bluuebunny/crossref_metadata_2025 huggingface dataset:
Convergence of biannual moulting strategies across birds and mammals
Authors: Beltran Roxanne S. , Burns Jennifer M. , Breed Greg A.
Published: May 2018

Birds and mammals have developed numerous strategies for replacing worn feathers and hair. Moulting usually occurs on an annual basis; however, moults that take place twice per year (biannual moults) also occur. Here, we review the forces driving the evolution of various moult strategies, focusing on the special case of the complete biannual moult as a convergence of selection pressures across birds and mammals. Current evidence suggests that harsh environmental conditions or seasonality (e.g. larger variation in temperatures) drive evolution of a biannual moult. In turn, the biannual moult can respond to secondary selection that results in phenotypic alteration such as colour changes for mate choice dynamics (sexual selection) or camouflage requirements (natural selection). We discuss the contributions of natural and sexual selection to the evolution of biannual moulting strategies in the contexts of energetics, niche selection, functionality and physiological mechanisms. Finally, we suggest that moult strategies are directly related to species niche because environmental attributes drive the utility (e.g. thermoregulation, camouflage, social dynamics) of the hair or feathers. Functional efficiency of moult may be undermined if the pace of evolution fails to match that of the changing climate. Thus, future research should seek to understand the plasticity of moult duration and phenology, especially in the context of annual cycles.
Reverse-engineering ecological theory from data
Authors: Martin Benjamin T. , Munch Stephan B. , Hein Andrew M.
Published: May 2018

Ecologists have long sought to understand the dynamics of populations and communities by deriving mathematical theory from first principles. Theoretical models often take the form of dynamical equations that comprise the ecological processes (e.g. competition, predation) believed to govern system dynamics. The inverse of this approach—inferring which processes and ecological interactions drive observed dynamics—remains an open problem in ecology. Here, we propose a way to attack this problem using a machine learning method known as
symbolic regression,
which seeks to discover relationships in time-series data and to express those relationships using dynamical equations. We found that this method could rapidly discover models that explained most of the variance in three classic demographic time series. More importantly, it reverse-engineered the models previously proposed by theoretical ecologists to describe these time series, capturing the core ecological processes these models describe and their functional forms. Our findings suggest a potentially powerful new way to merge theory development and data analysis.
Accurate autocorrelation modeling substantially improves fMRI reliability
Authors: Olszowy Wiktor , Aston John , Rua Catarina , Williams Guy B.
Published: May 2018

Given the recent controversies in some neuroimaging statistical methods, we compare the most frequently used functional Magnetic Resonance Imaging (fMRI) analysis packages: AFNI, FSL and SPM, with regard to temporal autocorrelation modeling. This process, sometimes known as pre-whitening, is conducted in virtually all task fMRI studies. We employ eleven datasets containing 980 scans corresponding to different fMRI protocols and subject populations. Though autocorrelation modeling in AFNI is not perfect, its performance is much higher than the performance of autocorrelation modeling in FSL and SPM. The residual autocorrelated noise in FSL and SPM leads to heavily confounded first level results, particularly for low-frequency experimental designs. Our results show superior performance of SPM’s alternative pre-whitening: FAST, over SPM’s default. The reliability of task fMRI studies would increase with more accurate autocorrelation modeling. Furthermore, reliability could increase if the packages provided diagnostic plots. This way the investigator would be aware of pre-whitening problems.
scQuery: a web server for comparative analysis of single-cell RNA-seq data
Authors: Alavi Amir , Ruffalo Matthew , Parvangada Aiyappa , Huang Zhilin , Bar-Joseph Ziv
Published: May 2018

Single cell RNA-Seq (scRNA-seq) studies often profile upward of thousands of cells in heterogeneous environments. Current methods for characterizing cells perform unsupervised analysis followed by assignment using a small set of known marker genes. Such approaches are limited to a few, well characterized cell types. To enable large scale supervised characterization we developed an automated pipeline to download, process, and annotate publicly available scRNA-seq datasets. We extended supervised neural networks to obtain efficient and accurate representations for scRNA-seq data. We applied our pipeline to analyze data from over 500 different studies with over 300 unique cell types and show that supervised methods greatly outperform unsupervised methods for cell type identification. A case study of neural degeneration data highlights the ability of these methods to identify differences between cell type distributions in healthy and diseased mice. We implemented a web server that compares new datasets to collected data employing fast matching methods in order to determine cell types, key genes, similar prior studies, and more.
Engineered Genetic Redundancy Relaxes Selective Constraints upon Endogenous Genes in Viral RNA Genomes
Authors: Ambrós Silvia , De la Iglesia Francisca , Rosario Sttefany M. , Butković Anamarija , Elena Santiago F.
Published: May 2018

