bluuebunny/crossref_metadata_2025_split huggingface dataset:
Timing of DNA damage responses impacts persistence to fluoroquinolones
Authors: Mok Wendy W. K. , Brynildsen Mark P. 
Published: June 2018

Significance
Bacterial persisters are able to survive high concentrations of antibiotics that kill their genetically identical kin. Their tolerances are thought to arise from decreased activity of cellular processes, which limits damage from antibiotics. However, persistence to fluoroquinolones in growth-inhibited populations is not as cut-and-dried, with survivors of treatment exhibiting similar DNA damage as cells that die. In this article, we use a model system of persistence to reveal that the timing of events, such as DNA repair, following fluoroquinolone treatment is critical to survival and show that the same is true for WT populations. These data highlight the importance of processes following antibiotic treatments to persister phenotypes and establish that timing matters for genetically susceptible bacteria struggling to survive fluoroquinolone treatments.
Dislocation-controlled formation and kinetics of grain boundary loops in two-dimensional crystals
Authors: Lavergne François A. , Curran Arran , Aarts Dirk G. A. L. , Dullens Roel P. A. 
Published: June 2018

Significance
Twisting a circular patch inside a large crystal does not always lead to a bicrystal. This is due to the topological properties of the resulting loop-shaped grain boundaries and the defects they are made of. By deforming a crystalline monolayer of colloidal particles using optical tweezers, we find that the product of the angle of rotation and the size of the patch needs to exceed a universal value that depends only on the lattice type for a grain boundary loop to form, while otherwise the deformation is elastically restored. We measure this universal value from the shrinkage kinetics of grain boundary loops and relate it to the complex dislocation structure and reactions, which we directly visualize in our experiments.
Origami mechanologic
Authors: Treml Benjamin , Gillman Andrew , Buskohl Philip , Vaia Richard 
Published: June 2018

Significance
Autonomy separates robots from machines. Incorporating autonomy into soft robots is an outstanding challenge due to the mismatch between rigid electronics and the compliant bodies. In this work, we demonstrate origami as a platform for compliant mechanical logic, containing mechanical bits, logic gates, and signal transmission mechanisms that can supplement conventional electronic controls. Furthermore, these processes can be responsive to and programmed by the environment via the integration of adaptive materials. Thus, origami provides a framework in which sensing, computation, and reflexes can be seamlessly integrated into the compliant bodies of soft robotics.
Structure of a lipid-bound viral membrane assembly protein reveals a modality for enclosing the lipid bilayer
Authors: Pathak Prabhat Kumar , Peng Shuxia , Meng Xiangzhi , Han Yue , Zhang Bing , Zhang Fushun , Xiang Yan , Deng Junpeng 
Published: June 2018

Significance
Cellular membranes are maintained as closed structures in the cytosol, and any breaches in membranes during reorganization are transient. However, open-ended membranes, likely derived from the endoplasmic reticulum, persist in vaccinia virus-infected cells during the assembly of the vaccinia envelope. A group of viral proteins have been identified to be required for this process, providing a unique opportunity for dissecting the molecular mechanism of membrane scission and remodeling. Our structural and functional studies of one of these viral proteins reveal a cage-like soluble protein that traps internally multiple lipids with a bilayer-like configuration. Our studies reveal a protein modality for enclosing the lipid bilayer and suggest a mechanism for stabilizing the open-ended membrane sheets.
Molecular cloning, expression and biochemical characterization of periplasmic nitrate reductase from Campylobacter jejuni
Authors: Mintmier Breeanna , McGarry Jennifer M , Sparacino-Watkins Courtney E , Sallmen Joseph , Fischer-Schrader Katrin , Magalon Axel , McCormick Joseph R , Stolz John F , Schwarz Günter , Bain Daniel J , Basu Partha 
Published: June 2018

