bluuebunny/crossref_metadata_2025_split huggingface dataset:
Soil variation response is mediated by growth trajectories rather than functional traits in a widespread pioneer Neotropical tree
Authors: Levionnois Sébastien , Tysklind Niklas , Nicolini Eric , Ferry Bruno , Troispoux Valérie , Le Moguedec Gilles , Morel Hélène , Stahl Clément , Coste Sabrina , Caron Henri , Heuret Patrick 
Published: June 2018

AbstractTrait-environment relationships have been described at the community level across tree species. However, whether interspecific trait-environment relationships are consistent at the intraspecific level is yet unknown. Moreover, we do not know how consistent is the response between organ vs. whole-tree level.We examined phenotypic variability for 16 functional leaf (dimensions, nutrient, chlorophyll) and wood traits (density) across two soil types, Ferralitic Soil (FS) vs. White Sands (WS), on two sites for 70 adult trees ofCecropia obtusaTrécul (Urticaceae) in French Guiana.Cecropiais a widespread pioneer Neotropical genus that generally dominates early successional forest stages. To understand how soil types impact resource-use through the processes of growth and branching, we examined the architectural development with a retrospective analysis of growth trajectories. We expect soil types to affect both, functional traits in relation to resource acquisition strategy as already described at the interspecific level, and growth strategies due to resource limitations with reduced growth on poor soils.Functional traits were not involved in the soil response, as only two traits-leaf residual water content and K content-showed significant differences across soil types. Soil effects were stronger on growth trajectories, with WS trees having the slowest growth trajectories and less numerous branches across their lifespan.The analysis of growth trajectories based on architectural analysis improved our ability to characterise the response of trees with soil types. The intraspecific variability is higher for growth trajectories than functional traits forC. obtusa, revealing the complementarity of the architectural approach with the functional approach to gain insights on the way trees manage their resources over their lifetime. Soil-related responses ofCecropiafunctional traits are not the same as those at the interspecific level, suggesting that the effects of the acting ecological processes are different between the two levels. Apart from soil differences, much variation was found across sites, which calls for further investigation of the factors shaping growth trajectories in tropical forests.
Three-dimensional organization of transzonal projections and other cytoplasmic extensions in mouse ovarian follicles
Authors: Baena Valentina , Terasaki Mark 
Published: June 2018

AbstractEach mammalian oocyte is nurtured by its own multi-cellular structure, the ovarian follicle. We used new methods for serial section electron microscopy to examine entire cells and their projections in mouse antral ovarian follicles. It is already known that cumulus cells send towards the oocyte thin cytoplasmic projections called transzonal projections (TZPs), which are crucial for normal oocyte development. We found that most TZPs do not reach the oocyte, and that they often branch and make gap junctions with each other. Furthermore, the connected TZPs are usually contacted on their shaft by oocyte microvilli. Mural granulosa cells were found to possess randomly oriented cytoplasmic projections that are strikingly similar to free-ended TZPs. We propose that granulosa cells use cytoplasmic projections to search for the oocyte, and cumulus cell differentiation results from a contact-mediated paracrine interaction with the oocyte.
The sequences near Chi sites allow the RecBCD pathway to avoid genomic rearrangements
Authors: Li Chastity , Danilowicz Claudia , Tashjian Tommy F. , Godoy Veronica G. , Prévost Chantal , Prentiss Mara 
Published: June 2018

AbstractBacterial recombinational repair is initiated by RecBCD, which creates a 3′ single-stranded DNA (ssDNA) tail on each side of a double strand break (DSB). Each tail terminates in a Chi site sequence that is usually distant from the break. Once an ssDNA-RecA filament forms on a tail, the tail searches for homologous double-stranded DNA (dsDNA) to use as template for DSB repair. Here we show that the nucleoprotein filaments rarely trigger sufficient synthesis to form an irreversible repair unless a long strand exchange product forms at the 3′ end of the filament. Our experimental data and modeling suggest that terminating both filaments with Chi sites allows recombinational repair to strongly suppress fatal genomic rearrangements resulting from mistakenly joining different copies of a repeated sequence after a DSB has occurred within a repeat. Taken together our evidence highlights cellular safe fail mechanisms that bacteria use to avoid potentially lethal situations.
Effects of Pathological Mutations on the Prion-Like Polymerisation of MyD88
Authors: O’Carroll Ailís , Chauvin Brieuc , Brown James , Meagher Ava , Coyle Joanne , Hunter Dominic , Bhumkhar Akshay , Ve Thomas , Kobe Bostjan , Sierecki Emma , Gambin Yann 
Published: June 2018

