bluuebunny/crossref_metadata_2025_split huggingface dataset:
Niche and neutral processes both shape community structure in parallelized, aerobic, single carbon-source enrichments
Authors: Flynn Theodore M. , Koval Jason C. , Greenwald Stephanie M. , Owens Sarah M. , Kemner Kenneth M. , Antonopoulos Dionysios A. 
Published: June 2017

AbstractHere we seek to test the extent to which laboratory enrichments mimic natural community processes and the degree to which the initial structure of a community determines its response to a press disturbance via the addition of environmentally-relevant carbon compounds. By utilizing aerobic substrate arrays to examine the effect of carbon amendment on microbial communities taken from six distinct environments (soil from a temperate prairie and forest, tropical forest soil, subalpine forest soil, and surface water and soil from a palustrine emergent wetland), we examined how carbon amendment and inoculum source shape the composition of the community in each enrichment. Dilute subsamples from each environment were used to inoculate 96-well microtiter plates containing triplicate wells amended with one of 31 carbon sources from 6 different classes of organic compound (phenols, polymers, carbohydrates, carboxylic acids, amines, amino acids). After incubating each well aerobically in the dark for 72 hours, we analyzed the composition of the microbial communities on the substrate arrays as well as the initial inocula by sequencing 16S rRNA gene amplicons using the Illumina MiSeq platform. Comparisons of alpha and beta diversity in these systems showed that, while the composition of the communities that grow to inhabit the wells in each substrate array diverges sharply from that of the original community in the inoculum, these enrichment communities are still is strongly affected by the inoculum source. We found most enrichments were dominated by one or several OTUs most closely related to aerobes or facultative anaerobes from theProteobacteria(e.g.Pseudomonas,Burkholderia, andRalstonia) orBacteroidetes(e.g.Chryseobacterium). Comparisons within each substrate array based on the class of carbon source further show that the communities inhabiting wells amended with a carbohydrate differ significantly from those enriched with a phenolic compound. Niche selection therefore seems to play a strong role in shaping the communities in the substrate arrays, although some stochasticity is seen whereby several replicate wells within a single substrate array display strongly divergent community compositions. Overall, the use of highly parallel substrate arrays offers a promising path forward to study the response of microbial communities to a changing environment.
A dual transcript-discovery approach to improve the delimitation of gene features from RNA-seq data in the chicken model
Authors: Orgeur Mickael , Martens Marvin , Börno Stefan T. , Timmermann Bernd , Duprez Delphine , Stricker Sigmar 
Published: June 2017

AbstractThe sequence of the chicken genome, like several other draft genome sequences, is presently not fully covered. Gaps, contigs assigned with low confidence and uncharacterized chromosomes result in gene fragmentation and imprecise gene annotation. Transcript abundance estimation from RNA sequencing (RNA-seq) data relies on read quality, library complexity and expression normalization. In addition, the quality of the genome sequence used to map sequencing reads and the gene annotation that defines gene features must also be taken into account. Partially covered genome sequence causes the loss of sequencing reads from the mapping step, while an inaccurate definition of gene features induces imprecise read counts from the assignment step. Both steps can significantly bias interpretation of RNA-seq data. Here, we describe a dual transcript-discovery approach combining a genome-guided gene prediction and ade novotranscriptome assembly. This dual approach enabled us to increase the assignment rate of RNA-seq data by nearly 20% as compared to when using only the chicken reference annotation, contributing therefore to a more accurate estimation of transcript abundance. More generally, this strategy could be applied to any organism with partial genome sequence and/or lacking a manually-curated reference annotation in order to improve the accuracy of gene expression studies.
Characterization of a spectrally diverse set of fluorescent proteins as FRET acceptors for mTurquoise2
Authors: Mastop Marieke , Bindels Daphne S. , Shaner Nathan C. , Postma Marten , Gadella Theodorus W. J. , Goedhart Joachim 
Published: June 2017

