bluuebunny/crossref_metadata_2025 huggingface dataset:
Dietary and Developmental Shifts in Butterfly-Associated Bacterial Communities
Authors: Phalnikar Kruttika , Kunte Krushnamegh , Agashe Deepa
Published: October 2017

Bacterial communities associated with insects can substantially influence host ecology, evolution and behavior. Host diet is a key factor that shapes bacterial communities, but the impact of dietary transitions across insect development is poorly understood. We analyzed bacterial communities of 12 butterfly species across different development stages, using 16S rDNA amplicon sequencing. Butterfly larvae typically consume leaves of a single host plant, whereas adults are more generalist nectar feeders. Thus, we expected bacterial communities to vary substantially across butterfly development. Surprisingly, very few species showed significant developmental transitions in bacterial communities, suggesting weak impacts of dietary transitions across butterfly development. On the other hand, bacterial communities were strongly influenced by butterfly species identity and dietary variation across species. Larvae of most butterfly species largely mirrored bacterial community composition of their diets, suggesting passive acquisition rather than active selection. Overall, our results suggest that although butterflies harbor distinct microbiomes across taxonomic groups and dietary guilds, the dramatic dietary shifts that occur during development do not impose strong selection to maintain distinct bacterial communities.
Enter the matrix: factorization uncovers knowledge from omics Names/Affiliations
Authors: Stein-O’Brien Genevieve L. , Arora Raman , Culhane Aedin C. , Favorov Alexander V. , Garmire Lana X. , Greene Casey S. , Goff Loyal A. , Li Yifeng , Ngom Aloune , Ochs Michael F. , Xu Yanxun , Fertig Elana J.
Published: October 2017

Omics data contains signal from the molecular, physical, and kinetic inter- and intra-cellular interactions that control biological systems. Matrix factorization techniques can reveal low-dimensional structure from high-dimensional data that reflect these interactions. These techniques can uncover new biological knowledge from diverse high-throughput omics data in topics ranging from pathway discovery to time course analysis. We review exemplary applications of matrix factorization for systems-level analyses. We discuss appropriate application of these methods, their limitations, and focus on analysis of results to facilitate optimal biological interpretation. The inference of biologically relevant features with matrix factorization enables discovery from high-throughput data beyond the limits of current biological knowledge—answering questions from high-dimensional data that we have not yet thought to ask.
Neural data science: accelerating the experiment-analysis-theory cycle in large-scale neuroscience
Authors: Paninski L , Cunningham J.P
Published: October 2017

Modern large - scale multineuronal recording methodologies, including multielectrode arrays, calcium imaging, and optogenetic techniques, produce single - neuron resolution data of a magnitude and precision that were the realm of science fiction twenty years ago. The major bottlenecks in systems and circuit neuroscience no longer lie in simply collecting data from large neural populations, but also in understanding this data: developing novel scientific questions, with corresponding analysis techniques and experimental designs to fully harness these new capabilities and meaningfully interrogate these questions. Advances in methods for signal processing, network analysis, dimensionality reduction, and optimal control – developed in lockstep with advances in experimental neurotechnology - - promise major breakthroughs in multiple fundamental neuroscience problems. These trends are clear in a broad array of subfields of modern neuroscience; this review focuses on recent advances in methods for analyzing neural time - series data with single - neuronal precision.
Figure 1.

The central role of data science in modern large - scale neuroscience.

Topics reviewed herein are indicated in black.
Directed evolution of TurboID for efficient proximity labeling in living cells and organisms
Authors: Branon Tess C. , Bosch Justin A. , Sanchez Ariana D. , Udeshi Namrata D. , Svinkina Tanya , Carr Steven A. , Feldman Jessica L. , Perrimon Norbert , Ting Alice Y.
Published: October 2017

Protein interaction networks and protein compartmentation underlie every signaling process and regulatory mechanism in cells. Recently, proximity labeling (PL) has emerged as a new approach to study the spatial and interaction characteristics of proteins in living cells. However, the two enzymes commonly used for PL come with tradeoffs – BioID is slow, requiring tagging times of 18-24 hours, while APEX peroxidase uses substrates that have limited cell permeability and high toxicity. To address these problems, we used yeast display-based directed evolution to engineer two mutants of biotin ligase, TurboID and miniTurbo, with much greater catalytic efficiency than BioID, and the ability to carry out PL in cells in much shorter time windows (as little as 10 minutes) with non-toxic and easily deliverable biotin. In addition to shortening PL time by 100-fold and increasing PL yield in cell culture, TurboID enabled biotin-based PL in new settings, including yeast,Drosophila, andC. elegans.
A simple and powerful analysis of lateral subdiffusion using single particle tracking
Authors: Renner Marianne , Wang Lili , Levi Sabine , Hennekinne Laetitia , Triller Antoine
Published: October 2017

