bluuebunny/crossref_metadata_2025_split huggingface dataset:
Habitat preference of an herbivore shapes the habitat distribution of its host plant
Authors: Alexandre Nicolas M. , Humphrey Parris T. , Gloss Andrew D. , Lee Jimmy , Frazier Joseph , Affeldt Henry A. , Whiteman Noah K. 
Published: June 2017

AbstractPlant distributions can be limited by habitat-biased herbivory, but the proximate causes of such biases are rarely known. Distinguishing plant-centric from herbivore-centric mechanisms driving differential herbivory between habitats is difficult without experimental manipulation of both plants and herbivores. Here we tested alternative hypotheses driving habitat-biased herbivory in bittercress (Cardamine cordifolia), which is more abundant under shade of shrubs and trees (shade) than in nearby meadows (sun) where herbivory is intense from the specialist flyScaptomyza nigrita. This system has served as a textbook example of habitat-biased herbivory driving a plant’s distribution across an ecotone, but the proximate mechanisms underlying differential herbivory are still unclear. First, we found that higherS. nigritaherbivory in sun habitats contrasts sharply with their preference to attack plants from shade habitats in laboratory choice experiments. Second,S. nigritastrongly preferred leaves in simulated sun over simulated shade habitats, regardless of plant source habitat. Thus, herbivore preference for brighter, warmer habitats overrides their preference for more palatable shade plants. This promotes the sun-biased herbivore pressure that drives the distribution of bittercress into shade habitats.
Engagement of spinal- vs prefrontal-projecting locus coeruleus neurons parses analgesia from aversion & anxiety in rats
Authors: Hirschberg Stefan , Li Yong , Randall Andrew , Kremer Eric J , Pickering Anthony E 
Published: June 2017

ABSTRACTThe locus coeruleus (LC) projects throughout the brain and spinal cord and is the major source of central noradrenaline. It remains unclear whether the LC acts functionally as a single global effector or as discrete modules. Specifically, while spinal-projections from LC neurons can exert analgesic actions, it is not known whether they can act independently of ascending LC projections. Using viral vectors taken up at axon terminals, we expressed chemogenetic actuators selectively in LC neurons with spinal (LC:SC) or prefrontal cortex (LC:PFC) projections. Activation of theLC:SCmodule produced robust, lateralised analgesia while activation ofLC:PFCproduced aversion. In a neuropathic pain model,LC:SCactivation reduced hind-limb sensitization and induced conditioned place preference. By contrast, activation ofLC:PFCexacerbated spontaneous pain, produced aversion and increased anxiety-like behaviour. This independent, contrasting modulation of pain-related behaviours mediated by distinct noradrenergic modules provides evidence for a discrete functional organisation of the LC.
Replacing reprogramming factors with antibodies selected from autocrine antibody libraries
Authors: Blanchard Joel W. , Xie Jia , El-Mecharrafie Nadja , Gross Simon , Lee Sohyon , Lerner Richard A. , Baldwin Kristin K. 
Published: June 2017

SummarySignaling pathways initiated at the membrane establish and maintain cell fate during development and can be harnessed in the nucleus to generate induced pluripotent stem cells (iPSCs) from differentiated cells. Yet, the impact of extracellular signaling on reprogramming to pluripotency has not been systematically addressed. Here, we screen a lentiviral library encoding ˜100 million secreted and membrane-bound antibodies and identify multiple antibodies that can replaceSox2/c-MycorOct4during reprogramming. We show that one Sox2-replacing antibody initiates reprogramming by antagonizing the membrane-associated protein Basp1, thereby inducing nuclear factorsWT1andEsrrb/Lin28independent ofSox2. By successively manipulating this pathway we identify three new methods to generate iPSCs. This study expands current knowledge of reprogramming methods and mechanisms and establishes unbiased selection from autocrine antibody libraries as a powerful orthogonal platform to discover new biologics and pathways regulating pluripotency and cell fate.
Evolution with a seed bank: the population genetic consequences of microbial dormancy
Authors: Shoemaker WR , Lennon JT 
Published: June 2017

ABSTRACTDormancy is a bet-hedging strategy that allows organisms to persist through conditions that are sub-optimal for growth and reproduction by entering a reversible state of reduced metabolic activity. Dormancy allows a population to maintain a reservoir of genetic and phenotypic diversity (i.e., a seed bank) that can contribute to the long-term survival of a population. This strategy can be potentially adaptive and has long been of interest to ecologists and evolutionary biologists. However, comparatively little is known about how dormancy influences the fundamental evolutionary forces of genetic drift, mutation, selection, recombination, and gene flow. Here, we investigate how seed banks affect the processes underpinning evolution by reviewing existing theory, implementing novel simulations, and determining how and when dormancy can influence evolution as a population genetic process. We extend our analysis to examine how seed banks can alter macroevolutionary processes, including rates of speciation and extinction. Through the lens of population genetic theory, we can understand the extent that seed banks influence microbial evolutionary dynamics.
Scikit-ribo: Accurate estimation and robust modeling of translation dynamics at codon resolution
Authors: Fang Han , Huang Yi-Fei , Radhakrishnan Aditya , Siepel Adam , Lyon Gholson J. , Schatz Michael C. 
Published: June 2017

