bluuebunny/crossref_metadata_2025 huggingface dataset:
Combinatorial Tissue Engineering Partially Restores Function after Spinal Cord Injury
Authors: Hakim Jeffrey S. , Rodysill Brian R. , Chen Bingkun K. , Schmeichel Ann M. , Yaszemski Michael J. , Windebank Anthony J. , Madigan Nicolas N.
Published: January 2018

Hydrogel scaffolds provide a beneficial microenvironment in transected rat spinal cord. A combinatorial biomaterials based strategy provided a microenvironment that facilitated regeneration while reducing foreign body reaction to the 3-dimensional spinal cord construct. We used poly lactic-co-glycolic acid microspheres to provide sustained release of rapamycin from Schwann cell (SC)-loaded, positively charged oligo-polyethylene glycol fumarate scaffolds. Three dose formulations of rapamycin were compared to controls in 53 rats. We observed a dose-dependent reduction in the fibrotic reaction to the scaffold and improved functional recovery over 6 weeks. Recovery was replicated in a second cohort of 28 animals that included retransection injury. Immunohistochemical and stereological analysis demonstrated that blood vessel number, surface area, vessel diameter, basement membrane collagen, and microvessel phenotype within the regenerated tissue was dependent on the presence of SCs and rapamycin. TRITC-dextran injection demonstrated enhanced perfusion into scaffold channels. Rapamycin also increased the number of descending regenerated axons, as assessed by Fast Blue retrograde axonal tracing. These results demonstrate that normalization of the neovasculature was associated with enhanced axonal regeneration and improved function after spinal cord transection.
Diagnosis and Prognosis Using Machine Learning Trained on Brain Morphometry and White Matter Connectomes
Authors: Wang Yun , Xu Chenxiao , Park Ji-Hwan , Lee Seonjoo , Stern Yaakov , Yoo Shinjae , Kim Jong Hun , Kim Hyoung Seop , Cha Jiook
Published: January 2018

Accurate, reliable prediction of risk for Alzheimer’s disease (AD) is essential for early, disease-modifying therapeutics. Multimodal MRI, such as structural and diffusion MRI, is likely to contain complementary information of neurodegenerative processes in AD. Here we tested the utility of commonly available multimodal MRI (T1-weighted structure and diffusion MRI), combined with high-throughput brain phenotyping—morphometry and connectomics—and machine learning, as a diagnostic tool for AD. We used, firstly, a clinical cohort at a dementia clinic (study 1: Ilsan Dementia Cohort; N=211; 110 AD, 64 mild cognitive impairment [MCI], and 37 subjective memory complaints [SMC]) to test and validate the diagnostic models; and, secondly, Alzheimer’s Disease Neuroimaging Initiative (ADNI)-2 (study 2) to test the generalizability of the approach and the prognostic models with longitudinal follow up data. Our machine learning models trained on the morphometric and connectome estimates (number of features=34,646) showed optimal classification accuracy (AD/SMC: 97% accuracy, MCI/SMC: 83% accuracy; AD/MCI: 97% accuracy) with iterative nested cross-validation in a single-site study, outperforming the benchmark model (FLAIR-based white matter hyperintensity volumes). In a generalizability study using ADNI-2, the combined connectome and morphometry model showed similar or superior accuracies (AD/HC: 96%; MCI/HC: 70%; AD/MCI: 75% accuracy) as CSF biomarker model (t-tau, p-tau, and Amyloid β, and ratios). We also predicted MCI to AD progression with 69% accuracy, compared with the 70% accuracy using CSF biomarker model. The optimal classification accuracy in a single-site dataset and the reproduced results in multi-site dataset show the feasibility of the high-throughput imaging analysis of multimodal MRI and data-driven machine learning for predictive modeling in AD.
Reactivation of neural patterns during memory reinstatement supports encoding specificity
Authors: Staudigl Tobias , Hanslmayr Simon
Published: January 2018

Encoding specificity or transfer appropriate processing state that memory benefits when items are encoded and retrieved in the same modality compared to when encoding and retrieval is conducted in different modalities. In neural terms, these effects can be expressed by a resonance process between a memory cue and a stored engram; the more the two overlap the better memory performance. We here used temporal pattern analysis in MEG to tap into this resonance process. We predicted that reactivation of sensory patterns established during encoding has opposing effects depending on whether there is a match or mismatch between the memory cue and the encoding modality. To test this prediction items were presented either visually or aurally during encoding and in a recognition test to create match (e.g. “dog” presented aurally during encoding and recognition) and mismatch conditions (e.g. “dog” presented aurally during encoding and shown visually during recognition). Memory performance was better for items in the match compared to the mismatch condition. MEG results showed that memory benefitted from neural pattern reinstatement only in the match condition, but suffered from reinstatement in the mismatch condition. These behavioural and neural effects were asymmetric in that they were only obtained for aurally encoded words but not for visually encoded words. A simple computational model was generated in order to simulate these opposing effects of neural pattern reactivation on memory performance. We argue that these results suggest that reactivation of neural patterns established during encoding underlies encoding specificity or transfer appropriate processing.
Motion regions are modulated by scene content
Authors: Korkmaz Hacialihafiz Didem , Bartels Andreas
Published: January 2018

