bluuebunny/crossref_metadata_2025_split huggingface dataset:
Order and gelation of cellulose nanocrystal suspensions: an overview of some issues
Authors: Gray Derek G. 
Published: December 2017

Cellulose nanocrystals (CNCs) are polydisperse rod-shaped particles of crystalline cellulose I, typically prepared by sulfuric acid hydrolysis of natural cellulose fibres to give aqueous colloidal suspensions stabilized by sulfate half-ester groups. Sufficiently dilute suspensions are isotropic fluids, but as the concentration of CNC in water is increased, a critical concentration is reached where a spontaneously ordered phase is observed. The (equilibrium) phase separation of the ordered chiral nematic phase is in competition with a tendency of the CNC suspension to form a gel. Qualitatively, factors that reduce the stability of the CNC suspension favour the onset of gelation. The chiral nematic structure is preserved, at least partially, when the suspension dries. Solid chiral nematic films of cellulose are of interest for their optical and templating properties, but the preparation of the films requires improvement. The processes that govern the formation of solid chiral nematic films from CNC suspensions include phase separation, gelation and also the effects of shear on CNC orientation during evaporation. Some insight into these processes is provided by polarized light microscopy, which indicates that the relaxation of shear-induced orientation to give a chiral nematic structure may occur via an intermediate twist-bend state.
This article is part of a discussion meeting issue ‘New horizons for cellulose nanotechnology’.
Optimization of cellulose nanocrystal length and surface charge density through phosphoric acid hydrolysis
Authors: Vanderfleet Oriana M. , Osorio Daniel A. , Cranston Emily D. 
Published: December 2017

Cellulose nanocrystals (CNCs) are emerging nanomaterials with a large range of potential applications. CNCs are typically produced through acid hydrolysis with sulfuric acid; however, phosphoric acid has the advantage of generating CNCs with higher thermal stability. This paper presents a design of experiments approach to optimize the hydrolysis of CNCs from cotton with phosphoric acid. Hydrolysis time, temperature and acid concentration were varied across nine experiments and a linear least-squares regression analysis was applied to understand the effects of these parameters on CNC properties. In all but one case, rod-shaped nanoparticles with a high degree of crystallinity and thermal stability were produced. A statistical model was generated to predict CNC length, and trends in phosphate content and zeta potential were elucidated. The CNC length could be tuned over a relatively large range (238–475 nm) and the polydispersity could be narrowed most effectively by increasing the hydrolysis temperature and acid concentration. The CNC phosphate content was most affected by hydrolysis temperature and time; however, the charge density and colloidal stability were considered low compared with sulfuric acid hydrolysed CNCs. This study provides insight into weak acid hydrolysis and proposes ‘design rules’ for CNCs with improved size uniformity and charge density.This article is part of a discussion meeting issue ‘New horizons for cellulose nanotechnology’.
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’.
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’.
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

AbstractHomologous 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

AbstractThe 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

AbstractFrom 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

ABSTRACTIn 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

AbstractBenthic 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

AbstractPlant 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

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

AbstactChloroplasts 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.
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

AbstractBackgroundReproducibility 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.ResultsTo 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.ConclusionsReproducible 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

AbstractMorphological 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.