AbstractCampylobacter jejuni, a human gastrointestinal pathogen, uses nitrate for growth under microaerophilic conditions using periplasmic nitrate reductase (Nap). The catalytic subunit, NapA, contains two prosthetic groups, an iron sulfur cluster and a molybdenum cofactor. Here we describe the cloning, expression, purification, and Michaelis-Menten kinetics (kcat of 5.91 ± 0.18 s−1 and a KM (nitrate) of 3.40 ± 0.44 μM) in solution using methyl viologen as an electron donor. The data suggest that the high affinity of NapA for nitrate could support growth of C. jejuni on nitrate in the gastrointestinal tract. Site-directed mutagenesis was used and the codon for the molybdenum coordinating cysteine residue has been exchanged for serine. The resulting variant NapA is 4-fold less active than the native enzyme confirming the importance of this residue. The properties of the C. jejuni enzyme reported here represent the first isolation and characterization of an epsilonproteobacterial NapA. Therefore, the fundamental knowledge of Nap has been expanded.
A review of abstract concept learning in embodied agents and robots
Authors: Cangelosi Angelo , Stramandinoli Francesca 
Published: June 2018

This paper reviews computational modelling approaches to the learning of abstract concepts and words in embodied agents such as humanoid robots. This will include a discussion of the learning of abstract words such as ‘use’ and ‘make’ in humanoid robot experiments, and the acquisition of numerical concepts via gesture and finger counting strategies. The current approaches share a strong emphasis on embodied cognition aspects for the grounding of abstract concepts, and a continuum, rather than dichotomy, view of concrete/abstract concepts differences.
This article is part of the theme issue ‘Varieties of abstract concepts: development, use and representation in the brain’.
Language as a disruptive technology: abstract concepts, embodiment and the flexible mind
Authors: Dove Guy 
Published: June 2018

A growing body of evidence suggests that cognition is embodied and grounded. Abstract concepts, though, remain a significant theoretical challenge. A number of researchers have proposed that language makes an important contribution to our capacity to acquire and employ concepts, particularly abstract ones. In this essay, I critically examine this suggestion and ultimately defend a version of it. I argue that a successful account of how language augments cognition should emphasize its symbolic properties and incorporate a view of embodiment that recognizes the flexible, multimodal and task-related nature of action, emotion and perception systems. On this view, language is an ontogenetically disruptive cognitive technology that expands our conceptual reach.
This article is part of the theme issue ‘Varieties of abstract concepts: development, use and representation in the brain’.
Interoception: the forgotten modality in perceptual grounding of abstract and concrete concepts
Authors: Connell Louise , Lynott Dermot , Banks Briony 
Published: June 2018

Conceptual representations are perceptually grounded, but when investigating which perceptual modalities are involved, researchers have typically restricted their consideration to vision, touch, hearing, taste and smell. However, there is another major modality of perceptual information that is distinct from these traditional five senses; that is, interoception, or sensations inside the body. In this paper, we use megastudy data (modality-specific ratings of perceptual strength for over 32 000 words) to explore how interoceptive information contributes to the perceptual grounding of abstract and concrete concepts. We report how interoceptive strength captures a distinct form of perceptual experience across the abstract–concrete spectrum, but is markedly more important to abstract concepts (e.g.hungry,serenity) than to concrete concepts (e.g.capacity,rainy). In particular, interoception dominates emotion concepts, especially negative emotions relating tofearandsadness, moreso than other concepts of equivalent abstractness and valence. Finally, we examine whether interoceptive strength represents valuable information in conceptual content by investigating its role in concreteness effects in word recognition, and find that it enhances semantic facilitation over and above the traditional five sensory modalities. Overall, these findings suggest that interoception has comparable status to other modalities in contributing to the perceptual grounding of abstract and concrete concepts.This article is part of the theme issue ‘Varieties of abstract concepts: development, use and representation in the brain'.
Across-subject offline decoding of motor imagery from MEG and EEG
Authors: Halme Hanna-Leena , Parkkonen Lauri 
Published: June 2018

