bluuebunny/crossref_metadata_2025 huggingface dataset:
Better together: synergy in nanocellulose blends
Authors: Mautner Andreas , Mayer Florian , Hervy Martin , Lee Koon-Yang , Bismarck Alexander
Published: December 2017

Cellulose nanopapers have gained significant attention in recent years as large-scale reinforcement for high-loading cellulose nanocomposites, substrates for printed electronics and filter nanopapers for water treatment. The mechanical properties of nanopapers are of fundamental importance for all these applications. Cellulose nanopapers can simply be prepared by filtering a suspension of nanocellulose, followed by heat consolidation. It was already demonstrated that the mechanical properties of cellulose nanopapers can be tailored by the fineness of the fibrils used or by modifying nanocellulose fibrils for instance by polymer adsorption, but nanocellulose blends remain underexplored. In this work, we show that the mechanical and physical properties of cellulose nanopapers can be tuned by creating nanopapers from blends of various grades of nanocellulose, i.e. (mechanically refined) bacterial cellulose or cellulose nanofibrils extracted from never-dried bleached softwood pulp by chemical and mechanical pre-treatments. We found that nanopapers made from blends of two or three nanocellulose grades show synergistic effects resulting in improved stiffness, strength, ductility, toughness and physical properties.

This article is part of a discussion meeting issue ‘New horizons for cellulose nanotechnology’.
Structure of native cellulose microfibrils, the starting point for nanocellulose manufacture
Authors: Jarvis Michael C.
Published: December 2017

There is an emerging consensus that higher plants synthesize cellulose microfibrils that initially comprise 18 chains. However, the mean number of chains per microfibril
in situ
is usually greater than 18, sometimes much greater. Microfibrils from woody tissues of conifers, grasses and dicotyledonous plants, and from organs like cotton hairs, all differ in detailed structure and mean diameter. Diameters increase further when aggregated microfibrils are isolated. Because surface chains differ, the tensile properties of the cellulose may be augmented by increasing microfibril diameter. Association of microfibrils with anionic polysaccharides in primary cell walls and mucilages leads to
in vivo
mechanisms of disaggregation that may be relevant to the preparation of nanofibrillar cellulose products. For the preparation of nanocrystalline celluloses, the key issue is the nature and axial spacing of disordered domains at which axial scission can be initiated. These disordered domains do not, as has often been suggested, take the form of large blocks occupying much of the length of the microfibril. They are more likely to be located at chain ends or at places where the microfibril has been mechanically damaged, but their structure and the reasons for their sensitivity to acid hydrolysis need better characterization.

This article is part of a discussion meeting issue ‘New horizons for cellulose nanotechnology’.
Residual wood polymers facilitate compounding of microfibrillated cellulose with poly(lactic acid) for 3D printer filaments
Authors: Winter Armin , Mundigler Norbert , Holzweber Julian , Veigel Stefan , Müller Ulrich , Kovalcik Adriana , Gindl-Altmutter Wolfgang
Published: December 2017

Microfibrillated cellulose (MFC) is a fascinating material with an obvious potential for composite reinforcement due to its excellent mechanics together with high specific surface area. However, in order to use this potential, commercially viable solutions to important technological challenges have to be found. Notably, the distinct hydrophilicity of MFC prevents efficient drying without loss in specific surface area, necessitating storage and processing in wet condition. This greatly hinders compounding with important technical polymers immiscible with water. Differently from cellulose, the chemistry of the major wood polymers lignin and hemicellulose is much more diverse in terms of functional groups. Specifically, the aromatic moieties present in lignin and acetyl groups in hemicellulose provide distinctly less polar surface-chemical functionality compared to hydroxyl groups which dominate the surface-chemical character of cellulose. It is shown that considerable advantages in the production of MFC-filled poly(lactic acid) filaments for three-dimensional printing can be obtained through the use of MFC containing residual lignin and hemicellulose due to their advantageous surface-chemical characteristics. Specifically, considerably reduced agglomerations of MFC in the filaments in combination with improved printability and improved toughness of printed objects are achieved.

This article is part of a discussion meeting issue ‘New horizons for cellulose nanotechnology’.
Cellulose synthase complex organization and cellulose microfibril structure
Authors: Turner Simon , Kumar Manoj
Published: December 2017

Cellulose consists of linear chains of β-1,4-linked glucose units, which are synthesized by the cellulose synthase complex (CSC). In plants, these chains associate in an ordered manner to form the cellulose microfibrils. Both the CSC and the local environment in which the individual chains coalesce to form the cellulose microfibril determine the structure and the unique physical properties of the microfibril. There are several recent reviews that cover many aspects of cellulose biosynthesis, which include trafficking of the complex to the plasma membrane and the relationship between the movement of the CSC and the underlying cortical microtubules (Bringmann
et al.
2012
Trends Plant Sci.
17
, 666–674 (
doi:10.1016/j.tplants.2012.06.003
); Kumar & Turner 2015
Phytochemistry
112
, 91–99 (
doi:10.1016/j.phytochem.2014.07.009
); Schneider
et al.
2016
Curr. Opin. Plant Biol.
34
, 9–16 (
doi:10.1016/j.pbi.2016.07.007
)). In this review, we will focus on recent advances in cellulose biosynthesis in plants, with an emphasis on our current understanding of the structure of individual catalytic subunits together with the local membrane environment where cellulose synthesis occurs. We will attempt to relate this information to our current knowledge of the structure of the cellulose microfibril and propose a model in which variations in the structure of the CSC have important implications for the structure of the cellulose microfibril produced.