In biological membranes many factors such as cytoskeleton, lipid composition, crowding and molecular interactions deviate lateral diffusion from the expected random walks. These factors have different effects on diffusion but act simultaneously so the observed diffusion is a complex mixture of diffusive behaviors (directed, >Brownian, anomalous or confined). Therefore commonly used approaches to quantify diffusion based on averaging of the displacements, such as the mean square displacement, are not adapted to the analysis of this heterogeneity. We introduce a new parameter, the packing coefficientPc, which gives an estimate of the degree of free movement that a molecule displays in a period of time independently of its global diffusivity. Applying this approach to two different situations (diffusion of a lipid probe and trapping of receptors at synapses), we show thatPcdetected and localized temporary changes of diffusive behavior both in time and in space. More importantly, it allowed the detection of periods with very high confinement (~immobility), their frequency and duration, and thus it can be used to calculate the effectivekonandkoffof scaffolding interactions such those that immobilize receptors at synapses.
Reproducibility of importance extraction methods in neural network based fMRI classification
Authors: Gotsopoulos Athanasios , Saarimäki Heini , Glerean Enrico , Jääskeläinen Iiro P. , Sams Mikko , Nummenmaa Lauri , Lampinen Jouko
Published: October 2017

Recent advances in machine learning allow faster training, improved performance and increased interpretability of classification techniques. Consequently, their application in neuroscience is rapidly increasing. While classification approaches have proved useful in functional magnetic resonance imaging (fMRI) studies, there are concerns regarding extraction, reproducibility and visualization of brain regions that contribute most significantly to the classification. We addressed these issues using an fMRI classification scheme based on neural networks and compared a set of methods for extraction of category-related voxel importances in three simulated and two empirical datasets. The simulation data revealed that the proposed scheme successfully detects spatially distributed and overlapping activation patterns upon successful classification. Application of the proposed classification scheme to two previously published empirical fMRI datasets revealed robust importance maps that extensively overlap with univariate maps but also provide complementary information. We conclude that importance maps are superior to univariate approaches for both detection of overlapping patterns and patterns with weak univariate information.
Current Models of Speech Motor Control: A Control-Theoretic Overview of Architectures & Properties
Authors: Parrell Benjamin , Lammert Adam C. , Ciccarelli Gregory , Quatieri Thomas F.
Published: October 2017

This paper reviews the current state of several formal models of speech motor control with particular focus on the low level control of the speech articulators. Further development of speech motor control models may be aided by a comparison of model attributes. The review builds an understanding of existing models from first principles, before moving into a discussion of several models, showing how each is constructed out of the same basic domain-general ideas and components – e.g., generalized feedforward, feedback, and model predictive components. This approach allows for direct comparisons to be made in terms of where the models differ, and their points of agreement. Substantial differences among models can be observed in their use of feedforward control, process of estimating system state, and method of incorporating feedback signals into control. However, many commonalities exist among the models in terms of their reliance on higher-level motor planning, use of feedback signals, lack of time-variant adaptation, and focus on kinematic aspects of control and biomechanics. Ongoing research bridging hybrid feedforward/feedback pathways with forward dynamic control, as well as feedback/internal model-based state estimation is discussed.
Inhibition of mitochondrial fission preserves photoreceptors after retinal detachment
Authors: She Xiangjun , Lu Xinmin , Li Tong , Sun Junran , Liang Jian , Zhai Yuanqi , Yang Shiqi , Gu Qing , Wei Fang , Zhu Hong , Wang Fenghua , Luo Xueting , Sun Xiaodong
Published: October 2017

Photoreceptor degeneration is a leading cause of visual impairment worldwide. Separation of neurosensory retina from the underlying retinal pigment epithelium is a prominent feature preceding photoreceptor degeneration in a variety of retinal diseases. Although ophthalmic surgeries have been well developed to restore retinal structures, post-op patients usually experience progressive photoreceptor degeneration and irreversible vision loss that is incurable at present. Previous studies point to a critical role of mitochondria-mediated apoptotic pathway in photoreceptor degeneration, but the upstream triggers remain largely unexplored. In this study, we show that after experimental RD induction, photoreceptors activate dynamin-related protein 1 (Drp1)-dependent mitochondrial fission pathway and subsequent apoptotic cascades. Mechanistically, endogenous ROS is necessary for Drp1 activation in vivo and exogenous ROS insult is sufficient to activate Drp1-dependent mitochondrial fission in cultured photoreceptors. Accordingly, inhibition of Drp1 activity effectively preserves mitochondrial integrity and rescues photoreceptors. Collectively, our data delineates a ROS-Drp1-mitochondria axis that promotes photoreceptor degeneration in retinal diseased models.
MreB Filaments Create Rod Shape By Aligning Along Principal Membrane Curvature
Authors: Hussain Saman , Wivagg Carl N. , Szwedziak Piotr , Wong Felix , Schaefer Kaitlin , Izoré Thierry , Renner Lars D. , Sun Yingjie , Bisson Filho Alexandre W. , Walker Suzanne , Amir Ariel , Löwe Jan , Garner Ethan C.
Published: October 2017