AbstractLong calibration time hinders the feasibility of brain-computer interfaces (BCI). If other subjects’ data were used for training the classifier, BCI-based neurofeedback practice could start without the initial calibration. Here, we compare methods for inter-subject decoding of left- vs. right-hand motor imagery (MI) from MEG and EEG.Six methods were tested on data involving MEG and EEG measurements of healthy participants. Only subjects with good within-subject accuracies were selected for inter-subject decoding. Three methods were based on the Common Spatial Patterns (CSP) algorithm, and three others on logistic regression with l1- or l2,1-norm regularization. The decoding accuracy was evaluated using 1) MI and 2) passive movements (PM) for training, separately for MEG and EEG.When the classifier was trained by MI, the best accuracies across subjects (mean 70.6% for MEG, 67.7% for EEG) were obtained using multi-task learning (MTL) with logistic regression and l2,1-norm regularization. MEG yielded slightly better average accuracies than EEG. When PM were used for training, none of the inter-subject methods yielded above chance level (58.7%) accuracy.In conclusion, MTL and training with other subject’s MI is efficient for inter-subject decoding of MI. Passive movements of other subjects are likely suboptimal for training the MI classifiers.
On the Orientation of Entorhinal Grids
Authors: Lebedev Mikhail A. , Ossadtchi Alexei 
Published: June 2018

AbstractIn the groundbreaking paper that eventually led to the 2014 Nobel prize in Physiology or Medicine, Hafting et al. (2005) reported that when rats forage for chocolate crumbs in a large open field, some neurons in their entorhinal cortex, called grid cells, exhibit crystalline-like responses to animal position, i.e. grids. Among several key findings documented in this article, the authors noted for the first time that the grids of different neurons can be tilted relative to each other, particularly if these neurons are far apart. In support of this claim, the researchers illustrated two neuronal subpopulations with a 7-10° difference in their grid orientations. Since these data are available online, we were able to reexamine these findings. Here we report several clarifications to the original observations of Hafting et al. First, we show that the relationship between the entorhinal grids is more complex than a single rotation: for the neuronal subpopulations analyzed by Hafting et al., one axis of the hexagonal grid is indeed tilted, but the other axes are not. Second, we show that local ensembles of entorhinal neurons are preferentially tuned to certain directions defined by the grid; this effect is unclear when single neurons are analyzed in isolation. Third, we argue that rat navigation traces are patterned instead of being random. For example, the orientation of the vector field representing average velocity appears to match the orientation of the neuronal grid. Overall, our observations indicate that additional insights into the function of entorhinal grids could be provided by ensemble-level analyses and thorough examination of the connection between the navigation behavior and neuronal patterns.HighlightsWhile our examination of the online dataset from Hafting et al. generally confirms their original findings, several clarifications should be made.For the two neuronal subpopulations, where Hafting et al. reported a 7-10° relative tilt between the grids, only one of the grid axes is tilted, whereas the others are not.When spatial response fields are plotted for neuronal subpopulations instead of single neurons, it is clear that each subpopulation exhibits spatially periodic bands aligned with one of the grid axes.Navigation traces are not random and appear to match the orientation and periodicity of the neuronal grid.
Substrate-dependent cluster density dynamics in bacterial phosphotransferase system permeases
Authors: Benevides Martins Gustavo , Giacomelli Giacomo , Bramkamp Marc 
Published: June 2018