Creating a stable perception of the world during pursuit eye movements is one of the everyday roles of visual system. Some motion regions have been shown to differentiate between motion in the external world from that generated by eye movements. However, in most circumstances, perceptual stability is consistently related to content: the surrounding scene is typically stable. However, no prior study has examined to which extent motion responsive regions are modulated by scene content, and whether there is an interaction between content and motion response. In the present study we used a factorial design that has previously been shown to reveal regional involvement in integrating efference copies of eye-movements with retinal motion to mediate perceptual stability and encode real-world motion. We then added scene content as a third factor, which allowed us to examine to which extent real-motion, retinal motion, and static responses were modulated by meaningful scenes versus their Fourier scrambled counterpart. We found that motion responses in human motion responsive regions V3A, V6, V5+/MT+ and cingulate sulcus visual area (CSv) were all modulated by scene content. Depending on the region, these motion-content interactions differentially depended on whether motion was self-induced or not. V3A was the only motion responsive region that also showed responses to still scenes. Our results suggest that contrary to the two-pathway hypothesis, scene responses are not isolated to ventral regions, but also can be found in dorsal areas.
A robot-based gait training therapy for pediatric population with Cerebral Palsy: goal setting, proposal and preliminary clinical implementation
Authors: Bayón C. , Martín-Lorenzo T. , Moral-Saiz B. , Ramírez O. , Pérez-Somarriba A. , Lerma-Lara S. , Martínez I. , Rocon E.
Published: January 2018

BACKGROUND

The use of robotic trainers has increased with the aim of improving gait function in patients with limitations. Nevertheless, there is an absence of studies that deeply describe detailed guidelines of how to correctly implement robot-based treatments for gait rehabilitation. This contribution proposes an accurate robot-based training program for gait rehabilitation of pediatric population with Cerebral Palsy (CP).

METHODS

The program is focused on the achievement of some specifications defined by the International Classification of Functioning, Disability and Health framework, Children and Youth version (ICF-CY). It is framed on 16 non-consecutive sessions where motor control, strength and power exercises of lower limbs are performed in parallel with a postural control strategy. A clinical evaluation with four pediatric patients with CP using the CPWalker robotic platform is presented.

RESULTS

The preliminary evaluation with patients with CP shows improvements in several aspects as strength (74.03±40.20%), mean velocity (21.46±33.79%), step length (17.95±20.45%) or gait performance (e.g. 18.88±14.31% in Gross Motor Function Measure-88 items, E and D dimensions).

CONCLUSIONS

The improvements achieved in the short term show the importance of working strength and power functions meanwhile over-ground training with postural control. This research could serve as preliminary support for future clinical implementations in any robotic device.

TRIAL REGISTRATION

The study was carried out with the number R-0032/12 from Local Ethical Committee of the Hospital Infantil Niño Jesús. Public trial registration: ISRCTN18254257. Registered 23 March 2017, retrospectively registered.
Evolution at two time frames: polymorphisms from an ancient singular divergence event fuel contemporary parallel evolution
Authors: Van Belleghem Steven M. , Vangestel Carl , De Wolf Katrien , De Corte Zoë , Möst Markus , Rastas Pasi , De Meester Luc , Hendrickx Frederik
Published: January 2018

When species occur in repeated ecologically distinct habitats across their range, adaptation may proceed surprisingly fast and result in parallel evolution. There is increasing evidence that such cases of rapid parallel evolution are fueled by standing genetic variation, but the origin of this genetic variation remains poorly understood. In Pogonus chalceus beetles, short- and long-winged ecotypes have diverged in response to contrasting hydrological regimes and can be repeatedly found along the Atlantic European coast. By analyzing genomic variation across the beetles’ distribution, we reveal that genomically widespread short-wing selected alleles evolved during a singular divergence event, estimated at ~0.19 Mya. The ancient and differentially selected alleles are currently polymorphic in all populations across the range, allowing for the fast evolution of one ecotype from a small number of random individuals, as low as 5 to 15, of the populations of the other ecotype. Our results suggest that cases of fast parallel ecological divergence might be the result of evolution at two different time frames: divergence in the past, followed by repeated selection on the divergently evolved alleles after admixture. We suggest that this mechanism may be common and potentially further driven by periods of geographic isolation imposed by large-scale environmental changes such as glacial cycles.
Machine learning models in electronic health records can outperform conventional survival models for predicting patient mortality in coronary artery disease
Authors: Steele Andrew J. , Aylin Cakiroglu S. , Shah Anoop D. , Denaxas Spiros C. , Hemingway Harry , Luscombe Nicholas M.
Published: January 2018

Prognostic modelling is important in clinical practice and epidemiology for patient management and research. Electronic health records (EHR) provide large quantities of data for such models, but conventional epidemiological approaches require significant researcher time to implement. Expert selection of variables, fine-tuning of variable transformations and interactions, and imputing missing values in datasets are time-consuming and could bias subsequent analysis, particularly given that missingness in EHR is both high, and may carry meaning.

