bluuebunny/crossref_metadata_2025_split huggingface dataset:
Some mechanistic requirements for major transitions
Authors: Schuster Peter 
Published: July 2016

Major transitions in nature and human society are accompanied by a substantial change towards higher complexity in the core of the evolving system. New features are established, novel hierarchies emerge, new regulatory mechanisms are required and so on. An obvious way to achieve higher complexity is integration of autonomous elements into new organized systems whereby the previously independent units give up their autonomy at least in part. In this contribution, we reconsider the more than 40 years old hypercycle model and analyse it by the tools of stochastic chemical kinetics. An open system is implemented in the form of a flow reactor. The formation of new dynamically organized units through integration of competitors is identified with transcritical bifurcations. In the stochastic model, the fully organized state is quasi-stationary whereas the unorganized state corresponds to a population with natural selection. The stability of the organized state depends strongly on the number of individual subspecies,n, that have to be integrated: two and three classes of individuals,and, readily form quasi-stationary states. The four-membered deterministic dynamical system,, is stable but in the stochastic approach self-enhancing fluctuations drive it into extinction. In systems with five and more classes of individuals,, the state of cooperation is unstable and the solutions of the deterministic ODEs exhibit large amplitude oscillations. In the stochastic system self-enhancing fluctuations lead to extinction as observed with. Interestingly, cooperative systems in nature are commonly two-membered as shown by numerous examples of binary symbiosis. A few cases of symbiosis of three partners, calledthree-way symbiosis, have been found and were analysed within the past decade. Four-way symbiosis is rather rare but was reported to occur in fungus-growing ants. The model reported here can be used to illustrate the interplay between competition and cooperation whereby we obtain a hint on the role that resources play in major transitions. Abundance of resources seems to be an indispensable prerequisite of radical innovation that apparently needs substantial investments. Economists often claim that scarcity is driving innovation. Our model sheds some light on this apparent contradiction. In a nutshell, the answer is: scarcity drives optimization and increase in efficiency but abundance is required for radical novelty and the development of new features.This article is part of the themed issue ‘The major synthetic evolutionary transitions’.
Generating minimal living systems from non-living materials and increasing their evolutionary abilities
Authors: Rasmussen Steen , Constantinescu Adi , Svaneborg Carsten 
Published: July 2016

We review lessons learned about evolutionary transitions from a bottom-up construction of minimal life. We use a particular systemic protocell design process as a starting point for exploring two fundamental questions: (i) how may minimal living systems emerge from non-living materials? and (ii) how may minimal living systems support increasingly more evolutionary richness? Under (i), we present what has been accomplished so far and discuss the remaining open challenges and their possible solutions. Under (ii), we present a design principle we have used successfully both for our computational and experimental protocellular investigations, and we conjecture how this design principle can be extended for enhancing the evolutionary potential for a wide range of systems.
This article is part of the themed issue ‘The major synthetic evolutionary transitions’.
Viruses and mobile elements as drivers of evolutionary transitions
Authors: Koonin Eugene V. 
Published: July 2016

The history of life is punctuated by evolutionary transitions which engender emergence of new levels of biological organization that involves selection acting at increasingly complex ensembles of biological entities. Major evolutionary transitions include the origin of prokaryotic and then eukaryotic cells, multicellular organisms and eusocial animals. All or nearly all cellular life forms are hosts to diverse selfish genetic elements with various levels of autonomy including plasmids, transposons and viruses. I present evidence that, at least up to and including the origin of multicellularity, evolutionary transitions are driven by the coevolution of hosts with these genetic parasites along with sharing of ‘public goods’. Selfish elements drive evolutionary transitions at two distinct levels. First, mathematical modelling of evolutionary processes, such as evolution of primitive replicator populations or unicellular organisms, indicates that only increasing organizational complexity, e.g. emergence of multicellular aggregates, can prevent the collapse of the host–parasite system under the pressure of parasites. Second, comparative genomic analysis reveals numerous cases of recruitment of genes with essential functions in cellular life forms, including those that enable evolutionary transitions.This article is part of the themed issue ‘The major synthetic evolutionary transitions’.
Stabilizing multicellularity through ratcheting
Authors: Libby Eric , Conlin Peter L. , Kerr Ben , Ratcliff William C. 
Published: July 2016

