bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of two descriptions of heterogeneity used in modelling plants dynamics
Authors: Droz Michel , Pękalski Andrzej 
Published: September 2016

AbstractWe analyse the role played by two different approaches of spatial heterogeneity in theoretical models of annual plants dynamics. The first approach is called quasi-continuous gradient in which one type of resource is changing gradually along the gradient line. In the second one, called the patches approach, part of the habitat is covered by patches and the resource has a different value in each patch. We show that when the spatial heterogeneity of the habitat is small, the two approaches yield the same average number of surviving species, even if a small number of patches is used. In a strong heterogeneity it takes many patches to get similar results as in the gradient case. The difference between the gradient and patchy description of the spatial heterogeneity increases with the number of species present in the system. We have also shown that even when the average number of surviving species is the same, the abundances of species are ordered in a different way, like different species are the dominant ones. The conclusion of this paper is that modelling spatial heterogeneity in a system of plants is not a simple task. Special care is needed when the heterogeneity of the habitat is large, since then depending of the choice of a method, some predictions may differ significantly, making the model non-robust. Therefore the type of theoretical approach must closely match the modelled ecosystem.
Ripping RNA by Force using Gaussian Network Models
Authors: Hyeon Changbong , Thirumalai D. 
Published: September 2016

AbstractUsing force as a probe to map the folding landscapes of RNA molecules has become a reality thanks to major advances in single molecule pulling experiments. Although the unfolding pathways under tension are complicated to predict studies in the context of proteins have shown that topology plays is the major determinant of the unfolding landscapes. By building on this finding we study the responses of RNA molecules to force by adapting Gaussian network model (GNM) that represents RNAs using a bead-spring network with isotropic interactions. Cross-correlation matrices of residue fluctuations, which are analytically calculated using GNM even upon application of mechanical force, show distinct allosteric communication as RNAs rupture. The model is used to calculate the force-extension curves at full thermodynamic equilibrium, and the corresponding unfolding pathways of four RNA molecules subject to a quasi-statically increased force. Our study finds that the analysis using GNM captures qualitatively the unfolding pathway ofT. ribozyme elucidated by the optical tweezers measurement. However, the simple model is not sufficient to capture subtle features, such as bifurcation in the unfolding pathways or the ion effects, in the forced-unfolding of RNAs.
Collateral sensitivity networks reveal evolutionary instability and novel treatment strategies in ALK mutated non-small cell lung cancer
Authors: Dhawan Andrew , Nichol Daniel , Kinose Fumi , Abazeed Mohamed E. , Marusyk Andriy , Haura Eric B. , Scott Jacob G. 
Published: September 2016

AbstractDrug resistance remains an elusive problem in cancer therapy, particularly with novel targeted therapy approaches. Much work is currently focused upon the development of an increasing arsenal of targeted therapies, towards oncogenic driver genes such as ALK-EML4, to overcome the inevitable resistance that develops as therapies are continued over time. The current clinical paradigm after failure of first line ALK TKI is to administer another drug in the same class. As to which drug however, the answer is uncertain, as clinical evidence is lacking. To address this shortcoming, we evolved resistance in an ALK rearranged non-small cell lung cancer line (H3122) to a panel of 4 ALK tyrosine kinase in-hibitors used in clinic, and performed a collateral sensitivity analysis to each of the other drugs. We found that all of the ALK inhibitor resistant cell lines displayed a significant cross-resistance to all other ALK inhibitors. To test for the stability of the resistance phenotypes, we evaluated the ALK-inhibitor sensitivities after drug holidays of varying length (1, 3, 7, 14, and 21 days). We found the resistance patterns to be stochastic and dynamic, with few conserved patterns. This unpredictability led us to an expanded search for treatment options for resistant cells. In this expansion, we tested a panel of 6 more anti-cancer agents for collateral sensitivity among the resistant cells, uncovering a multitude of possibilities for further treatment, including cross-sensitivity to several standard cytotoxic therapies as well as the HSP-90 inhibitors. Taken together, these results imply that resistance to targeted therapy in non-small cell lung cancer is truly a moving target; but also one where there are many opportunities to re-establish sensitivities where there was once resistance.
Multiple factors influence population sex ratios in the Mojave Desert mossSyntrichia caninervis
Authors: Baughman Jenna T. , Payton Adam C. , Paasch Amber E. , Fisher Kirsten M. , McDaniel Stuart F. 
Published: September 2016