Using a cohort of over 80,000 patients from the CALIBER programme, we performed a systematic comparison of several machine-learning approaches in EHR. We used Cox models and random survival forests with and without imputation on 27 expert-selected variables to predict all-cause mortality. We also used Cox models, random forests and elastic net regression on an extended dataset with 586 variables to build prognostic models and identify novel prognostic factors without prior expert input.

We observed that data-driven models used on an extended dataset can outperform conventional models for prognosis, without data preprocessing or imputing missing values, and with no need to scale or transform continuous data. An elastic net Cox regression based with 586 unimputed variables with continuous values discretised achieved a C-index of 0.801 (bootstrapped 95% CI 0.799 to 0.802), compared to 0.793 (0.791 to 0.794) for a traditional Cox model comprising 27 expert-selected variables with imputation for missing values.

We also found that data-driven models allow identification of novel prognostic variables; that the absence of values for particular variables carries meaning, and can have significant implications for prognosis; and that variables often have a nonlinear association with mortality, which discretised Cox models and random forests can elucidate.

This demonstrates that machine-learning approaches applied to raw EHR data can be used to build reliable models for use in research and clinical practice, and identify novel predictive variables and their effects to inform future research.
Asymptotically optimal minimizers schemes
Authors: Marçais Guillaume , DeBlasio Dan , Kingsford Carl
Published: January 2018

Motivation

The minimizers technique is a method to sample k-mers that is used in many bioinformatics software to reduce computation, memory usage and run time. The number of applications using minimizers keeps on growing steadily. Despite its many uses, the theoretical understanding of minimizers is still very limited. In many applications, selecting as few k-mers as possible (i.e. having a low density) is beneficial. The density is highly dependent on the choice of the order on the k-mers. Different applications use different orders, but none of these orders are optimal. A better understanding of minimizers schemes, and the related local and forward schemes, will allow designing schemes with lower density, and thereby making existing and future bioinformatics tools even more efficient.

Results

From the analysis of the asymptotic behavior of minimizers, forward and local schemes, we show that the previously believed lower bound on minimizers schemes does not hold, and that schemes with density lower than thought possible actually exist. The proof is constructive and leads to an efficient algorithm to compare k-mers. These orders are the first known orders that are asymptotically optimal. Additionally, we give improved bounds on the density achievable by the 3 type of schemes.

Contact

gmarcais@cs.cmu.educkingsf@cs.cmu.edu
Opposing effects of population density and stress on Escherichia coli mutation rate
Authors: Krašovec Rok , Richards Huw , Gifford Danna R. , Belavkin Roman V. , Channon Alastair , Aston Elizabeth , McBain Andrew J. , Knight Christopher G.
Published: January 2018

Evolution depends on mutations. For an individual genotype, the rate at which mutations arise is known to increase with various stressors (stress-induced mutagenesis – SIM) and decrease at high population density (density-associated mutation-rate plasticity – DAMP). We hypothesised that these two forms of mutation rate plasticity would have opposing effects across a nutrient gradient. Here we test this hypothesis, culturing Escherichia coli bacteria in increasingly rich media. We distinguish an increase in mutation rate with added nutrients through SIM (dependent on error-prone polymerases Pol IV and Pol V) and an opposing effect of DAMP (dependent on MutT, which removes oxidised G nucleotides). The combination of DAMP and SIM result in a mutation rate minimum at intermediate nutrient levels (which can support 7×108 cells ml−1). These findings demonstrate a strikingly close and nuanced relationship of ecological factors – stress and population density – with mutation, the fuel of all evolution.
Durability of environment-recruitment relationships in aquatic ecosystems: insights from long-term monitoring in a highly modified estuary and implications for management
Authors: Tamburello Natascia , Connors Brendan M. , Fullerton David , Phillis Corey C.
Published: January 2018

The environment can strongly influence the survival of aquatic organisms and their resulting dynamics. Our understanding of these relationships, typically based on correlations, underpins many contemporary resource management decisions and conservation actions. However, such relationships can break down over time as ecosystems evolve. Even when durable, they may not be very useful for management if they exhibit high variability, context dependency, or non-stationarity. Here, we systematically review the literature to identify trends across environment-recruitment relationships for aquatic taxa from California’s San Francisco Bay and Sacramento-San Joaquin Delta Estuary. This is one of the most heavily modified aquatic ecosystems in North America, and home to numerous species of concern whose relationships with the environment inform regulatory actions and constraints. We retested 23 of these relationships spanning 9 species using data that have accumulated in the years since they were first published (9-40 additional years) to determine whether they persisted. Most relationships were robust (i.e., same or stronger in magnitude) to the addition of new data, but the ability to predict how a species will respond to environmental change did not generally improve with more data. Instead, prediction error generally increased over time and in some cases very quickly, suggesting a rapid regime shift. Our results suggest that more data alone will not necessarily improve the ability of these relationships to inform decision making. We conclude by synthesizing emerging insights from the literature on best practices for the analysis, use, and refinement of environment-recruitment relationships to inform decision making in dynamic ecosystems.
A phenomenological model of the time course of maximal voluntary isometric contraction force for optimization of complex loading schemes
Authors: Herold Johannes L. , Kirches Christian , Schlöder Johannes P.
Published: January 2018