This article is part of a discussion meeting issue ‘New horizons for cellulose nanotechnology’.
Bioinspired Bouligand cellulose nanocrystal composites: a review of mechanical properties
Authors: Natarajan Bharath , Gilman Jeffrey W.
Published: December 2017

The twisted plywood, or Bouligand, structure is the most commonly observed microstructural motif in natural materials that possess high mechanical strength and toughness, such as that found in bone and the mantis shrimp dactyl club. These materials are isotropically toughened by a low volume fraction of soft, energy-dissipating polymer and by the Bouligand structure itself, through shear wave filtering and crack twisting, deflection and arrest. Cellulose nanocrystals (CNCs) are excellent candidates for the bottom-up fabrication of these structures, as they naturally self-assemble into ‘chiral nematic’ films when cast from solutions and possess outstanding mechanical properties. In this article, we present a review of the fabrication techniques and the corresponding mechanical properties of Bouligand biomimetic CNC nanocomposites, while drawing comparison to the performance standards set by tough natural composite materials.

This article is part of a discussion meeting issue ‘New horizons for cellulose nanotechnology’.
Extensive sex differences at the initiation of genetic recombination
Authors: Brick Kevin , Thibault-Sennett Sarah , Smagulova Fatima , Lam Kwan-Wood G. , Pu Yongmei , Pratto Florencia , Camerini-Otero R. Daniel , Petukhova Galina V.
Published: December 2017

Homologous recombination in meiosis is initiated by programmed DNA double strand breaks (DSBs) and DSB repair as a crossover is essential to prevent chromosomal abnormalities in gametes. Sex differences in recombination have been previously observed by analyses of recombination end-products. To understand when and how sex differences are established, we built genome-wide maps of meiotic DSBs in both male and female mice. We found that most recombination initiates at sex-biased DSB hotspots. Local context, the choice of DSB targeting pathway and sex-specific patterns of DNA methylation give rise to these differences. Sex differences are not limited to the initiation stage, as the rate at which DSBs are repaired as crossovers appears to differ between the sexes in distal regions. This uneven repair patterning may be linked to the higher aneuploidy rate in females. Together, these data demonstrate that sex differences occur early in meiotic recombination.
Auxin regulates endosperm cellularization inArabidopsis
Authors: Figueiredo Duarte D. , Batista Rita A. , Kohler Claudia
Published: December 2017

The endosperm is an ephemeral tissue that nourishes the developing embryo, similar to the placenta in mammals. In most angiosperms endosperm development starts as a syncytium, where nuclear divisions are not followed by cytokinesis. The timing of endosperm cellularization largely varies between species and the event triggering this transition remains unknown. Here we show that increased auxin biosynthesis in the endosperm prevents its cellularization, leading to seed arrest. Auxin-overproducing seeds phenocopy paternal-excess triploid seeds derived from hybridizations of diploid maternal plants with tetraploid fathers. Concurrently, auxin-related genes are strongly overexpressed in triploid seeds, correlating with increased auxin activity. Reducing auxin biosynthesis and signaling reestablishes endosperm cellularization in triploid seeds and restores their viability, highlighting a causal role of increased auxin in preventing endosperm cellularization. We propose that auxin determines the time of endosperm cellularization and thereby uncovered a central role of auxin in establishing hybridization barriers in plants.
The null additivity of multi-drug combinations
Authors: Russ D. , Kishony R.
Published: December 2017

From natural ecology 1–4 to clinical therapy 5–8, cells are often exposed to mixtures of multiple drugs. Two competing null models are used to predict the combined effect of drugs: response additivity (Bliss) and dosage additivity (Loewe) 9–11. Here, noting that these models diverge with increased number of drugs, we contrast their predictions with measurements of Escherichia coli growth under combinations of up to 10 different antibiotics. As the number of drugs increases, Bliss maintains accuracy while Loewe systematically loses its predictive power. The total dosage required for growth inhibition, which Loewe predicts should be fixed, steadily increases with the number of drugs, following a square root scaling. This scaling is explained by an approximation to Bliss where, inspired by RA Fisher’s classical geometric model 12, dosages of independent drugs adds up as orthogonal vectors rather than linearly. This dose-orthogonality approximation provides results similar to Bliss, yet uses the dosage language as Loewe and is hence easier to implement and intuit. The rejection of dosage additivity in favor of effect additivity and dosage orthogonality provides a framework for understanding how multiple drugs and stressors add up in nature and the clinic.
An optimized strategy for cloning-based locus-specific bisulfite sequencing PCR
Authors: Van Poucke Mario , Boulougouris Xanthippe , De Spiegeleer Bart , Burvenich Christian , Duchateau Luc , Peelman Luc J.
Published: December 2017

