bluuebunny/crossref_metadata_2025_split huggingface dataset:
Generalised Complementarity Analysis: identifying the most precious places for the conservation of Species, Functional and Phylogenetic Diversity
Authors: Nipperess David Anthony 
Published: September 2017

AbstractThe most precious places for conservation are those that make the largest contribution to regional, national or global biodiversity. The two key concepts for determining the contribution of a specific site areComplementarity(the gain in diversity achieved when adding that site to a set of other sites) andIrreplaceability(here defined as the overall complementarity of that site when compared to a range of possible combinations of other sites).Generalised Complementarity Analysis(GCA) is a mathematical framework that provides an exact analytical solution for the expected complementarity (gain in diversity) of a focal site, when added to a set of other sites of a given size (m). Diversity is defined very generally to allow for complementarity to be calculated for species richness, Functional Diversity or Phylogenetic Diversity. The expected irreplaceability of a focal site is then defined in GCA as the area under the curve of expected complementarity values for all possible values ofm. GCA is much more computationally efficient than existing algorithmic approaches and is scalable to very large numbers of sites. Because complementarity and irreplaceability are calculated for all possible combinations of sites, GCA serves as a null model for systematic conservation planning algorithms that seek to optimise site selection. However, because truly irreplaceable sites remain so under all possible site selections, GCA is a powerful conservation planning tool in its own right, providing an efficient means of identifying the world’s most precious places for conservation.
Dynamic and Depth Dependent Nanomechanical Properties of Dorsal Ruffles in Live Cells and Biopolymeric Hydrogels
Authors: Vyas Varun , Solomon Melani , D’Souza Gerard G. M. , Huey Bryan D. 
Published: September 2017

AbstractThe nanomechanical properties of various biological and cellular surfaces are increasingly investigated with Scanning Probe Microscopy. Surface stiffness measurements are currently being used to define metastatic properties of various cancerous cell lines and other related biological tissues. Here we present a unique methodology to understand depth dependent nanomechanical variations in stiffness in biopolymers and live cells. In this study we have used A2780 & NIH3T3 cell lines and 0.5% & 1% Agarose to investigate depth dependent stiffness and porosity on nanomechanical properties in different biological systems. This analytical methodology can circumvent the issue associated with the contribution of substrates on cell stiffness. Here we demonstrate that by calculating ‘continuous-step-wise-modulus’ on force vs. distance curves one can observe minute variation as function of depth. Due to the presence of different kinds of cytoskeletal filament, dissipation of contact force might vary from one portion of a cell to another. On NIH3T3 cell lines, stiffness profile of Circular Dorsal Ruffles could be observed in form of large parabolic feature with changes in stiffness at different depth. In biopolymers like agarose, depending upon the extent of polymerization in there can be increase or decrease in stiffness due variations in pore size and extent to which crosslinking is taking place at different depths. 0.5% agarose showed gradual decrease in stiffness whereas with 1% agarose there was slight increase in stiffness as one indents deeper into its surface.
Structural Priming Is Supported By Different Components Of Non-Declarative Memory: Evidence From Priming Across The Lifespan
Authors: Heyselaar Evelien , Wheeldon Linda , Segaert Katrien 
Published: September 2017

AbstractStructural priming is the tendency to repeat syntactic structure across sentences and can be divided into short-term (prime to immediately following target) and long-term (across an experimental session) components. This study investigates how non-declarative memory could support both the transient, short-term and the persistent, long-term structural priming effects commonly seen in the literature. We propose that these characteristics are supported by different subcomponents of non-declarative memory: Perceptual and conceptual non-declarative memory respectively. Previous studies have suggested that these subcomponents age differently, with only conceptual memory showing age-related decline. By investigating how different components of structural priming vary across the lifespan, we aim to elucidate how non-declarative memory supports two seemingly different components of structural priming. In 167 participants ranging between 20 and 85 years old, we find no change in short-term priming magnitude and performance on perceptual tasks, whereas both long-term priming and conceptual memory vary with age. We suggest therefore that the two seemingly different components of structural priming are supported by different components of non-declarative memory. These findings have important implications for theoretical accounts of structural priming.
The hidden spatial dimension of alpha: 10 Hz perceptual echoes propagate as periodic travelling waves in the human brain
Authors: Lozano-Soldevilla Diego , VanRullen Rufin 
Published: September 2017