We construct a simple and predictive ordinary differential equation model to describe the time course of maximal voluntary isometric contraction (MVIC) force during voluntary isometric contractions and at rest. These time courses are of particular interest whenever force capacities are a limiting factor, e.g. during heavy manual work or resistance training (RT) sessions. Our model is able to describe MVIC force under complex loading schemes and is validated with a comprehensive set of published data from the elbow flexors. We use the calibrated model to analyze fatigue and recovery patterns observed in the literature. Due to the model’s structure, it can be efficiently employed to optimize complex loading schemes. We demonstrate this by computing a work-rest schedule that minimizes fatigue and an optimal isometric RT session as examples.
Integration of single-cell RNA-seq data into metabolic models to characterize tumour cell populations
Authors: Damiani Chiara , Maspero Davide , Di Filippo Marzia , Colombo Riccardo , Pescini Dario , Graudenzi Alex , Westerhoff Hans Victor , Alberghina Lilia , Vanoni Marco , Mauri Giancarlo
Published: January 2018

Motivation

Metabolic reprogramming is a general feature of cancer cells. Regrettably, the comprehensive quantification of metabolites in biological specimens does not promptly translate into knowledge on the utilization of metabolic pathways. Computational models hold the promise to bridge this gap, by estimating fluxes across metabolic pathways. Yet they currently portray the average behavior of intermixed subpopulations, masking their inherent heterogeneity known to hinder cancer diagnosis and treatment. If complemented with the information on single-cell transcriptome, now enabled by RNA sequencing (scRNA-seq), metabolic models of cancer populations are expected to empower the characterization of the mechanisms behind metabolic heterogeneity. To this aim, we propose single-cell Flux Balance Analysis (scFBA) as a computational framework to translate sc-transcriptomes into single-cell fluxomes.

Results

We show that the integration of scRNA-seq profiles of cells derived from lung ade-nocarcinoma and breast cancer patients, into a multi-scale stoichiometric model of cancer population: 1) significantly reduces the space of feasible single-cell fluxomes; 2) allows to identify clusters of cells with different growth rates within the population; 3) points out the possible metabolic interactions among cells via exchange of metabolites.

Availability

The scFBA suite of MATLAB functions is available at https://github.com/BIMIB-DISCo/scFBA, as well as the case study datasets.

Contact

chiara.damiani@unimib.it
Antimalarial pantothenamide metabolites target acetyl-CoA synthesis inPlasmodium falciparum
Authors: Schalkwijk Joost , Allman Erik L. , Jansen Patrick A.M. , de Vries Laura E. , Jackowski Suzanne , Botman Peter N. M. , Beuckens-Schortinghuis Christien A. , Koolen Karin M.J. , Bolscher J. M. , Vos Martijn W. , Miller Karen , Reeves Stacy A. , Pett Helmi , Trevitt Graham , Wittlin Sergio , Scheurer Christian , Sax Sibylle , Fischli Christoph , Josling Gabrielle , Kooij Taco W.A. , Bonnert Roger , Campo Brice , Blaauw Richard H. , Rutjes Floris P.J.T. , Sauerwein Robert W. , Llinás Manuel , Hermkens Pedro H.H. , Dechering Koen J.
Published: January 2018

Malaria eradication is critically dependent on novel drugs that target resistantPlasmodiumparasites and block transmission of the disease. Here we report the discovery of potent pantothenamide bioisosteres that are active against blood-stageP. falciparumand also block onward mosquito transmission. These compounds are resistant to degradation by serum pantetheinases, show favorable pharmacokinetic properties and clear parasites in a humanized rodent infection model. Metabolomics revealed that CoA biosynthetic enzymes convert pantothenamides into drug-conjugates that interfere with parasite acetyl-CoA anabolism.In vitrogenerated resistant parasites showed mutations in acetyl-CoA synthetase and acyl-CoA synthetase 11, confirming the key roles of these enzymes in the sensitivity to pantothenamides. These new pantothenamides provide a promising class of antimalarial drugs with a unique mode of action.

One sentence summary

Pantothenamides form antimetabolites that interfere with acetyl-CoA metabolism in the human malaria parasitePlasmodium falciparum
SPADIS: An Algorithm for Selecting Predictive and Diverse SNPs in GWAS
Authors: Yilmaz Serhan , Tastan Oznur , Cicek A. Ercument
Published: January 2018