In this methods paper, we describe a successful strategy to investigate locus-specific methylation by cloning-based bisulfite sequencing. We cover sample handling, DNA isolation, DNA quality control before bisulfite conversion, bisulfite conversion, DNA quality control after bisulfite conversion, in silico identification of CpG islands, methylation-independent bisulfite sequencing PCR (BSP) assay design, methylation-independent BSP, cloning strategy, sequencing and data analysis. Methods that are described nicely elsewhere will not be covered in detail. Instead, the focus will be on tips/tricks and new methods/strategies used in this protocol, including quality control assessment of the DNA before and after bisulfite conversion and a pooled cloning strategy to reduce time, costs and effort during this step. In addition we comment on dealing with bias and improving overall protocol efficiency.
Recruitment and abundance of intertidal barnacles and mussels along the Atlantic Canadian coast: pelagic influences and relationships with predator abundance
Authors: Scrosati Ricardo A. , Ellrich Julius A.
Published: December 2017

Benthic species from rocky intertidal systems are irregularly distributed along marine coastlines. Nearshore pelagic conditions often help to explain such variation, but most such studies have been done on eastern ocean boundary coasts. Through a large-scale mensurative study, we investigated possible benthic-pelagic coupling along the Atlantic coast of Nova Scotia, a western ocean boundary coast. We studied the high intertidal zone of nine wave-exposed bedrock locations spanning 415 km of coastline from north to south. At each location in the spring, we measured the recruitment of barnacles and mussels, the two main filter-feeding invertebrates. Recruitment varied irregularly along the coast. Satellite data on coastal phytoplankton and particulate organic carbon (food for intertidal filter-feeders and their pelagic larvae) and in-situ data on seawater temperature explained, to varying degrees, the geographic structure of recruitment. In turn, the summer abundance of both filter-feeders was positively related to their spring recruitment. Ultimately, predator (dogwhelk) abundance was positively related to the recruitment and/or abundance of barnacles and mussels (the main prey of dogwhelks). These results are consistent with bottom-up forcing influencing intertidal community structure on this coast. Sea ice may also influence this predator–prey interaction. Drift ice leaving the Gulf of St. Lawrence in late winter disturbed the northern locations surveyed on the Atlantic coast, making barnacles (owing to their high spring recruitment) the only food source for dogwhelks at such places. Investigating the oceanographic drivers of pelagic food supply and seawater temperature should help to further understand how this large metacommunity is organized.
Cooperativity in Plant Plasma Membrane Intrinsic Proteins (PIPs): Mechanism of Increased Water Transport in Maize PIP1 Channels in Hetero-tetramers
Authors: Vajpai Manu , Mukherjee Mishtu , Sankararamakrishnan Ramasubbu
Published: December 2017

Plant aquaporins (AQPs) play vital roles in several physiological processes. Plasma membrane intrinsic proteins (PIPs) belong to the subfamily of plant AQPs and they are further divided into two closely related subgroups PIP1s and PIP2s. Members of the two subgroups have been shown to have different transport properties. While PIP2 members are efficient water channels, PIP1s from some plant species have been shown to be functionally inactive. Aquaporins form tetramers under physiological conditions. PIP2s can enhance the water transport of PIP1s when they form hetero-tetramers. However, the role of monomer-monomer interface and the significance of specific residues in enhancing the water permeation of PIP1s have not been investigated at atomic level. We have performed all-atom molecular dynamics (MD) simulations of homo-tetramers of ZmPIP1;2 and ZmPIP2;5 from Zea mays and hetero-tetramers containing ZmPIP1;2 and ZmPIP2;5 with different stoichiometries and configurations. ZmPIP1;2 in a tetramer assembly will have two interfaces, one formed by transmembrane segments TM4 and TM5 and the other formed by TM1 and TM2. We have analyzed channel radius profiles, water transport and potential of mean force profiles of ZmPIP1;2 monomers with different types of interfaces. Results of MD simulations clearly revealed that TM4-TM5 interface and not the TM1-TM2 interface is important in modulating the water transport of ZmPIP1;2. We generated in silico mutants of specific residues that are involved in contacts with adjacent monomers. MD simulations of mutant tetramers highlighted the importance of I93 residue from the TM2 segment of ZmPIP2;5 for the increased water transport in ZmPIP1;2.
Dynamic compression schemes for graph coloring
Authors: Mustafa Harun , Schilken Ingo , Karasikov Mikhail , Eickhoff Carsten , Rätsch Gunnar , Kahles André
Published: December 2017

Motivation

Technological advancements in high-throughput DNA sequencing have led to an exponential growth of sequencing data being produced and stored as a byproduct of biomedical research. Despite its public availability, a majority of this data remains hard to query to the research community due to a lack of efficient data representation and indexing solutions. One of the available techniques to represent read data is a condensed form as an assembly graph. Such a representation contains all sequence information but does not store contextual information and metadata.

Results

We present two new approaches for a compressed representation of a graph coloring: a lossless compression scheme based on a novel application of wavelet tries as well as a highly accurate lossy compression based on a set of Bloom filters. Both strategies retain a coloring with dynamically changing graph topology. We present construction and merge procedures for both methods and evaluate their performance on a wide range of different datasets. By dropping the requirement of a fully lossless compression and using the topological information of the underlying graph, we can reduce memory requirements by up to three orders of magnitude. Representing individual colors as independently stored modules, our approaches are fully dynamic and can be efficiently parallelized. These properties allow for an easy upscaling to the problem sizes common to the biomedical domain.