1

Genetic redundancy, understood as the functional overlap of different genes, is a double-edge sword. At the one side, it is thought to serve as a robustness mechanism that buffers the deleterious effect of mutations hitting one of the redundant copies, thus resulting in pseudogenization. At the other side, it is considered as a source of genetic and functional innovation. In any case, genetically redundant genes are expected to show an acceleration in the rate of molecular evolution. Here we tackle the role of genetic redundancy in viral RNA genomes. To this end, we have evaluated the rates of compensatory evolution for deleterious mutations affecting an essential function, the suppression of RNA silencing plant defense, of tobacco etch potyvirus (TEV). TEV genotypes containing deleterious mutations in presence/absence of engineered genetic redundancy were evolved and the pattern of fitness and virulence recovery evaluated. Genetically redundant genotypes suffered less from the effect of deleterious mutations and showed relatively minor changes in fitness and virulence. By contrast, non-genetically redundant genotypes had very low fitness and virulence at the beginning of the evolution experiment that were fully recovered by the end. At the molecular level, the outcome depended on the combination of the actual mutations being compensated and the presence/absence of genetic redundancy. Reversions to wild-type alleles were the norm in the non-redundant genotypes while redundant ones either did not fix any mutation at all or showed a higher nonsynonymous mutational load.
Nitrone-Trolox conjugate as an inhibitor of lipid oxidation: Towards synergistic antioxidant effects
Authors: Socrier L. , Rosselin M. , Gomez Giraldo A. M. , Chantemargue B. , Di Meo F. , Trouillas P. , Durand G. , Morandat S.
Published: May 2018

1

Free radical scavengers like α-phenyl-N-tert-butylnitrone (PBN) and 6-hydroxy-2,5,7,8-tetramethylchroman-2-carboxylic acid (Trolox) have been widely used as protective agents in various biomimetic and biological models. A series of three amphiphilic Trolox and PBN derivatives have been designed by adding to the parent molecules both a perfluorinated chain and a sugar group in order to render them amphiphilic. In this work, we have studied the interaction of these derivatives with lipid membranes and how it correlates to their antioxidant properties.

The three derivatives form monolayers at the air/water interface. We next investigated the ability of each derivative to interact with 1,2-dilinoleoyl-sn-glycero-3-phosphocholine (DLPC) as well as their efficiency to inhibit the AAPH-induced oxidation of DLPC liposomes. The location of these derivatives in the membrane is a key parameter to rationalize their antioxidant efficiency. The derivative bearing both the PBN and the Trolox antioxidant moieties on the same fluorinated carrier exhibited a synergistic antioxidant effect by delaying the oxidation process. Molecular dynamics (MD) simulations supported the understanding of the mechanism of action, highlighting various key physical-chemical descriptors.

Graphical abstract

Highlights

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Amphiphilic fluorinated antioxidants efficiently inhibit lipid oxidation

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The perfluorinated chain allows the insertion into membranes

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The nature of the antioxidant is a key parameter in the antioxidant efficiency

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The combination of Trolox and PBN results in a synergistic antioxidant effect

Condensed running title

Trolox derivatives limit lipid oxidation
Vector-mediated viral transmission favours less virulent viruses
Authors: Remnant Emily J. , Mather Niklas , Gillard Thomas L. , Yagound Boris , Beekman Madeleine
Published: May 2018

While it is well-established that the ectoparasitic miteVarroa destructoris largely responsible for the widely-reported decline of populations of the Western honeybeeApis mellifera, the exact role the mite plays in honeybee health remains unclear. The last few years have seen a surge in studies associating RNA viruses vectored by the mite with the death of honeybee colonies.Varroafacilitates the spread of RNA viruses because it feeds on developing bee brood and transfers haemolymph from bee-to-bee. Such a change in transmission, from horizontal and vertical to vector-based, is predicted to lead to an increase in virulence of RNA viruses, thus potentially providing an explanation for the observed association betweenVarroaand certain viruses. Here we document the effect of changing the route of transmission of honeybee viruses contained in the haemolymph of honeybee pupae. We find that a change in mode of transmission rapidly increases viral titres of two honeybee viruses, Sacbrood virus (SBV) and Black queen cell virus (BQCV). This increase in viral titre is accompanied by an increase in virulence. In contrast, the virus most often associated withVarroa, Deformed wing virus (DWV), shows a reduction in viral titre in the presence of SBV and BQCV. In addition, DWV does not cause mortality to honeybee pupae in isolation. Most likely a change in mode of transmission due to the arrival of a vector quickly eliminates the most virulent honeybee viruses resulting in an association betweenVarroaand less virulent viruses such as DWV. Our work therefore provides empirical evidence for an alternative explanation for the widely-observed association betweenVarroaand DWV.
Next-generation Sequence-analysis Toolkit (NeST): A standardized bioinformatics framework for analyzing Single Nucleotide Polymorphisms in next-generation sequencing data
Authors: Ravishankar Shashidhar , Schmedes Sarah E. , Patel Dhruviben S. , Plucinski Mateusz , Udhayakumar Venkatachalam , Talundzic Eldin , Vannberg Fredrik
Published: May 2018