AbstractA novel concept has emerged whereby the higher-order self-assembly of proteins provides a simple and robust mechanism for signal amplification. This appears to be a universal signalling mechanism within the innate immune system, where the recognition of pathogens or danger-associated molecular patterns need to trigger a strong, binary response within cells. Previously, multiple structural studies have been limited to single domains, expressed and assembled at high protein concentrations. We therefore set out to develop new in vitro strategies to characterise the behaviour of full-length proteins at physiological levels. In this study we focus on the adaptor protein MyD88, which contains two domains with different self-assembly properties: a TIR domain that can polymerise similarly to the TIR domain of Mal, and a Death Domain that has been shown to oligomerise with helical symmetry in the Myddosome complex. To visualize the behaviour of full-length MyD88 without purification steps, we use single-molecule fluorescence coupled to eukaryotic cell-free protein expression. These experiments demonstrate that at low protein concentration, only full-length MyD88 forms prion-like polymers. We also demonstrate that the metastability of MyD88 polymerisation creates the perfect binary response required in innate signalling: the system is silenced at normal concentrations but upstream signalling creates a “seed” that triggers polymerisation and amplification of the response. These findings pushed us to re-interpret the role of polymerisation in MyD88-related diseases and we studied the impact of disease-associated point mutations L93P, R196C and L252P/L265P at the molecular level. We discovered that all mutations completely block the ability of MyD88 to polymerise. We also confirm that L252P, a gain-of-function mutation, allows the MyD88 mutant to form extremely stable oligomers, even when expressed at low nanomolar concentrations. Thus, our results are consistent with and greatly add to the findings on the Myddosomes digital ‘all-or-none’ responses and the behaviour of the oncogenic mutation of MyD88.
Epitope - based peptide vaccine againstFructose-bisphosphate aldolase (FBA)ofMadurella mycetomatisusing immunoinformatics approaches
Authors: Mohammed Arwa A. , ALnaby Ayman M. H. , Sabeel Solima M. , AbdElmarouf Fagr M. , Dirar Amina I. , Ali Mostafa M. , Khandgawi Mustafa A. , Yousif Abdelhameed M. , Abdulgadir Eman M. , Sabahalkhair Magdi A. , Abbas Ayman E. , Hassan Mohammed A. 
Published: June 2018

AbstractBackgroundMycetoma is a distinct flesh eating and destructive neglected tropical disease. It is endemic in many tropical and subtropical countries. Mycetoma is caused by bacterial infections (actinomycetoma) such as Streptomyces somaliensis and Nocardiae or true fungi (eumycetoma) such as Madurella mycetomatis. Until date, treatments fail to cure the infection and the available marketed drugs are expensive and toxic upon prolonged usage. Moreover, no vaccine was prepared yet against mycetoma.The aimof this study is to predict effective epitope-based vaccine against fructose-bisphosphate aldolase enzymes of M. mycetomatis using immunoinformatics approaches.Methods and MaterialsFructose-bisphosphate aldolase ofMadurella mycetomatisSequence was retrieved from NCBI. Different prediction tools were used to analyze the nominee’s epitopes in Immune Epitope Database for B-cell, T-cell MHC class II & I. Then the proposed peptides were docked using Autodock 4.0 software program.Results and ConclusionsThe proposed and promising peptides KYLQ shows a potent binding affinity to B-cell, FEYARKHAF with a very strong binding affinity to MHC1 alleles and FFKEHGVPL that show a very strong binding affinity to MHC11and MHC1 alleles. This indicates a strong potential to formulate a new vaccine, especially with the peptide FFKEHGVPL which is likely to be the first proposed epitope-based vaccine against Fructose-bisphosphate aldolase of Madurella mycetomatis. This study recommends an in-vivo assessment for the most promising peptides especially FFKEHGVPL.
Liquid biopsy for infectious diseases: Sequencing of cell-free plasma to detect pathogen DNA in patients with invasive fungal disease
Authors: Hong David K. , Blauwkamp Timothy A. , Kertesz Mickey , Bercovici Sivan , Truong Cynthia , Banaei Niaz 
Published: June 2018

AbstractDiagnosis of life-threatening deep-seated infections currently requires invasive sampling of the infected tissue to provide a microbiologic diagnosis. These procedures can lead to high morbidity in patients and add to healthcare costs. Here we describe a novel next-generation sequencing assay that was used to detect pathogen-derived cell-free DNA in peripheral blood of patients with biopsy-proven invasive fungal infections. The non-invasive nature of this approach could provide rapid, actionable treatment information for invasive fungal infections when a biopsy is not possible.
Communication and quorum sensing in non-living mimics of eukaryotic cells
Authors: Niederholtmeyer Henrike , Chaggan Cynthia , Devaraj Neal K. 
Published: June 2018