Availability

We provide prototype implementations in C++, summaries of our experiments as well as links to all datasets publicly at https://github.com/ratschlab/graph_annotation.

Contact

andre.kahles@inf.ethz.ch, carsten@brown.edu, Gunnar.Ratsch@ratschlab.org
WSL5, a pentatricopeptide repeat protein, is essential for chloroplast biogenesis in rice under cold stress
Authors: Liu X. , Lan J. , Huang Y.S. , Cao P.H. , Zhou C.L. , Ren Y.K. , He N.Q. , Liu S.J. , Tian Y.L. , Nguyen T.L. , Jiang L. , Wan J.M.
Published: December 2017

Abstact

Chloroplasts play an essential role in plant growth and development, and cold has a great effect on chloroplast development. Although many genes or regulators involved in chloroplast biogenesis and development have been isolated and characterized, identification of novel components associated with cold is still lacking. In this study, we reported the functional characterization of white stripe leaf 5 (wsl5) mutant in rice. The mutant developed white-striped leaves during early leaf development and was albinic when planted under cold stress. Genetic and molecular analysis revealed that WSL5 encodes a novel chloroplast-targeted pentatricopeptide repeat protein. RNA-seq analysis showed that expression of nuclear-encoded photosynthetic genes in the mutant was significantly repressed, and expression of many chloroplast-encoded genes was also significantly changed. Notably, the WSL5 mutation caused defects in editing of rpl2 and atpA, and in splicing of rpl2 and rps12. Chloroplast ribosome biogenesis was impaired under cold stress. We propose that WSL5 is required for normal chloroplast development in rice under cold stress.
Viral replication modes in single-peak fitness landscapes: a dynamical systems analysis
Authors: Forners Joan , Lázaro J. Tomás , Alarcón Tomás , Elena Santiago F. , Sardanyés Josep
Published: December 2017

Positive-sense, single-stranded RNA viruses are important pathogens infecting almost all types of organisms. Experimental evidences from mutant distributions and amplification kinetics of viral RNA suggest that these pathogens may follow different RNA replication modes, ranging from the stamping machine replication (SMR) to the geometric replication (GR) modes. Despite previous theoretical works have focused on the evolutionary dynamics of RNA viruses amplifying their genomes with different strategies, few is known in terms of the bifurcations and transitions involving error thresholds (mutation-induced dominance of mutants) and lethal mutagenesis (mutation-induced extinction of all sequences). Here we analyze a dynamical system describing the intracellular amplification of viral RNA genomes evolving on a single-peak fitness landscape focusing on three cases considering neutral, deleterious, and lethal mutants spectra. In our model, the different replication modes are introduced with parameter α: with α ≳ 0 for the SMR and α = 1 for the GR. We analytically derive the critical mutation rates causing lethal mutagenesis and error catastrophe, governed by transcritical bifurcations that depend on parameters α, k1 (replicative fitness of mutants), and on the spontaneous degradation rates of the sequences, ϵ. For the lethal case the critical mutation rate involving lethal mutagenesis is . Here, the SMR involves lower critical mutation rates, being the system more robust to lethal mutagenesis replicating closer to the GR mode. This result is also found for the neutral and deleterious cases, but for these later cases lethal mutagenesis can shift to the error catastrophe once the replication mode surpasses a threshold given by .
Reproducible Bioinformatics Project: A community for reproducible bioinformatics analysis pipelines
Authors: Kulkarni Neha , Alessandrì Luca , Panero Riccardo , Arigoni Maddalena , Olivero Martina , Cordero Francesca , Beccuti Marco , Calogero Raffaele A
Published: December 2017

Background

Reproducibility of a research is a key element in the modern science and it is mandatory for any industrial application. It represents the ability of replicating an experiment independently by the location and the operator. Therefore, a study can be considered reproducible only if all used data are available and the exploited computational analysis workflow is clearly described. However, today for reproducing a complex bioinformatics analysis, the raw data and a list of tools used in the workflow could be not enough to guarantee the reproducibility of the results obtained. Indeed, different releases of the same tools and/or of the system libraries (exploited by such tools) might lead to sneaky reproducibility issues.

Results

To address this challenge, we established the Reproducible Bioinformatics Project (RBP), which is a non-profit and open-source project, whose aim is to provide a schema and an infrastructure, based on docker images and R package, to provide reproducible results in Bioinformatics. One or more Docker images are then defined for a workflow (typically one for each task), while the workflow implementation is handled via R-functions embedded in a package available at github repository. Thus, a bioinformatician participating to the project has firstly to integrate her/his workflow modules into Docker image(s) exploiting an Ubuntu docker image developed ad hoc by RPB to make easier this task. Secondly, the workflow implementation must be realized in R according to an R-skeleton function made available by RPB to guarantee homogeneity and reusability among different RPB functions. Moreover she/he has to provide the R vignette explaining the package functionality together with an example dataset which can be used to improve the user confidence in the workflow utilization.