Rapid advancements in next-generation sequencing (NGS) technologies have led to the development of numerous bioinformatics tools and pipelines. As these tools vary in their output function and complexity and some are not well-standardized, it is harder to choose a suitable pipeline to identify variants in NGS data. Here, we present NeST (NGS-analysis Toolkit), a modular consensus-based variant calling framework. NeST uses a combination of variant callers to overcome potential biases of an individual method used alone. NeST consists of four modules, that integrate open-source bioinformatics tools, a custom Variant Calling Format (VCF) parser and a summarization utility, that generate high-quality consensus variant calls. NeST was validated using targeted-amplicon deep sequencing data from 245 Plasmodium falciparum isolates to identify single-nucleotide polymorphisms conferring drug resistance. The results were verified using Sanger sequencing data for the same dataset in a supporting publication [28]. NeST offers a user-friendly pipeline for variant calling with standardized outputs and minimal computational demands for easy deployment for use with various organisms and applications.
Structure of the human volume regulated anion channel
Authors: Kefauver J. M. , Saotome K. , Dubin A. E. , Pallesen J. , Cottrell C.A. , Cahalan S.M. , Qiu Z. , Hong G. , Crowley C.S. , Whitwam T. , Lee W.H. , Ward A.B. , Patapoutian A.
Published: May 2018

SWELL1 (LRRC8A) is the only essential subunit of the Volume Regulated Anion Channel (VRAC), which regulates cellular volume homeostasis and is activated by hypotonic solutions. SWELL1, together with four other LRRC8 family members, forms a vastly heterogeneous cohort of VRAC channels with different properties; however, SWELL1 alone is also functional. Here, we report a high-resolution cryo-electron microscopy structure of full-length human homo-hexameric SWELL1. The structure reveals a trimer of dimers assembly with symmetry mismatch between the pore-forming domain and the cytosolic leucine-rich repeat (LRR) domains. Importantly, mutational analysis demonstrates that a charged residue at the narrowest constriction of the homomeric channel is an important pore determinant of heteromeric VRAC. This structure provides a scaffold for further dissecting the heterogeneity and mechanism of activation of VRAC.
Diversity of coelomycetous fungi in human infections: a 10-year experience of two European reference centres
Authors: Garcia-Hermoso Dea , Valenzuela-Lopez Nicomedes , Rivero-Menendez Olga , Alastruey-Izquierdo Ana , Guarro Josep , Cano-Lira José F. , Stchigel Alberto M. ,   the French Mycoses Study Group
Published: May 2018

The coelomycetous fungi are difficult to properly identify from their phenotypic characterization and their role as etiologic agents of human infections is not clear. We studied the species distribution of these fungi among clinical isolates that had been collected and stored over a ten-year period in two European reference laboratories (France and Spain). We identified phenotypically and molecularly 97 isolates by sequencing the D1-D2 fragment of the 28S nrRNA (LSU) gene. Species of the ordersPleosporalesandGlomerellaleswere present in both collections, andBotryosphaerialesandDiaporthalesonly in the French one. The most prevalent species wereMedicopsis romeroi,Neocucurbitaria keratinophila,Neocucurbitaria unguis-hominisandParaconiothyrium cyclothyrioides, which had been recovered primarily from superficial tissues. TheDidymellaceaewas the most common family represented, with 27 isolates distributed into five genera.
Rapid Pliocene Diversification of Modern Kangaroos
Authors: Couzens Aidan M. C. , Prideaux Gavin J.
Published: May 2018

Differentiating between ancient and rapidly-evolved clades is critical for understanding impacts of environmental change on biodiversity. Australia possesses many aridity-adapted lineages, the origins of which have been linked by molecular evidence to late Miocene drying. Using dental macrowear and molar crown-height measurements spanning the past 25 million years, we show that the most iconic of Australia’s terrestrial mammals, ‘true’ kangaroos and wallabies (Macropodini), diversified in response to Pliocene grassland emergence. In contrast, low-crowned short-faced kangaroos radiated into browsing niches as the late Cenozoic became more arid, contradicting the view that this was a period of global decline among browsers. Our results link warm intervals with bursts of diversification and undermine arguments attributing Pleistocene megafaunal extinction to aridity-forced dietary change.
A segmentation scheme for complex neuronal arbors and application to vibration sensitive neurons in the honeybee brain
Authors: Ikeno Hidetoshi , Kumaraswamy Ajayrama , Kai Kazuki , Wachtler Thomas , Ai Hiroyuki
Published: May 2018

The morphology of a neuron is strongly related to its physiological properties, and thus to information processing functions. Optical microscope images are widely used for extracting the structure of neurons. Although several approaches have been proposed to trace and extract complex neuronal structures from microscopy images, available methods remain prone to errors. In this study, we present a practical scheme for processing confocal microscope images and reconstructing neuronal structures. We evaluated this scheme using image data samples and associated gold standard reconstructions from the BigNeuron Project. In these samples, dendritic arbors belonging to multiple projection branches of the same neuron overlapped in space, making it difficult to automatically and accurately trace their structural connectivity. Our proposed scheme, which combines several software tools for image masking and filtering with an existing tool for dendritic segmentation and tracing, outperformed state-of-the-art automatic methods in reconstructing such neuron structures. For evaluating our scheme, we applied it to a honeybee local interneuron, DL-Int-1, which has complex arbors and is considered to be a critical neuron for encoding the information indicated in the waggle dance of the honeybee.
Targeted induction ofde novoFatty acid synthesis enhances MDV replication in a COX-2/PGE2αdependent mechanism through EP2 and EP4 receptors engagement
Authors: Boodhoo Nitish , Kamble Nitin , Kaufer Benedikt B. , Behboudi Shahriar
Published: May 2018