AbstractCells in tissues or biofilms communicate with one another through chemical and mechanical signals to coordinate collective behaviors. Non-living cell mimics provide simplified models of natural systems, however, it has remained challenging to implement communication capabilities comparable to living cells. Here we present a porous artificial cell-mimic containing a nucleus-like DNA-hydrogel compartment that is able to express and display proteins, and communicate with neighboring cell-mimics through diffusive protein signals. We show that communication between cell-mimics allows distribution of tasks, quorum sensing, and cellular differentiation according to local environment. Cell-mimics can be manufactured in large quantities, easily stored, chemically modified, and spatially organized into diffusively connected tissue-like arrangements, offering a means for studying communication in large ensembles of artificial cells.
Disturbance During Biofilm Community Succession Promotes Cooperation and Diversity
Authors: Stratford James P. , Hodgson Douglas M. , Beecroft Nelli J. , Smith Ann , Marchesi Julian R. , Avignone-Rossa Claudio 
Published: June 2018

AbstractDiversity-disturbance relationships have found widespread application in ecology, conservation and biodiversity management. In spite of their explanatory power, these conceptual frameworks have yet to be systematically applied to understanding succession in diverse microbial biofilms. Here we investigate community assembly in biofilms formed in replicate microbial bioelectrochemical systems using time-course sequencing of community 16S rRNA genes, corresponding to hundreds of operational taxonomic units (OTUs). For the first time we present a statistical model showing that a simple diversity-disturbance relationship can be used to explain dynamic changes in high diversity biofilm communities. This simple model reveals that succession in these systems is guided towards either a low diversity, generalist-dominated biofilm or a high diversity, cooperative-specialist biofilm, depending on the level of endogenous disturbance measured within the community. The pattern observed shows remarkable symmetry with findings from macro-scale communities such as grasslands, forests and coral reefs.
Recent secondary contacts, background selection and variable recombination rates shape genomic diversity in the model speciesAnolis carolinensis
Authors: Bourgeois Yann , Ruggiero Robert P. , Manthey Joseph D. , Boissinot Stéphane 
Published: June 2018

AbstractGaining a better understanding on how selection and neutral processes affect genomic diversity is essential to gain better insights into the mechanisms driving adaptation and speciation. However, the evolutionary processes affecting variation at a genomic scale have not been investigated in most vertebrate lineages. Previous studies have been limited to a small number of model species, mostly mammals, and no studies have investigated genomic variation in non avian reptiles. Here we present the first population genomics survey using whole genome re sequencing in the green anole (Anolis carolinensis). This species has emerged as a model for the study of genomic evolution in squamates. We quantified how demography, recombination and selection have led to the current genetic diversity of the green anole by using whole-genome resequencing of five genetic clusters covering the entire species range. The differentiation of green anole’s populations is consistent with a northward expansion from South Florida followed by genetic isolation and subsequent gene flow among adjacent genetic clusters. Dispersal out-of-Florida was accompanied by a drastic population bottleneck followed by a rapid population expansion. This event was accompanied by male-biased dispersal and/or selective sweeps on the X chromosome. We show that the combined effect of background selection and recombination rates is the main contributor to the genomic landscape of differentiation in the anole genome. We further demonstrate that recombination rates are positively correlated with GC content at third codon position (GC3) and confirm the importance of biased gene conversion in shaping genome wide patterns of diversity in reptiles.
Spatial distribution of benthic macrofauna in the Central Arctic Ocean
Authors: Vedenin Andrey , Gusky Manuela , Gebruk Andrey , Kremenetskaia Antonina , Rybakova Elena , Boetius Antje 
Published: June 2018

AbstractPermanent ice coverage and the low primary production in the mostly ice-covered Central Arctic ocean basins result in significantly lower biomass and density of macrobenthos in the abyssal plains compared to the continental slopes. However, little is known on bathymetric and regional effects on macrobenthos diversity. This study synthesizes new and available macrobenthos data to provide a baseline for future studies of the effects of Arctic change on macrofauna community composition in the Arctic basins. Samples taken during three expeditions (in 1993, 2012 and 2015) at 37 stations on the slope of the Barents and Laptev Seas and in the abyssal of the Nansen and Amundsen Basins in the depth range from 38 m to 4381 m were used for a quantitative analysis of species composition, abundance and biomass. Benthic communities clustered in five depth ranges across the slope and basin. A parabolic pattern of species diversity change with depth was found, with the diversity maximum for macrofauna at the shelf edge at depths of 100-300 m. This deviates from the typical species richness peak at mid-slope depths of 1500-3000 m in temperate oceans. Due to the limited availability of standardized benthos data, it remains difficult to assess the massive sea ice retreat observed in the past decade has affected benthic community composition. The polychaeteYmerana pteropodaand the bryozoanNolellasp. were found for the first time in the deep Nansen and Amundsen Basins, as a potential first sign of increasing productivity and carbon flux with the thinning ice.
ComPath: An ecosystem for exploring, analyzing, and curating mappings across pathway databases
Authors: Domingo-Fernández Daniel , Hoyt Charles Tapley , Bobis-Álvarez Carlos , Marín-Llaó Josep , Hofmann-Apitius Martin 
Published: June 2018