AbstractGenetically encoded Förster Resonance Energy Transfer (FRET) based biosensors report on changes in biochemical states in single living cells. The performance of biosensors depends on their brightness and dynamic range, which are dependent on the characteristics of the fluorescent proteins that are employed. Cyan fluorescent protein (CFP) is frequently combined with yellow fluorescent protein (YFP) as FRET pair in biosensors. However, current YFPs are prone to photobleaching and pH changes. In addition, more efficient acceptors may yield biosensors that have higher contrast. In this study, we evaluated the properties of a diverse set of acceptor fluorescent proteins in combination with the optimized CFP variant mTurquoise2 as the donor. To determine the theoretical performance of acceptors, the Förster radius was determined. The practical performance was determined by measuring FRET efficiency and photostability of tandem fusion proteins in mammalian cells. Our results show that mNeonGreen is the most efficient acceptor for mTurquoise2 and that the photostability is better than SYFP2. The non-fluorescent YFP variant sREACh is an efficient acceptor, which is useful in lifetime-based FRET experiments. Among the orange and red fluorescent proteins, mChery and mScarlet-I are the best performing acceptors. Several new pairs were applied in a multimolecular FRET based sensor for detecting activation of a heterotrimeric G-protein by G-protein coupled receptors. The sensor with mScarlet-I as acceptor and mTurquoise2 as donor shows a higher dynamic range in ratiometric FRET imaging experiments and less variability than with mCherry as acceptor, due to the high quantum yield and efficient maturation of mScarlet-I. Overall, the sensor with mNeonGreen as acceptor and mTurquoise2 as donor showed the highest dynamic range in ratiometric FRET imaging experiments with the G-protein sensor.
Voltage-gating of mechanosensitive PIEZO channels
Authors: Moroni Mirko , Servin-Vences Martha Rocio , Fleischer Raluca , Lewin Gary R. 
Published: June 2017

SummaryMechanosensitive PIEZO ion channels are evolutionarily conserved proteins whose presence is critical for normal physiology in multicellular organisms. Here we show that, in addition to mechanical stimuli, PIEZO channels are also powerfully modulated by voltage and can even switch to a purely voltage gated mode. Mutations that cause human diseases such as Xerocytosis profoundly shift voltage sensitivity of PIEZO1 channels towards the resting membrane potential and strongly promote pure voltage gating. Our data may be explained by the presence of an inactivation gate in the pore, the opening of which is promoted by outward permeation. Invertebrate (fly) and vertebrate (fish) PIEZO proteins are also voltage sensitive but voltage gating is a much more prominent feature of these older channels. We propose that the voltage sensitivity of PIEZO channels is a deep property co-opted to add a regulatory mechanism for PIEZO activation in widely different cellular contexts.
Cftr Modulates Wnt/β-Catenin Signaling and Stem Cell Proliferation in Murine Intestine
Authors: Strubberg Ashlee M. , Liu Jinghua , Walker Nancy M. , Stefanski Casey D. , MacLeod R. John , Magness Scott T. , Clarke Lane L. 
Published: June 2017

AbstractBackground & AimsCystic fibrosis (CF) patients and CF mouse models have increased risk for gastrointestinal tumors. CF mice exhibit augmented intestinal proliferation of unknown etiology and an altered intestinal environment. We examined the role of Cftr in Wnt/β-catenin signaling, stem cell proliferation and its functional expression in the active intestinal stem cell (ISC) population. Dysregulation of intracellular pH (pHi) in CF ISCs was investigated for facilitation of Wnt/β-catenin signaling.MethodsCrypt epithelia from wild-type (WT) and CF mice were compared ex vivo and in intestinal organoids (enteroids) for proliferation and Wnt/β-catenin signaling by standard assays. Cftr in ISCs was assessed by immunoblot of sorted Sox9EGFPintestinal epithelia and pHiregulation by confocal microfluorimetry of Lgr5+-EGFP ISCs. Plasma membrane association of the Wnt transducer Disheveled 2 (Dvl2) was assessed by fluorescence imaging of live enteroids from WT and CF mice crossed with Dvl2-EGFP/RosamT/mGmice.ResultsRelative to WT, CF intestinal crypts showed a ~30% increase in epithelial and Lgr5+ ISC proliferation and increased Wnt/β-catenin signaling. Cftr was expressed in Sox9EGFPLoISCs and loss of Cftr induced an alkaline pHiin Lgr5+-EGFP ISCs. CF crypt-base columnar cells (CBCs) demonstrated a generalized increase in plasma membrane Dvl2-EGFP association as compared to WT. Dvl2-EGFP membrane association was charge- and pH-dependent and increased in WT CBCs by Cftr inhibition.ConclusionsCF intestine exhibits increased ISC proliferation and Wnt/β-catenin signaling. Loss of Cftr increases pHiin ISCs which stabilizes the plasma membrane association of the Wnt transducer Dvl, likely facilitating Wnt/β-catenin signaling. Absence of Cftr-dependent suppression of ISC proliferation in the CF intestine may contribute to increased risk for intestinal tumors.Graphical Abstract
ADAGE signature analysis: differential expression analysis with data-defined gene sets
Authors: Tan Jie , Huyck Matthew , Hu Dongbo , Zelaya René A. , Hogan Deborah A. , Greene Casey S. 
Published: June 2017