AbstractAlpha oscillations play a special role in vision. During sensory processing, reverse-correlation techniques revealed that white-noise luminance sequences elicit a robust occipital ∼10 Hz response that periodically reverberates the input sequence for up to 1 s. These perceptual echoes constitute the impulse response function of the visual system. However, the spatial dimension of perceptual echoes remains unknown: do they reverberate across the cortex simultaneously? Does stimulation over multiple visual coordinates evoke multiple synchronized echoes, or do they show consistent phase differences? Here, we tested the spatial dimension of perceptual echoes in two electroencephalogram (EEG) experiments manipulating the location of the visual stimulation. When a single disc flickered a white-noise luminance sequence in the upper visual field, we observed a single “echo wave” originating in posterior sensors and spatially propagating towards frontal ones (i.e. periodic travelling wave). The presentation of two independent flickering discs in separate visual hemifields produced two simultaneous and superimposed echo waves propagating in opposite directions, one in response to each stimulus. Strikingly, at many electrode sites, the phase of the two echoes differed, with a phase advance for the contralateral stimulus location. EEG source reconstruction tentatively located the waves within contralateral parieto-occipital cortex. In conclusion, the alpha rhythm processes stimulus information as a travelling wave that propagates across the cortical representation of retinotopic space in the human brain. In line with the “cortical scanning” hypothesis (Pitts & McCulloch, 1947), these results suggest the existence of an additional spatial dimension embedded in the phase of the alpha rhythm.Significance statement:How does the spatial dimension of sensory processing relate to the temporal dimension of brain rhythms? Using correlation techniques, we characterized perceptual echoes, the average electroencephalogram response induced by visual stimuli that change luminance randomly. We found that perceptual echoes are actually periodic waves that travel through human visual cortex. Strikingly these periodic waves show consistent phase differences across the visual field, processing screen locations sequentially across distinct phases of the cycle following basic retinotopy. These results suggest the existence of an additional “hidden” spatial dimension in sensory cortex, encoded in the phase of the alpha oscillatory cycle. This could mean that perceptual echoes behave like sweeps of a sonar, processing the visual field in cycles of ∼100 ms duration.
RNA-binding and HEPN-nuclease activation are decoupled in CRISPRCas13a
Authors: Tambe Akshay , East-Seletsky Alexandra , Knott Gavin J. , Doudna Jennifer A. , O’Connell Mitchell R. 
Published: September 2017

SUMMARYCRISPR-Cas13a enzymes are RNA-guided, RNA-activated ribonucleases. Their properties have been exploited as powerful tools for RNA detection, RNA imaging and RNA regulation. However, the relationship between target RNA binding and HEPN (higher-eukaryotes-and-prokaryotes nucleotide-binding)- domain nuclease activation is not well understood. Using sequencing experiments coupled within vitrobiochemistry, we find that Cas13a’s target RNA binding affinity and HEPN-nuclease activity are differentially affected by the number of and position of mismatches between the guide and target. We identify a central ‘binding seed’ where perfect base pairing is absolutely required for target binding, and a separate ‘nuclease switch’ where imperfect base-pairing results in tight binding but no HEPN-nuclease activation. These results demonstrate that the binding and cleavage activities of Cas13a are decoupled, highlighting a complex specificity landscape. Our findings underscore a need to consider the range of effects off-target recognition has on Cas13a’s RNA binding and cleavage behavior for RNA-targeting tool development.
Evolutionary rate shifts suggest species-specific adaptation events in HIV-1 and SIV
Authors: Gelbart Maoz , Stern Adi 
Published: September 2017

AbstractThe process of molecular adaptation following a cross-species virus transmission event is currently poorly understood. Here, we identified 137 protein sites that experienced deceleration in their rate of evolution along the HIV-1/SIV phylogeny, likely indicating gain-of-function and consequent adaptation. The majority of such events occurred in parallel to cross-species transmission events and varied between HIV-1 groups, indicating independent adaptation strategies. The evolutionary rate decelerations we found were particularly prominent in accessory proteins that counteract host antiviral restriction factors, suggesting that these factors are a major barrier to viral adaptation to a new host. Surprisingly, we observed that the non-pandemic HIV-1 group O, derived from gorillas, exhibited more rate deceleration events than the pandemic group M, derived from chimpanzees. We suggest that the species barrier is higher when the genetic distance of the hosts increases. Our approach paves the way for subsequent studies on cross-species transfers in other major pathogens.
Effects of mechanical loading on cortical defect repair using a novel mechanobiological model of bone healing
Authors: Liu Chao , Carrera Robert , Flamini Vittoria , Kenny Lena , Cabahug-Zuckerman Pamela , Benson George , Hunter Daniel , Liu Bo , Singh Gurpreet , Leucht Philipp , Mann Kenneth A. , Helms Jill A. , Castillo Alesha B. 
Published: September 2017