Many viruses alterde novoFatty Acid (FA) synthesis pathway, which can increase availability of energy for replication and provide specific cellular substrates for particle assembly. Marek’s disease virus (MDV) is a herpesvirus that causes deadly lymphoma and has been linked to alterations of lipid metabolism in MDV-infected chickens. However, the role of lipid metabolism in MDV replication is largely unknown. We demonstrate here that infection of primary chicken embryonic fibroblast with MDV activatesde novolipogenesis, which is required for virus replication. In contrast, activation of Fatty Acid Oxidation (FAO) reduced MDV titer, while inhibition of FAO moderately increased virus replication. Thus optimized virus replication occurs if synthetized fatty acids are not used for generation of energy in the infected cells, and they are likely converted to lipid compounds, which are important for virus replication. We showed that infection with MDV activates COX-2/PGE2αpathway and increases the biosynthesis of PGE2α, a lipid mediator generated from arachidonic acid. Inhibition of COX-2 or PGE2αreceptors, namely EP2 and EP4 receptors, reduced MDV titer, indicating that COX-2/PGE2αpathway are involved in virus replication. Our data show that the FA synthesis pathway inhibitors reduce COX-2 expression level and PGE2αsynthesis in MDV infected cells, arguing that there is a direct link between virus-induced fatty acid synthesis and activation of COX-2/PGE2αpathway. This notion was confirmed by the results showing that PGE2αcan restore MDV replication in the presence of the FA synthesis pathway inhibitors. Taken together, our data demonstrate that MDV uses FA synthesis pathway to enhance PGE2αsynthesis and promote MDV replication through EP2 and EP4 receptors engagement.
Cerox1 and microRNA-488-3p noncoding RNAs jointly regulate mitochondrial complex I catalytic activity
Authors: Sirey Tamara M , Roberts Kenny , Haerty Wilfried , Bedoya-Reina Oscar , Rogatti-Granados Sebastian , Tan Jennifer Y , Li Nick , Heather Lisa C , Cooper Sarah , Marques Ana C , Ponting Chris P
Published: May 2018

To generate energy efficiently, the cell is uniquely challenged to co-ordinate the abundance of electron transport chain protein subunits expressed from both nuclear and mitochondrial genomes. How an effective stoichiometry of this many constituent subunits is co-ordinated post-transcriptionally remains poorly understood. Here we show that Cerox1, an unusually abundant cytoplasmic long noncoding RNA (lncRNA), modulates the levels of mitochondrial complex I subunit transcripts in a manner that requires binding to microRNA-488-3p. Increased abundance of Cerox1 cooperatively elevates complex I subunit protein abundance and enzymatic activity, decreases reactive oxygen species production, and protects against the complex I inhibitor rotenone. Cerox1 function is conserved across placental mammals: human and mouse orthologues effectively modulate complex I enzymatic activity in mouse and human cells, respectively. Cerox1 is the first lncRNA demonstrated, to our knowledge, to regulate mitochondrial oxidative phosphorylation (OXPHOS) and, with miR-488-3p, represent novel targets for the modulation of complex I activity.
Using neural networks to bridge scales in cancer: Mapping signaling pathways to phenotypes
Authors: Kim Eunjung , Gerlee Philip , Anderson Alexander R.A.
Published: May 2018

Cancer is an evolving system subject to mutation and selection. Selection is driven by the microenvironment that the cancer cells are growing in and acts on the cell phenotype, which is in turn modulated by intracellular signaling pathways regulated by the cell genotype. Integrating all of these processes requires bridging different biological scales. We present a mathematical model that uses a neural network as a means to connecting these scales. In particular, we consider the mapping from intracellular pathway activity to phenotype under different microenvironmental conditions.
PIM-related kinases selectively regulate sensory functions in C. elegans
Authors: Kalichamy Karunambigai S. , Ikkala Kaisa , Pörsti Jonna , Santio Niina M. , Jha Sweta , Holmberg Carina I. , Koskinen Päivi J.
Published: May 2018

The mammalian PIM family of serine/threonine kinases regulate several cellular functions, such as cell survival and motility. Since we have observed PIM expression in the olfactory epithelium and other sensory organs of mice, this has raised the question of whether PIM kinases regulate also sensory cell functions. As our model organism to investigate this question, we used the Caenorhabditis elegans nematodes, which express two PIM-related kinases, PRK-1 and PRK-2. We demonstrated them to be true PIM orthologs with similar substrate specificity as well as sensitivity to PIM-inhibitory compounds. Furthermore, we obtained evidence to indicate that PRKs are selectively involved in regulation of olfactory sensations via AWB or AWCON neurons to volatile attractants or repellants, but do not affect gustatory sensations.
Phenotero: annotate as you write
Authors: Hombach Daniela , Schwarz Jana Marie , Knierim Ellen , Schuelke Markus , Seelow Dominik , Köhler Sebastian
Published: May 2018

Controlled vocabularies and ontologies have become a valuable resource for knowledge representation, data integration, and downstream analyses in the biomedical domain. In precision medicine, especially in clinical genetics, the Human Phenotype Ontology (HPO) as well as disease ontologies like the Orphanet Rare Disease Ontology (ORDO) or Medical Subject Headings (MeSH) are often used for deep phenotyping of patients and coding of clinical diagnoses. However, the process of assigning ontology classes (annotating) to patient descriptions is often disconnected from the process of writing patient reports or manuscripts in word processing software such as Microsoft Word or LibreOffice. This additional workload and the requirement to install dedicated software may discourage usage of ontologies for parts of the target audience.