AbstractBacteria take up carbohydrates by membrane-integral sugar specific phosphoenolpyruvate-dependent carbohydrate:phosphotransferase systems (PTS). Although PTS is at the heart of bacterial carbon uptake and centrally involved in regulation of carbon metabolism, little is known about localization and putative oligomerization of the permease subunits (EII) of PTS. Here, we analyzed localization of the fructose specific PtsF and the glucose specific PtsG transporters from C. glutamicum using widefield and single molecule localization microscopy. PtsG and PtsF form membrane embedded clusters that localize in a punctate pattern within the cell membrane. The size, number and fluorescence of the observed clusters changes upon presence or absence of the transported substrate. In presence of the transport substrate clusters significantly increased in size. Photo-activated localization microscopy (PALM) data revealed that, in presence of different carbon sources, the number of EII protein events per cluster remain the same, however the density of PTS molecules within a cluster reduces. Our work reveals a simple mechanism for efficient membrane occupancy regulation. Clusters of PTS EII transporters are densely packed in absence of a suitable substrate. In presence of a transport substrate the EII proteins in individual clusters occupy larger membrane areas, thereby decreasing protein density in individual clusters. This mechanism allows for efficient use of the limited membrane space under varying growth conditions without need of protein removal and re-synthesis.ImportanceThe carbohydrate transport system PTS is centrally involved in the regulation of sugar metabolism. Although much is known about the regulatory interaction, the genetic control and the structure/function relationship of the individual PTS components, we know almost nothing about the spatio-temporal organization of the PTS proteins within the cell. We find dynamic clustering of PTS permeases in Corynebacterium glutamicum. Using single molecule resolution photo-activated localization microscopy we could show that PTS EII protein cluster are dynamically changing protein density upon substrate availability. Our findings imply a novel strategy of regulating limited membrane space efficiently. Furthermore, these data will provide important insights in modelling carbohydrate fluxes in cells, since current models assume a homogeneous distribution of PTS permeases within the membrane.
Highly accelerated rates of heritable large-scale mutations under prolonged exposure to a metal mixture of copper and nickel
Authors: Chain Frédéric J.J. , Flynn Jullien M. , Bull James K. , Cristescu Melania E. 
Published: June 2018

AbstractMutation rate variation has been under intense investigation for decades. Despite these efforts, little is known about the extent to which environmental stressors accelerate mutation rates and influence the genetic load of populations. Moreover, most studies have focused on point mutations rather than large-scale deletions and duplications (copy number variations or “CNVs”). We estimated mutation rates inDaphnia pulexexposed to low levels of environmental stressors as well as the effect of selection onde novomutations. We conducted a mutation accumulation (MA) experiment in which selection was minimized, coupled with an experiment in which a population was propagated under competitive conditions in a benign environment. After an average of 103 generations of MA propagation, we sequenced 60 genomes and found significantly accelerated rates of deletions and duplications in MA lines exposed to ecologically relevant concentrations of metals. Whereas control lines had gene deletion and duplication rates comparable to other multicellular eukaryotes (1.8 × 10−6per gene per generation), a mixture of nickel and copper increased rates fourfold. The realized mutation rate under selection was reduced to 0.4x that of control MA lines, providing evidence that CNVs contribute to mutational load. Our CNV breakpoint analysis revealed that nonhomologous recombination associated with regions of DNA fragility is the primary source of CNVs, plausibly linking metal-induced DNA strand breaks with higher CNV rates. Our findings suggest that environmental stress, in particular multiple stressors, can have profound effects on large-scale mutation rates and mutational load of populations.
Low-frequency variation in TP53 has large effects on head circumference and intracranial volume
Authors: Haworth Simon , Shapland Chin Yang , Hayward Caroline , Prins Bram P. , Felix Janine F. , Medina-Gomez Carolina , Rivadeneira Fernando , Wang Carol , Ahluwalia Tarunveer S , Vrijheid Martine , Guxens Mònic , Sunyer Jordi , Tachmazidou Ioanna , Walter Klaudia , Iotchkova Valentina , Jackson Andrew , Cleal Louise , Huffmann Jennifer , Min Josine L. , Sass Lærke , Timmers Paul R. H. J. ,   UK10K consortium, Smith George Davey , Fisher Simon E. , Wilson James F. , Cole Tim J. , Fernandez-Orth Dietmar , Bønnelykke Klaus , Bisgaard Hans , Pennell Craig E. , Jaddoe Vincent W. V. , Dedoussis George , Timpson Nicholas , Zeggini Eleftheria , Vitart Veronique , Pourcain Beate 
Published: June 2018

