bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Crystal Structure of Klebsiella pneumoniae FeoA Reveals a Site For Protein-Protein Interactions
Authors: Linkous Richard O. , Sestok Alexandrea E. , Smith Aaron T. 
Published: January 2019

ABSTRACTIn order to establish infection, pathogenic bacteria must obtain essential nutrients such as iron. Under acidic and/or anaerobic conditions, most bacteria utilize the Feo system in order to acquire ferrous iron (Fe2+) from their host environment. The mechanism of this process, including its regulation, remains poorly understood. In this work, we have determined the crystal structure of FeoA from the nosocomial agent Klebsiella pneumoniae (KpFeoA). Our structure reveals an SH3-like domain that mediates interactions between neighboring polypeptides via intercalations into a Leu zipper motif. Using docking of a small peptide corresponding to a postulated FeoB partner binding site, we demonstrate the KpFeoA can assume both ‘open’ and ‘closed’ conformations, controlled by peptide binding. We propose a model in which a ‘C-shaped’ clamp along the FeoA surface mediates interactions with its partner protein, FeoB. These findings are the first to demonstrate atomic-level details of FeoA-based protein-protein interactions, which could be exploited for future antibiotic developments.
Mapping Structure and Biological Functions within Mesenchymal Bodies using Microfluidics
Authors: Sart Sébastien , Tomasi Raphaël F.-X. , Barizien Antoine , Amselem Gabriel , Cumano Ana , Baroud Charles N. 
Published: January 2019

AbstractOrganoids that recapitulate the functional hallmarks of anatomic structures comprise cell populations able to self-organize cohesively in 3D. However, the rules underlying organoid formationin vitroremain poorly understood because a correlative analysis of individual cell fate and spatial organization has been challenging. Here, we use a novel microfluidics platform to investigate the mechanisms determining the formation of organoids by human mesenchymal stromal cells that recapitulate the early steps of condensation initiating bone repairin vivo. We find that heterogeneous mesenchymal stromal cells self-organize in 3D in a developmentally hierarchical manner. We demonstrate a link between structural organization and local regulation of specific molecular signaling pathways such as NF-κB and actin polymerization, which modulate osteo-endocrine functions. This study emphasizes the importance of resolving spatial heterogeneities within cellular aggregates to link organization and functional properties, enabling a better understanding of the mechanisms controlling organoid formation, relevant to organogenesis and tissue repair.
Comparative analysis of Synthetic Physical Interactions with the yeast centrosome
Authors: Howell Rowan S M , Csikász-Nagy Attila , Thorpe Peter H 
Published: January 2019

1AbstractThe yeast centrosome or Spindle Pole Body (SPB) is situated in the nuclear membrane, where it nucleates spindle microtubules and acts as a signalling hub. Previously, we used Synthetic Physical Interactions to map the regions of the cell that are sensitive to forced relocalization of proteins across the proteome [Berry et al., 2016]. Here, we expand on this work to show that the SPB, in particular, is sensitive to the relocalization of many proteins. This work inspired a new data analysis approach that indicates that relocalization screens may produce more growth defects than previously reported. A set of associations with the SPB result in elevated SPB number and since hyper-proliferation of centrosomes is a hallmark of cancer cells, these associations point the way for the use of yeast models in the study of spindle formation and chromosome segregation in cancer.
How conspicuous are peacock eyespots and other colorful feathers in the eyes of mammalian predators?
Authors: Amador Kane Suzanne , Wang Yuchao , Fang Rui , Lu Yabin , Dakin Roslyn 
Published: January 2019

AbstractFeathers perceived by humans to be vividly colorful are often presumed to be equally conspicuous to other mammals, and thus to present an enhanced predation risk. However, many mammals that prey on adult birds have dichromatic visual systems with only two types of color-sensitive visual receptors (one sensitive to ultraviolet light), rather than the three characteristic of humans and four of most birds. Thus, understanding how these predators perceive color requires quantitative visual modeling. Here, we use a combination of reflectance spectroscopy, multispectral imaging, color vision modelling and visual texture analysis to compare the visual signals available to conspecifics and to mammalian predators for multicolored feathers from the Indian peacock (Pavo cristatus) as well as red and yellow parrot feathers; we also take into account the effects of distance-dependent blurring due to visual acuity. When viewed by tetrachromatic birds against a background of green vegetation, most of the feathers studied had color and brightness contrasts similar to values previously found for ripe fruit. By contrast, when viewed by dichromat mammalian predators, the color and brightness contrasts of these feathers were only weakly detectable and often did not reach detection thresholds for typical viewing distances. We furthermore show that the peacock’s erect train has undetectable color and brightness contrasts and visual textures when photographed against various foliage backgrounds. Given the similarity of photoreceptor sensitivities and feather reflectance properties across relevant species, these findings are consistent with many feathers of similar hue being inconspicuous, and in some cases potentially cryptic, in the eyes of their mammalian predators. These results suggest that many types of colorful feathers are likely to be cryptic to mammals while providing a communication channel perceptible to birds, while emphasizing the importance of understanding diverse sensory receivers in the evolution of animal coloration.
Dynamics, cariogenicity, and geographic distribution of Streptococcus mutans adhesin types suggest adaptation to individual hosts
Authors: Sheng Nongfei , Esberg Anders , Mårell Lena , Johansson Elisabeth , Källestål Carina , Strömberg Nicklas 
Published: January 2019