To improve this situation, we present Phenotero, a freely available and simple solution to annotate patient phenotypes and diseases at the time of writing clinical reports or manuscripts. We adopt Zotero, a well-established, actively developed citation management software to generate a tool which allows to reference classes from ontologies within clinical reports or manuscripts at the time of writing. We expect this approach to decrease the additional workload to a minimum while ensuring high quality associations with ontology classes. Standardised collection of phenotypic information at the time of describing the patient allows for streamlining of clinic workflow, efficient data entry, and will subsequently promote clinical and molecular diagnosis, remove ambiguousness from manuscripts, and allow sharing of anonymised patient phenotype data with ultimate goal of a better understanding of the disease. Thus, we hope that our integrated approach will further promote the usage of ontologies and controlled vocabularies in the clinical setting and in the biomedical domain.
Neurofibromin is essential to maintain metabolic function and sustain life in the adult mouse
Authors: Turner Ashley N , Johnson Maria S , Brosius Stephanie N , Yoder Brennan S. , Yang Kevin , Yang Qinglin , Moore John F , Yang Qinglin , Moore John F , Sharer J. Daniel , Smith Daniel L , Nagy Tim R , Schoeb Trent R , Korf Bruce R , Kesterson Robert A
Published: May 2018

The consequences of pathogenic variants in the NF1 gene can manifest in numerous tissues as a result of loss of neurofibromin protein function(s). A known function of NF1 is negative regulation of p21ras signaling via a GTPase activating (Ras-GAP) domain. Besides modulation of Ras signaling as a tumor suppressor, other functions of this multi-domain protein are less clear. Biallelic inactivation of NF1 leads to an embryonic lethal phenotype, while neurofibromin is expressed at varying levels in most tissues beyond developmental stages. Taking advantage of the mouse genetics toolkit, we established novel tamoxifen-inducible systemic knockout Nf1 mouse models (C57BL/6) to gain a better understanding of the role of Nf1 in the adult (3-4 months) mouse. Following inactivation of floxed Nf1 alleles, adult CAGGCre-ERTM;Nf14F/4F mice lose function of Nf1 systemically. Both male and female animals do not survive beyond 11 days post-tamoxifen induction and exhibit histological changes in multiple tissues. During this acute crisis, CAGGCre-ERTM;Nf14F/4F mice are not able to maintain body temperature or body mass, and expend all adipose tissue; however, they continue to consume food and absorb calories comparable to littermate-paired controls. Targeted metabolite analyses and indirect calorimetry studies revealed altered fat metabolism, amino acid metabolism and energy expenditure, with animals undergoing metabolic crisis and torpor-like states. Thermoneutral conditions accelerated the acute, lethal phenotype coincident with lower food intake. This study reveals that systemic loss of neurofibromin in the adult mouse induces metabolic dysfunction and lethality, thus highlighting potential functions of this multi-domain protein in addition to tumor suppression.
Neuronal Modulation of Brown Adipose Activity Through Perturbation of White Adipocyte Lipogenesis
Authors: Guilherme Adilson , Pedersen David J , Henriques Felipe , Bedard Alexander H. , Henchey Elizabeth , Kelly Mark , Rahmouni Kamal , Morgan Donald A. , Czech Michael P
Published: May 2018

White adipose tissue (WAT) secretes factors to communicate with other metabolic organs to maintain energy homeostasis. We previously reported that perturbation of adipocyte de novo lipogenesis (DNL) by deletion of fatty acid synthase (FASN) causes expansion of sympathetic neurons within white adipose tissue (WAT) and the appearance of “beige” adipocytes. Here we report evidence that white adipocyte DNL activity is also coupled to neuronal regulation and thermogenesis in brown adipose tissue (BAT). Induced deletion of FASN in all adipocytes in mature mice (iAdFASNKO) enhanced sympathetic innervation and neuronal activity as well as UCP1 expression in both WAT and BAT. In contrast, selective ablation of FASN in brown adipocytes of mice (iUCP1FASNKO) failed to modulate sympathetic innervation and the thermogenic program in BAT. Surprisingly, DNL in brown adipocytes was also dispensable in maintaining euthermia when UCP1FASNKO mice were cold-exposed. These results indicate that DNL in white adipocytes influences long distance signaling to BAT, which can modify BAT sympathetic innervation and expression of genes involved in thermogenesis.
The return of the trophic chain: fundamental vs realized interactions in a simple arthropod food web
Authors: Torres-Campos Inmaculada , Magalhães Sara , Moya-Laraño Jordi , Montserrat Marta
Published: May 2018