AbstractRibosome profiling (Riboseq) is a powerful technique for measuring protein translation, however, sampling errors and biological biases are prevalent and poorly understand. Addressing these issues, we present Scikit-ribo (https://github.com/hanfang/scikit-ribo), the first open-source software for accurate genome-wide A-site prediction and translation efficiency (TE) estimation from Riboseq and RNAseq data. Scikit-ribo accurately identifies A-site locations and reproduces codon elongation rates using several digestion protocols (r= 0.99). Next we show commonly used RPKM-derived TE estimation is prone to biases, especially for low-abundance genes. Scikit-ribo introduces a codon-level generalized linear model with ridge penalty that correctly estimates TE while accommodating variable codon elongation rates and mRNA secondary structure. This corrects the TE errors for over 2000 genes inS. cerevisiae, which we validate using mass spectrometry of protein abundances (r= 0.81) and allows us to determine the Kozak-like sequence directly from Riboseq. We conclude with an analysis of coverage requirements needed for robust codon-level analysis, and quantify the artifacts that can occur from cycloheximide treatment.
Is it possible to keep the exoskeleton of the crabCallinectes ornatussoft for several days?
Authors: Hungria Diogo Barbalho , Teixeira da Silva Ubiratã de Assis , Pereira Leandro Ângelo , Cella-Ribeiro Ariana , Ostrensky Antonio 
Published: June 2017

AbstractSoft-shell crab is considered a gastronomic delicacy, reaching high values in the international market. The process of hardening of the crab’s exoskeleton after moulting takes approximately two days to complete; however, the duration for which the shell remains at the consistency of high commercial value is only 3 hours on average. After this period, the shell assumes a consistency classified as “paper”, later becoming “hard” again. The goal of this work was to evaluate the use of the crabs themselves to alter the chemical characteristics of the water and thereby increase the amount of time during which they can be marketed as “soft-shell crab”. In this work, 241 individuals ofCallinectes ornatuswere used in two experiments. In the first experiment, the animals were maintained in a collective system with filtration and partial daily water renewal. In the second experiment, the crabs were maintained in a collective system with filtration but no water renewal. In Experiment 1, the chemical characteristics of the water remained unchanged over time (p > 0.05), and the median time to hardening of the exoskeleton to the paper consistency after moulting was 3 hours. Over the course of Experiment 2, there was a significant reduction (p < 0.05) in pH and significant increases in the ammonia and nitrite concentrations. When moulting occurred in water with a pH below 7.3 and total ammonia concentrations above 6.0 mg/L, the crabs’ shells did not harden, and it was possible to keep them soft for up to 5 days.
GrapHi-C: Graph-based visualization of Hi-C Datasets
Authors: MacKay Kimberly , Kusalik Anthony , Eskiw Christopher H. 
Published: June 2017

AbstractBackgroundHi-C is a proximity-based ligation reaction used to detect regions of the genome that are close in 3D space (or “interacting”). Typically, results from Hi-C experiments (whole-genome contact maps) are visualized as heatmaps or Circos plots. While informative, these visualizations do not intuitively represent the complex organization and folding of the genome in 3D space, making the interpretation of the underlying 3D genomic organization difficult. Our objective was to utilize existing tools to generate a graph-based representation of a whole-genome contact map that leads to a more intuitive visualization.MethodologyWhole-genome contact maps were converted into graphs where each vertex represented a genomic region and each edge represented a detected or known interaction between two vertices. Three types of interactions were represented in the graph: linear, intra-chromosomal (cis-), and inter-chromosomal (trans-) interactions. Each edge had an associated weight related to the linear distance (Hi-C experimental resolution) or the associated interaction frequency from the contact map. Graphs were generated based on this representation scheme for whole-genome contact maps from a fission yeast dataset where yeast mutants were used to identify specific principles influencing genome organization (GEO accession: GSE56849). Graphs were visualized in Cytoscape with an edge-weighted spring embedded layout where vertices and linear interaction edges were coloured according to their corresponding chromosome.ResultsThe graph-based visualizations (compared to the equivalent heatmaps) more intuitively represented the effects of therad21mutant on genome organization. Specifically, the graph based visualizations clearly highlighted the loss of structural globules and a greater intermingling of chromosomes in the mutant strain when compared to the wild-type. The graph-based representation and visualization protocol developed here will aid in understanding the complex organization and folding of the genome.
Detecting repeated cancer evolution in human tumours from multi-region sequencing data
Authors: Caravagna Giulio , Giarratano Ylenia , Ramazzotti Daniele , Graham Trevor A , Sanguinetti Guido , Sottoriva Andrea 
Published: June 2017