Conclusions

Reproducible Bioinformatics Project provides a general schema and an infrastructure to distribute robust and reproducible workflows. Thus, it guarantees to final users the ability to repeat consistently any analysis independently by the used UNIX-like architecture.
Frequent Non-random Shifts in the Temporal Sequence of Developmental Landmark Events during Teleost Evolutionary Diversification
Authors: Ito Fumihiro , Matsumoto Tomotaka , Hirata Tatsumi
Published: December 2017

Morphological transformations can be generated by evolutionary changes in the sequence of developmental events. In this study, we examined the evolutionary dynamics of the developmental sequence on a macroevolutionary scale using the teleost. Using the information from previous reports describing the development of 31 species, we extracted the developmental sequences of 19 landmark events involving the formation of phylogenetically conserved body parts; we then inferred ancestral developmental sequences by two different parsimony-based methods—event-pairing (Jeffery, Bininda-Emonds, Coates & Richardson, 2002a) and continuous analysis (Germain & Laurin, 2009). The phylogenetic comparisons of these sequences revealed event-dependent heterogeneity in the frequency of sequence changes. Most of the sequence changes occurred as exchanges of temporally neighboring events. The phylogenetic analyses suggested that the ancestral species had experienced frequent changes in developmental sequences. Although the analyses showed that these heterochronic changes accumulated along phylogenic time, the precise distribution of the changes over the teleost phylogeny remains unclear due to technical limitations. Finally, this first comprehensive analysis of teleost developmental sequences will provide solid ground on which to elucidate the significance of developmental timing in animal morphological diversification.
In vivoimaging of radial spoke proteins reveals independent assembly and turnover of the spoke head and stalk
Authors: Lechtreck Karl F. , Mengoni Ilaria , Okivie Batare , Hilderhoff Kiersten B.
Published: December 2017

Radial spokes (RSs) are multiprotein complexes regulating dynein activity. In the cell body and ciliary matrix, RS proteins are present in a 12S precursor, which is converted into axonemal 20S spokes consisting of a head and stalk. To study RS assemblyin vivo, we expressed fluorescent protein (FP)-tagged versions of the head protein RSP4 and the stalk protein RSP3 to rescue the correspondingChlamydomonasmutantspfl, lacking spoke heads, andpf14, lacking RSs entirely. RSP3 and RSP4 mostly co-migrated by intraflagellar transport (IFT). Transport was elevated during ciliary assembly. IFT of RSP4-FP depended on RSP3. To study RS assembly independently of ciliogenesis, strains expressing FP-tagged RS proteins were mated to untagged cells with, without, or with partial RSs. RSP4-FP is added a tip-to-base fashion to preexistingpf1spoke stalks while de novo RS assembly occurred lengthwise. In wild-type cilia, the exchange rate of head protein RSP4 exceeded that of the stalk protein RSP3 suggesting increased turnover of spoke heads. The data indicate that RSP3 and RSP4 while transported together separate inside cilia during RS repair and maintenance. The 12S RS precursor encompassing both proteins could represent transport form of the RS ensuring stoichiometric delivery by IFT. (196 of 200)
Dealing with mutualists and antagonists: Specificity of plant‐mediated interactions between herbivores and flower visitors, and consequences for plant fitness
Authors: Rusman Quint , Lucas‐Barbosa Dani , Poelman Erik H.
Published: December 2017

Plants need to deal with antagonists, such as herbivores, while maintaining interactions with mutualists, such as pollinators that help plants to maximize their reproductive output. Although many plant species have inducible defences to save metabolic costs of defence in the absence of herbivores, plant responses induced by herbivore attack can have ecological costs. For example, herbivore‐induced responses can affect flower traits and alter interactions with flower visitors. Such plant‐mediated interactions between herbivores and flower visitors can affect plant reproductive output. Current knowledge on the generality and specificity of plant‐mediated herbivore–flower–visitor interactions and its consequences for plant fitness is limited.

In this study, we investigated whether a broad range of herbivores feeding on the annual plant Brassica nigra affect interactions with flower visitors, whether the direction of interactions is predicted by the feeding modes (chewing and sap‐feeding) and sites (above‐ and belowground) of the herbivores, and whether it results in fitness consequences for the plant.

Our results show that attack of B. nigra by a range of different herbivores influenced plant interactions with mutualist pollinators and an antagonist florivore, the pollen beetle Meligethes aeneus. Pollinator community composition was affected by herbivory, whereas overall pollinator attraction was maintained. Pollinator community composition of uninfested plants differed from that of chewing and root herbivore‐infested plants. Main responders in the pollinator communities to changes induced by herbivory were syrphid flies, bumblebees, and solitary bees. Although the preference of pollen beetle adults was not affected by herbivory, beetle larvae performed best on plants infested with the nematode Heterodera schachtii. The changes in pollinator community composition and syrphid fly visitation can explain the observed increase in seed set of root herbivore‐infested plants.

Interactions of flowering B. nigra plants with mutualist and antagonist insects are well integrated and conflicting interactions do not reduce reproductive output. Our results suggest some degree of specificity in herbivore–flower–visitor interactions with consequences for plant fitness. Specificity of plant responses were determined at the species level as well as the herbivore functional group level, and differed depending on the flower visitor. Because plant reproduction was affected by indirect plant‐mediated interactions, these can potentially result in selection on plant strategies to optimize growth, defence and reproduction.

