bluuebunny/crossref_metadata_2025 huggingface dataset:
18. A Decade of Democratic Decline and Stagnation
Authors: Fish M. Steven , Wittenberg Jason , Jakli Laura
Published: January 2019

This chapter examines key factors that lead to failed democratization. It first describes five categories of countries: established democracies, established autocracies, robust democratizers, tenuous democratizers, and failed democratizers. Using the Freedom House Index, it explains why some democratizers slid backwards while others did not. In particular, it looks at the conditions that undermine democracy and political actors, such as the chief executive, that contribute to democratization’s derailment. The chapter identifies several major structural factors that influence whether democratization succeeds fully, succeeds partially, or fails. These include poverty, a late history of national independence, a large Muslim population, economic reliance on oil and gas, and gender inequality. The chapter concludes by considering ways of reducing the hazards of democratic reversal and preventing relapses into authoritarianism, such as strengthening legislatures and curtailing executive power.
19. Southern Europe
Authors: Gunther Richard
Published: January 2019

This chapter examines the political consequences of different types of regime change in Southern Europe by comparing democratic transitions via ‘elite pacts’ or ‘elite convergence’ with those involving much higher levels of mass mobilization. It begins with overviews of the distinguishing features of the transitions to democracy in Portugal, Greece, and Spain, along with some observations about how the processes of regime transformation affected the conduct of politics for several years after democracy was established. It then considers the relevance of international actors and events, economic factors, as well as social-structural and cultural characteristics to processes of regime change. It also discusses lessons that can be drawn from the experiences of Portugal, Greece, and Spain and shows that the type of regime transition can have a significant impact on the success of democratization.
21. Post-Communist Central and Eastern Europe
Authors: Haerpfer Christian W. , Kizilova Kseniya
Published: January 2019

This chapter examines the democratic revolutions that occurred in post-communist Europe since 1989. It first considers the beginning of the decline of communism and the failed attempts to reform communist one-party states from 1970 to 1988 as stage one of democratization. It then discusses the end of communist regimes as the second stage of democratization—between 1989 and 1991. It also looks at stage three of the democratization process, which focuses on the creation of new democracies. The chapter concludes with an assessment of the main drivers of successful democratization in post-communist Europe.
23. The Middle East and North Africa
Authors: Cavatorta Francesco
Published: January 2019

This chapter examines why democratic openings failed to consolidate in the Middle East and North Africa despite the profound influence of the global wave of democratization on both regions. Authoritarianism persists in the region comprising the Middle East and North Africa. Nevertheless, countries in the region experienced changes since the consolidation of authoritarian rule soon after decolonization. The chapter considers a number of explanations for the durability of authoritarian rule in the Middle East and North Africa in the face of both domestic and international pressures for democratic governance. In particular, it discusses the role of Islamist political actors and Israel. It also looks at the region’s political culture and society, business and economy, and agents of democratization and democratic failure. Finally, it describes institutional challenges for the region’s chances to become more democratic.
3. Neofunctionalism
Authors: Niemann Arne , Lefkofridi Zoe , Schmitter Philippe C.
Published: January 2019

This chapter focuses on neofunctionalism, one of the earlier theories of regional integration. Neofunctionalist theory was first formulated in the late 1950s and early 1960s, but began to receive increasing criticism from the mid1960s, particularly because of several adverse empirical developments, the culmination of which was the Empty Chair crisis of 1965–66 when French President Charles de Gaulle effectively paralysed the European Community. With the resurgence of the European integration process in the mid1980s, neofunctionalism made a substantial comeback. After providing an overview of neofunctionalism’s intellectual roots, the chapter examines early neofunctionalism’s core assumptions and hypotheses, including its central notion of ‘spillover’. It then considers the criticisms that have been levelled against it before turning to later revisions of the theory. Finally, this chapter applies the theory critically to explain the nature and probable outcome of the sovereign debt crisis.
9. European Integration and Gender
Authors: Galligan Yvonne
Published: January 2019

This chapter analyses theories of European integration through a gender lens. It points to the diversity of perspectives in gender scholarship on European integration, and draws on these different points of view to examine other theoretical approaches. It assumes that gender is a basic organising principle of the social world, and therefore is an integral aspect of European integration. The chapter discusses gender theory and its contribution to the study of European integration. It then goes on to interrogate other European integration theories - liberal intergovernmentalism, neofunctionalism, and social constructivism – examining the nature of gendered power that they emphasize and evaluating the extent to which they are open to incorporating a gender-informed perspective. The chapter then analyses the integrationist effect of the European economic crisis on gender equality. This discussion reveals the marginalization of gender equality, and gender mainstreaming, as the neo-liberal response to the economic crisis created new gender inequalities and perpetuated old patterns of gender hierarchy.
7. Governance in the European Union
Authors: Christiansen Thomas
Published: January 2019