AbstractMechanical loading is an important aspect of post-surgical care. The timing of load application relative to the injury event is thought to differentially regulate repair depending on the stage of healing. Here, we show using a novel mechanobiological model of cortical defect repair that daily loading (5 N peak load, 2 Hz, 60 cycles, 4 consecutive days) during hematoma consolidation and inflammation disrupts the injury site and activates cartilage formation on the periosteal surface adjacent to the defect. We also show that daily loading during the matrix deposition phase enhances both bone and cartilage formation at the defect site, while loading during the remodeling phase results in an enlarged woven bone regenerate. All loading regimens resulted in abundant cellular proliferation within the regenerate and at the periosteal surface and fibrous tissue formation directly above the defect. Stress was concentrated at the edges of the defect during exogenous loading, and finite element (FE)-modeled longitudinal strain (εzz) values along the anterior and posterior borders of the defect (~2200 με) were an order of magnitude larger than strain values on the proximal and distal borders (~50-100 με). These findings demonstrate that all phases of cortical defect healing are sensitive to physical stimulation. In addition, the proposed novel mechanobiological model offers several advantages including its technical simplicity and its well-characterized and spatially confined repair program, making effects of physical and biological interventions more easily assessed.
Recentrifuge: robust comparative analysis and contamination removal for metagenomics
Authors: Martí Jose Manuel 
Published: September 2017

AbstractMetagenomic sequencing is becoming widespread in biomedical and environmental research, and the pace is increasing even more thanks to nanopore sequencing. With a rising number of samples and data per sample, the challenge of efficiently comparing results within a specimen and between specimens arises. Reagents, laboratory, and host related contaminants complicate such analysis. Contamination is particularly critical in low microbial biomass body sites and environments, where it can comprise most of a sample if not all. Recentrifuge implements a robust method for the removal of negative-control and crossover taxa from the rest of samples. With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications. In addition to contamination-subtracted samples, Recentrifuge provides shared and exclusive taxa per sample, thus enabling robust contamination removal and comparative analysis in clinical and environmental metagenomics.Author summaryWhether in a clinical or environmental sample, metagenomics can reveal what microorganisms exist and what they do. It is indeed a powerful tool for the study of microbial communities which requires equally powerful methods of analysis. Current challenges in the analysis of metagenomic data include the comparative study of samples, the degree of uncertainty in the results, and the removal of contamination. The scarcer the microbes are in an environment, the more essential it is to have solutions to these issues. Examples of sites with few microbes are not only habitats with low levels of nutrients, but also many body tissues and fluids. Recentrifuge’s novel approach combines statistical, mathematical and computational methods to tackle those challenges with efficiency and robustness: it seamlessly removes diverse contamination, provides a confidence level for every result, and unveils the generalities and specificities in the metagenomic samples.
Functional Modeling of Plant Growth Dynamics
Authors: Xu Yuhang , Qiu Yumou , Schnable James C. 
Published: September 2017

ABSTRACTRecent advances in automated plant phenotyping have enabled the collection time series measurements from the same plants of a wide range of traits over different developmental time scales. The availability of time series phenotypic datasets has increased interest in statistical approaches for comparing patterns of change between different plant genotypes and different treatment conditions. Two widely used methods of modeling growth over time are point-wise analysis of variance (ANOVA) and parametric sigmoidal curve fitting. Point-wise ANOVA yields discontinuous growth curves, which do not reflect the true dynamics of growth patterns in plants. In contrast, fitting a parametric model to a time series of observations does capture the trend of growth, however these models require assumptions regarding the true pattern of plant growth. Depending on the species, treatment regime, and subset of the plant lifecycle sampled this assumptions will not always hold true. Here we introduce a different approach – functional ANOVA – which yields continuous growth curves without requiring assumptions regarding patterns of plant growth. We compare and validate this approach using data from an experiment measuring growth of two maize (Zea maysssp.mays) genotypes under two water availability treatments over a 21-day period. Functional ANOVA enables a nonparametric estimation of the dynamics of changes in plant traits over time without assumptions regarding curve shape. In addition to estimating smooth curves of trait values over time, functional ANOVA also estimates the the derivatives of these curves – e.g. growth rates – simultaneously. Using two different subsampling strategies, we demonstrate that this functional ANOVA method enables the comparison of growth curves between plants phenotyped on non-overlapping days with little reduction in estimation accuracy. This means functional ANOVA based approaches can allow larger numbers of samples and biological replicates to be scored in a single experiment given fixed amounts of phenotyping infrastructure and personnel.
Progressive change in expression of killer-like receptorsr and GPR56 expression defines the cytokine production potential of human CD4+ T memory cells
Authors: Truong Kim-Long , Schlickeiser Stephan , Vogt Katrin , Boës David , Schumann Julia , Appelt Christine , Streitz Mathias , Grütz Gerald , Meisel Christian , Tomiuk Stefan , Polansky Julia K. , Pascher Andreas , Sauer Igor , Gerlach Undine , Sawitzki Birgit 
Published: September 2017