AbstractCarcinogenesis is an evolutionary process driven by the accumulation of genomic aberrations. Recurrent sequences of genomic changes, both between and within patients, reflect repeated evolution that is valuable for anticipating cancer progression. Multi-region sequencing and phylogenetic analysis allow inference of the partial temporal order of genomic changes within a patient’s tumour. However, the inherent stochasticity of the evolutionary process makes phylogenetic trees from different patients appear very distinct, preventing the robust identification of recurrent evolutionary trajectories. Here we present a novel quantitative method based on a machine learning approach called Transfer Learning (TL) that allows overcoming the stochastic effects of cancer evolution and highlighting hidden recurrences in cancer patient cohorts. When applied to multi-region sequencing datasets from lung, breast and renal cancer (708 samples from 160 patients), our method detected repeated evolutionary trajectories that determine novel patient subgroups, which reproduce in large singlesample cohorts (n=2,641) and have prognostic value. Our method provides a novel patient classification measure that is grounded in the cancer evolution paradigm, and which reveals repeated evolution during tumorigenesis, with implications for our ability to anticipate malignant evolution.
Diffusion as a ruler: modeling kinesin diffusion as a length sensor for intraflagellar transport
Authors: Hendel Nathan L. , Thomson Matt , Marshall Wallace F. 
Published: June 2017

ABSTRACTAn important question in cell biology is whether cells are able to measure size, either whole cell size or organelle size. Perhaps cells have an internal chemical representation of size that can be used to precisely regulate growth, or perhaps size is just an accident that emerges due to constraint of nutrients. The eukaryotic flagellum is an ideal model for studying size sensing and control because its linear geometry makes it essentially one-dimensional, greatly simplifying mathematical modeling. The assembly of flagella is regulated by intraflagellar transport (IFT), in which kinesin motors carry cargo adaptors for flagellar proteins along the flagellum and then deposit them at the tip, lengthening the flagellum. The rate at which IFT motors are recruited to begin transport into the flagellum is anticorrelated with the flagellar length, implying some kind of communication between the base and the tip and possibly indicating that cells contain some mechanism for measuring flagellar length. Although it is possible to imagine many complex scenarios in which additional signaling molecules sense length and carry feedback signals to the cell body to control IFT, might the already-known components of the IFT system be sufficient to allow length dependence of IFT? Here, we investigate a model in which the anterograde kinesin motors unbind after cargo delivery, diffuse back to the base, and are subsequently reused to power entry of new IFT trains into the flagellum. By modeling such a system at three different levels of abstraction we are able to show that the diffusion time of the motors can in principle be sufficient to serve as a proxy for length measurement. In all three implementations, we found that the diffusion model can not only achieve a stable steady-state length without the addition of any other signaling molecules or pathways, but also is able to produce the anticorrelation between length and IFT recruitment rate that has been observed in quantitative imaging studies.
The impact of consumer-brand engagement on brand experience and behavioural intentions
Authors: Risitano Marcello , Romano Rosaria , Sorrentino Annarita , Quintano Michele 
Published: June 2017

Purpose
The purpose of this paper is to investigate the impact of consumer-brand engagement and brand experience on behavioural intentions (i.e. intent to re-purchase, willingness to accept brand extension, willingness to pay a premium price) in relation to food brands.

Design/methodology/approach
The authors propose a conceptual model comprising five latent variables and 26 manifest variables. A questionnaire with questions relating to pasta and coffee was given to an Italian consumer sample (n=400). The model was tested using structural equation modelling of the resulting data to examine the research hypotheses.

Findings
The empirical study confirms the predictive role of the two selected drivers of brand value. Both consumer-brand engagement and brand experience influenced behavioural intentions, but these brand constructs had different roles in the two product categories examined in the study, pasta and coffee.

Research limitations/implications
This study does have limitations. First, the generalisability of the findings should be considered. The study refers to only two product categories in a specific country. It would be interesting to investigate the issue of food brand engagement and brand experience in different countries, and to compare the results. Furthermore, it would be valuable to investigate the impact of brand engagement and brand experience in other product categories.

Practical implications
The results have an important implication for marketing managers: they should develop long-term and strong brand relationships. Such consumer engagement and/or experiential actions can be key competitive advantages for food companies.