AbstractAlthough pathways are widely used for the analysis and representation of biological systems, their lack of clear boundaries, their dispersion across numerous databases, and the lack of interoperability impedes the evaluation of the coverage, agreements, and discrepancies between them. Here, we present ComPath, an ecosystem that supports curation of pathway mappings between databases and fosters the exploration of pathway knowledge through several novel visualizations. We have curated mappings between three of the major pathway databases and present a case study focusing on Parkinson’s disease that illustrates how ComPath can generate new biological insights by identifying pathway modules, clusters, and cross-talks with these mappings. The ComPath source code and resources are available at https://github.com/ComPath and the web application can be accessed at http://compath.scai.fraunhofer.de/.
Does forecasting have all the answers? A case study of elections in India
Authors: Dhagarra Devendra , Goswami Mohit , Sarma PRS 
Published: June 2018

Subject area
Forecasting.

Study level/applicability
The case is intended for Postgraduate level management students.

Case overview
The purpose of this case study is to explain various forecasting techniques, their applicability and the importance of forecasting to the students. This case also explains the management situations where the application of one technique may not be sufficient, thereby explaining the importance of simultaneous usage of qualitative and quantitative techniques for making crucial decisions. The case is focused on the district of Etah of the state of Uttar Pradesh in India. The real-life situation of elections in this district of an Indian state has been taken to explain the critical nature of forecasting accuracy in a management situation where the manager has only one chance to execute his project. Discussion in this case is limited to explaining various techniques available for forecasting and their applications and does not provide a solution to a management problem.

Expected learning outcomes
The students are expected to understand various forecasting methods and the managerial situations where these can be applied. The case also explains situations where it becomes extremely important to have fairly accurate estimates of future requirements and the application of one technique may not be sufficient, thereby explaining the importance of simultaneous usage of qualitative and quantitative techniques for making crucial decisions.

Supplementary materials
Teaching Notes are available for educators only. Please contact your library to gain login details or email support@emeraldinsight.com to request teaching notes.

Subject code
CSS 9: Operations and Logistics.
The paradoxes of informalizing street trade in the Latin American city
Authors: Linares Lissette Aliaga 
Published: June 2018

Purpose
The purpose of this paper is to challenge the default portrayal of street trade as an informal occupation and spatial practice, by examining comparatively the changes in the regulatory frameworks of two politically distinct city administrations in Latin America since the introduction of the informal economy debate.

Design/methodology/approach
This paper draws from a comparative case study design to synthesize evidence from historical administrative records, secondary research and materials from a two-year fieldwork carried out in Lima and Bogotá in 2008 and 2009.

Findings
The author argues that the incorporation of the informal economy framework into local governments’ policymaking has reframed street trade as a subject of policy. Since the 1970s, the author traces a shift from worker-centered initiatives, through the deregulation of street trade, to entrepreneurial-centered approaches. Nowadays, both, Lima’s neoliberal governance focusing on “formalizing” and Bogotá’s socialist/progressive governance aiming at “upgrading” street trade respond more explicitly to distinct assessments about the informal economy – legalist and dualist, respectively. Yet, both cities converge in that the closer street trade is perceived as an informal occupation; the more likely policy initiatives decouple the right to work from the right to access public space, spurring more marginal forms of street vending.

Originality/value
Even though the informal economy framework has helped to draw attention to important policy issues locally, nationally and internationally, this paper calls for a critical revision of such framing at the local level to allow for inclusive urban governance.
The value of human capital within Canadian business schools
Authors: Velayutham Ajantha , Rahman Asheq Razaur 
Published: June 2018

Purpose
The purpose of this paper is to empirically investigate whether an individual’s knowledge, skills and capabilities (human capital) are reflected in their compensation.

Design/methodology/approach
Data are drawn from university academics in the Province of Ontario, Canada, earning more than CAD$100,000 per annum. Data on academics human capital are drawn from Research Gate. The authors construct a regression analysis to examine the relationship between human capital and salary.

Findings
The analyses performed indicates a positive association between academic human capital and academic salaries.

Research limitations/implications
This study is limited in that it measures an academic’s human capital solely through their research outputs as opposed to also considering their teaching outputs. Continuing research needs to be conducted in different country contexts and using negative proxies of human capital.

Practical implications
This study will create awareness about the value of human capital and its contribution towards improving organisational structural capital.

Social implications
The study contributes to the literature on human capital in accounting and business by focussing on the economic relevance of individual level human capital.

Originality/value
The study contributes to the literature on human capital in accounting and business by focussing on the economic relevance of individual level human capital. It will help create awareness of the importance of valuing human capital at the individual level.