AbstractDental caries, the most common chronic infectious disease, involve Streptococcus mutans SpaP A/B/C and Cnm/Cbm adhesin types of different virulence. We have explored their stability and dynamics over 5 years, their geographic distribution, as well as the potentially increased cariogenicity of specific SpaP B subtypes. We performed qPCR and TaqMan typing using whole saliva and isolates from 452 Swedish adolescents followed from 12 to 17 years of age. Approximately 50% of the children were infected at baseline with a single dominant (44%) or mixed (6%) SpaP A, B, or C type, some of which were also Cnm (6%) or Cbm (1%) positive. Stability (+, +) was high for S. mutans infection (85%) and dominant SpaP A or C (80% and 67%) and Cnm or Cbm (85% and 100%) types, but low for SpaP B (51%) and mixed SpaP A/B/C types (26%). Only five children switched from one SpaP type to another, and none between Cnm and Cbm types. Mixed SpaP A/B/C types were typically lost or changed into dominant types. Moreover, children infected with Cnm (n=26) types were more frequent in the northern (Skellefteå) region (p = 0.0041), and those with Cbm types (n=7) in the southern (Umeå) region. Children infected with SpaP B-2 subtypes had a doubled caries experience (p = 0.009) and 5-year caries increment (p = 0.02) compared to those infected with SpaP A. In conclusion, the stable dominant but instable mixed adhesin types and geographic differentiation of Cnm and Cbm types suggest adaptation of low and high cariogenicity types to specific individuals.
Stochastic neural field model of stimulus-dependent variability in cortical neurons
Authors: Bressloff Paul C. 
Published: January 2019

AbstractWe use stochastic neural field theory to analyze the stimulus-dependent tuning of neural variability in ring attractor networks. We apply perturbation methods to show how the neural field equations can be reduced to a pair of stochastic nonlinear phase equations describing the stochastic wandering of spontaneously formed tuning curves or bump solutions. These equations are analyzed using a modified version of the bivariate von Mises distribution, which is well-known in the theory of circular statistics. We first consider a single ring network and derive a simple mathematical expression that accounts for the experimentally observed bimodal (or M-shaped) tuning of neural variability. We then explore the effects of inter-network coupling on stimulus-dependent variability in a pair of ring networks. These could represent populations of cells in two different layers of a cortical hypercolumn linked via vertical synaptic connections, or two different cortical hypercolumns linked by horizontal patchy connections within the same layer. We find that neural variability can be suppressed or facilitated, depending on whether the inter-network coupling is excitatory or inhibitory, and on the relative strengths and biases of the external stimuli to the two networks. These results are consistent with the general observation that increasing the mean firing rate via external stimuli or modulating drives tends to reduce neural variability.Author SummaryA topic of considerable current interest concerns the neural mechanisms underlying the suppression of cortical variability following the onset of a stimulus. Since trial-by-trial variability and noise correlations are known to affect the information capacity of neurons, such suppression could improve the accuracy of population codes. One of the main candidate mechanisms is the suppression of noise-induced transitions between multiple attractors, as exemplified by ring attractor networks. The latter have been used to model experimentally measured stochastic tuning curves of directionally selective middle temporal (MT) neurons. In this paper we show how the stimulus-dependent tuning of neural variability in ring attractor networks can be analyzed in terms of the stochastic wandering of spontaneously formed tuning curves or bumps in a continuum neural field model. The advantage of neural fields is that one can derive explicit mathematical expressions for the second-order statistics of neural activity, and explore how this depends on important model parameters, such as the level of noise, the strength of recurrent connections, and the input contrast.
Nonlinear transfer and temporal gain control in ON bipolar cells
Authors: Deshmukh Nikhil R. , Berry Michael J. 
Published: January 2019