The mathematical theory describing small assemblages of interacting species (community modules or motifs) has proved to be essential in understanding the emergent properties of ecological communities. These models use differential equations to study pairwise interactions between species. However, as community modules become more complex, it is not certain that all potential interactions will be effectively realized. Here, we use community modules to experimentally explore whether the number of trophic links among species scales with community complexity (i.e., by adding species known to feed on each other from pair-wise trials). To investigate this question, we used a simple mite community present in avocado orchards (Persea americana), composed of two predators (Euseius stipulatus and Neoseiulus californicus), one herbivore as shared prey (Oligonychus perseae), and pollen of Carpobrotus edulis as an alternative food resource. These configurations enabled the potential for (intraguild) predation and (apparent) competition to be expressed. Using a series of controls, we assessed whether the presence of one species affected the survival of another, or its conversion of food into offspring). We found that increasing the number of potential interactions did not result in more complex realized community modules. Instead, all communities were reduced to one or two linear trophic chains. Our results show that trophic links assumed to occur when species are assembled in pairs do not necessarily occur when other components of the community are present. Consequently, food-web structure may be unrealistic in theoretical community modules that are parameterized based on pair-wise interactions observed when alternative prey is absent. This further suggests the need for empirical research to work in concert with theoretical approaches to develop more realistic and predictive food-web models.
Recurrent gene amplification on Drosophila Y chromosomes suggests cryptic sex chromosome drive is common on young sex chromosomes
Authors: Ellison Chris , Bachtrog Doris
Published: May 2018

Theory predicts that selfish genetic elements that increase their transmission are prone to originate on sex chromosomes but create strong selective pressure to evolve suppressors due to reduced fertility and distorted population sex ratios. Here we show that recurrent genetic conflict over sex chromosome transmission appears to be an important evolutionary force that has shaped gene content evolution of sex chromosomes in Drosophila. We demonstrate that convergent acquisition and amplification of spermatid expressed gene families are common on Drosophila sex chromosomes, and especially on recently formed ones, and harbor characteristics typical of meiotic drivers. We carefully characterize one putative novel cryptic sex chromosome distortion system that arose independently several times in members of the Drosophila obscura group. Co-amplification of the S-Lap1/GAPsec gene pair on both the X and the Y chromosome occurred independently several times in members of the D. obscura group, where this normally autosomal gene pair is sex-linked due to a sex chromosome - autosome fusion. Investigation of gene expression and short RNA profiles at the S-Lap1/GAPsec system suggest that meiotic drive and suppression likely involves RNAi mechanisms. Our finding suggests that recurrent conflict over sex chromosome transmission has shaped widespread genomic and evolutionary patterns, including the epigenetic regulation of sex chromosomes, the distribution of sex-biased genes, and the evolution of hybrid sterility.
Structural basis for transcript elongation control by NusG/RfaH universal regulators
Authors: Young Kang Jin , Anne Mooney Rachel , Nedialkov Yuri , Saba Jason , Mishanina Tatiana V. , Artsimovitch Irina , Landick Robert , Darst Seth A.
Published: May 2018

NusG/RfaH/Spt5 transcription elongation factors are the only transcription regulators conserved across all life. In bacteria, NusG regulates RNA polymerase (RNAP) elongation complexes (ECs) across most genes, enhancing elongation by suppressing RNAP backtracking and also coordinating ρ-dependent termination and translation. RfaH is a specialized NusG paralog that engages the EC atopssites and subsequently excludes NusG and suppresses both backtrack and hairpin-stabilized pausing. We used single-particle cryo-EM to determine structures of ECs atopswith NusG or RfaH. Both factors chaperone base pairing of the EC upstream duplex DNA to suppress backtracking. RfaH loads onto the EC by specific recognition of anopshairpin in the single-stranded nontemplate DNA. Binding of both NusG and RfaH is incompatible with the swiveled RNAP conformation necessary for hairpin-stabilized pausing, but only RfaH fully counteracts swiveling to suppress pausing. The universal conservation of NusG/RfaH/Spt5 suggests that the molecular mechanisms uncovered here are widespread.
Market earnings expectation, measurement error in analysts’ consensus forecasts and prediction of stock returns
Authors: Kim Jung Hoon
Published: May 2018

Purpose

In capital markets research, analysts’ consensus forecasts are widely used as a proxy for unobservable market earnings expectation. However, they measure the market earnings expectation with error that may vary cross-sectionally, as the market does not consistently rely on analysts’ consensus forecasts to form earnings expectation (Walther, 1997). Based on this notion, this paper aims to relate the prediction of future stock returns to the cross-sectional variation of the error in measuring market earnings expectation embedded in analysts’ consensus forecasts.

Design/methodology/approach

This study uses empirical analyses based on stock returns and annual analysts’ consensus forecasts.