This chapter provides an overview of the ‘governance turn’ in the study of European integration. Opening with a discussion of the reasons why governance as a concept and as a practice has become so prevalent in Europe, the chapter goes on to discuss the various ways in which the governance approach has evolved. Two strands of this literature—‘multilevel governance’ and the ‘regulatory state’—are examined in greater detail here. The chapter then introduces some of the important normative debates to which the ‘governance turn’ has given rise, before concluding with some observations about the relevance of the governance approach in the current phase of European integration.
12. The European Parliament
Authors: Burns Charlotte
Published: January 2019

This chapter focuses upon the European Parliament (EP), an institution that has seen its power dramatically increase in recent times. The EP has been transformed from being a relatively powerless institution into one that is able to have a genuine say in the legislative process and hold the European Union’s executive bodies (the Commission and Council, introduced in Chapters 9 and 10) to account in a range of policy areas. However, increases in the Parliament’s formal powers have not been matched by an increase in popular legitimacy: turnout in European elections is falling. Thus, while the EP’s legislative power is comparable to that enjoyed by many national parliaments, it has struggled to connect with the wider European public. The chapter explores these issues in detail. In the first section, the EP’s evolution from talking shop to co-legislator is reviewed; its powers and influence are explained in the next section; the EP’s internal structure and organization are then discussed with a focus upon the role and behaviour of the political groups, and finally, the European Parliament’s representative function as the EU’s only directly elected institution is discussed.
27. Brexit
Authors: Cini Michelle , Pérez-Solórzano Borragán Nieves
Published: January 2019

This chapter examines the so-called ‘Brexit’ phenomenon, the first time an existing EU member state has voted in a referendum to leave the Union. The chapter examines the historical context that shaped the UK’s decision to join the EEC and its subsequent relationship with the EU. It charts the events leading to the EU referendum, including the campaign and explains the reasons for the narrow ‘Leave’ vote in the referendum. The Brexit negotiations under Article 50 are discussed by focusing on process, actors, and outcomes, specifically the content of the March 2018 Draft Withdrawal Agreement. The penultimate section of the chapter explains Brexit by drawing on the extant European integration literature with a focus on the concepts of disintegration, differentiated integration, Europeanization, and politicization, while surveying the likely scenarios for a future EU–UK relationship. The chapter ends discussing the impact and implications of Brexit for the EU.
Enhanced functionalisation of major facilitator superfamily transporters via fusion of C-terminal protein domains is both extensive and varied in bacteria
Authors: Willson Benjamin J. , Dalzell Lindsey , Chapman Liam N. M. , Thomas Gavin H.
Published: January 2019

The evolution of gene fusions that result in covalently linked protein domains is widespread in bacteria, where spatially coupling domain functionalities can have functional advantages in vivo. Fusions to integral membrane proteins are less widely studied but could provide routes to enhance membrane function in synthetic biology. We studied the major facilitator superfamily (MFS), as the largest family of transporter proteins in bacteria, to examine the extent and nature of fusions to these proteins. A remarkably diverse variety of fusions are identified and the 8 most abundant examples are described, including additional enzymatic domains and a range of sensory and regulatory domains, many not previously described. Significantly, these fusions are found almost exclusively as C-terminal fusions, revealing that the usually cytoplasmic C-terminal end of MFS protein would the permissive end for engineering synthetic fusions to other cytoplasmic proteins.
Direct synthesis of EM-visible gold nanoparticles on genetically encoded tags for single-molecule visualization in cells
Authors: Jiang Zhaodi , Jin Xiumei , Li Yuhua , Liu Sitong , Liu Xiao-Man , Wang Ying-Ying , Zhao Pei , Cai Xinbin , Liu Ying , Tang Yaqi , Sun Xiaobin , Liu Yan , Hu Yanyong , Li Ming , Cai Gaihong , Qi Xiangbing , Chen She , Du Li-Lin , He Wanzhong
Published: January 2019

Single-molecule visualization in cells with genetically encoded tags for electron microscopy (EM) has been a long-awaited but unimplemented tool for cell biologists. Here, we report an approach for directly synthesizing EM-visible gold nanoparticles (AuNPs) on cysteine-rich tags for single-molecule visualization in cells. We first uncovered an auto-nucleation suppression mechanism that allows specific synthesis of AuNPs on isolated cysteine-rich tags. We next exploited this mechanism to develop an approach for single-molecule detection of proteins in prokaryotic cells and achieved an unprecedented labeling efficiency. We then expanded it to more complicated eukaryotic cells and successfully detected the proteins targeted to various organelles, including the membranes of endoplasmic reticulum (ER) and nuclear envelope, ER lumen, nuclear pores, spindle pole bodies, and mitochondrial matrix. Thus, our implementation of genetically encoded tags for EM should allow cell biologists to address an enormous range of biological questions at single-molecule level in diverse cellular ultrastructural contexts without using antibodies.
Endogenous pioneer neutrophils release NETs during the swarming response in zebrafish
Authors: Isles Hannah M. , Loynes Catherine A. , Hamilton Noémie , Muir Clare F. , Kadochnikova Anastasia , Henry Katherine M. , Kadirkamanathan Visakan , Renshaw Stephen A. , Elks Philip M.
Published: January 2019