AbstractThe separation of visual input into discrete channels begins at the photoreceptor to bipolar cell synapse. Current models of the ON pathway describe the time-varying membrane voltage of ON bipolar cells as a linear function of light fluctuations. While this linearity holds under some visual conditions, stimulating the retina with full-field, high contrast flashes reveals a number of nonlinearities already present in the input current of ON bipolar cells. First, we show that the synaptic input to ON bipolar cells is asymmetric in response to equal flashes of opposite polarity. Next, we show that this asymmetry emerges because the responses to dark flashes increase linearly with contrast, whereas responses to bright flashes are highly rectified. We also describe how the outward current saturates in response to dark flashes of increasing duration. Furthermore, varying the inter-flash interval between a pair of high contrast flashes reveals a rapid, transient form of gain control that modulates both the amplitude and time course of the flash response. We develop a phenomenological model that captures the primary features of the ON bipolar cell response at high contrast. Finally, we discuss the implications of these nonlinearities in our understanding of how retinal circuitry shapes the visual signal.
Class II Contact-Dependent growth Inhibition (CDI) systems allow for broad-range cross-species toxin delivery
Authors: Virtanen Petra , Wäneskog Marcus , Koskiniemi Sanna 
Published: January 2019

AbstractContact-dependent growth inhibition (CDI) allows bacteria to recognize kin cells in mixed bacterial populations. In Escherichia coli, CDI mediated effector delivery has been shown to be species-specific, with a preference for the own strain over others. This specificity is achieved through an interaction between a receptor-binding domain in the CdiA protein and its cognate receptor protein on the target cell. But how conserved this specificity is has not previously been investigated in detail. Here we show that three different class II CdiA receptor-binding domains and their Enterobacter cloacae analog are highly promiscuous, allowing for efficient effector delivery into several different Enterobacteriaceae species, including Escherichia, Enterobacter, Klebsiella and Salmonella spp. In addition, although we observe a preference for some receptors over others, this did not limit cross-species effector delivery, suggesting that class II CdiA proteins can allow for broad-range and cross-species growth inhibition in mixed bacterial populations.
Deep-sea megabenthos communities of the Eurasian Central Arctic are influenced by ice-cover and sea-ice algal falls
Authors: Elena Rybakova , Antonina Kremenetskaia , Andrey Vedenin , Antje Boetius , Andrey Gebruk 
Published: January 2019

AbstractQuantitative camera surveys of benthic megafauna were carried out during the expedition ARK-XXVII/3 to the Eastern Central Arctic basins with the research icebreaker Polarstern in summer 2012 (2 August-29 September). Nine transects were performed for the first time in deep-sea areas previously fully covered by ice, four of them in the Nansen Basin (3571-4066m) and five in the Amundsen Basin (4041-4384m). At seven of these stations benthic Agassiz trawls were taken near the camera tracks for species identification. The observed Arctic deep-sea megafauna was largely endemic. Several taxa showed a substantially greater depth or geographical range than previously assumed. Variations in the composition and structure of megabenthic communities were analysed and linked to several environmental variables, including state of the sea ice and phytodetritus supply to the seafloor. Three different types of communities were identified based on species dominating the biomass. Among these species were the actiniarian Bathyphellia margaritacea and the holothurians Elpidia heckeri and Kolga hyalina. Variations in megafaunal abundance were first of all related to the proximity to the marginal ice zone. Stations located closer to this zone were characterized by relatively high densities and biomass of B. margaritacea (mean 0.2-1.7 ind m-2; 0.2-1.5 g ww.m-2). The food supply was higher at these stations, as suggested by enhanced concentrations of pigments, organic carbon, bacterial cell abundances and porewater nutrients in the sediments. The fully ice-covered stations closer to the North Pole and partially under multi-year ice were characterized by lower concentrations of the same biogeochemical indicators for food supply. These stations nevertheless hosted relatively high density and biomass of the holothurians E. heckeri (mean 0.9-1.5 ind m-2; 0.3-0.4 g ww.m-2) or K. hyalina (mean 0.004-1.7 ind m-2; 0.01-3.5 g ww.m-2), which were observed to feed on large food falls of the sea-ice colonial diatom Melosira arctica. The link between the community structure of megafauna and the extent and condition of the Central Arctic sea-ice cover suggests that future climate changes may substantially affect deep ocean biodiversity.
Substance use, comorbid psychiatric disorders and suicide attempts in adult FASD patients
Authors: Dirks Henrike , Francke Lisa , Würz Verena , Kretschmann Constance , Dehghan-Sanij Sonja , Scherbaum Norbert 
Published: January 2019

Purpose
Fetal alcohol spectrum disorders (FASD) are a group of developmental disabilities related to prenatal alcohol exposure. FASD is a life-long lasting condition with various neurocognitive impairments and deficits in daily-life functioning. Research also indicates that FASD patients have an increased prevalence for substance use, substance related disorders and other psychiatric disorders. In Germany, data on adult FASD patients and their mental health are rare. The purpose of this paper is to describe substance use and comorbid psychiatric disorders (in addition to FASD) and suicide attempts in adult FASD patients.