Phenotypic heritability of complex traits and diseases is seldom explained by individual genetic variants. Algorithms that select SNPs which arecloseand connected on a biological network have been successful in finding biologically-interpretable and predictive loci. However, we argue that the connectedness constraint favors selecting redundant features that affect similar biological processes and therefore does not necessarily yield better predictive performance. In this paper, we propose a novel method called SPADIS that selects SNPs thatcoverdiverse regions in the underlying SNP-SNP network. SPADIS favors the selection of remotely located SNPs in order to account for the complementary additive effects of SNPs that are associated with the phenotype. This is achieved by maximizing a submodular set function with a greedy algorithm that ensures a constant factor (1−1/e) approximation. We compare SPADIS to the state-of-the-art method SConES, on a dataset of Arabidopsis Thaliana genotype and continuous flowering time phenotypes. SPADIS has better regression performance in 12 out of 17 phenotypes on average, it identifies more candidate genes and runs faster. We also investigate the use of Hi-C data to construct SNP-SNP network in the context of SNP selection problem for the first time, which yields slight but consistent improvements in regression performance. SPADIS is available athttp://ciceklab.cs.bilkent.edu.tr/spadis
Spatio-Temporal Gene Discovery For Autism Spectrum Disorder
Authors: Norman Utku , Cicek A. Ercument
Published: January 2018

Whole exome sequencing (WES) studies for Autism Spectrum Disorder (ASD) could identify only around six dozen risk genes to date because the genetic architecture of the disorder is highly complex. To speed the gene discovery process up, a few network-based ASD gene discovery algorithms were proposed. Although these methods use static gene interaction networks, functional clustering of genes is bound to evolve during neurodevelopment and disruptions are likely to have a cascading effect on the future associations. Thus, approaches that disregard the dynamic nature of neurodevelopment are limited in power. Here, we present a spatio-temporal gene discovery algorithm for ASD, which leverages information from evolving gene coexpression networks of neurodevelopment. The algorithm solves a variant of prize-collecting Steiner forest-based problem on coexpression networks to model neurodevelopment and transfer information from precursor neurodevelopmental windows. The decisions made by the algorithm can be traced back, adding interpretability to the results. We apply the algorithm on WES data of 3,871 samples and identify risk clusters using BrainSpan coexpression networks of earlyand mid-fetal periods. On an independent dataset, we show that incorporation of the temporal dimension increases the prediction power: Predicted clusters are hit more and show higher enrichment in ASD-related functions compared to the state-of-the-art. Code is available at http://ciceklab.cs.bilkent.edu.tr/ST-Steiner/.
A proposal for a standardized bacterial taxonomy based on genome phylogeny
Authors: Parks Donovan H. , Chuvochina Maria , Waite David W. , Rinke Christian , Skarshewski Adam , Chaumeil Pierre-Alain , Hugenholtz Philip
Published: January 2018

Taxonomy is a fundamental organizing principle of biology, which ideally should be based on evolutionary relationships. Microbial taxonomy has been greatly restricted by the inability to obtain most microorganisms in pure culture and, to a lesser degree, the historical use of phenotypic properties as the basis for classification. However, we are now at the point of obtaining genome sequences broadly representative of microbial diversity by using culture-independent techniques, which provide the opportunity to develop a comprehensive genome-based taxonomy. Here we propose a standardized bacterial taxonomy based on a concatenated protein phylogeny that conservatively removes polyphyletic groups and normalizes ranks based on relative evolutionary divergence. From 94,759 bacterial genomes, 99 phyla are described including six major normalized monophyletic units from the subdivision of the Proteobacteria, and amalgamation of the Candidate Phyla Radiation into the single phylum Patescibacteria. In total, 73% of taxa had one or more changes to their existing taxonomy.
Cryo-EM structure of Escherichia coli σ70 RNAP and promoter DNA complex revealed a role of σ non-conserved region during the open complex formation
Authors: Narayanan Anoop , Vago Frank S. , Li Kungpeng , Qayyum M. Zuhaib , Yernool Dinesh , Jiang Wen , Murakami Katsuhiko S.
Published: January 2018

First step of gene expression is transcribing the genetic information stored in DNA to RNA by the transcription machinery including RNA polymerase (RNAP). In Escherichia coli, a primary σ70 factor form the RNAP holoenzyme to express housekeeping genes. The σ70 contains a large insertion at between the conserved regions 1.2 and 2.1, the σ non-conserved region (σNCR), but its function remains to be elucidated. In this study, we determined the cryo-EM structures of the E. coli RNAP σ70 holoenzyme and its complex with promoter DNA (open complex, RPo) at 4.2 and 5.75 Å resolutions, respectively, to reveal native conformations of RNAP and DNA. The RPo structure presented here found an interaction between R157 residue in the σNCR and promoter DNA just upstream of the −10 element, which was not observed in a previously determined E. coli RNAP transcription initiation complex (RPo plus short RNA) structure by X-ray crystallography due to restraint of crystal packing effect. Disruption of the σNCR and DNA interaction by the amino acid substitution (R157E) influences the DNA opening around the transcription start site and therefore decreases the transcription activity of RNAP. We propose that the σNCR and DNA interaction is conserved in proteobacteria and RNAP in other bacteria replace its role with a transcription factor.
Transcriptomic analyses reveal tissue-specific selection on genes related to apoptotic processes in the subterranean rodent,Ctenomys sociabilis
Authors: Lang Andrew , Kordonowy Lauren , Lacey Eileen , MacManes Matthew
Published: January 2018