MreB is essential for rod shape in many bacteria. Membrane-associated MreB filaments move around the rod circumference, helping to insert cell wall in the radial direction to reinforce rod shape. To understand how oriented MreB motion arises, we altered the shape ofBacillus subtilis.MreB motion is isotropic in round cells, and orientation is restored when rod shape is externally imposed. Stationary filaments orient within protoplasts, and purified MreB tubulates liposomesin vitro,orienting within tubes. Together, this demonstrates MreB orients along the greatest principal membrane curvature, a conclusion supported with biophysical modeling. We observed that spherical cells regenerate into rods in a local, self-reinforcing manner: rapidly propagating rods emerge from small bulges, exhibiting oriented MreB motion and increased glycan crosslinking. We propose that the coupling of MreB filament alignment to shape-reinforcing peptidoglycan synthesis creates a locally-acting, self-organizing mechanism allowing the rapid establishment and stable maintenance of emergent rod shape.
Biomechanics of the peafowl’s crest reveals frequencies tuned to social displays
Authors: Kane Suzanne Amador , Beveren Daniel Van , Dakin Roslyn
Published: October 2017

Feathers act as vibrotactile sensors that can detect mechanical stimuli during avian flight and tactile navigation, suggesting that they may also detect stimuli during social displays. In this study, we present the first measurements of the biomechanical properties of the feather crests found on the heads of birds, with an emphasis on those from the Indian peafowl (Pavo cristatus). We show that in peafowl these crest feathers are coupled to filoplumes, small feathers known to function as mechanosensors. We also determined that airborne stimuli with the frequencies used during peafowl courtship and social displays couple efficiently via resonance to the vibrational response of their feather crests. Specifically, vibrational measurements showed that although different types of feathers have a wide range of fundamental resonant frequencies, peafowl crests are driven near-optimally by the shaking frequencies used by peacocks performing train-rattling displays. Peafowl crests were also driven to vibrate near resonance in a playback experiment that mimicked the effect of these mechanical sounds in the acoustic very near-field, reproducing the way peafowl displays are experienced at distances ≤ 1.5min vivo. When peacock wing-shaking courtship behaviour was simulated in the laboratory, the resulting airflow excited measurable vibrations of crest feathers. These results demonstrate that peafowl crests have mechanical properties that allow them to respond to airborne stimuli at the frequencies typical of this species’ social displays. This suggests a new hypothesis that mechanosensory stimuli could complement acoustic and visual perception and/or proprioception of social displays in peafowl and other bird species. We suggest behavioral studies to explore these ideas and their functional implications.
Control of Thiol-Maleimide Reaction Kinetics in PEG Hydrogel Networks
Authors: Jansen Lauren E. , Negrón-Piñeiro Lenny J. , Galarza Sualyneth , Peyton Shelly R.
Published: October 2017

Michael-type addition reactions are widely used to polymerize biocompatible hydrogels. The thiol-maleimide modality achieves the highest macromer coupling efficiency of the reported Michael-type pairs, but the resulting hydrogel networks are heterogeneous, because polymerization is faster than the individual components can be manually mixed. The reactivity of the thiol dictates the overall reaction speed, which can be slowed in organic solvents and acidic buffers. Since these modifications also reduce the biocompatibility of resulting hydrogels, we investigated a series of biocompatible buffers and crosslinkers to decelerate gelation while maintaining high cell viability. We found that lowering the polymer weight percentage (wt%), buffer concentration, and pH slowed gelation kinetics, but crosslinking with an electronegative peptide was optimal for both kinetics and cell viability. Slowing the speed of polymerization resulted in more uniform hydrogels, both in terms of visual inspection and the diffusion of small molecules through the network. However, reactions that were too slow resulted in non-uniform particle dispersion due to settling, thus there is a trade-off in hydrogel network uniformity versus cell distribution in the hydrogels when using these networks in cell applications.
Transcriptome dynamics at theArabidopsisgraft junction reveal an inter-tissue recognition mechanism that activates vascular regeneration
Authors: Melnyk Charles W , Gabel Alexander , Hardcastle Thomas J , Robinson Sarah , Miyashima Shunsuke , Grosse Ivo , Meyerowitz Elliot M
Published: October 2017

The ability for cut tissues to join together and form a chimeric organism is a remarkable property of many plants, however, grafting is poorly characterized at the molecular level. To better understand this process we monitored genome-wide temporal and spatial gene expression changes in graftedArabidopsis thalianahypocotyls. Tissues above and below the graft rapidly developed an asymmetry such that many genes were more highly expressed on one side than the other. This asymmetry correlated with sugar responsive genes and we observed an accumulation of starch above the graft that decreased along with asymmetry once the sugar-transporting vascular tissues reconnected. Despite the initial starvation response below the graft, many genes associated with vascular formation were rapidly activated in grafted tissues but not in cut and separated tissues indicating that a recognition mechanism activated that was independent of functional vascular connections. Auxin which is transported cell-to-cell, had a rapidly elevated response that was symmetric, suggesting that auxin was perceived by the root within hours of tissue attachment to activate the vascular regeneration process. A subset of genes were expressed only in grafted tissues, indicating that wound healing proceeded via different mechanisms depending on the presence or absence of adjoining tissues. Such a recognition process could have broader relevance for tissue regeneration, inter-tissue communication and tissue fusion events.
Molecular function limits divergent protein evolution on planetary timescales
Authors: Konaté Mariam M. , Plata Germán , Park Jimin , Usmanova Dinara R. , Wang Harris H. , Vitkup Dennis
Published: October 2017

