bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNASEK is required for internalization of diverse acid-dependent viruses
Authors: Hackett Brent A. , Yasunaga Ari , Panda Debasis , Tartell Michael A. , Hopkins Kaycie C. , Hensley Scott E. , Cherry Sara 
Published: June 2015

Significance
Many viruses, including those of global concern, are dependent on internalization for their entry. We found that ribonuclease kappa (RNASEK) is required for infection of every virus we tested that enters cells through an acid-dependent pathway, including dengue, West Nile, Sindbis, Rift Valley Fever, and influenza viruses. Mechanistically, we found that RNASEK has no effect on virus binding to cells but, rather, is required for their uptake. RNASEK was required for diverse viruses that are dependent on clathrin-mediated endocytosis for entry, but we found that RNASEK was dispensable for general endocytic uptake. Therefore, RNASEK appears to play a unique role in viral uptake and may be a therapeutically viable target to inhibit major human viral pathogens.
High-resolution helix orientation in actin-bound myosin determined with a bifunctional spin label
Authors: Binder Benjamin P. , Cornea Sinziana , Thompson Andrew R. , Moen Rebecca J. , Thomas David D. 
Published: June 2015

Significance
The interaction between actin and myosin is responsible for driving a vast array of essential biological processes, including the production of force in contracting muscle. However, the structural behavior of the two proteins in complex is not well understood, because high-resolution atomic models are not yet available by traditional methods. We use a bifunctional spin label and site-directed electron paramagnetic resonance spectroscopy to determine orientations of individual α-helices within the complex. We thus quantify for the first time, to our knowledge, structural changes within the motor domain of actin-bound myosin on nucleotide binding and dissociation. Our results provide valuable insight into the mechanism of muscle contraction while showcasing a method with wide applicability to other oriented biological systems.
Identification of a triplet pair intermediate in singlet exciton fission in solution
Authors: Stern Hannah L. , Musser Andrew J. , Gelinas Simon , Parkinson Patrick , Herz Laura M. , Bruzek Matthew J. , Anthony John , Friend Richard H. , Walker Brian J. 
Published: June 2015

SignificanceWe use transient spectroscopy to investigate the mechanism of singlet exciton fission, a quantum mechanical phenomenon in some organic molecules in which a spin-singlet excited state can split into two spin-triplet states. This process may be harnessed to boost solar cell efficiencies, but the underlying mechanism remains poorly understood. Central to most models is a triplet pair state, consisting of two triplets entangled into an overall spin-singlet configuration, but it has never before been optically detected. In a solution-based system, we detect a state with simultaneous singlet and triplet exciton character that dissociates to form triplet excitons in 120% yield. We consider that this intermediate constitutes a triplet pair state, and its observation allows important insight into the nature of triplet exciton coupling.
Essential role of the cytochrome P450 CYP4F22 in the production of acylceramide, the key lipid for skin permeability barrier formation
Authors: Ohno Yusuke , Nakamichi Shota , Ohkuni Aya , Kamiyama Nozomi , Naoe Ayano , Tsujimura Hisashi , Yokose Urara , Sugiura Kazumitsu , Ishikawa Junko , Akiyama Masashi , Kihara Akio 
Published: June 2015

Significance
The sphingolipid backbone ceramide is the major lipid species in the stratum corneum and plays a pivotal function in skin permeability barrier formation. Acylceramide is an important epidermis-specific ceramide species. However, the details of acylceramide production, including its synthetic genes, reactions and their orders, and intracellular site for production, have remained unclear. In the present study, we identified the cytochrome P450, family 4, subfamily F, polypeptide 22 (CYP4F22) as the missing fatty acid ω-hydroxylase required for acylceramide synthesis. We also determined that CYP4F22 is a type I endoplasmic reticulum membrane protein and that its substrate is ultra-long-chain fatty acids. Our findings provide important insights into the molecular mechanisms of not only acylceramide production but also skin permeability barrier formation.
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

Abstract
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.
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

AbstractThe 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.
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

SummaryWhile 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

SummaryCholine 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

AbstractEnvironmental 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.