ABSTRACTPremise of research:Natural populations of many mosses appear highly female-biased based on the presence of reproductive structures. This bias could be caused by increased male mortality, lower male growth rate, or a higher threshold for achieving sexual maturity in males. Here we test these hypotheses using samples from two populations of the Mojave Desert mossSyntrichia caninervis.Methods:We used double digest restriction-site associated DNA (RAD) sequencing to identify candidate sex-associated loci in a panel of sex-expressing plants. Next, we used putative sex-associated markers to identify the sex of individuals without sex structures.Key results:We found an 18:1 phenotypic female: male sex ratio in the higher elevation site (Wrightwood), and no sex expression at the low elevation site (Phelan). In contrast, based on genetic data we found a 2:1 female bias in the Wrightwood site and only females in the Phelan site. The area occupied by male and female genets was indistinguishable.Conclusions:These data suggest that both differential mortality and sexual dimorphism in thresholds for sex expression likely contribute to population genetic and phenotypic sex ratio biases, and that phenotypic sex expression alone fails to capture the extent of actual sex ratio bias present in natural populations ofS. caninervis.
Determinants and patterns of the endangered brown bearUrsus arctoshabitat use in the French Pyrenees revealed by occupancy modeling
Authors: Piédallu Blaise , Quenette Pierre-Yves , Bombillon Nicolas , Gastineau Adrienne , Miquel Christian , Gimenez Olivier 
Published: September 2016

AbstractThe Pyrenean brown bear (Ursus arctos) in the mountainous border between France and Spain is one of the smallest and most endangered populations of large carnivores in Europe. Here, we aimed at assessing trends in brown bear habitat use in the Pyrenees and determining the underlying environmental and anthropogenic drivers. Using detection/non-detection data collected between 2008 and 2014 through non-invasive methods, we developed occupancy models to investigate the dynamic of brown bear habitat use in the Pyrenees accounting for local colonization and extinction processes. First, we found two non-connected occupancy cores, one located in the West and another in the Center of the Pyrenees, with an overall significant decrease in habitat use between 2008 and 2014. Second, we showed a negative correlation between human density and bear occupancy in agreement with previous studies on brown bear habitat suitability. Our results confirm the critically endangered status of the Pyrenean population of brown bears.
Massive influence of DNA isolation and library preparation approaches on palaeogenomic sequencing data
Authors: Barlow Axel , Fortes Gloria G. , Dalén Love , Pinhasi Ron , Gasparyan Boris , Rabeder Gernot , Frischauf Christine , Paijmans Johanna L.A. , Hofreiter Michael 
Published: September 2016

ABSTRACTThe ability to access genomic information from ancient samples has provided many important biological insights. Generating such palaeogenomic data requires specialised methodologies, and a variety of procedures for all stages of sample preparation have been proposed. However, the specific effects and biases introduced by alternative laboratory procedures is insufficiently understood. Here, we investigate the effects of three DNA isolation and two library preparation protocols on palaeogenomic data obtained from four Pleistocene subfossil bones. We find that alternative methodologies can significantly and substantially affect total DNA yield, the mean length and length distribution of recovered fragments, nucleotide composition, and the total amount of usable data generated. Furthermore, we also detect significant interaction effects between these stages of sample preparation on many of these factors. Effects and biases introduced in the laboratory can be sufficient to confound estimates of DNA degradation, sample authenticity and genomic GC content, and likely also estimates of genetic diversity and population structure. Future palaeogenomic studies need to carefully consider the effects of laboratory procedures during both experimental design and data analysis, particularly when studies involve multiple datasets generated using a mixture of methodologies.
Cortical dynamics of saccade-target selection during free-viewing of natural scenes
Authors: Henriksson Linda , Ölander Kaisu , Hari Riitta 
Published: September 2016

ABSTRACTNatural visual behaviour entails explorative eye movements, saccades, that bring different parts of a visual scene into the central vision. The neural processes guiding the selection of saccade targets are still largely unknown. Therefore, in this study, we tracked with magnetoencephalography (MEG) cortical dynamics of viewers who were freely exploring novel natural scenes. Overall, the viewers were largely consistent in their gaze behaviour, especially if the scene contained any persons. We took a fresh approach to relate the eye-gaze data to the MEG signals by characterizing dynamic cortical representations by means of representational distance matrices. Specifically, we compared the representational distances between the stimuli in the evoked MEG responses with predictions based (1) on the low-level visual similarity of the stimuli (as visually more similar stimuli evoke more similar responses in early visual areas) and (2) on the eye-gaze data. At 50–75 ms after the scene onset, the similarity of the occipital MEG patterns correlated with the low-level visual similarity of the scenes, and already at 75–100 ms the visual features attracting the first saccades predicted the similarity of the right parieto-occipital MEG responses. Thereafter, at 100–125 ms, the landing positions of the upcoming saccades explained MEG responses. These results indicate that MEG signals contain signatures of the rapid processing of natural visual scenes as well as of the initiation of the first saccades, with the processing of the saccade target preceding the processing of the landing position of the upcoming saccade.SIGNIFICANCE STATEMENTHumans naturally make eye movements to bring different parts of a visual scene to the fovea where our visual acuity is the best. Tracking of eye gaze can reveal how we make inferences about the content of a scene by looking at different objects, or which visual cues automatically attract our attention and gaze. The brain dynamics governing natural gaze behaviour is still largely unknown. Here we suggest a novel approach to relate eye-tracking results with brain activity, as measured with magnetoencephalography (MEG), and demonstrate signatures of natural gaze behaviour in the MEG data already before the eye movements occur.
Investigating the potential of opportunistic sighting data to inform wildlife conservation strategies
Authors: Tenan Simone , Pedrini Paolo , Bragalanti Natalia , Groff Claudio , Sutherland Chris 
Published: September 2016