Functional conservation is known to constrain protein evolution. Nevertheless, the long-term divergence patterns of proteins maintaining the same molecular function and the possible limits of this divergence have not been explored in detail. We investigate these fundamental questions by characterizing the divergence between ancient protein orthologs with conserved molecular function. Our results demonstrate that the decline of sequence and structural similarities between such orthologs significantly slows down after ~1-2 billion years of independent evolution. As a result, their sequence and structural similarities have not substantially decreased for the past billion years. The effective divergence limit (>25% sequence identity) is not primarily due to protein sites universally conserved in all linages. Instead, less than four amino acid types are accepted, on average, per site in orthologs strictly conserving their molecular function. Our analysis also reveals different divergence patterns for protein sites with experimentally determined small and large fitness effects of mutations.
Grid cell co-activity patterns during sleep reflect spatial overlap of grid fields during active behaviors
Authors: Trettel Sean G. , Trimper John B. , Hwaun Ernie , Fiete Ila R. , Colgin Laura Lee
Published: October 2017

Continuous attractor network models of grid formation posit that recurrent connectivity between grid cells controls their patterns of co-activation. Grid cells from a common module exhibit stable offsets in their periodic spatial tuning curves across environments, which may reflect recurrent connectivity or correlated sensory inputs. Here we explore whether cell-cell relationships predicted by attractor models persist during sleep states in which spatially informative sensory inputs are absent. We recorded ensembles of grid cells in superficial layers of medial entorhinal cortex during active exploratory behaviors and overnight sleep. Per pair and collectively, we found preserved patterns of spike-time correlations across waking, REM, and non-REM sleep, which reflected the spatial tuning offsets between these cells during active exploration. The preservation of cell-cell relationships across states was not explained by theta oscillations or CA1 activity. These results suggest that recurrent connectivity within the grid cell network drives grid cell activity across behavioral states.
Cell Cycle Control by Nuclear Sequestration ofCDC20andCDH1mRNA in Plant Stem Cells
Authors: Yang Weibing , Wightman Raymond , Meyerowitz Elliot M.
Published: October 2017

In eukaryotic cells, most RNA molecules are exported into the cytoplasm after being transcribed in the nucleus. Long noncoding RNAs (lncRNAs) have been found to reside and function primarily inside the nucleus, but nuclear localization of protein-coding messenger RNAs (mRNAs) has been considered rare in both animals and plants. Here we show that two mRNAs, transcribed from theCDC20andCCS52B(plant orthologue ofCDH1) genes, are specifically sequestered inside the nucleus during the cell cycle. CDC20 and CDH1 both function as coactivators of the anaphase-promoting complex or cyclosome (APC/C) E3 ligase to trigger cyclin B (C YCB) destruction. In theArabidopsis thalianashoot apical meristem (SAM), we findCDC20andCCS52Bare co-expressed withCYCBsin mitotic cells.CYCBtranscripts can be exported and translated, whereasCDC20andCCS52BmRNAs are strictly confined to the nucleus at prophase and the cognate proteins are not translated until the redistribution of the mRNAs to the cytoplasm after nuclear envelope breakdown (NEBD) at prometaphase. The 5’ untranslated region (UTR) is necessary and sufficient forCDC20mRNA nuclear localization as well as protein translation. Mitotic enrichment ofCDC20andCCS52Btranscripts enables the timely and rapid activation of APC/C, while their nuclear sequestration at prophase appears to protect cyclins from precocious degradation.
Genomic MET amplification occurs early in NF1-related malignant peripheral nerve sheath tumor (MPNST) progression and is a potent therapeutic target
Authors: Peacock Jacqueline D. , Pridgeon Matthew G. , Tovar Elizabeth A. , Essenburg Curt J. , Bowman Megan , Madaj Zachary , Koeman Julie , Grit Jamie , Dodd Rebecca D. , Cardona Diana M. , Chen Mark , Kirsch David G. , Maina Flavio , Dono Rosanna , Winn Mary E. , Graveel Carrie R. , Steensma Matthew R.
Published: October 2017