AbstractBackgroundGene set enrichment analysis and overrepresentation analyses are commonly used methods to determine the biological processes affected by a differential expression experiment. This approach requires biologically relevant gene sets, which are currently curated manually, limiting their availability and accuracy in many organisms without extensively curated resources. New feature learning approaches can now be paired with existing data collections to directly extract functional gene sets from big data.ResultsHere we introduce a method to identify perturbed processes. In contrast with methods that use curated gene sets, this approach uses signatures extracted from public expression data. We first extract expression signatures from public data using ADAGE, a neural network-based feature extraction approach. We next identify signatures that are differentially active under a given treatment. Our results demonstrate that these signatures represent biological processes that are perturbed by the experiment. Because these signatures are directly learned from data without supervision, they can identify uncurated or novel biological processes. We implemented ADAGE signature analysis for the bacterial pathogenPseudomonas aeruginosa. For the convenience of different user groups, we implemented both an R package (ADAGEpath) and a web server (http://adage.greenelab.com) to run these analyses. Both are open-source to allow easy expansion to other organisms or signature generation methods. We applied ADAGE signature analysis to an example dataset in which wild-type andΔanrmutant cells were grown as biofilms on the Cystic Fibrosis genotype bronchial epithelial cells. We mapped active signatures in the dataset to KEGG pathways and compared with pathways identified using GSEA. The two approaches generally return consistent results; however, ADAGE signature analysis also identified a signature that revealed the molecularly supported link between the MexT regulon and Anr.ConclusionsWe designed ADAGE signature analysis to perform gene set analysis using data-defined functional gene signatures. This approach addresses an important gap for biologists studying non-traditional model organisms and those without extensive curated resources available. We built both an R package and web server to provide ADAGE signature analysis to the community.
Germline Cas9 Expression Yields Highly Efficient Genome Engineering in a Major Worldwide Disease Vector,Aedes aegypti
Authors: Li Ming , Bui Michelle , Yang Ting , White Bradley J. , Akbari Omar S. 
Published: June 2017

AbstractThe development of CRISPR/Cas9 technologies has dramatically increased the accessibility and efficiency of genome editing in many organisms. In general,in vivogermline expression of Cas9 results in substantially higher activity than embryonic injection. However, no transgenic lines expressing Cas9 have been developed for the major mosquito disease vectorAedes aegypti. Here, we describe the generation of multiple stable, transgenicAe. aegyptistrains expressing Cas9 in the germline, resulting in dramatic improvements in both the consistency and efficiency of genome modifications using CRISPR. Using these strains, we disrupted numerous genes important for normal morphological development, and even generated triple mutants from a single injection. We have also managed to increase the rates of homology directed repair by more than an order of magnitude. Given the exceptional mutagenic efficiency and specificity of the Cas9 strains we built, they can be used for high-throughput reverse genetic screens to help functionally annotate theAe. aegyptigenome. Additionally, these strains represent a first step towards the development of novel population control technologies targetingAe. aegyptithat rely on Cas9-based gene drives.Significance StatementAedes aegyptiis the principal vector of multiple arboviruses that significantly affect human health including dengue, chikungunya, and zika. Development of tools for efficient genome engineering in this mosquito will not only lay the foundation for the application of novel genetic control strategies that do not rely on insecticides, but will also accelerate basic research on key biological processes involved in disease transmission. Here, we report the development of a transgenic CRISPR approach for rapid gene disruption in this organism. Given their high editing efficiencies, the Cas9 strains we developed can be used to quickly generate novel genome modifications allowing for high-throughput gene targeting, and can possibly facilitate the development of gene drives, thereby accelerating comprehensive functional annotation and development of innovative population control strategies forAe. aegypti.
Robustness of spike deconvolution for calcium imaging of neural spiking
Authors: Pachitariu Marius , Stringer Carsen , Harris Kenneth D. 
Published: June 2017

