry animals were the primary perennial sensitizers. Asthma was associated with higher levels of component sensitization, and sensitization to more than one component from the same animal conferred the greatest risk.
Technical Note – Pricing Below Cost Under Exchange‐Rate Risk
Authors: Park John , Kazaz Burak , Webster Scott
Published: June 2015

Pricing below cost is often classified as “dumping” in international trade and as “predatory pricing” in local markets. It is legally prohibited from practice because of earlier findings that it leads to predatory behavior by either eliminating competition or stealing market share. This study shows that a stochastic exchange rate can create incentives for a profit‐minded monopoly firm to set price below marginal cost. Our result departs from earlier findings because the optimal pricing decision is based on a rational behavior that does not exhibit any malicious intent against the competition to be considered as violating anti‐trust laws. The finding is a robust result, because our analysis demonstrates that this behavior occurs under various settings such as when the firm (i) is risk‐averse, (ii) can postpone prices until after exchange rates are realized, (iii) is capable of manufacturing in multiple countries, and (iv) operates under demand uncertainty in addition to the random exchange rate.
Jurassic artematopodid beetles and their implications for the early evolution of Artematopodidae (Coleoptera)
Authors: CAI CHEN‐YANG , LAWRENCE JOHN F. , ŚLIPIŃSKI ADAM , HUANG DI‐YING
Published: June 2015

Fossil Artematopodidae are rarely collected and previously confined to middle Eocene Baltic amber. Here we report the first definitive artematopodid, Sinobrevipogon jurassicus gen. et sp.n., from the Middle Jurassic Daohugou beds (c. 165 Ma) in Inner Mongolia, northeastern China. It exhibits a number of defining features of Artematopodidae, including paired carinae on prosternum and an internal apical interlocking tongue on the ventral side of each elytron. However, it differs from any modern Artematopodidae by having the mesocoxal cavitiy closed by the mesepimeron and the anterolateral edge of metanepisternum. The discovery of this new genus represents the earliest fossil record for Artematopodidae, highlighting the antiquity of the family. The systematic positions of Forticatinius Tan & Ren and Tarsomegamerus Zhang are discussed, and the latter is formally transferred to Artematopodidae. Phylogenetic relationships within Artematopodidae were investigated to elucidate the relationships between the two Jurassic genera and Recent genera. Eleven in‐group taxa and two out‐groups were included in a cladistic analysis based on 30 adult characters; the resulting tree recovered the family Artematopodidae in three clades: (i) Electribius authority, (ii) Ctesibius authority + Brevipogon authority + Sinobrevipogon + Tarsomegamerus and (iii) the remaining Recent genera, including Allopogonia authority.
Lactobacillus rhamnosus bacteremia in a kidney transplant recipient
Authors: Falci D.R. , Rigatto M.H. , Cantarelli V.V. , Zavascki A.P.
Published: June 2015

Lactobacillus rhamnosus is a rare clinical pathogen. A case of bacteremia caused by L. rhamnosus in a kidney transplant recipient is described. Once considered only as a contaminant or a low‐virulence organism, L. rhamnosus might be an opportunistic pathogen in immunocompromised patients. To our knowledge, this is the first report of primary bloodstream infection caused by L. rhamnosus in a kidney transplant recipient.
I-Girders Method Used to Support Existing Railway Operations During Highway Underpass Construction
Authors: Ho Chun-Hsing , Shan Junyi , Wang Feiyue , Chen Yiyang
Published: June 2015

In metropolitan areas, when a highway underpass project is being planned to go beneath an existing railway corridor, there are a number of concerns that could have an impact on the project. For example, will the underpass construction impact the existing railway operations? How to maintain the construction safety in both rail and highway operations? This paper brings construction technology using I-girder systems to provide a solution for highway underpass projects constructing beneath the existing rail corridors. The I-girder systems have been proved as a reliable method for highway underpass construction without the interruption of railway operations. This type of I-girder systems has been widely used in several countries as a temporary “bridge” structure in support of dynamic rail movements during underpass construction. Depending on the spans of underpass structures, a contractor can decide the number of I-girder units to be assembled and installed on site. This paper describes the construction procedures of the I-girder systems installation and daily inspection processes. A case study is used to demonstrate the applicability of I-girder systems in ensuring underpass construction smoothly while maintaining existing railway operations in a safety manner. During the construction of underpass, the contractor encountered geotechnical issues that had a severe impact on the construction safety and the integrity of foundation. This paper further discusses strategies that were used to mitigate the potential building collapses and foundation failures. It is concluded the method of I-girder systems is capable of supporting railway dynamic movements during highway underpass construction.
Meta Planning Approach to Train Scheduling
Authors: Vilela Plínio , Brocchetto Sérgio , Dias Rafael , Chiba Elaine , Vieira Anderson , Christofoletti Luciano
Published: June 2015

Computing the circulation plan for trains in a railroad is a hard problem. The number of variables considered, size of the search space and limitations on processing time define rigid limits to the solutions considered for any practical use.

Our approach to train circulation planning [1] implements a simulation of discrete events that performs really well. Nevertheless, the approach is known to have some shortsightedness, specially when a global analysis is considered.

To reduce the impact of such shortsightedness, a couple of solutions have been developed, including a second layer of intelligence on top of the core algorithm. This layer is called Adaptive Engine (AE), and is able to execute pre-processing and post-processing rules to fine tune the core engine’s output. The solution that is presented in this paper, called Meta Planning Engine (MPE), tackles another limitation of the tool, no matter how adjusted the implemented heuristics are, the core engine is computing only one output for any given input. With the MPE, multiple versions of the core engine execute in parallel and compute several outputs for any given input. We can even leverage the benefits of having different approaches running at the same time, without compromising the performance of the whole system.

Preliminary results have shown it is possible to increase the solution quality by 7 to 10% while still maintaining the same range in terms of processing time.