Malignant Peripheral Nerve Sheath Tumors (MPNSTs) are highly resistant sarcomas that occur in up to 13% of individuals with Neurofibromatosis Type 1 (NF1). Genomic analysis of longitudinally collected tumor samples in a case of MPNST disease progression revealed early hemizygous microdeletions inNF1andTP53, with concomitant amplifications ofMET,HGF, andEGFR. To examine the role of MET in MPNST progression, we developed mice with enhanced MET expression and NF1 ablation (NF1fl/KO;lox-stop-loxMETtg/+;Plp-creERTtg/+; referred to as NF1-MET). NF1-MET mice express a robust MPNST phenotype in the absence of additional mutations. A comparison of NF1-MET MPSNTs with MPNSTs derived from NF1KO/+;p53R172H;Plp-creERTtg/+(NF1-P53) and NF1KO/+;Plp-creERTtg/+(NF1) mice revealed unique Met, Ras, and PI3K signaling patterns. To investigate the therapeutic potential of MET inhibition among tumorgrafts derived from the respective MPNST models, we tested the highly selective MET inhibitor, capmatinib. NF1-MET MPNSTs were uniformly sensitive to MET inhibition whereas only a small subset of NF1-P53 and NF1 MPNSTs were inhibited. These results confirm that MET activation is sufficient for Schwann cell dedifferentiation into MPNSTs in the context of NF1 deficiency. RAS-MET signal interactions may be an important driver of MPSNT disease progression.
Haystack: systematic analysis of the variation of epigenetic states and cell-type specific regulatory elements
Authors: Pinello Luca , Farouni Rick , Yuan Guo-Cheng
Published: October 2017

Motivation

With the increasing amount of genomic and epigenomic data in the public domain, a pressing challenge is how to integrate these data to investigate the role of epigenetic mechanisms in regulating gene expression and maintenance of cell-identity. To this end, we have implemented a computational pipeline to systematically study epigenetic variability and uncover regulatory DNA sequences that play a role in gene regulation.

Results

Haystack is a bioinformatics pipeline to characterize hotspots of epigenetic variability across different cell-types as well as cell-type specific cis-regulatory elements along with their corresponding transcription factors. Our approach is generally applicable to any epigenetic mark and provides an important tool to investigate cell-type identity and the mechanisms underlying epigenetic switches during development. Additionally, we make available a set of precomputed tracks for a number of epigenetic marks across several cell types. These precomputed results may be used as an independent resource for functional annotation of the human genome.

Availability

The Haystack pipeline is implemented as an open-source, multiplatform, Python package called haystack_bio available athttps://github.com/pinellolab/haystack_bio.

Contact

lpinello@mgh.harvard.edu,gcyuan@jimmy.harvard.edu
Microscopic Observation of Living Cells Stained with Fluorescent Probes
Authors: Asakawa Haruhiko , Ding Da-Qiao , Haraguchi Tokuko , Hiraoka Yasushi
Published: October 2017

Fluorescence imaging of living cells provides a unique opportunity to follow dynamic behavior of specific molecules under physiological conditions. In the fission yeast Schizosaccharomyces pombe, expression of a target protein genetically fused with a fluorescent protein such as the jellyfish green fluorescent protein (GFP) is widely used. In addition, fluorescent chemical reagents are also used to stain specific molecules (e.g., Hoechst 33324 to stain DNA). Specimens of S. pombe cells for live cell imaging are prepared by either of two methods: sandwiching the cells between glass coverslips and by mounting the cells on a glass-bottom culture dish. For time-lapse observation, it is necessary to immobilize fission yeast cells on the glass surface of the glass-bottom dish because they are nonadherent and tend to move easily as a result of stage movement, convection flow of culture medium, and the contact and pushing of neighboring cells during cell growth. Either concanavalin A or soybean lectin, which bind to S. pombe cell walls, can be used for immobilization. Considerations for sample preparations and observation conditions are described.
Live Cell Imaging of the Schizosaccharomyces pombe Sexual Life Cycle
Authors: Merlini Laura , Vjestica Aleksandar , Dudin Omaya , Bendezú Felipe , Martin Sophie G.
Published: October 2017

The fission yeast Schizosaccharomyces pombe is an invaluable model system for studying the principles that drive sexual differentiation and the meiotic cell division cycle. We describe a simple protocol for microscopic observation of the entire sexual life cycle that can be adapted to focus on specific stages of sexual differentiation. After growth to exponential phase in a nitrogen-rich medium, cell cultures are switched to a nitrogen-deprived medium until the population is enriched for the specific stage of the sexual lifecycle to be studied. Cells are then mounted in easily constructed customized agarose pad chambers for imaging.
Visualization of a Specific Genome Locus by the lacO/LacI-GFP System
Authors: Ding Da-Qiao , Hiraoka Yasushi
Published: October 2017

Observing the dynamics of a specific chromosome locus in living cells can provide important information as to the molecular mechanisms underlying events such as chromosome segregation, homologous chromosome pairing, chromosome arrangement, and gene expression. The lacO/LacI-GFP system provides a simple and useful method in which a chromosome locus is visualized by inserting lacO repeat arrays and then expressing an LacI–GFP fusion that specifically binds to the lacO sequence. This system has been adapted for use in Schizosaccharomyces pombe by expressing the LacI–GFP under a promoter of the dis1+ gene. Furthermore, a two-step integration method has been developed that ensures high-efficiency integration of lacO arrays to a desired target position.
Plating Bacteriophage M13
Authors: Green Michael R. , Sambrook Joseph
Published: October 2017