ABSTRACTAbundance and space use are key population-level parameters used to inform management and conservation decisions of rare and elusive species, for which monitoring resources can be limited, potentially affecting quality of model-based inference. Recently-developed methods that integrate multiple data sources arising from the same ecological process have typically been focused on data from well-defined sampling protocols, i.e. structured data sets. Despite a rapid increase in availability of large datasets, the value of unstructured or opportunistic data to improve inference about spatial ecological processes is, however, unclear. Using spatial capture-recapture (SCR) methods, we jointly analyze opportunistic recovery of biological samples, traditional SCR data resulting from systematic sampling of hair traps and rub trees, and satellite telemetry data, collected on a reintroduced brown bear population in the central Alps. We compared the precision of sex-specific estimates of density and space use derived from models using combinations of data sources ranging from traditional SCR to a fully integrated SCR model that includes both telemetry and opportunistic data. Estimates of density and space use were more precise when unstructured data were added compared to estimates from a classical SCR model. Our results demonstrate that citizen science data lend itself naturally to integration with in the SCR framework and highlight the value of opportunistic data for improving inference about space use, and in turn, of abundance and density. When individual identity and location can be obtained from opportunistic observations, such data are informative about space use and thus have the potential to improve estimates of movement and density using SCR methods. This is particularly relevant in studies of rare or elusive species, where the amount of SCR encounters is usually small, but also budget restrictions and the difficulty of collaring animals limit the number of individuals for which telemetry information is available. Spatially-referenced opportunistic data thus potentially increase both the geographic extent of a study and the number of individuals with available spatial information, providing an improved understanding of how individuals are distributed and how they use space – fundamental components for calibrating conservation management actions.
Genome‑wide identification and characterization of Transcription Factors of Basic Leucine Zipper Family inMalus domestica
Authors: Zhang Zhengrong , Cui Haoran , Xing Shanshan , Liu Xin , Chen Xuesen , Wang Xiaoyun 
Published: September 2016

AbstractBasic leucine zipper proteins (bZIP) contain a basic DNA-binding region and a leucine zipper region, acting as transcriptional factors in regulation of gene expression exclusively in eukaryotes. In this investigation, total 116 bZIP members were identified in apple genome and mapped on all 17 chromosomes with various densities asM.bZIPs. All these members were divided into six groups according to the phylogenetic relationship combining with bZIPs from rice andArabidopsis. Investigating gene structure ofM.bZIPs, five splicing patterns of intron were found in the DNA-binging region with no splicing position and splicing positions at different nucleotide of codons or different positions. Analyzing of protein structure ofM.bZIPs, twenty-five motifs were identified with certain characteristic in different phylogenetic groups. To predict dimerization of leucine zipper region, the key positions of amino acid in heptad(s) were investigated. The results showed that mostM.bZIPs may form hetero-dimer or homo-dimer and someM.bZIPs may form both. Expression experiment revealed thatM.bZIP genes have organ-specific expression and widely expressed in flowers, leaves, and fruits. To investigate the response ofM.bZIPs to abiotic stresses, the promoter sequences of randomly selectedM.bZIP genes were analyzed.Cis-acting elements related to multiple stresses were found existing widely in promoter sequences. Quantitative real-time PCR results further demonstrated that the expression of someM.bZIP genes were quite sensitive to exogenous abscisic acid and osmotic treatments.
Low-frequency cortical oscillations are modulated by temporal prediction and temporal error coding
Authors: Barne Louise Catheryne , Claessens Peter Maurice Erna , Reyes Marcelo Bussotti , Caetano Marcelo Salvador , Cravo André Mascioli 
Published: September 2016