Specialization for a subterranean existence is expected to impact multiple aspects of an organism’s biology, including behavior, physiology, and genomic structure. While the phenotypic correlates of life underground have been extensively characterized, the genetic bases for these traits are not well understood, due in part to the challenges of generating large, multi-locus data sets using traditional DNA sequencing strategies. To begin exploring the genomic architecture of adaptation to a subterranean existence, we generated high-qualityde novotranscriptome assemblies for 8 different tissue types (hippocampus, hypothalamus, kidney, liver, spleen, ovary, testis, skin) obtained from the colonial tuco-tuco (Ctenomys sociabilis), a group-living species of subterranean rodent that is endemic to southwestern Argentina. From these transcriptomes, we identified genes that are evolving more rapidly in theC. sociabilislineage compared to other subterranean species of rodents. These comparisons suggest that genes associated with immune response, cell-cycle regulation, and heavy metal detoxification have been subject to positive selection inC. sociabilis. Comparisons of transcripts from different tissues suggest that the spleen and liver - organs involved in immune function and detoxification - may be particularly important sites for these adaptations, thereby underscoring the importance of including multiple tissue types in analyses of transcriptomic variation. In addition to providing an important resource for future genomic studies ofC. sociabilis, our analyses generate new insights into the genomic architecture of functionally significant phenotypic traits in free-living mammals.
Decomposing parasite fitness in a two-host, two-parasite system reveals the underpinnings of parasite specialization
Authors: Lievens Eva J. P. , Perreau Julie , Agnew Philip , Michalakis Yannis , Lenormand Thomas
Published: January 2018

Abstract

The ecological specialization of parasites – whether they can obtain high fitness on very few or very many different host species – is a determining feature of their ecology. In order to properly assess specialization, it is imperative to measure parasite fitness across host species; to understand its origins, fitness must be decomposed into the underlying traits. Despite the omnipresence of parasites with multiple hosts, very few studies assess and decompose their specialization in this way. To bridge this gap, we quantified the infectivity, virulence, and transmission rate of two parasites, the horizontally transmitted microsporidiansAnostracospora rigaudiandEnterocytospora artemiae, in their natural hosts, the brine shrimpArtemia parthenogeneticaandArtemia franciscana. Our results demonstrate that each parasite performs well on one of the two host species (A. rigaudionA. parthenogenetica, andE. artemiaeonA. franciscana), and poorly on the other. This partial specialization is driven by high infectivity and transmission rates in the preferred host, and is associated with maladaptive virulence and large costs of resistance in the other. Our study represents a rare empirical contribution to the study of parasite evolution in multi-host systems, highlighting the negative effects of under- and over-exploitation when adapting to multiple hosts.
Inferring the probability of the derived versus the ancestral allelic state at a polymorphic site
Authors: Keightley Peter D. , Jackson Benjamin C.
Published: January 2018

It is known that the allele ancestral to the variation at a polymorphic nucleotide site cannot be assigned with certainty, and that the most frequently used method to assign the ancestral state – maximum parsimony – is prone to mis-inference. Estimates of counts of sites that have a certain number of copies of the derived allele (the unfolded site frequency spectrum, uSFS) made by parsimony are therefore also biased. We previously developed a maximum likelihood method to estimate the uSFS for a focal species, using information from two outgroups and assuming simple models of nucleotide substitution. Here, we extend this approach to infer the uSFS, allowing multiple outgroups, potentially any phylogenetic tree topology and more complex models of nucleotide substitution. We find, however, that two outgroups and assuming the Kimura 2-parameter model is adequate for uSFS inference in most cases. We show that using parsimony for ancestral state inference at a specific site seriously breaks down in two situations. The first is where the outgroups provide no information about the ancestral state of variation in the focal species. In this case, nucleotide variation will be under-estimated if such sites are removed from the data. The second is where the minor allele in the focal species agrees with the allelic state of the outgroups. In this situation, parsimony tends to over-estimate the probability of the major allele being derived, because it fails to account for the fact that sites with a high frequency of the derived allele tend to be rare in most data sets. We present a method that corrects this deficiency, which is capable of providing unbiased estimates of ancestral state probabilities on a site-by-site basis and the uSFS.
N′-[(1E)-2,5-Dimethoxybenzylidene]pyridine-2-carbohydrazide
Authors: R.Albayati Mustafa , Mague Joel T. , Akkurt Mehmet , Mohamed Shaaban K. , Elgarhy Sahar M. I.
Published: January 2018

The molecule of the title compound, C15H15N3O3, is twisted, with the dihedral angle between the pyridyl and benzene rings being 58.34 (6)°. In the crystal, amide-N—H...O(amide) and imine-C—H...O(amide) hydrogen bonds lead to zigzag (glide symmetry) chains extending along the c axis which are joined into layers parallel to the [100] direction by offset π–π stacking interactions between inversion-related benzene rings [centroid–centroid distance = 3.7468 (7) Å] and by C—H...π(pyridyl) interactions. Pyridyl rings protrude from the surfaces of the layers and partially intercalate with those of adjacent layers.
Cervejaria Noi: brewing a go-to-market strategy
Authors: Arthur Mauro Paulo , Ketne Daltoé Kateline , da Costa Lopes João Ricardo , Albergaria Freitas Flavia d , Almeida Victor M.C.
Published: January 2018

Subject area

Marketing Channels.