Design/methodology/approach
The German version of the structured “Mini International Neuropsychiatric Interview (MINI)” was administered to a convenience sample of patients attending a specialized FASD diagnostic service at a German university hospital to assess psychiatric disorders. Current and lifetime substance use were examined using sections from the German version of the “European Addiction Severity Index (EUROP-ASI-R)” interview.

Findings
In total, 31 adults with FASD were included. Two patients were diagnosed with a substance related disorder, one for alcohol and one for cannabis. Nearly half of all patients fulfilled the diagnostic criteria for mild mental retardation, a further 16 per cent fulfilled the criteria for another current comorbid psychiatric disorder. In total, 26 per cent reported at least one suicide attempt.

Originality/value
Given that the body of research literature on FASD in adulthood is sparse, even a clinical sample of thirty individuals expands knowledge on mental health and substance use in the adult FASD population. The sample was comprehensively assessed using validated structured interviews on mental health, substance use and FASD.
Examining the financial performance of agricultural cooperatives in the USA
Authors: Pokharel Krishna Prasad , Regmi Madhav , Featherstone Allen M. , Archer David W. 
Published: January 2019

Purpose
The purpose of this paper is to identify financial stress and the causes of financial stress for agricultural cooperatives and provide management recommendations to stakeholders including cooperatives’ managers, boards of directors and lenders.

Design/methodology/approach
This research used the geometric mean of the real rate of return on equity to identify financially stressed agricultural cooperatives. The real rate of return on equity allows the allocation of total financial stress among the return on assets, leverage and interest rate issues.

Findings
This study found that financially non-stressed agricultural cooperatives had a higher rate of return on equity and rate of return on assets, but lower leverage ratios and interest rates than stressed agricultural cooperatives. Further, non-stressed cooperatives had higher total assets and sales compared to stressed cooperatives. This suggests that smaller cooperatives are more likely to face financial stress than larger cooperatives. The decomposition of the financial problem showed that a substantial percentage of financial stress was correlated with a low return on assets or profitability. A smaller percentage of financial stress was due to financing decisions.

Originality/value
This study provides value by measuring the impact of profitability, leverage and interest rate on the financial performance of agricultural cooperatives. Results showed that a substantial proportion of financial stress was associated with a low return on assets. This indicates that profitability is a problem for agricultural cooperatives. This study also examines profitability during a period of volatile returns in production agriculture.
The modified characteristics finite element method for time-dependent Darcy-Brinkman problem
Authors: Liao Cheng , Huang Pengzhan 
Published: January 2019

Purpose
This study aims to capture the effective behavior of double-diffusion problem, which arises from the combined heat and mass transfer in porous medium and develop the modified characteristics finite element method.

Design/methodology/approach
The proposed finite element method deals with the nonlinear term temporal term by modified characteristics method. Then, the authors compute the velocity, pressure, temperature and concentration using the decoupled technique. Finally, to show the efficiency of the method, the authors give some numerical examples.

Findings
From the numerical results, one can see that the method has a good accuracy, which shows that the method can simulate this Darcy–Brinkman problem well.

Originality/value
The originality lies in the fact that the proposed scheme is the first time for solving the Darcy–Brinkman problem, which is a more complicated model, and includes the velocity, pressure, temperature and concentration.
Children’s agency in building social capital and collective actions
Authors: Stjernqvist Nanna Wurr , Bonde Ane Høstgaard , Trolle Ellen , Sabinsky Marianne , Maindal Helle Terkildsen 
Published: January 2019

Purpose
Whole-school approaches emphasising pupil participation are recognised as being conducive for building social capital, yet how participatory health educational processes relate to different types of social capital remains unclear. The purpose of this paper is to explore which mechanisms within a participatory health educational process influence social capital and collective actions in the school context, and to discuss children’s agency in such processes.

Design/methodology/approach
A multiple case study design, with the Danish “We Act – Together for Health” intervention, considered as an instrumental case regarding participatory health educational processes for children, principally since it applied the participatory Investigation–Vision–Action–Change (IVAC) methodology. The paper is based on a theory-driven, abductive research strategy. Qualitative methods, including focus group interviews with children, semi-structured interviews with teachers and school principals, and participant observation were used.

Findings
The study’s conceptual framework, which elucidates several mechanisms that interact with types of social capital and collective actions within the school setting, indicates that working with child participation through the IVAC methodology can influence types of social capital and collective actions. It also emphasises children’s limited agency in terms of affecting bridging and linking social capital, norms of reciprocity and collective actions without sufficient support mechanisms at the school and class levels.

Originality/value
The study provides a novel comprehensive conceptual framework identifying the specific mechanisms at different levels that influence social capital and collective actions.