A plaque of bacteriophage M13 derives from infection of a single bacterium by a single virus particle. The progeny particles infect neighboring bacteria, which, in turn, release another generation of daughter virus particles. If the bacteria are growing in semisolid medium (e.g., containing agar or agarose), then the diffusion of the progeny particles is limited. Cells infected with bacteriophage M13 are not killed, but have a longer generation time than uninfected Escherichia coli. In consequence, plaques appear as areas of slower-growing cells on a faster-growing lawn of bacterial cells. This protocol describes plating of bacteriophage M13 stocks. Plaques are readily detectable on top agar after 4–8 h of incubation at 37°C.
Organ Culture of the Xenopus Tadpole Intestine
Authors: Ishizuya-Oka Atsuko
Published: October 2017

During Xenopus metamorphosis, most tadpole organs remodel from the larval to adult form to prepare for adaptation to terrestrial life. Organ culture serves as an important tool for studying larval-to-adult organ remodeling independent of the effects of other parts of the body. Here, I introduce a protocol for organ culture in vitro using the Xenopus laevis tadpole intestine before metamorphic climax. During culture in the absence of exogenous 3,3′,5-triiodo-l-thyronine (T3), the most potent natural thyroid hormone, the intestine remains in its larval state without any metamorphic changes. In contrast, when T3 is added to the culture medium, the larval epithelium undergoes apoptosis, whereas adult stem cells appear, actively proliferate, and finally generate the differentiated adult epithelium within a week. At the same time, the surrounding nonepithelial tissues also develop. Thus, this culture model is useful for clarifying the control mechanisms of apoptosis in larval tissues, formation of adult stem cells, and cell proliferation and differentiation of adult tissues, all of which occur in harmony during natural metamorphosis. Moreover, a procedure for tissue recombination combined with organ culture provides a platform for investigating complex tissue interactions during organ remodeling. Such tissue recombination experiments will help to reveal the important role of nonepithelial tissues in larval epithelial apoptosis and/or adult stem cell development in the X. laevis intestine.
Metabolic Labeling of Protein Antigens with [35S]Methionine
Authors: DeCaprio James , Kohl Thomas O.
Published: October 2017

Metabolic labeling of antigens can be achieved by supplementation of the cell culture medium with radioactive amino acid precursors such as [35S]methionine during the incubation period of target cells. In this protocol, intracellular unlabeled methionine levels are reduced by starvation of cells for 0.5–1 h before the addition of labeled [35S]methionine and incubation for 0.5–4 h. Upon completion of the metabolic labeling process, cells can be prepared for immunoprecipitation by lysis or alternatively pelleted and frozen for cell lysate preparations at a later time.
1-Methyl-3-(2-methylphenyl)-4-phenyl-1H-pyrazolo[3,4-d]pyrimidine
Authors: El Hafi Mohamed , Boulhaoua Mohammed , Ramli Youssef , Benchidmi Mohammed , Essassi El Mokhtar , Mague Joel T.
Published: October 2017

In the title compound, C19H16N4, the pyrazolopyrimidine unit is slightly twisted. A combination of π-stacking and offset π-stacking interactions forms columns along theb-axis direction.
Influence of social capital on customer’s relationship satisfaction in the Pakistani banking industry
Authors: Muhammad Lakhi , Mahadi Batiah , Hussin Nazimah
Published: October 2017

Purpose

The purpose of this paper is to investigate the effects of structural social capital, relational social capital and cognitive social on relationship satisfaction, and also to investigate how relationship satisfaction is associated with negative word-of-mouth and re-patronage intentions, in service recovery.

Design/methodology/approach

A sample of 478 Pakistani banking industry clients, who registered a complaint to their bank recently, answered the survey. Variance-based partial least squares structural equation modeling was employed for data analysis.

Findings

Results demonstrate that all three facets of social capital have a significant positive impact on relationship satisfaction. However, relationship satisfaction enhances customer re-patronage intentions and restrains negative word-of-mouth intentions.

Practical implications

Findings are important for service firms, particularly for banks to adjust their service recovery strategies.

Originality/value

The paper verified the influence of structural social capital, cognitive social capital and relational social capital on relationship satisfaction and tested the influence of relationship satisfaction on negative word-of-mouth and re-patronage intentions.
A study of the Chinese consumers’ product-country image of Spain
Authors: Gorostidi-Martinez Haritz , Xu Weimin , Zhao Xiaokang
Published: October 2017

Purpose

As part of a cross-cultural research, the purpose of this paper is to provide further insights into the existing product-country image (PCI) of the Chinese consumers’ perceptions of Spain, its products, and its people, thereby providing an overall contemporary Spanish PCI within the Chinese market.

Design/methodology/approach

In total, 215 valid structured questionnaires were gathered throughout China. Following a pre-investigation of 259 usable questionnaires, a 52-item construct was drawn from the existing widely used PCI item scales, designing a structured PCI construct, covering: “country image,” “personal image,” “product image,” “general knowledge about Spain,” and “personal data.”