AbstractCalcium imaging is a powerful method to record the activity of neural populations, but inferring spike times from calcium signals is a challenging problem. We compared multiple approaches using multiple datasets with ground truth electrophysiology, and found that simple non-negative deconvolution (NND) outperformed all other algorithms. We introduce a novel benchmark applicable to recordings without electrophysiological ground truth, based on the correlation of responses to two stimulus repeats, and used this to show that unconstrained NND also outperformed the other algorithms when run on “zoomed out” datasets of ~10,000 cell recordings. Finally, we show that NND-based methods match the performance of a supervised method based on convolutional neural networks, while avoiding some of the biases of such methods, and at much faster running times. We therefore recommend that spikes be inferred from calcium traces using simple NND, due to its simplicity, efficiency and accuracy.
Chemical-microstructural-nanomechanical variations in the structural units of the cuttlebone ofSepia officinalis
Authors: North L , Labonte David , Oyen ML , Coleman MP , Caliskan HB , Johnston RE 
Published: June 2017

Abstract‘Cuttlebone’, the internalized shell found in all members of the cephalopod family Sepiidae, is a sophisticated buoyancy device combining high porosity with considerable strength. Using a complementary suite of characterization tools, we identified significant structural, chemical and mechanical variations across the different structural units of the cuttlebone: the dorsal shield consists of two stiff and hard layers with prismatic mineral organization which encapsulate a more ductile and compliant layer with a lamellar structure, enriched with organic matter. A similar organization is found in the lamellar matrix, which consists of individual chambers separated by septa, and supported by meandering plates (‘pillars’). Like the dorsal shield, septa contain two layers with lamellar and prismatic organization, respectively, which differ significantly in their mechanical properties: layers with prismatic organization are a factor of three stiffer, and up to a factor of ten harder than those with lamellar organization. The combination of stiff and hard, and compliant and ductile components may serve to reduce the risk of catastrophic failure, and reflect the role of organic matter for the growth process of the cuttlebone. Mechanically ‘weaker’ units may function as sacrificial structures, ensuring a step-wise failure of the individual chambers in cases of overloading, allowing the animals to retain near-neutral buoyancy even with partially damaged cuttlebones. Our findings have implications for the structure-property-function relationship of cuttlebone, and may help to identify novel bioinspired design strategies for light-weight yet high-strength foams.
Place branding-exploring knowledge and positioning choices across national boundaries
Authors: Pucci Tommaso , Casprini Elena , Rabino Samuel , Zanni Lorenzo 
Published: June 2017

Purpose
The purpose of this paper is to examine the effects of the product-specific region-of-origin (ROO) and product-specific country-of-origin (COO) on the willingness to pay a premium price for a wine label designated as a superbrand by the Italian Government: the Chianti Classico.

Design/methodology/approach
The paper introduces the concept of “ROO-COO distance”, defined as the importance attributed to a product-specific ROO as compared to its COO. In order to better understand whether the construct “ROO-COO distance” influences the willingness to pay a premium price, the paper considers consumers’ cross-national differences and their knowledge, distinguishing among three types of knowledge: consumers’ subjective general product knowledge, consumers’ subjective country product knowledge and consumers’ regional product experience (PE). Four hypotheses were tested focussing on Chianti Classico – a premium wine – as related to its ROO and COO (Tuscany, Italy). The authors employed a sample of 4,254 consumers originating from New World countries (Australia, USA and Canada) and Old World countries (Germany, UK, Sweden and Belgium).