A plain language summary is available for this article.
Prediction and attenuation of seasonal spillover of parasites between wild and domestic ungulates in an arid mixed‐use system
Authors: Walker Josephine G. , Evans Kate E. , Rose Vineer Hannah , van Wyk Jan A. , Morgan Eric R.
Published: December 2017

Transmission of parasites between host species affects host population dynamics, interspecific competition, and ecosystem structure and function. In areas where wild and domestic herbivores share grazing land, management of parasites in livestock may affect or be affected by sympatric wildlife due to cross‐species transmission.

We develop a novel method for simulating transmission potential based on both biotic and abiotic factors in a semi‐arid system in Botswana. Optimal timing of antiparasitic treatment in livestock is then compared under a variety of alternative host scenarios, including seasonally migrating wild hosts.

In this region, rainfall is the primary driver of seasonality of transmission, but wildlife migration leads to spatial differences in the effectiveness of treatment in domestic animals. Additionally, competent migratory wildlife hosts move parasites across the landscape.

Simulated transmission potential matches observed patterns of clinical disease in livestock in the study area. Increased wildlife contact is correlated with a decrease in disease, suggesting that non‐competent wild hosts may attenuate transmission by removing infective parasite larvae from livestock pasture.

Optimising the timing of treatment according to within‐year rainfall patterns was considerably more effective than treating at a standard time of year. By targeting treatment in this way, efficient control can be achieved, mitigating parasite spillover from wildlife where it does occur.

Synthesis and applications. This model of parasite transmission potential enables evidence‐based management of parasite spillover between wild and domestic species in a spatio‐temporally dynamic system. It can be applied in other mixed‐use systems to mitigate parasite transmission under altered climate scenarios or changes in host ranges.
Environmental drivers and phylogenetic constraints of growth phenologies across a large set of herbaceous species
Authors: Huang Lin , Koubek Tomáš , Weiser Martin , Herben Tomáš
Published: December 2017

Because perennial herbs of temperate climates develop their above‐ground parts every year anew, their success critically depends on the timing and speed of this growth (growth phenology). These parameters can play a role in species coexistence and may differ along environmental gradients. Still, we know little about them, as most phenological data come from observations of flowering and to a lesser degree leafing onset.

We collected data on growth phenology of about 400 perennial herbs in a botanical garden to make the results independent of local differences in climatic drivers as much as possible. Using these data, we determined species‐specific parameters ofDay of peak growth,Day of maturityand two types of growth rates associated with the change in plant size. Environmental conditions in which these species occur in the field were assessed using Ellenberg indicator values, which express species’ optima along gradients of moisture, nutrients and temperature.

Both timing and speed of growth estimated in the common garden were affected by light and moisture conditions of the habitats where the species typically occur. All parameters showed phylogenetic conservatism.

We identified two relationships among these parameters of growth phenology: (1) species with early peak growth had high relative growth rates in contrast to late species; (2) tall species showed later peak growth than short species. The first relationship is associated with survival under forest canopy, where species are selected to grow early and fast before trees leaf out, which restricts their size. The latter is associated with (asymmetric) competition for light in open habitats, where the main selection factor is for tall stature, which cannot be attained early in the season.

Synthesis. We show that large differences in size growth dynamics among herbaceous species are constrained by a few key trade‐offs involving height at maturity, rate of growth and time when maximum height is attained. These trade‐offs correspond to major selective forces acting on herbaceous plants in temperate climates.
Financement Bancaire des Petites et Moyennes Entreprises au Cameroun
Authors: Tsambou André Dumas , Akono Christian Zamo , Ndokang Esone Ludwick , Tsafack Nanfosso Roger
Published: December 2017

Le présent travail a pour objectif d'identifier les déterminants du financement bancaire des PME camerounaises. Il s'appuie pour cela sur l'enquête « Formulation d'un Plan de Développement Local des PME au Cameroun » réalisée auprès de 413 PME par le ministère des petites et moyennes entreprises, de l'économie sociale et de l'artisanat (MINPMEESA) du Gouvernement camerounais et l'Agence Japonaise de Coopération Internationale (JICA). Nous utilisons un modèle logit simple et les méthodes d'estimations récentes. L'analyse statistique des données révèle que les PME autofinancent leurs activités à court terme et font recours aux institutions financières à long terme. L'analyse économétrique a montré que les principaux déterminants du financement des PME sont la présence régulière des effets financiers, la qualité des garanties offertes, la taille de la PME, la rentabilité et le capital social (appartenance aux réseaux sociaux, participation des étrangers au capital, soutien des autorités gouvernementales). Cependant, les relations sociales qui sont des indicateurs du degré de confiance des PME améliorent significativement la probabilité d'accès au financement bancaire en réduisant le degré d'opacité des PME aux yeux du banquier.
A struggle on two fronts: boundary drawing in the lower region of the social space and the symbolic market for ‘down‐to‐earthness’
Authors: Jarness Vegard , Flemmen Magne Paalgard
Published: December 2017