Findings

Based on the analytical work by Abarbanell et al. (1995), this study reports that when the measurement error in annual analysts’ consensus forecasts is the smallest, forward earnings-to-price ratio (constructed with annual analysts’ consensus forecasts) best explains future stock returns, and the forward earnings-to-price ratio-based investment strategy is the most profitable.

Originality/value

Findings of this study are useful to capital markets research that relies on the market earnings expectation and to practitioners seeking more profitable investment strategies.
Determinants of non-performing loans in banking sector in small developing island states
Authors: Kumar Ronald Ravinesh , Stauvermann Peter Josef , Patel Arvind , Prasad Selvin Sanil
Published: May 2018

Purpose

The banking sector stability depends in large part on the size of non-performing loans (NPLs). Hence, the factors which explain the problem loans are very useful information for banks. Notably, studies in this regard with respect to the small developing countries’ banking sector have received less attention. Therefore, this study aims to examine the determinants of NPLs with a case of Fiji’s banking sector, over the period 2000-2013.

Design/methodology/approach

The balanced sample consists of the entire banking sector (five commercial banks and two non-bank financial institutions). First, the authors estimate a base model which comprise bank-specific indicators that are related to bank management and then they extend the estimations to include macroeconomic/structural factors such as economic growth, inflation, changes of the real effective exchange rate, unemployment, remittances, political instability and external events like the global financial crisis. The estimations are done using pooled OLS, the random effects and the fixed effects regression methods.

Findings

The results show that the following indicators have negative association with NPL and are statistically significant with the conventional levels: return on equity, capital adequacy requirement, market share based on assets, unemployment and time. On the other hand, the net interest margin has a positive and statistically significant association with NPL.

Research limitations/implications

Subsequently, the stability of the banking sector in small developing countries such as Fiji is largely dependent on banks’ profitability, solvency, size in terms of market share and the presence of a learning curve and keeping a close tab on the interest rate spread between loans and deposits.

Practical implications

The paper highlights the specific factors determining NPL in small developing economy of Fiji.

Originality/value

This study is the first to examine specific factors determining NPLs with respect to small developing economies in the Oceania region.
Company reputation and auditor choice: evidence from fortune 1000 companies
Authors: Huang Xuan , Kang Fei
Published: May 2018

Purpose

The purpose of this paper is to investigate how companies’ reputation affects their selection of auditors.

Design/methodology/approach

This paper measures company reputation using the reputation scores from Fortune’s “America’s Most Admired Companies” list. Multivariate analysis is performed to examine the impact of company reputation on public companies’ auditor choice. Robustness checks include conducting Heckman procedures and instrumental-variable two-stage least square regressions to control for self-selection bias and using alternative measures to proxy for company reputation and auditor industry expertise.

Findings

This paper finds that companies with higher reputations are more likely to hire industry-specialist auditors than their counterparts. The results suggest that because of reputation concerns, high-reputation companies have strong incentives to maintain and signal their financial reporting quality, which in turn increase their demand for audit quality.

Practical implication

This paper suggests that company reputation constitutes an important determinant of auditor selection and, therefore, has both policy and practical implications for the demand of audit services. The paper provides policy-makers and practitioners with insights into critical factors influencing companies’ complex decision process of auditor selection.

Originality/value

The findings of this paper on the empirical link between company reputation and auditor choice contribute to the auditing literature by enhancing the understanding of the effects of different company-level characteristics in financial reporting and audit planning process. This paper also adds to the growing literature on the influence of company reputation on corporate behavior by documenting the important role that company reputation plays in the managerial decision-making process.
Productivity improvement in solid waste recycling centres through lean implementation aided by multi-criteria decision analysis
Authors: Tortorella Guilherme , Silva Glauco , Campos Lucila M.S. , Pizzeta Cassiano , Latosinski Amanda , Soares Alessandro
Published: May 2018

Purpose

The purpose of this paper is to investigate, through a comparative analysis, the applicability of lean manufacturing practices, such as value stream mapping (VSM), for productivity improvement in recycling centres (RCs) aided by multi-criteria decision analysis.

Design/methodology/approach

The study is carried out in five RCs that sort the municipal solid waste of Porto Alegre, one of the main cities in Brazil. Since all of the centres present their labour composed by poor communities’ members, cultural and social characteristics may represent an incremental challenge for lean implementation. Further, these centres are organised in cooperatives, in which decisions are taken through a participatory way and all their members are entitled to vote, undermining and retarding the decision-making process.

Findings

The integration of a multi-criteria decision-making tool to the lean practices enables the prioritisation of improvements, complementing the final stage of VSM. In particular, this contribution becomes especially important in cooperatives managed by community, where decisions are often complex and time-consuming. Finally, despite the increasing pressure for better performance of RCs, the existent mindset is still far from the private sector, where lean practices were conceived. Further, the findings suggest that, despite processes similarities, it is not feasible to declare the existence of a one-best practice to such scenario.