Findings
The findings confirm that a place-of-origin influence on price-related product evaluations is country specific. Furthermore, the moderating role of consumers’ subjective product knowledge and consumers’ region-related PEs differ across countries. The ROO-COO distance was found to positively affect only Old World consumers. It was established that respondents’ subjective country/product knowledge and consumers’ regional knowledge or PEs positively moderate this relationship.

Originality/value
The paper links the COO and ROO effects in a single framework and analyses it at the cross-national level, while also considering the moderating effect of consumer’s knowledge.
How do food safety regulations influence market price? A theoretical analysis
Authors: Nait Mohand Nacim , Hammoudi Abdelhakim , Radjef Mohammed Said , Hamza Oualid , Perito Maria Angela 
Published: June 2017

Purpose
This study is in line with the debate concerning the compatibility between the qualitative and quantitative food production objectives. The purpose of this paper is to identify the causal relationship that may exist between public food safety regulations (specifically, the maximum authorised levels of chemical or microbiological contaminants), and the expected price in the spot markets (wholesale markets, for example).

Design/methodology/approach
The authors propose a theoretical industrial economic model that identifies the causal link which may exist between public food safety regulations (e.g. the maximum authorised levels of chemical or microbiological contaminants), the expected price in domestic markets, and the rate of exclusion of local producers. This general model allows one to characterize the price formation process in markets subject to maximum residue level constraints by focusing on the role of the official inspection systems established by public authorities.

Findings
The authors show how strengthening official controls does not systematically impact negatively on producers’ participation and does not always decrease supply. Moreover, the authors show that reinforcing the maximum permitted contamination thresholds is not always sufficient for ensuring consumer health.

Originality/value
The originality of the model is that it shows how all variables (economic and sanitary variables) interact in the formation of agricultural prices and determine the final size of the productive system (number of active producers). The characterisation of the market price as a function of producers’ investment efforts and of the level of official control reliability allows one to determine both the total supply and the proportion of this supply that is contaminated (i.e. does not comply with the maximum threshold of contamination).
Why do you drink? A means-end approach to the motivations of young alcohol consumers
Authors: Fabbrizzi Sara , Marinelli Nicola , Menghini Silvio , Casini Leonardo 
Published: June 2017

Purpose
The purpose of this paper is to analyse the motivations of young consumers of alcoholic beverages in order to supply information for the definition of corporate and social marketing strategies. The target of young consumers was chosen because of its association with the choice of consumption behaviours often resulting in health and social issues related to alcohol. The focus on motivations, on the other hand, is justified by the need to assess the contents of appropriate and efficient communication campaigns for both producers and public institutions.

Design/methodology/approach
A means-end approach was used on a sample of young consumers from Tuscany via face-to-face interviews. The interviews were carried out with students who were completing their last year of high school. The results were processed using an MEC analyst software for the construction of the hierarchical value maps and cognitive maps showing the links between products and consumers.

Findings
The results highlighted the perception of a “socialisation” attribute that is stronger when linked to the consumption of beer and spirits; however, wine is still perceived as a non-friendly beverage. The aspect of socialisation underlines both the pleasure of sharing consumption experiences and the dangerous binge drinking behaviour. Thanks to this approach, the study identifies the main elements in the cognitive structure that, if used to define a communication strategy, may guarantee a high degree of efficacy.

Originality/value
The findings of the study constitute valuable information that can be used to prepare stages of communication plans within larger corporate and social marketing strategies. The wine sector can benefit from understanding the motivations that prevent young people from drinking wine and can attempt to fill the psychological and cognitive gap between young consumers and the product. Public institutions, on the other hand, may benefit from understanding the motivations that lead young people towards dangerous drinking behaviours. In turn, the institutions may be able to send appropriate messages within their communication activities aimed at containing such behaviours.