Neutrophils are rapidly recruited to inflammatory sites where they coordinate their migration to form clusters, a process termed neutrophil swarming. The factors which modulate neutrophil swarming during its early stages are not fully understood, requiring the development of newin vivomodels. Using transgenic zebrafish larvae to study endogenous neutrophil migration in a tissue damage model, we demonstrate that neutrophil swarming is a conserved process in zebrafish immunity, sharing essential features with mammalian systems. We show that neutrophil swarms initially develop around a pioneer neutrophil, in a three-phase sequence of events. By adopting a high-resolution confocal microscopy approach, we observed the release of cell fragments by early swarming neutrophils. We developed a neutrophil specific histone H2A transgenic reporter lineTgBAC(mpx:GFP)i114;Tg(lyz:H2A-mCherry)sh530to study neutrophil extracellular traps (NETs), and found that endogenous neutrophils recruited to sites of tissue damage released NETs at the start of the swarming process. The optical transparency achieved using the zebrafish model has provided some of the highest resolution imaging of NET releasein vivoto date. Using a combination of transgenic reporter lines and DNA intercalating agents, we demonstrate that pioneer neutrophils release extracellular traps during the swarming response, suggesting that cell death signalling via NETosis might be important in driving the swarming response.
On the Complexity of Sequence to Graph Alignment
Authors: Jain Chirag , Zhang Haowen , Gao Yu , Aluru Srinivas
Published: January 2019

Availability of extensive genetics data across multiple individuals and populations is driving the growing importance of graph based reference representations. Aligning sequences to graphs is a fundamental operation on several types of sequence graphs (variation graphs, assembly graphs, pan-genomes, etc.) and their biological applications. Though research on sequence to graph alignments is nascent, it can draw from related work on pattern matching in hypertext. In this paper, we study sequence to graph alignment problems under Hamming and edit distance models, and linear and affine gap penalty functions, for multiple variants of the problem that allow changes in query alone, graph alone, or in both. We prove that when changes are permitted in graphs either standalone or in conjunction with changes in the query, the sequence to graph alignment problem is -complete under both Hamming and edit distance models for alphabets of size ≥ 2. For the case where only changes to the sequence are permitted, we present an O(|V| + m|E|) time algorithm, where m denotes the query size, and V and E denote the vertex and edge sets of the graph, respectively. Our result is generalizable to both linear and affine gap penalty functions, and improves upon the run-time complexity of existing algorithms.
Comparative analysis of mitochondrial genome between UG93A and UG93B reveal common feature of 5’-end heterogeneity in mitochondrial genes of kenaf
Authors: Liao Xiaofang , Zhao Yanhong , Khan Aziz , Kong Xiangjun , Zhou Bujin , Li Min , Wei Meiling , Peng Shuangshuang , Munsif Fazal , Zhou Ruiyang
Published: January 2019

Plant cytoplasmic male sterility (CMS) being maternal phenomenon trait that result from pollen abortion and closely linked with mitochondrial DNA rearrangement in many crops including kenaf. However, the molecular mechanism in kenaf is poorly known. In present work, we described the mitochondrial genome in isonuclear CMS line UG93A and its maintainer line UG93B. Findings of the current study revealed that a total of 398 SNPs and 230 InDels were identified in UG93A mtDNA. Total of 26 SNPs variations and three InDels were identified in the coding region of atp6, indicating its active role in mitochondrial genome re-arrangement. Northern blot analysis showed that the transcripts of atp1, atp4, atp6, cox3 and sdh4 in F1 were consistent with UG93A but different for UG93B. The transcript of atp9 was found similar between UG93B and F1 while different for UG93A, which depict that atp9 may be regulated by nuclear genes in F1 hybrid. The expression of atp9 in UG93A was substantially lower compared with UG93B, suggesting its key role for energy supplying in microspore development of kenaf. Circularized RNA (CR)-RT-PCR revealed that mitochondrial RNAs with heterogeneous 5’-ends but uniform 3’ - ends are common feature in kenaf mitochondrial genes, and the promoter architecture analysis showed that the promoter sequences in kenaf mitochondrial genome are highly diverged in comparison to those in other plants. Our data highlight that the translation of mitochondrial genes in kenaf is closely associated with heterogeneity of the 5’-end of plant mRNA. The present result provides the basic information in understanding the transcription of kenaf mitochondrial genome and can be used as reference in other plants.
Transposable elements drive reorganisation of 3D chromatin during early embryogenesis
Authors: Kruse Kai , Díaz Noelia , Enriquez-Gasca Rocio , Gaume Xavier , Torres-Padilla Maria-Elena , Vaquerizas Juan M.
Published: January 2019