AbstractMonitoring and updating temporal predictions are critical abilities for adaptive behavior. Here, we investigated whether neural oscillations are related to violation and updating of temporal predictions. Human participants performed an experiment in which they had to generate a target at an expected time point, by pressing a button while taking into account a variable delay between the act and the stimulus occurrence. Our behavioral results showed that participants quickly adapted their temporal predictions in face of an error. Concurrent electrophysiological (EEG) data showed that temporal errors elicited markers that are classically related to error coding. Furthermore, intertrial phase coherence of frontal theta oscillations was modulated by error magnitude, possibly indexing the degree of surprise. Finally, we found that delta phase at stimulus onset was correlated with future behavioral adjustments. Together, our findings suggest that low frequency oscillations play a key role in monitoring and in updating temporal predictions.
Expression biomarkers used for the selective breeding of complex polygenic traits
Authors: Guarna M. Marta , Hoover Shelley E. , Huxter Elizabeth , Higo Heather , Moon Kyung-Mee , Domanski Dominik , Bixby Miriam E.F. , Melathopoulos Andony P. , Ibrahim Abdullah , Peirson Michael , Desai Suresh , Micholson Derek , White Rick , Borchers Christoph H. , Currie Robert W. , Pernal Stephen F. , Foster Leonard J. 
Published: September 2016

AbstractWe present a novel way to select for highly polygenic traits. For millennia, humans have used observable phenotypes to selectively breed stronger or more productive livestock and crops. Selection on genotype, using single-nucleotide polymorphisms (SNPs) and quantitative trait loci (QTLs), is also now applied broadly in livestock breeding programs; however, selection on protein or mRNA expression markers have not been proved useful yet. Here we demonstrate the utility of protein markers to select for disease-resistant behaviour in the European honey bees (Apis melliferaL.). Robust, mechanistically-linked protein expression markers, by integrating cis and trans effects from many genomic loci, may overcome limitations of genomic markers to allow for selection. After three generations of selection, the resulting stock performed as well or better than bees selected using phenotype–based assessment of this trait, when challenged with disease. This is the first demonstration of the efficacy of protein markers for selective breeding in any agricultural species, plant or animal.Significance statementThe honey bee has been in the news a lot recently, largely because of world-wide die-offs due to the parasitic Varroa mite, which is becoming resistant to the chemical controls the bee industry uses. In this study, we show that robust expression biomarkers of a disease-resistance trait can be used, in an out-bred population, to select for that trait. After three generations of selection, the resulting stock performed as well or better than bees selected using the phenotypic best method for assessing this trait when challenged with disease. This is the first demonstration of an expression marker for selective breeding in any agricultural species, plant or animal. This also represents a completely novel way to select for highly polygenic traits.
Managing multiple logics in partnerships for scaling social innovation
Authors: Voltan Annika , De Fuentes Claudia 
Published: September 2016

Purpose
The purpose of this paper is to contribute to the field of social innovation by examining institutional logics at the level of inter- and intra-organizational partnerships for scaling impact.

Design/methodology/approach
The authors use a set of case studies from the Stanford Social Innovation Review to analyze success in scaling social innovations applying the logic compatibility-centrality matrix proposed by Besharov and Smith (2014), which aims to reveal the potential for conflict in organizations based on the diversity of logics present and the degree to which they are compatible with each other.

Findings
The findings shed insight on how individuals and organizations are able to manage logic multiplicity in the context of partnerships for scaling social innovation.

Originality/value
The authors build on recent work that recognizes logic multiplicity in social enterprises resulting from their hybrid nature, and the authors add to the existing debate by introducing to the discussion contributions from cognitive theory that help explain why organizational cultures evolve and scale out the way they do.
Feature fit
Authors: Gattol Valentin , Sääksjärvi Maria , Gill Tripat , Schoormans Jan 
Published: September 2016

Purpose
Previous research in the context of feature fit has examined the effects of congruence (i.e. more specifically, the extent to which a new feature and the product are similar in the hedonic-utilitarian benefits they provide to consumers). The purpose of this paper is to examine a second dimension of feature fit: complementarity (i.e. the extent to which a new feature is related and contributing to the main functionality of the product).

Design/methodology/approach
The role of feature fit is examined in two experimental studies (n=593) in the context of feature additions, and also for feature deletions.

Findings
The results showed that complementarity adds value to a product as an additional dimension of feature fit beyond congruence, complementarity matters more for a hedonic than for a utilitarian product, and complementarity can compensate for lack of congruence.

Originality/value
For a product developer, adding new features to a product offers an array of choices in terms of what feature(s) to include. Although having a large pool of potential features to choose from is attractive it can also prove problematic, as products may become overly complex and features do not fit well together. The results demonstrate the importance of both congruence and complementarity as predictors of feature fit when features are added to or deleted from products.