Findings

The study provides: a PCI pre-investigation research results as well as a literature review on PCI topic; research results for the five hypotheses concerning Chinese citizens’ view of Spanish product price, quality, technicality, inventiveness, and known brands view; descriptive statistics as well as result graphs for each of the covered PCI sections; our PCI construct variable correlations with the tested five product image variables; and general implications.

Research limitations/implications

Standardizing PCI longitudinal studies, as well as focusing on how the Spanish Government and private sector should determine the long-term criteria to facilitate a clearer representation of the Spanish PCI evolution within the Chinese market, is advised.

Originality/value

The current study intends to capture insights for Spain and other country’s public and private sector decision makers to better integrate market and non-market strategies. The results would further assist delineating strategies to avoid the liability of foreignness of Spanish organizations within China.
Escalation of commitment and information security: theories and implications
Authors: Chulkov Dmitriy V.
Published: October 2017

Purpose

This study aims to explore the challenges that the escalation of commitment poses to information security.

Design/methodology/approach

Two distinct scenarios of escalation behavior are presented based on literature review. Psychological, organizational and economic theories on escalation of commitment are reviewed and applied to the area of information security.

Findings

Escalation of commitment involves continuation of a course of action after receiving negative information about it. In the information security compliance context, escalation affects a firm when an employee decides to break the firm’s information security policy to complete a failing task. In the information security investment context, escalation occurs if a manager continues investment in policies and solutions that are ineffective because of psychological, organizational or economic factors. Both of these types of escalation may be prevented with de-escalation techniques including a change in management or rotation of duties, monitoring, auditing and governance mechanisms.

Practical implications

Implications of escalation of commitment behavior for information security decision-makers and for future research are discussed.

Originality/value

This study complements the literature by establishing the context of escalation of commitment in decisions related to information security and reviewing managerial and economic theories on escalation of commitment.
Incorporating privacy in the design of cloud-based systems: a conceptual meta-model
Authors: Kalloniatis Christos
Published: October 2017

Purpose

The purpose of this paper is to extend PriS (privacy safeguard), a privacy requirements engineering method for eliciting and modelling privacy requirements during system design, with the addition of privacy-aware cloud-based concepts to assist analysts to reason and model about privacy in cloud environments.

Design/methodology/approach

An analysis of previous findings on the file of cloud privacy based on previous work has been conducted and a set of privacy-related concepts that need to be considered during privacy analysis for cloud-based systems have been revealed. These concepts were used for extending the conceptual model of PriS.

Findings

The main finding of the paper is the design of a new, novel conceptual model that assists analysts and designers in reasoning about privacy in cloud environments. A new template using the JSON (Javascript notation object) format has been introduced for better expressing the privacy requirements along with the related concepts presented through the conceptual model, thus letting the developers to better understand the findings during the design stage and better guide them to the implementation of the respective solution.

Research limitations/implications

The design of a cloud-based process that will guide analysts in detail for eliciting and modelling the identified privacy-related requirements is the limitation and in parallel the next step of the specific work presented here.

Practical implications

The conceptual model has been applied on a real case scenario regarding its efficiency on capturing and mapping all necessary concepts for assisting analysts proceed with the design of the privacy-aware system. The results were positive, all concepts were easy to use and totally understandable from the design team and the stakeholders and the use of the JSON template received very positive comments, especially from the developer’s team.

Originality/value

The paper presents a novel conceptual model for reasoning about privacy requirements in the cloud. The applicability of the proposed model has also been tested on a real case study.
To cloud or not to cloud: how risks and threats are affecting cloud adoption decisions
Authors: Kajiyama Takahiko , Jennex Murray , Addo Theophilus
Published: October 2017

Purpose

This paper aims to discover factors that are truly affecting cloud adoption decisions in organizations. Many reasons have been given for the adoption, or lack thereof, of the cloud.

Design/methodology/approach

The paper uses an empirical approach by means of an exploratory survey, using descriptive statistics and t-tests to determine significant differences among various response groups.

Findings

The findings reveal that current and prospective cloud users feel that public cloud computing is less secure than on premise systems. These users feel that the public cloud may still be currently too immature for mission-critical system deployments; however, they do expect it to be more secure in the future as the service models become more mature and better technologies become available. None of the cloud adoption risk factors were universally considered to be showstoppers with respect to adoption.

Research limitations/implications

The sample size is relatively small compared to the number of cloud participants. Additionally, respondents were concentrated in the high technology industries in Southern California.

Originality/value

The paper provides some valuable insight into cloud adoption and concludes that despite hyped security fears, the risks and threats of the cloud are well understood and that with proper planning and implementation, organizations can adopt cloud technologies with no additional risk.
Understanding of e-service security dimensions and its effect on quality and intention to use
Authors: Taherdoost Hamed
Published: October 2017

Purpose

Security has been a critical matter in the development of electronic services. The purpose of this research is to develop a new model to help e-service practitioners and researchers in the evaluation of e-service security and its effect on quality and intention to use e-services.