Originality/value
The study provides empirical support for the effect of consumer-brand engagement and brand experience on consumers’ behavioural intentions in the food industry.
Willingness to pay for organic cotton
Authors: Nassivera Federico , Troiano Stefania , Marangon Francesco , Sillani Sandro , Markova Nencheva Iskra 
Published: June 2017

PurposeConsumers seem to be increasingly concerned about the environmental and social consequences of their purchases. For this reason, companies are involved in corporate social responsibility (CSR) strategies for their supply chain to responsibly manage the consumption of the environmental resources and to support sustainability. The purpose of this paper is to contribute to a better understanding of the Italian organic apparel consumer by investigating the importance of consumers’ attitudes towards CSR in agricultural products processing industries and their willingness to pay (WTP) for organic cotton clothing.Design/methodology/approachQuestionnaire data were gathered in Italy on a Likert scale. Questions focussed on WTP for organic cotton, with the aim to test consumer responsiveness to a CSR initiative in Italy. A structural equation model is proposed to shed some light into this relatively unexplored area.FindingsOne of the direct implications of the authors’ study is that companies in apparel industry should try to improve their social and environmental performance to elicit the desired consumer responses.Originality/valueThis implies important managerial implications for new marketing strategies. If consumers’ perception of CSR practices drives their behavioural intention, firms will be motivated to be involved and to invest in socially responsible practices.
Institution building in retreat
Authors: Funk Charles , Treviño Len J. 
Published: June 2017

PurposeThe purpose of this paper is to describe co-devolutionary processes of multinational enterprise (MNE)/emerging economy institutional relationships utilizing concepts from “old” institutional theory as well as the institutional aspects of socially constructed realities.Design/methodology/approachThe authors develop a set of propositions that explore the new concept of a co-devolutionary relationship between MNEs and emerging economy institutions. Guided by prior research, the paper investigates MNE/emerging economy institutional co-devolution at the macro-(MNE home and host countries), meso-(MNE industry/host country regulative and normative institutions) and micro-(MNE and host country institutional actors) levels.FindingsMNE/emerging economy institutional co-devolution occurs at the macro-level via negative public communications in the MNE’s home and host countries, at the meso-level via host country corruption and MNE adaptation, and at the micro-level via pressures for individual actors to cognitively “take for granted” emerging economy corruption, leading to MNE divestment and a reduction in new MNE investment.Research limitations/implicationsBy characterizing co-devolutionary processes within MNE/emerging economy institutional relationships, the research augments co-evolutionary theory. It also assists in developing more accurate specification and measurement methods for the organizational co-evolution construct by using institutional theory’s foundational processes to discuss MNE/emerging economy institutional co-devolution.Practical implicationsThe research suggests the use of enhanced regulation, bilateral investment treaties and MNE/local institution partnerships to stabilize MNE/emerging economy institutional relationships, leading to more robust progress in building emerging economy institutions.Originality/valueThe research posits that using the concepts of institutional theory as a foundation provides useful insights into the “stickiness” of institutional instability and corruption in emerging economies and into the resulting co-devolutionary MNE/emerging economy institutional relationships.
Implementing innovative financial models in different cultures
Authors: Cervantes Mauricio , Lemus Daniel , Montalvo Raúl 
Published: June 2017

Purpose
The purpose of this paper is to present evidence about cultural differences between Mexico and China, and analyze their significance when implementing an innovative financial model. Specifically, the authors analyzed the case of the Yunus model (or Grameen model), originally developed in Bangladesh and further implemented in China and Mexico.

Design/methodology/approach
This paper uses a comparative quantity study to test the cultural difference which affects the innovative financial model implementation. A materialism and credit overuse value scale (Ponchio and Aranha, 2008; Richins, 2011; Roberts and Jones, 2001) is applied to analyze cultural differences with a sample of 250 people in each country.

Findings
The results show that the survey responses are statistically significantly different in these two countries. The Mexican sample shows a greater affinity with luxury and bragging. The Chinese sample shows more responsibility toward credit. Recommendations for the implementation of the innovative financial model considering cultural differences are suggested.

Practical implications
Based on the survey results, gender equality, greater caution with young borrowers, financial education programs, and strict liability agreements to ensure credit repayment, especially for Mexico, are suggested, with the aim of enabling microfinance institutions to increase the successful implementation of the Yunus model in China and Mexico.

Originality/value
There are few existing cultural comparisons between China and Mexico. Therefore, one of the relevant contributions of this work is to shed light on the cultural differences of these two important emerging economies for future research. Additionally, the authors applied a materialism and credit overuse value scale developed to assess consumer behavior as a proxy for culture. The results are relevant for further usage of this scale as a tool to help adapt innovative financial models for application in other cultures.