AbstractCranial growth and development affects the closely related traits of head circumference (HC) and intracranial volume (ICV). Here we model the developmental genetic architecture of HC, showing this is genetically stable and correlated with genetic determinants of ICV. Investigating up to 46,000 children and adults of European descent, we identify association with final HC and/or final ICV+HC at 9 novel common and low-frequency loci, illustrating that genetic variation from a wide allele frequency spectrum contributes to cranial growth. The largest effects are reported for low-frequency variants within TP53, with 0.5 cm wider heads in increaser-allele carriers versus non-carriers during mid-childhood.
When an insecticide affects the adaptive value of intraguild predation by an invader
Authors: Cabrera Paula , Cormier Daniel , Bessette Marianne , Cruz Vanessa , Lucas Éric 
Published: June 2018

AbstractBiological invasions can generate major ecological disturbances, such as changes in species diversity and structure of communities. It is believed that the multicolored Asian ladybeetle,Harmonia axyridisPallas (Col, Coccinellidae), recognized as one of the most invasive insects in the world, has reduced native coccinellids populations in several areas and is considered as a threat for biodiversity at large. A significant trait, favoring its invasiveness and its dominance over indigenous ladybeetles, is intraguild predation (IGP). IGP has advantageous adaptive value for individuals, removing competitors, potential predators and providing an alternative nutritive resource, when main resources are scarce. Previous research demonstrated that this invasive ladybeetle is highly susceptible to the reduced-risk insecticide novaluron, a chitin synthesis inhibitor, whereas the North American indigenous competitor,Coleomegilla maculataDeGeer (Col, Coccinellidae), is not. Our study explores the adaptive value of IGP for each of the two coccinellids after preying on each other’s larvae, previously treated with insecticide. Our first hypothesis is that the invasive ladybeetle, susceptible to the insecticide, should lose the adaptive value of IGP, while the native predator not. Our second hypothesis is that the adaptive value of IGP for the invasive predator will be recovered over time, as a result of neutralisation of the insecticide by the intraguild prey (native species). The results support both hypotheses, and show that an insecticide can completely remove the adaptive value of IGP for the invader, while it does not change for the indigenous ladybeetle. Moreover, the study demonstrates that if the intraguild prey (non-susceptible to the insecticide) undergoes molt after being exposed to the insecticide, the adaptive value for the intraguild predator is restored.
Wine business performance benchmarking: a comparison of German and Ukrainian wineries
Authors: Goncharuk Anatoliy G. 
Published: June 2018

Purpose
The purpose of this paper is to evaluate and compare the efficiency of wine making in Germany and Ukraine in order to find the controllable factors of wine business performance using benchmarking tools.

Design/methodology/approach
The models of data envelopment analysis and other benchmarking tools are used to analyse the efficiency of wineries in two countries. Returns to scale, scale efficiency, super-efficiency and some other indicators are examined. The research is based on the sample of 36 German and Ukrainian wineries.

Findings
The hypothesis of higher wine making relative efficiency in Germany was compared with Ukrainian wine making, then analytically and statistically verified. A relatively high average scale efficiency score indicates good potential (above 30 per cent) for efficiency growth, due to the optimisation of a scale of production and sales. Generally, wine making in Germany and Ukraine has increasing returns to scale. The high-efficient wine business cannot bring great losses. It was found that the most efficient combinations of size and legal form of business organisation for wine business are presented in Germany.

Research limitations/implications
The research is limited by a single industry of only the two countries.

Practical implications
This study provides useful information for researchers, investors and policy makers, enabling them to understand the current state, basic problems, controllable factors and efficiency levels of wine making in Germany and Ukraine. It may be useful to wine producers in these countries for improving their business performance.

Originality/value
This is the first paper that compares wine business performance and discloses its factors for Germany and Ukraine.