Design/methodology/approach

According to the literature, 13 security dimensions are extracted. Then, exploratory factor analysis is applied to reduce the number of security dimensions. This step is implemented based on end-users’ perception. Afterward, a hierarchical structure of e-service security is established to calculate the weights of security dimensions applying analytical hierarchy process method by contribution of e-service experts and providers. Finally, structural equation modeling using LISREL is applied to test the proposed theoretical model.

Findings

Results indicates that confidentiality, integrity, privacy, authentication, non-repudiation and availability are antecedents of consumers’ perceived security in e-service. Considering the high significance of perceived security, it is concluded that enhanced feelings of security will result in improved perception of quality. Furthermore, it is found that users will intend to use e-service if they feel that the quality of e-service is high.

Originality/value

Few studies have been done on users’ adoption behaviors of e-services and even those few have not investigated users’ security perception as a major factor affecting users’ intention to use e-services. Considering the increasing concerns of users about the security of their personal information and how it affects their adoption behaviors, there is a need to conduct more studies on the factors involved in this procedure. In this study, the concept of security from both perspective of objective security and subjective security is evaluated.
Measuring attitude towards personal data for adaptive cybersecurity
Authors: Addae Joyce Hoese , Brown Michael , Sun Xu , Towey Dave , Radenkovic Milena
Published: October 2017

Purpose

This paper presents an initial development of a personal data attitude (PDA) measurement instrument based on established psychometric principles. The aim of the research was to develop a reliable measurement scale for quantifying and comparing attitudes towards personal data that can be incorporated into cybersecurity behavioural research models. Such a scale has become necessary for understanding individuals’ attitudes towards specific sets of data, as more technologies are being designed to harvest, collate, share and analyse personal data.

Design/methodology/approach

An initial set of 34 five-point Likert-style items were developed with eight subscales and administered to participants online. The data collected were subjected to exploratory and confirmatory factor analyses and MANOVA. The results are consistent with the multidimensionality of attitude theories and suggest that the adopted methodology for the study is appropriate for future research with a more representative sample.

Findings

Factor analysis of 247 responses identified six constructs of individuals’ attitude towards personal data: protective behaviour, privacy concerns, cost-benefit, awareness, responsibility and security. This paper illustrates how the PDA scale can be a useful guide for information security research and design by briefly discussing the factor structure of the PDA and related results.

Originality/value

This study addresses a genuine gap in research by taking the first step towards establishing empirical evidence for dimensions underlying personal data attitudes. It also adds a significant benchmark to a growing body of literature on understanding and modelling computer users’ security behaviours.
Uncovering the service profit chain in the casino industry
Authors: Prentice Catherine , Wong IpKin Anthony , Lam Desmond
Published: October 2017

Purpose

This paper, from a marketing and management perspective, aims to review the relevant literature germane to casino studies. The review discusses the major findings from previous studies, provides a critique and identifies research gaps for future studies. In particular, the research foci presented in this paper rest on the service profit chain (SPC) model. The review involves studies relating to the constructs of the chain model and comprises sections that are categorized based on the internal link between management and employees, interaction between casino service employees and customers and profitability link.

Design/methodology/approach

The approach used in the current study involves a systematic review of the relevant academic literature with a focus on SPC studies in the casino industry, along with critical evaluation and analysis to identify research gaps. Google Scholar, EBSCOHost, Science Direct, Emerald and other academic databases were used to search relevant studies relating to casino and gambling research streams.

Findings

The review identifies several research gaps on the basis of the SPC link. Specifically, internal service quality needs more attention from both the practice and research points of view. Casino employee research should be extended to include personal traits and characteristics that may contribute to employee performance and loyalty. In the interaction between casino service providers and gamblers, more studies should be undertaken on the efficiency and effectiveness of marketing initiatives and promotions. Externally, the paper points out that more appropriate measurement of customer loyalty and casino profitability should be explored.

Research limitations/implications

This review provides references to focusing on key competitive advantages and presents guidelines on improving business growth and profitability for casino managers. The paper also identifies research areas that future studies should attend to.

Originality/value

The paper is the first thorough literature review of gaming research on marketing and management with a focus on the SPC model. This review represents a new era of gaming research, extending the problem gambling research focus into a broader scope embracing other disciplines.
The effect of older adults’ age identity on attitude toward online travel websites and e-loyalty
Authors: Kim Joonhyeong Joseph , Ahn Young-joo , Kim Insin
Published: October 2017

Purpose

This study aims to identify the effect of age identity on attitude to online sites, examine the impact of this attitude on e-loyalty and investigate the moderating effect of motivational orientation.

Design/methodology/approach

A survey was distributed to an online panel consisting of US-based adults older than 50 and usable data were collected from 284 participants, followed by an analysis using structural equation modeling.

Findings

Psychological and social age negatively influenced older adults’ attitude toward travel websites. Recreation-oriented motivation influenced the effect of online attitude on e-loyalty more strongly than did task-oriented motivation.

Originality/value

Unlike previous studies, the current study provided several managerial implications for e-marketers intending to attract older adults by adopting the multidimensional scale of age identity to predict older adults’ online attitude.