Transposable elements are abundant genetic components of eukaryotic genomes with important regulatory features affecting transcription, splicing, and recombination, among others. Here we demonstrate that the Murine Endogenous Retroviral Element (MuERV-L/MERVL) family of transposable elements drives the 3D reorganisation of the genome in the early mouse embryo. By generating Hi-C data in 2-cell-like cells, we show that MERLV elements promote the formation of insulating domain boundaries through-out the genome in vivo and in vitro. The formation of these boundaries is coupled to the upregulation of directional transcription from MERVL, which results in the activation of a subset of the gene expression programme of the 2-cell stage embryo. Domain boundaries in the 2-cell stage embryo are transient and can be remodelled without undergoing cell division. Remarkably, we find extensive inter-strain MERVL variation, suggesting multiple non-overlapping rounds of recent genome invasion and a high regulatory plasticity of genome organisation. Our results demonstrate that MERVL drive chromatin organisation during early embryonic development shedding light into how nuclear organisation emerges during zygotic genome activation in mammals.
Single-neuron representations of spatial targets in humans
Authors: Tsitsiklis Melina , Miller Jonathan , Qasim Salman E. , Inman Cory S. , Gross Robert E. , Willie Jon T. , Smith Elliot H. , Sheth Sameer A. , Schevon Catherine A. , Sperling Michael R. , Sharan Ashwini , Stein Joel M. , Jacobs Joshua
Published: January 2019

The hippocampus and surrounding medial-temporal-lobe (MTL) structures are critical for both memory and spatial navigation, but we do not fully understand the neuronal representations used to support these behaviors. Much research has examined how the MTL neurally represents spatial information, such as with “place cells” that represent the current location or “head-direction cells” that code for the current heading. In addition to behaviors that require an animal to attend to the current spatial location, navigating to remote destinations is a common part of daily life. To examine the neural basis of these behaviors we recorded single-neuron activity from neurosurgical patients playing Treasure Hunt, a virtual-reality spatial-memory task. By analyzing how the activity of these neurons related to behavior in Treasure Hunt, we found that the firing rates of many MTL neurons during navigation significantly changed depending on the position of the current spatial target. In addition, we observed neurons whose firing rates during navigation were tuned to specific heading directions in the environment, and others whose activity changed depending on the timing within the trial. By showing that neurons in our task represent remote locations rather than the subject’s own position, our results suggest that the human MTL can represent remote spatial information according to task demands.
Ultra-fast fit-free analysis of complex fluorescence lifetime imaging via deep learning
Authors: Smith Jason T. , Yao Ruoyang , Sinsuebphon Nattawut , Rudkouskaya Alena , Mazurkiewicz Joseph , Barroso Margarida , Yan Pingkun , Intes Xavier
Published: January 2019

Fluorescence lifetime imaging (FLI) provides unique quantitative information in biomedical and molecular biology studies, but relies on complex data fitting techniques to derive the quantities of interest. Herein, we propose a novel fit-free approach in FLI image formation that is based on Deep Learning (DL) to quantify complex fluorescence decays simultaneously over a whole image and at ultra-fast speeds. Our deep neural network (DNN), named FLI-Net, is designed and model-based trained to provide all lifetime-based parameters that are typically employed in the field. We demonstrate the accuracy and generalizability of FLI-Net by performing quantitative microscopic and preclinical experimental lifetime-based studies across the visible and NIR spectra, as well as across the two main data acquisition technologies. Our results demonstrate that FLI-Net is well suited to quantify complex fluorescence lifetimes, accurately, in real time in cells and intact animals without any parameter settings. Hence, it paves the way to reproducible and quantitative lifetime studies at unprecedented speeds, for improved dissemination and impact of FLI in many important biomedical applications, especially in clinical settings.
Affective reactivity during adolescence: Associations with age, puberty and testosterone
Authors: Vijayakumar Nandita , Pfeifer Jennifer H. , Flournoy John C. , Hernandez Leanna M. , Dapretto Mirella
Published: January 2019

Adolescence is a period of heightened social engagement that is accompanied by normative changes in neural reactivity to affective stimuli. It is also a period of concurrent endocrine and physical changes associated with puberty. A growing body of research suggests that hormonal shifts during adolescence impact brain development, but minimal research in humans has examined the relationship between intra-individual changes in puberty and brain function. The current study examines linear and nonlinear changes in affective reactivity in a longitudinal sample of 82 adolescents who underwent three fMRI sessions between the ages of 9 and 18 years. Changes in response to affective facial stimuli were related to age, pubertal stage, and testosterone levels. Using multilevel modelling, we highlight extensive nonlinear development of socio-emotional responsivity across the brain. Results include mid-pubertal peaks in amygdala and hippocampus response to fearful expressions, as well as sex differences in regions subserving social and self-evaluative processes. However, testosterone levels exhibited inverse patterns of association with neural response compared to pubertal stage in females (e.g. U-shaped relationship with the amygdala and hippocampus). Findings highlight potentially unique roles of age, pubertal stage and testosterone on socio-emotional development during adolescence, as well as sex differences in these associations.
Changes in fungal communities across a forest disturbance gradient
Authors: Shi Lingling , Dossa Gbadamassi G.O. , Paudel Ekananda , Zang Huadong , Xu Jianchu , Harrison Rhett D.
Published: January 2019