The evolutionary transition to multicellularity probably began with the formation of simple undifferentiated cellular groups. Such groups evolve readily in diverse lineages of extant unicellular taxa, suggesting that there are few genetic barriers to this first key step. This may act as a double-edged sword: labile transitions between unicellular and multicellular states may facilitate the evolution of simple multicellularity, but reversion to a unicellular state may inhibit the evolution of increased complexity. In this paper, we examine how multicellular adaptations can act as evolutionary ‘ratchets’, limiting the potential for reversion to unicellularity. We consider a nascent multicellular lineage growing in an environment that varies between favouring multicellularity and favouring unicellularity. The first type of ratcheting mutations increase cell-level fitness in a multicellular context but are costly in a single-celled context, reducing the fitness of revertants. The second type of ratcheting mutations directly decrease the probability that a mutation will result in reversion (either as a pleiotropic consequence or via direct modification of switch rates). We show that both types of ratcheting mutations act to stabilize the multicellular state. We also identify synergistic effects between the two types of ratcheting mutations in which the presence of one creates the selective conditions favouring the other. Ratcheting mutations may play a key role in diverse evolutionary transitions in individuality, sustaining selection on the new higher-level organism by constraining evolutionary reversion.This article is part of the themed issue ‘The major synthetic evolutionary transitions’.
Epigenetic inheritance systems contribute to the evolution of a germline
Authors: Lachmann Michael , Libby Eric 
Published: July 2016

Differentiation within multicellular organisms is controlled by epigenetic markers transmitted across cell division. The process of differentiation will modify these epigenetic markers so that information that one cell type possesses can be lost in the transition to another. Many of the systems that encode these markers also exist in unicellular organisms but do not control differentiation. Thus, during the evolution of multicellularity, epigenetic inheritance systems were probably exapted for their current use in differentiation. We show that the simultaneous use of an information carrier for differentiation and transmission across generations can lead to the evolution of cell types that do not directly contribute to the progeny of the organism and ergo a germ–soma distinction. This shows that an intrinsic instability during a transition from unicellularity to multicellularity may contribute to widespread evolution of a germline and its maintenance, a phenomenon also relevant to the evolution of eusociality. The difference in epigenetic information contents between different cell lines in a multicellular organism is also relevant for the full-success cloning of higher animals, as well as for the maintenance of single germlines over evolutionary timescales.This article is part of the themed issue ‘The major synthetic evolutionary transitions’.
Energy and time determine scaling in biological and computer designs
Authors: Moses Melanie , Bezerra George , Edwards Benjamin , Brown James , Forrest Stephanie 
Published: July 2016

Metabolic rate in animals and power consumption in computers are analogous quantities that scale similarly with size. We analyse vascular systems of mammals and on-chip networks of microprocessors, where natural selection and human engineering, respectively, have produced systems that minimize both energy dissipation and delivery times. Using a simple network model that simultaneously minimizes energy and time, our analysis explains empirically observed trends in the scaling of metabolic rate in mammals and power consumption and performance in microprocessors across several orders of magnitude in size. Just as the evolutionary transitions from unicellular to multicellular animals in biology are associated with shifts in metabolic scaling, our model suggests that the scaling of power and performance will change as computer designs transition to decentralized multi-core and distributed cyber-physical systems. More generally, a single energy–time minimization principle may govern the design of many complex systems that process energy, materials and information.
This article is part of the themed issue ‘The major synthetic evolutionary transitions’.
Agent-based models for the emergence and evolution of grammar
Authors: Steels Luc 
Published: July 2016