Study level/applicability

The case was developed to stimulate the discussion about decisions and strategies of channel and was recommended for MBA students in courses such as Marketing Channels or Trade Marketing in Business Administration.

Case overview

The case reports the dilemma experienced in 2013 by Osmar Buzin, one of the partners of Cervejaria Noi, whose specialty beers had achieved prestige among their customers, mainly in the city of Niterói, RJ, where the company was born. This success aroused the interest of other markets that wanted to sell their products. The opportunity for expansion brought together the need to decide how to meet these new markets: deliver directly to the points of sale, as it did before; or use distributors. Osmar knew that he could count on Gilmar Gutbrodt, his partner and brewmaster, along with Bianca Buzin, the General Manager of the brewery to evaluate together the best strategy for reaching new markets.

Expected learning outcomes

It is expected that at the end of the discussion of the case, students will be able to achieve the following learning outcomes: to design the path-to-market, identifying the role of intermediaries; to identify distribution alternatives and key channel members; and to perceive the advantages and disadvantages of intermediation and its unfolding in channel management.

Supplementary materials

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

Subject code

CSS: 8: Marketing.
The role of ideal self-congruence and brand attachment in consumers’ negative behaviour
Authors: Japutra Arnold , Ekinci Yuksel , Simkin Lyndon , Nguyen Bang
Published: January 2018

Purpose

The purpose of this paper is to investigate the role of ideal self-congruence in instigating two types of negative consumer behaviours – compulsive buying and external trash-talking – and the mediating role of brand attachment on these relationships.

Design/methodology/approach

Two studies were designed using a structural equation modelling methodology. Study 1a was based on a mail survey of 280 respondents, whereas Study 1b was based on an electronic survey of 152 respondents. Study 1b was conducted to test the external validity of the research model.

Findings

In Study 1a, ideal self-congruence affects emotional brand attachment and in turn emotional brand attachment affects compulsive buying behaviour and external trash-talking. The mediation analysis indicates that emotional brand attachment mediates the relationships. Study 1b offers support to the results of Study 1a.

Practical implications

From a practical point of view, this study is useful for policymakers seeking to regulate and prevent excessive consumerism. For marketers, they should understand that brand attachment leads to compulsive buying and external trash-talking, which may provide immediate benefit for the brand or the firm. However, marketers should understand that these two negative behaviours may harm the firm image and consumers’ well-being in the long run.

Social implications

Apart from practical implications, firms should consider alleviating compulsive buying, as it is harmful to society. Similarly, excessive external trash-talking may lead to physical aggression. Consumers expect firms to be socially responsible. Thus, firms should start conducting activities that promote responsible shopping and reduce external trash-talking.

Originality/value

The study highlights a dark side of ideal self-congruence and brand attachment. The results suggest that ideal self-congruence with the help of emotional brand attachment predicts compulsive buying behaviour and external trash-talking. This may not only damage brand image but also the consumers’ well-being.
A systematic review of risk variables for child abuse material offenders
Authors: Garrington Catherine , Rickwood Debra , Chamberlain Peter , P. Boer Douglas
Published: January 2018

Purpose

The purpose of this paper is to collate the available research into the characteristics of child abuse material (CAM) offenders to inform future assessment and treatment options. This systematic review collates the contribution and directionality of variables from existing research assessing an offenders’ use of CAM.

Design/methodology/approach

Background and definitions of terminology are reviewed, and a summary of sexual reoffending rates provided. Articles were then identified for inclusion through a systematic review using online searches, EBSCOHost and other databases. Articles were also identified from reference lists. After exclusions, the final sample (n=17) were reviewed for identified variables and their directional contribution to risk.

Findings

Internet only (IO) offenders present with a range of similarities and differences. The demographic, psychological and offence-specific risk variables identified suggest IO offenders differ from other types of sexual offenders. Using the collated variables, IO offender profiles are suggested.

Research limitations/implications

Limitations have been identified in the availability of research in this area, the variety of terminology and the definitions in common usage. Additionally, there are challenges in ascertaining the truthfulness of self-reported data.

Practical implications

Development of IO offender-specific risk assessment tools would contribute to advances in targeted supervision and treatment. In turn, this contributes to community safety by protecting children from online sexual victimisation.

Originality/value

Based on identified gaps, this review contributes to ongoing research by signalling future pathways for IO offender-specific risk assessment.
Relationship orientation in banking and insurance services – a review of the evidence
Authors: Shetty Ankitha , Basri Savitha
Published: January 2018

Purpose

This study aims to review the published empirical research on relationship orientation in banking and insurance services. The objective of the study is to understand whether a strong customer–sales representative relationship contributes to sales effectiveness and to know the significance of relational behaviors in developing and maintaining long-term relationship.