Deforestation has a substantial impact on above ground biodiversity, but the response of below ground soil fungi remains poorly understood. In a tropical montane rainforest in southwestern China, plots were established along a forest degradation gradient ranging from mature and regenerated forests to open land to examine the impacts of forest degradation and deforestation on ecosystem diversity and function. Here, we evaluate the changes in below ground fungal diversity and community composition using a metabarcoding approach. Soil saprotrophic fungal richness declined with increasing forest disturbance. For example, Penicillium spp. (Phosphorus (P) solubilizing fungi) dominated in mature forest, but were less abundant in regenerating forest and showed the lowest abundance in open land sites. Conversely, the abundance of facultative pathogenic fungi increased along the disturbance gradient. The decline in soil saprophytic fungi may be a direct result of forest disturbance or it may be associated with increased availability of soil phosphorus indirectly through an increase in soil pH. The increase in abundance of facultative pathogenic fungi may be related to reduce competition with saprotrophic fungi, changes in microclimate or increased spore rain. These results demonstrate a loss of dominant P solubilizing saprotrophic fungi along the disturbance gradient, indicated a change from soil P limitation in mature tropical forest to soil C limitation in deforested sites. The increased prevalence of pathogenic fungi may inhibit plant succession following deforestation. Overall, this research demonstrates that soil fungi can be used as a sensitive indicator for soil health to evaluate the consequences of forest disturbance.

Importance

The soil fungal functional group changes in response to forest disturbance indicated a close interaction between the above-ground plant community and the below-ground soil biological community. Soil saprotrophic fungi declined in relative abundance with increasing forest disturbance. At the same time, the relative abundance of facultative pathogenic fungi increased. The loss of saprotrophic fungal richness and abundance may have been a direct result of forest disturbance or an indirect result of changes in soil pH and soil P. Furthermore, the dominant P solubilizing saprotrophic fungi was replaced by diverse facultative pathogenic fungi, which have weaker C decomposition ability. These changes potentially indicate a shift from soil phosphate limitation to carbon limitation following deforestation. This study suggests that changes in fungal functional group composition can be used as an indicator of the effects of forest disturbance on soil carbon and nutrients.
Metabolic rates of prokaryotic microbes may inevitably rise with global warming
Authors: Smith Thomas P. , Thomas Thomas J. H. , García-Carreras Bernardo , Sal Sofía , Yvon-Durocher Gabriel , Bell Thomas , Pawar Samrāt
Published: January 2019

Understanding how the metabolic rates of prokaryotes respond to temperature is fun-damental to our understanding of how ecosystem functioning will be altered by climate change, as these micro-organisms are major contributors to global carbon efflux. Ecological metabolic theory suggests that species living at higher temperatures evolve higher growth rates than those in cooler niches due to thermodynamic constraints. Here, using a global prokaryotic dataset, we find that maximal growth rate at thermal optimum increases with temperature for mesophiles (temperature optima ≲ 45°C), but not thermophiles (≳ 45°C). Furthermore, short-term (within-day) thermal responses of prokaryotic metabolic rates are typically more sensitive to warming than those of eukaryotes. Given that climatic warming will mostly impact ecosystems in the mesophilic temperature range, we conclude that as microbial communities adapt to higher temperatures, their metabolic rates and therefore, carbon efflux, will inevitably rise. Using a mathematical model, we illustrate the potential global impacts of these findings.
No evidence that portion size influences food consumption in male Sprague Dawley rats
Authors: Naneix Fabien , Pinder Sophie C. , Summers Megan Y. , Rouleau Renee M. , Robinson Eric , Myers Kevin P. , McCutcheon James E.
Published: January 2019

In studies of eating behavior that have been conducted in humans, the tendency to consume more when given larger portions of food, known as the portion size effect (PSE), is one of the most robust and widely replicated findings. Despite this, the mechanisms that underpin it are still unknown. In particular, it is unclear whether the PSE arises from higher-order social and cognitive processes that are unique to humans or, instead, reflects more fundamental processes that drive feeding, such as conditioned food-seeking. Importantly, studies in rodents and other animals have yet to show convincing evidence of a PSE. In this series of studies, we used several methods to test for a PSE in adult male Sprague Dawley rats. Our approaches included using visually identifiable portions of a palatable food; training on a plate cleaning procedure; providing portion sizes of food pellets that were signaled by auditory and visual food-predictive cues; providing food with amorphous shape properties; and providing standard chow diet portions in home cages. In none of these manipulations did larger portions increase food intake. In summary, our data provide no evidence that a PSE is present in male Sprague Dawley rats, and if it is, it is more nuanced, dependent on experimental procedure, and/or smaller in size than it is in humans. In turn, these findings suggest that the widely-replicated PSE in humans may be more likely to reflect higher-order cognitive and social processes than fundamental conditioned behaviors.

Highlights

Portion size effect (PSE) refers to increased food intake induced by large portions.