Originality/value

In theoretical terms, the authors demonstrate through a multi-case study the adequacy of analytic hierarchy process as a decision analysis tool complementary to the VSM, enabling a broader perspective about this subject. Concerning the practical contribution, the comprehension of the adaptation needs for lean practices implementation within the production context of solid waste RCs provides a framework with guidelines for this sector, when incorporating lean activities. Lean practitioners and eventual municipal authorities involved in improving productivity of community-managed RCs might benefit from this framework, since they will be able to emphasise the development of recommended and already tested lean practices that tend to improve their operational performance.
Technological change, information processing and supply chain integration
Authors: Bartnik Roman , Park Youngwon
Published: May 2018

Purpose

Technologies change quickly in the automotive industry. This can provide opportunities to firms from emerging economies who try to enter the world stage of automotive production, provided they can react to this more nimbly than established competitors. How technological change affects the supply chain coordination of incumbents from developed economies and new entrants from emerging economies should strongly determine the speed of competitive reaction. By using the example of automotive transmission development, the purpose of this paper is to provide a conceptual model for the analysis and offer research propositions.

Design/methodology/approach

The authors build a conceptual model based on information processing theory and offer research propositions based on case study evidence of four automotive original equipment manufacturers (OEMs) and five suppliers.

Findings

The authors find symptoms of two larger trends: increasing specialization and technological linkages and a need to increase external supply chain integration beyond traditional structures. Comparing the effects on Japanese and German incumbents, the authors find that increasing external supply chain linkages proves to be harder for Japanese OEMs. Tight links and routines in the Japanese supply chain networks may harm OEM efficiency under the new technological conditions, e.g. the lack of complete part specifications and high demands for customization. Looking at effects on emerging market firms, Chinese OEMs use quasi-open modular production settings in transmission development and lean strongly on inputs from specialized foreign tier-one suppliers. Speed advantages must be weighed against long-term disadvantages of dependence and insufficient R&D investments.

Research limitations/implications

The study explores how technological change affects inter-firm development processes. The authors propose a framework and hypotheses based on information processing theory and link the findings to the discussion on the impact of national institutional context on supply chain coordination.

Practical implications

OEMs wanting to adapt complex existing internal structures to the changing demands for information processing should focus first on improving internal capacities by improving the amount and richness of information flow. Implementing new standards for simultaneous and standardized software development across the supply chain is a key point for this. A second step should be to boost the internal capacity to process higher richness of information, i.e. to understand the meta-knowledge necessary to integrate across technological areas in the development of electronic control units (ECUs).

Originality/value

The authors draw on original interview data in developed and emerging markets and information processing theory to explore the complexity of inter-firm coordination in automotive supply chains.
Modelling cause and effect relationship among enablers of innovation in SMEs
Authors: Gupta Himanshu , Barua Mukesh Kumar
Published: May 2018

Purpose

Innovation is a prerequisite for economic and technological growth of any organization. Identifying enablers of innovation can help managers accelerate the process of economic growth. The purpose of this paper is to identify the prominent enablers of innovation in small and medium enterprises (SMEs) that can help overhauling organizations and benefit them economically.

Design/methodology/approach

A comprehensive literature review and expert’s opinions have been applied to identify enablers of innovation. A case of automotive component supplier is considered for conducting the research. A coalescence of Grey and DEMATEL methodologies has been incorporated to first rank the enablers of innovation based on their importance and then identify the causal relationship among these enablers by characterizing enablers into causal and effect groups.

Findings

A few important enablers, namely, entrepreneur traits, knowledge management, resources for innovation, and linkage capabilities, have been identified as prominent enablers for successful innovation in SMEs.

Practical implications

This paper identifies enablers of innovation in SMEs and the causal relationship between these enablers. The identified enablers and the causal relationship between these enablers will help managers of small organizations in selecting the enablers that need to be focused on, which, in turn, can drive other enablers of innovation, thus saving time and resources of the organizations.

Originality/value

This paper uses a novel Grey–DEMATEL methodology to identify the causal relationship among enablers and also contributes to the literature on innovation by identifying enablers of innovation in SMEs.
A critical discourse on tacit knowledge management and the performative agenda
Authors: Garrick John
Published: May 2018

Purpose

This paper examines the relationship between the tacit knowledge held by learning and development professionals and performance measurement regimes of post-modern organisations.

Design/methodology/approach

Drawing on Polanyi’s (1958; 1968) influential ideas about tacit knowledge and Lyotard’s (1984) theory of performativity with regard to criteria such as profit-performance, it assesses the applicability and relevance of tacit, working knowledge in the internet age to the daily working lives of industry training and development personnel. A central question for the study is whether such professionals can still tap into and use their tacit know-how without having it reduced by contemporary performance-oriented regimes of “knowledge”.

Findings

It is argued that there is a powerful interaction between tacit knowledge and narratively produced performance regimes – which are now supported by digital-age technologies including developments in artificial intelligence (AI). It has also been argued that fostering organisational environments that encourage open communication and allow a role for critique remains vital.

Research limitations/implications

With systems of knowledge production including AI at the point of potentially overriding human decision-making processes, more research is required into possible implications of uploading workers’ tacit, working knowledge in different contexts and ways to foster open communication and critique in organisations.

Originality/value

The overt linking of classic theories – Polanyi and Lyotard – and applying these to contemporary (digital-age) training and development contexts is original.