Design/methodology/approach

Through Boolean search, a systematic review with narrative synthesis was conducted. Relevant electronic bibliographic databases and reference lists of pertinent review articles were searched. Screening and eligibility of articles were based on participants, interventions, comparisons, outcomes (PICO) model and PRISMA (Preferred Reporting Items for Systematic reviews) guidelines.

Findings

A total of 22 papers were finalized for the study, and results reveal that customer orientation behavior and adaptive selling behavior of sales representatives improve relationship quality, culminating in higher customer satisfaction, enhanced loyalty and escalated commitment, whereas selling orientation diminishes the relationship quality. The attributes of sales person especially contact intensity, contact frequency and client knowledge augment sales effectiveness and longstanding relationship with the customers.

Practical implications

This paper would provide valuable insights for financial sales representatives, academicians and practitioners of relationship marketing in the area of banking and insurance services. Personalization and customizations are important aspects of the provision of social benefits that strengthen competitive advantage.

Originality/value

Although the relevance of relationship marketing has been acknowledged, the conceptual base of relationship orientation in banking and insurance services has received only limited attention.
Satisfaction level and competitiveness in subsistence small businesses
Authors: Jardón Carlos M.
Published: January 2018

Purpose

Subsistence small businesses (SSBs) do not seek the maximum benefit; they only seek a benefit that enough satisfies their basic needs. In consequence, a dual behaviour of companies is expected and possibly the competitiveness of these companies is different. The purpose of this paper is to study the dual behaviour of SSBs and the differences about their competitive advantages.

Design/methodology/approach

Data were obtained by conducting surveys with owners and managers of wood processing companies located in a region of Misiones (Argentina). The results were checked by interviews in 2012 and 2015. The research uses principal component analysis and K-means to classify the different behaviour and MANOVA analysis to study the relationships.

Findings

The findings suggest two types of SSBs and show that competitive advantages are different into two groups of companies.

Research limitations/implications

The data used refer to a certain period of time, with interviews in next periods. Sample is in a particular region and sector and generalisations should be done carefully. The variables are measured with subjective questions.

Practical implications

The findings suggest instruments to change the strategy of unsatisfied SSBs to grow.

Social implications

The growth of SSBs is very important in poorest areas. The paper suggest governments’ politics that facilitate a stable environment for improving competitiveness of SSBs.

Originality/value

SSBs are very important in developing countries, but they are not sufficiently studied. The research shows the importance of satisfying principle in the competitiveness of subsistence entrepreneurs.
Family control and innovativeness in private firms: the mediating role of board task performance
Authors: Deman Robin , Jorissen Ann , Laveren Eddy
Published: January 2018

Purpose

Although the majority of research explores the direct relationship between family control and innovativeness, the purpose of this paper is to investigate mediators that explain how family control is related to innovativeness. Grounded in agency theory, resource dependence theory, and the resource-based view of the firm, the authors suggest that this relationship operates through board task performance, that is, the level of directors’ involvement in control and service tasks.

Design/methodology/approach

To test the hypotheses, structural equation modeling is applied to cross-sectional survey data collected from 329 private firms that are located in Belgium. Family control is defined as 50 percent family ownership in combination with at least one family member being involved in the management or board of directors of the firm.

Findings

Four key results emerge from the analysis. First, family control is negatively associated with control task performance but does not affect service task performance. Second, control and service task performance positively influence innovativeness. Third, the negative relationship between family control and innovativeness is partially mediated by control task performance. Fourth, the presence of a family CEO and the percentage of family directors address heterogeneity among family controlled firms (FCFs).

Originality/value

This paper complements and extends existing research on the relationship between family control and innovativeness by adopting a governance perspective. The authors contribute to a deeper understanding of why FCFs are more or less innovative than nonfamily controlled firms and reveal underlying mechanisms previously uncovered.
Organizational climate and job satisfaction: do employees’ personalities matter?
Authors: Ahmad Kamarul Zaman Bin , Jasimuddin Sajjad M. , Kee Wang Ling
Published: January 2018

Purpose

The purpose of this paper is to provide some insights on the interplay of organizational climate and job satisfaction, taking personality traits as a moderator.

Design/methodology/approach

The paper reviews the extant literature from which it develops a theoretical model which is then tested empirically in the Malaysian context, using hierarchical regression methodology.

Findings

The results imply that there are moderating effects of personality traits on the relationship between certain aspects of organizational climate and job satisfaction.

Research limitations/implications

The cross-sectional nature of this study inhibits the testing of causality between the variables. The research model and hypotheses were tested, using data drawn only from companies operating in a single country.

Practical implications

The paper provides valuable information to leaders and managers in understanding which personality works better in the potential casual linkage between organizational climate and overall job satisfaction. This paper also helps practitioners to understand better why the same climate can have different impacts on different people.

Originality/value

It contributes to the conceptualization of the organizational climate by emphasizing Litwin and Stringer’s (1968) dimensions of organizational climate as the important determinants of the job satisfaction. Moreover, it expands the traditional discussion by incorporating the personal traits that moderates the relationship between organizational climate and the job satisfaction.