Although widely replicated in human feeding studies, it may not exist animals.

Presence of a PSE in animals would shed light on mechanisms, which are not known.

Here, we find no evidence of PSE in male Sprague Dawley rats under a number of experimental conditions.

This suggests that the human PSE is more likely due to socio-cognitive processes.
An encoding of genome content for machine learning
Authors: Viehweger A. , Krautwurst S. , Parks D. H. , König B. , Marz M.
Published: January 2019

An ever-growing number of metagenomes can be used for biomining and the study of microbial functions. The use of learning algorithms in this context has been hindered, because they often need input in the form of low-dimensional, dense vectors of numbers. We propose such a representation for genomes callednanotextthat scales to very large data sets.

The underlying model is learned from a corpus of nearly 150 thousand genomes spanning 750 million protein domains. We treat the protein domains in a genome like words in a document, assuming that protein domains in a similar context have similar “meaning”. This meaning can be distributed by a neural net over a vector of numbers.

The resulting vectors efficiently encode function, preserve known phylogeny, capture subtle functional relationships and are robust against genome incompleteness. The “functional” distance between two vectors complements nucleotide-based distance, so that genomes can be identified as similar even though their nucleotide identity is low.nanotextcan thus encode (meta)genomes for direct use in downstream machine learning tasks. We show this by predicting plausible culture media for metagenome assembled genomes (MAGs) from theTara Oceans Expeditionusing their genome content only.nanotextis freely released under a BSD licence (https://github.com/phiweger/nanotext).
Postnatal development of skeletal muscle in IUGR pigs: morphofunctional phenotype and molecular mechanisms
Authors: Pereira A.D. , Felicioni F. , Caldeira-Brant A.L. , Magnabosco D. , Bortolozzo F.P. , Tsoi S.C. , Dyck M. K. , Dixon W.T. , Martinelli P.M. , Jorge E.C. , Chiarini-Garcia H. , Almeida F.R.C.L.
Published: January 2019

Intrauterine growth restriction (IUGR) is a serious condition which impairs the achievement of the fetus full growth potential and occurs in a natural and severe manner in pigs. Knowledge on skeletal muscle morphofunctional phenotype and its molecular regulation in IUGR pigs is important to understand postnatal muscle development and may help the establishment of therapies to improve skeletal muscle growth in those individuals. To investigate the impairment of skeletal muscle postnatal development due to IUGR, we evaluated the histomorphometrical pattern of the semitendinosus muscle, the Myosin Heavy Chain (embryonic, I, IIa, IIb and IIx MyHC) fiber composition and the relative expression of genes related to myogenesis, adipogenesis and growth during three specific periods: postnatal myogenesis (newborn to 100 days of age), postnatal development (newborn to 150 days of age), and hypertrophy (100 days to 150 days of age), comparing IUGR and normal birth weight (NW) pigs. Growth restriction in utero affected muscle fiber diameter, total fiber number and muscle cross sectional area which were smaller in IUGR pigs at birth (P < 0.05). Even though the percentage of MyHC-I myofibers was higher in IUGR females at birth (P < 0.05), in older gilts, a lower percentage of MyHC-IIx isoform (P < 0.05) and the presence of emb-MyHC were also observed in that experimental group. Regarding the pattern of gene expression in the postnatal myogenesis period, growth restriction in utero led to a down regulation of myogenic factors, which delayed the expression of signals that induces skeletal muscle myogenesis (PAX7, MYOD, MYOG, MYF5 and DES). Taken together, the muscle morphofunctional aspects described and their ontogenetic regulation define the possible molecular origins of the notorious damage to the postnatal musculature development in IUGR pigs.
Ponds, puddles, floodplains and dams in the Upper Xingu Basin: could we be witnessing the ‘lentification’ of deforested Amazonia?
Authors: Schiesari Luis , Ilha Paulo R. , Negri Daniel Din Betin , Prado Paulo Inácio , Grillitsch Britta
Published: January 2019

Hydrological change is a conspicuous signal of land use intensification in human-dominated landscapes. We hypothesized that land conversion and land use change increase the availability of lentic habitats and associated biodiversity in Southern Amazonian landscapes through at least four drivers. River damming promotes the formation of reservoirs, which are novel permanent lentic water bodies. A rise in the water table driven by local deforestation promotes the expansion of shallow riparian floodplains. Soil compaction and the deliberate construction of cattle and drainage ponds promote the increase in temporary water bodies in interfluvia. We tested these hypotheses using data on habitat characterization and biological surveys of amphibians and fish in forests, pastures and soybean fields in the headwaters of the Xingu River in Mato Grosso, Brazil. Lentic habitat availability sharply increased in deforested land, with consequences to freshwater biodiversity. Reservoir formation influenced both fish and amphibian assemblage structure. Fish species ranged from strongly favored to strongly disfavored by reservoir conditions. Amphibian richness and abundance increased in pasture and soybean streams relative to forests, with a strong positive effect of density of reservoirs in the landscape. Expansion of stream floodplains increased the abundance ofMelanorivulus megaroni, a fish species indicator of shallow lentic habitats. Rainwater accumulation in temporary ponds and puddles, entirely absent from well-drained forested interfluvia, allowed the invasion of converted interfluvia by twelve species of open-area amphibians. A literature review indicates that these four drivers of hydrological change are geographically widespread suggesting that we may be witnessing a major yet previously unaccounted form of habitat change in deforested Amazonia.
Role of organizational image in employee engagement and performance
Authors: Dhir Swati , Shukla Archana
Published: January 2019