In this article we use qualitative interviews to examine how Norwegians possessing low volumes of cultural and economic capital demarcate themselves symbolically from the lifestyles of those above and below them in social space. In downward boundary drawing, a range of types of people are regarded as inferior because of perceived moral and aesthetic deficiencies. In upward boundary drawing, anti‐elitist sentiments are strong: people practising resource‐demanding lifestyles are viewed as harbouring ‘snobbish’ and ‘elitist’ attitudes. However, our analysis suggests that contemporary forms of anti‐elitism are far from absolute, as symbolic expressions of privilege are markedly less challenged if they are parcelled in a ‘down‐to‐earth’ attitude. Previous studies have shown attempts by the privileged to downplay differences in cross‐class encounters, accompanied by displays of openness and down‐to‐earthness. Our findings suggest that there is in fact a symbolic ‘market’ for such performances in the lower region of social space. This cross‐class sympathy, we argue, helps naturalize, and thereby legitimize, class inequalities. The implications of this finding are outlined with reference to current scholarly debates about politics and populism, status and recognition and intersections between class and gender in the structuring of social inequalities. The article also contributes key methodological insights into the mapping of symbolic boundaries. Challenging Lamont's influential framework, we demonstrate that there is a need for a more complex analytical strategy rather than simply measuring the ‘relative salience’ of various boundaries in terms of their occurrence in qualitative interview data. In distinguishing analytically between usurpationary and exclusionary boundary strategies, we show that moral boundaries in particular can take on qualitatively different forms and that subtypes of boundaries are sometimes so tightly intertwined that separating them to measure their relative salience would neglect the complex ways in which they combine to engender both aversion to and sympathies for others.
Credit Default Swaps and Managers’ Voluntary Disclosure
Authors: KIM JAE B. , SHROFF PERVIN , VYAS DUSHYANTKUMAR , WITTENBERG‐MOERMAN REGINA
Published: December 2017

We investigate how the availability of traded credit default swaps (CDSs) affects the referenced firms’ voluntary disclosure choices. CDSs enable lenders to hedge their credit risk exposure, weakening their incentives to monitor borrowers. We predict that reduced lender monitoring in turn leads shareholders to intensify their monitoring and demand increased voluntary disclosure from managers. Consistent with this expectation, we find that managers are more likely to issue earnings forecasts and forecast more frequently when traded CDSs reference their firms. We further find a stronger impact of CDS availability on firm disclosure when (1) lenders have higher ability and propensity to hedge credit risk using CDSs, and (2) lender monitoring incentives and monitoring strength are weaker. Consistent with an increase in shareholder demand for public information disclosure induced by a reduction in lender monitoring, we find a stronger effect of CDSs on voluntary disclosure for firms with higher institutional ownership and stronger corporate governance. Overall, our findings suggest that firms with traded CDS contracts enhance their voluntary disclosure to offset the effect of reduced monitoring by CDS‐protected lenders.
Citrate Content of Bone as a Measure of Postmortem Interval: An External Validation Study
Authors: Brown Michael A. , Bunch Ann W. , Froome Charles , Gerling Rebecca , Hennessy Shawn , Ellison Jeffrey
Published: December 2017

The postmortem interval (PMI) of skeletal remains is a crucial piece of information that can help establish the time dimension in criminal cases. Unfortunately, the accurate and reliable determination of PMI from bone continues to evade forensic investigators despite concerted efforts over the past decades to develop suitable qualitative and quantitative methods. A relatively new PMI method based on the analysis of citrate content of bone was developed by Schwarcz et al. The main objective of our research was to determine whether this work could be externally validated. Thirty‐one bone samples were obtained from the Forensic Anthropology Center, University of Tennessee, Knoxville, and the Onondaga County Medical Examiner's Office. Results from analyzing samples with PMI greater than 2 years suggest that the hypothetical relationship between the citrate content of bone and PMI is much weaker than reported. It was also observed that the average absolute error between the PMI value estimated using the equation proposed by Schwarcz et al. and the actual (“true”) PMI of the sample was negative indicating an underestimation in PMI. These findings are identical to those reported by Kanz et al. Despite these results this method may still serve as a technique to sort ancient from more recent skeletal cases, after further, similar validation studies have been conducted.
Physicochemical, Thermal, and Sensory Properties of Blue Corn (Zea Mays L.)
Authors: Mutlu Ceren , Arslan‐Tontul Sultan , Candal Cihadiye , Kilic Ozlem , Erbas Mustafa
Published: December 2017

The aim of this study was to investigate some physicochemical and sensory properties of blue corn cultivated in Turkey. The length and width of the cob with kernels, hectoliter, and 1000‐kernel weight of blue corn were measured as 7.66, 2.02 mm, 84.40 kg/100 L, and 44.27 g, respectively. The gelatinization onset, peak, and end temperatures were measured as 61.12 °C, 64.35 °C, and 75.65 °C, respectively. The water activity, moisture content, total protein, lipid, and crude fiber contents of the blue corn sample were detected as 0.44, 9.39%, 13.13%, 4.30%, and 2.68%, respectively. Total starch and resistant starch contents of blue corn were determined as 63.94% and 8.89%, respectively. Also, total monomeric anthocyanin content and antioxidant capacity of blue corn were detected as 915.43 mg CGE/kg and 7.99 μmol TE/g, respectively. Additionally, the major fatty acids detected in blue corn samples were palmitic, stearic, oleic, and linoleic acids.