AbstractMemory T cells mount an accelerated response upon re-challenge but are heterogeneous in phenotype and function. Traditionally memory T cells were classified into central memory, effector memory and terminally differentiated effector memory (TEMRA) cells based on expression of CCR7 and CD45RA. Functional heterogeneity even within these subsets demonstrated the need for more suitable markers. We applied bulk and single gene expression profiling of human CD4+ memory T cells and identified surface markers, KLRB1, KLRG1, GPR56 and KLRF1, allowing classification into “low”, “high” or “exhausted” cytokine producers. In contrast to common understanding KLRG1 expression was not associated with exhaustion and highest production of multiple cytokines was observed in KLRB1+KLRG1+GPR56+ T cells. Only additional KLRF1 expression was associated with a decline in cytokine production. The superiority of KLRF1 to define exhausted cytokine producers compared to classical TEMRA identification was best exemplified for intrahepatic T cells in patients with inflammatory liver diseases.
Wine, family businesses and web: marketing strategies to compete effectively
Authors: Iaia Lea , Scorrano Paola , Fait Monica , Cavallo Federica 
Published: September 2017

Purpose
The purpose of this paper is to deepen the web marketing strategies used by wine family businesses (FBs) with the aim to identify the role assigned to websites, the online models and the competitive strategies implemented through them.

Design/methodology/approach
In order to examine the content and structure of the information found on the website of selected FBs, an ad hoc analysis model was designed and validated with the support of marketing and industry experts through an inspecting focus group (Mich, 2007).

Findings
The subsequent observation of the websites of the businesses studied showed that family-run Italian wineries use their websites mainly to present information about the business and as a relational tool through edutainment activities; FBs yet neglect the potential of e-commerce.

Research limitations/implications
The study highlights the importance and the attention that FBs, among others, should dedicate to the role of web communications within their communications strategy. Although this path has allowed the traits essential to launch effective online communications for FBs, the small number of businesses surveyed (ten) does not permit a theoretical generalisation of the results. Thus, we expect to integrate the information obtained from this preliminary study with in-depth interviews with the digital strategists for the companies examined or by increasing the number of FBs studied.

Originality/value
The paper provides an evaluation model to effectively organise the websites’ contents; wine businesses should consider and customise these essential elements with the brand’s specific details.
International law applicable to urban conflict and disaster
Authors: McDermott Ronan , Luelf Charlotte , Hofmann Laura , Gibbons Pat 
Published: September 2017

Purpose
The purpose of this paper is to provide a comprehensive overview of the international legal framework governing urban crises arising from conflict, “natural” and technological disasters.

Design/methodology/approach
The paper deploys legal analysis to the most relevant bodies of international law pertaining to urban crises and systematically outlines the key legal issues arising.

Findings
International humanitarian law (IHL) and international human rights law (IHRL) provide important protections to vulnerable persons in both human-made and “natural” disaster settings. While the two bodies of law do not draw explicit distinctions between urban and rural settings, their various provisions, and indeed their silence on, crucial issues that would enhance legal protection in urban settings merit greater attention.

Research limitations/implications
The paper provides an overview of the sources of international law of most relevance to urban crises. Further research is required into how the urban environment influences their application concretely in urban settings.

Practical implications
In an era when international law is being challenged from many sources and attention is turning to the increasing potential for urban violence and vulnerability, this paper serves to sensitise the disaster management and humanitarian community to the relevance of international legal frameworks to its activities in urban settings.

Originality/value
This paper considers the most salient international legal issues arising during crises and compares and contrasts how the different bodies of international law (IHL and IHRL) address each of the kinds of crises (conflict, “natural” or technological disaster), respectively.
Authenticity at work: a moderated mediation analysis
Authors: Kuntz Joana R.C. , Abbott Mary 
Published: September 2017

PurposeThis paper aims to test a moderated mediation model linking person-environment fit with workplace outcomes (engagement, meaning at work and performance) through authenticity (authentic living and self-alienation). Self-deception was included as a moderator of these relationships.Design/methodology/approachData were collected from 163 employees in a large department using an online survey. The hypotheses were tested using the PROCESS Macro for SPSS, which conducts bootstrapped moderated mediation analyses.FindingsResults showed that person-environment fit facets were positively related to engagement, meaning and performance through authentic living and negatively related through self-alienation. These relationships were significant at low to moderate levels of self-deception.Research/limitations implicationsDespite its small sample size, this study used a time-lagged design to mitigate the limitations associated with cross-sectional studies. Further, it expanded the research on authenticity in the workplace by illustrating the interplay of authenticity with fit, self-deception and workplace outcomes.Practical implicationsOrganisations stand to gain from encouraging authenticity at work, and this can be achieved by ensuring person-environment fit. While self-deception can act as a protective factor against low perceptions of person-environment fit, organisations should strive to create a culture that values diversity and self-expression.Originality/valueThis study is among the first to explore authenticity at work and the first to empirically examine the authenticity and person-environment fit relationship in relation to outcomes, considering individual propensity for motivated bias.