Purpose

The purpose of this paper is to investigate the role of organizational image in engaging employees and improving their performance. The study has explored the role of employee’s perception about the organizational image, and its linkage with the investment of employee’s energies into their work roles resulting in employee engagement (EE) and hence performance.

Design/methodology/approach

Adopting a model that was built on the basis of research conducted in the form of surveys. By using cross-sectional data and following a quantitative research method, the study collected data from 701 managers in India holding various positions, in different industries. The study has used “Component-Based Structural Equation Modeling” by Smart PLS.

Findings

The key findings of the study help employees as well as employers to have a thorough, comprehensive understanding to improve EE and their performance by creating a positive and consistent organizational image.

Research limitations/implications

This study will be very useful for employers and policymakers to understand the value of organizational image in engaging the workforce effectively. Aligning with the organizational behaviors theoretical support, this study yields some important and useful suggestions for managers to engage and retain their workforce in the present dynamic work environment.

Originality/value

The paper tries to focus on one’s perceptions of the organization and its linkage between EE and performance. The positive perception of employees reflects that they identify themselves and feel connected with the overall vision of the organization.
Comparison of the reluctance laminated and solid rotor synchronous machine operating at high temperatures
Authors: Lefik Marcin , Komeza Krzysztof , Napieralska-Juszczak Ewa , Roger Daniel , Napieralski Piotr Andrzej
Published: January 2019

Purpose

The purpose of this paper is to present a comparison between reluctance synchronous machine-enabling work at high internal temperature (HT° machine) with laminated and solid rotor.

Design/methodology/approach

To obtain heat sources for the thermal model, calculations of the electromagnetic field were made using the Opera 3D program including effect of rotation and the resulting eddy current losses. To analyse the thermal phenomenon, the 3D coupled thermal-fluid (CFD) model is used.

Findings

The presented results show clearly that laminated construction is much better from a point of view of efficiency and temperature. However, solid construction can be interesting for high speed machines due to their mechanical robustness.

Research limitations/implications

The main problem, despite the use of parallel calculations, is the long calculation time.

Practical implications

The obtained simulation and experimental results show the possibility of building a machine operating at a much higher ambient temperature than it was previously produced for example in the vicinity of the aircraft turbines.

Originality/value

The paper presents the application of fully three-dimensional coupled electromagnetic and thermal analysis of new machine constructions designed for elevated temperature.
Model structure effect on static aeroelastic deformation of the NASA CRM
Authors: Bdeiwi Houda , Ciarella Andrea , Peace Andrew , Hahn Marco
Published: January 2019

Purpose

This paper aims to present a computational aeroelastic capability based on a fluid–structure interaction (FSI) methodology and validate it using the NASA Common Research Model (CRM). Focus is placed on the effect of the wind tunnel model structural features on the static aeroelastic deformations.

Design/methodology/approach

The FSI methodology couples high-fidelity computational fluid dynamics to a simplified beam representation of the finite element model. Beam models of the detailed CRM wind tunnel model and a simplified CRM model are generated. The correlation between the numerical simulations and wind tunnel data for varying angles of attack is analysed and the influence of the model structure on the static aeroelastic deformation and aerodynamics is studied.

Findings

The FSI results follow closely the general trend of the experimental data, showing the importance of considering structural model deformations in the aerodynamic simulations. A thorough examination of the results reveals that it is not unequivocal that the fine details of the structural model are important in the aeroelastic predictions.

Research limitations/implications

The influence of some changes in structural deformation on transonic wing aerodynamics appears to be complex and non-linear in nature and should be subject to further investigations.

Originality/value

It is shown that the use of a beam model in the FSI approach provides a reliable alternative to the more costly coupling with the full FE model. It also highlights the non-necessity to develop precise, detailed structural models for accurate FSI simulations.
Mega events and seasonality: the case of the Milan World Expo 2015
Authors: Sainaghi Ruggero , Mauri Aurelio G. , Ivanov Stanislav , d’Angella Francesca
Published: January 2019

Purpose

This paper aims to explore the effects generated by the Milan World Expo 2015 on both firm performance and seasonality structure. It aims to answer the following research question: Did the Milan Expo 2015 influence only hotel results without changing seasonal patterns, or was this mega event able to reconfigure seasonal periods?