Practical Application

Blue corn can be utilized in the production of enjoyable and healthier snacks, such as popcorn and chips, because of its color and high phenolic, anthocyanin, and fiber contents.
Climate and Water Conflicts Coevolution from Tropical Development and Hydro‐Climatic Perspectives: A Case Study of Costa Rica
Authors: Esquivel‐Hernández Germain , Sánchez‐Murillo Ricardo , Birkel Christian , Boll Jan
Published: December 2017

Costa Rica is a nation with a vast wealth of water resources; however, recently the country has faced water conflicts (WC) due to social, economic, legal, and political impediments in response to limited water availability during El Niño events and inefficient use of its water resources. This study presents a spatial distribution and temporal analysis of WC in Costa Rica from 2005 to 2015. In total, 719 WC were analyzed of which 54% were among private individuals and government. The largest urban areas and the Grande de Tárcoles Basin were identified as the main “hot spot” for the conflicts. WC were mainly caused by spills of wastewater, water pollution, water shortage, infrastructure damage, and flooding, and can be predicted using a multiple linear model including the population size and the number of hydro‐meteorological events (HME) (R2 = 0.77). The identified HME also coevolved significantly with the changes in precipitation regimes (r = 0.67, p = 0.021). Our results suggest that there is a need to recognize that water infrastructure longevity across the country concatenates and amplifies WC, mainly in the most populated area located in the Central Valley. Implications of our findings include the need for truly integrated water resources management plans that include, for example, WC as indicators of hydro‐climatic changing conditions and water supply and sanitation infrastructure status.
Recursive multi‐frequency segmentation of movement trajectories (ReMuS)
Authors: Ahearn Sean C. , Dodge Somayeh
Published: December 2017

The quantity of GPS trajectories on the movement of individuals has far outstripped our ability to analyse them. Segmentation, a first step in trajectory analysis, is fundamental to imputing behaviour from patterns of movement.

Behaviour occurs at multiple scales that are captured at different temporal frequencies. To identify behaviour from a complex trajectory it is essential to use a segmentation procedure that captures different frequency ranges. A limitation of existing segmentation algorithms is that they require training and parameterisation that can lead to special use segmentations that are not generalisable.

This paper presents a new approach to the automated segmentation of movement trajectories at multiple scales. It has two distinguishing characteristics: it can capture movement patterns at multiple temporal frequencies through its recursive application; and requires no training or thresholding.

The methodology is tested on two sets of simulated data and GPS tracking data of two species, the Turkey Vulture (Cathartes aura) and the Galapagos Albatross (Phoebastria irrorata). For the Turkey Vulture dataset, segments and transition points are evaluated using behavioural segmentations delineated by domain experts, and results are also compared with an existing approach. For the Albatross dataset, the segmentation results are evaluated using the geographic context of the movement tracks through visualisation. An Albatross trajectory is used to illustrate the application of recursive segmentation for extracting movement patterns at multiple temporal scales. The evaluation suggests that the segmentation technique is capable of extracting the right number of segments and in estimating transition points for most of the evaluated datasets.

The proposed methodology has the potential to automate the segmentation process by enabling researchers to analyse a broad range of heterogeneous datasets without training. It will enable them to segment datasets recursively to derive multiple scales of movement patterns in a trajectory that may relate to different scales of behaviour.
Avoiding quantification bias in metabarcoding: Application of a cell biovolume correction factor in diatom molecular biomonitoring
Authors: Vasselon Valentin , Bouchez Agnès , Rimet Frédéric , Jacquet Stéphan , Trobajo Rosa , Corniquel Méline , Tapolczai Kálmán , Domaizon Isabelle
Published: December 2017

In recent years, remarkable progress has been made in developing environmental DNA metabarcoding. However, its ability to quantify species relative abundance remains uncertain, limiting its application for biomonitoring. In diatoms, although the rbcL gene appears to be a suitable barcode for diatoms, providing relevant qualitative data to describe taxonomic composition, improvement of species quantification is still required.

Here, we hypothesized that rbcL copy number is correlated with diatom cell biovolume (as previously described for the 18S gene) and that a correction factor (CF) based on cell biovolume should be applied to improve taxa quantification. We carried out a laboratory experiment using pure cultures of eight diatom species with contrasted cell biovolumes in order to (1) verify the relationship between rbcL copy numbers (estimated by qPCR) and diatom cell biovolumes and (2) define a potential CF. In order to evaluate CF efficiency, five mock communities were created by mixing different amounts of DNA from the eight species, and were sequenced using HTS and targeting the same rbcL barcode.

As expected, the correction of DNA reads proportions by the CF improved the congruence between morphological and molecular inventories. Final validation of the CF was obtained on environmental samples (metabarcoding data from 80 benthic biofilms) for which the application of CF allowed differences between molecular and morphological water quality indices to be reduced by 47%.

Overall, our results highlight the usefulness of applying a CF factor, which is effective in reducing over‐estimation of high biovolume species, correcting quantitative biases in diatom metabarcoding studies and improving final water quality assessment.