Design/methodology/approach

The present analysis is based on Smith Travel Research (STR) data. This source offers daily data on a large sample of Milan hotels (approximately 80 per cent of the total), representing more than 30,000 rooms. The empirical data relate to a period of 12 years, 11 of which are focused on the pre-event period (2004-2014), while 2015 is centered on the Milan Expo. This data comprise 4,383 daily observations. For each day, three operating measures were analyzed: occupancy, average daily rate (ADR) and revenue per available room (RevPAR).

Findings

The empirical findings fully support the first hypothesis: the four seasonal periods built around the main market segments are relevant lenses for understanding Milan’s demand structure before Expo 2015. The findings also support the second hypothesis relating to the effects generated by the event: Expo 2015 was able to improve hotel performance during the four seasonal periods analyzed. The most fragile seasonality registered the highest rise. Finally, the last two hypotheses to be investigated are as follows: did the Milan Expo 2015 simply improve hotel performance, without changing the underlying seasonal patterns (H3), or did this event reconfigure the demand structure (H4)? The analyses carried out lend more support to the fourth hypothesis, suggesting that new seasonal patterns emerged during Expo 2015.

Originality/value

This paper explores the impact of a mega event on seasonal patterns of hotel performance metrics. At least three original aspects are introduced. First, to analyze the Milan demand variation, a market segment approach that proposes an innovative seasonal matrix is developed. This is based on the three main client groups attracted by the destination. Second, the effects generated by the Expo are measured with consideration given to the four seasonal periods. Third, based on graphical and statistical analysis, the paper confirms that new seasonal patterns emerged during the Expo.
The nexus of electricity access, population growth, economic growth in Pakistan and projection through 2040
Authors: Rehman Abdul
Published: January 2019

Purpose

The purpose of this study was to investigate the relationship between electricity access, population growth and economic growth in Pakistan.

Design/methodology/approach

Phillips–Perron unit root test was applied to check the stationarity of the variables and an Autoregressive Distributed Lag (ARDL) bounds testing approach to co-integration was used to investigate the causality link between the study variables. Finally, a projection method was applied to check the future trend of the variables.

Findings

The study results show the long-term connections among the variables; further, the results illustrate that the electricity access to the urban population and the urban population growth has a significant impact on the economic growth, while the electricity access to the rural population and the rural population growth has a negative impact on the economic growth in Pakistan.

Research limitations/implications

The electricity sector needs further attention from the Government of Pakistan to boost the production from different energy sources, such as oil, gas, solar, nuclear and hydropower to be able to fulfill the country’s growing demand.

Originality/value

By using the ARDL bounds testing approach to co-integration, this study addressed the literature gap regarding electricity access, population growth and economic growth in Pakistan.
“Under the radar”: exploring “invisible” graduate attributes in tertiary dance education
Authors: Longley Alys , Kensington-Miller Barbara
Published: January 2019

Purpose

Many graduate attributes (such as adaptability, resilience, cultural awareness and professionalism) are often considered aspirational or invisible and conventionally go “under the radar” of standard university dance education. The purpose of this paper is to add to existing theories of dance as an academic discipline and contributes to studies identifying and mapping graduate attributes across the academy.

Design/methodology/approach

The research project Making the Invisible Visible contextualises this paper. It has involved a two-year, cyclical data-gathering process, involving interviews with leading dance employers and academics, and surveys of students from diverse disciplines entering and completing full-time dance degrees.

Findings

Due to the centrality of embodiment in studio learning, dance is an unusual discipline within research on graduate attributes and holds a unique place in academia. The creative, embodied, collaborative activities typical to dance learning offer fresh insight to the literature on graduate attributes – both visible and invisible – all graduates from a given institution are expected to hold.

Originality/value

A narrative methodology is employed to present a series of amalgam characters manifesting specific ways in which invisible graduate attributes inform pedagogies, student–teacher relationships and student understandings of their professional skills.
Collaborative innovation for more value: how to make it work
Authors: Lin Haibo , Yip George , Yang Jinchun , Fu Xiaolan
Published: January 2019

Purpose

The purpose of this paper is to focus on “how to create value from collaborative innovation,” which is a core question when companies plan open-innovation initiatives. China’s Huawei Technologies is taken as the main case study, with other companies’ practices as further examples to elaborate and validate a new yet practical model.

Design/methodology/approach

This paper is based on the direct experience over many years of two Huawei technology executives – the very recent head of the technology cooperation department and the current manager of the same unit.

Findings

This study provides a spiral four-stage model, named SWIM, with each stage being a decision guided by a 2 × 2 matrix. These stages, named scope, weave, identify and modularize, try to balance resource allocation toward a foreseeable value, though it might be long term.

Research limitations/implications

The research is primarily based on one company. The validity of its recommended model can be tested only after other companies have applied it.

Practical implications

The research offers a practical framework for how companies can improve their open innovation.

Social implications

Large companies are important players in innovation networks. Improving the ability of large companies to operate open innovation will help many other companies and the society as a whole.

Originality/value

The proposed model is original and provides insights from China and is not a traditional source of management innovation. The paper will also help Western readers get a better understanding of management in what will soon be the world’s largest economy.