Human languages are extraordinarily complex adaptive systems. They feature intricate hierarchical sound structures, are able to express elaborate meanings and use sophisticated syntactic and semantic structures to relate sound to meaning. What are the cognitive mechanisms that speakers and listeners need to create and sustain such a remarkable system? What is the collective evolutionary dynamics that allows a language to self-organize, become more complex and adapt to changing challenges in expressive power? This paper focuses on grammar. It presents a basic cycle observed in the historical language record, whereby meanings move from lexical to syntactic and then to a morphological mode of expression before returning to a lexical mode, and discusses how we can discover and validate mechanisms that can cause these shifts using agent-based models.This article is part of the themed issue ‘The major synthetic evolutionary transitions’.
Functional Cliques in Developmentally Correlated Neural Networks
Authors: Luccioli S. , Barzilai A. , Ben-Jacob E. , Bonifazi P. , Torcini A. 
Published: July 2016

AbstractWe consider a sparse random network of excitatory leaky integrate-andfire neurons with short-term synaptic depression. Furthermore to mimic the dynamics of a brain circuit in its first stages of development we introduce for each neuron correlations among in-degree and out-degree as well as among excitability and the corresponding total degree, We analyze the influence of single neuron stimulation and deletion on the collective dynamics of the network. We show the existence of a small group of neurons capable of controlling and even silencing the bursting activity of the network. These neurons form afunctional cliquesince only their activation in a precise order and within specific time windows is capable to ignite population bursts.
FEELnc: A tool for Long non-coding RNAs annotation and its application to the dog transcriptome
Authors: Wucher V , Legeai F , Hédan B , Rizk G , Lagoutte L , Leeb T , Jagannathan V , Cadieu E , David A , Lohi H , Cirera S , Fredholm M , Botherel N , Leegwater P , Le Béguec C , Fieten H , Johansson C , Johnsson J ,   LUPA consortium, Alifoldi J , André C , Lindblad-Toh K , Hitte C , Derrien T 
Published: July 2016

ABSTRACTWhole transcriptome sequencing (RNA-seq) has become a standard for cataloguing and monitoring RNA populations. Among the plethora of reconstructed transcripts, one of the main bottlenecks consists in correctly identifying the different classes of RNAs, particularly those that will be translated (mRNAs) from the class of long non-coding RNAs (lncRNAs). Here, we present FEELnc (FlExible Extraction of LncRNAs), an alignment-free program which accurately annotates lncRNAs based on a Random Forest model trained with general features such as multik-mer frequencies and relaxed open reading frames. Benchmarking versus five state-of-art tools shows that FEELnc achieves similar or better classification performance on GENCODE and NONCODE datasets. The program also provides several specific modules that enable to fine-tune classification accuracy, to formalize the annotation of lncRNA classes and to annotate lncRNAs even in the absence of training set of noncoding RNAs. We used FEELnc on a real dataset comprising 20 new canine RNA-seq samples produced in the frame of the European LUPA consortium to expand the canine genome annotation and classified 10,374 novel lncRNAs and 58,640 new mRNA transcripts. FEELnc represents a standardized protocol for identifying and annotating lncRNAs and is freely accessible athttps://github.com/tderrien/FEELnc.
Neuronal control of the fingertips is socially configured in touchscreen smartphone users
Authors: Balerna Myriam , Ghosh Arko 
Published: July 2016

AbstractAs a common neuroscientific observation, the more a body part is used, the less variable the corresponding computations become. We here report a more complicated scenario concerning the fingertips of smartphone users. We sorted 21-days histories of touchscreen use of 57 volunteers into social and non-social categories. Sensorimotor variability was measured in a laboratory setting by simple button depressions and scalp electrodes (electroencephalogram, EEG). The ms range trial-to-trial variability in button depression was directly proportional to the number of social touches and inversely proportional to non-social touches. Variability of the early tactile somatosensory potentials was also proportional to the number of social touches, but not to non-social touches. The number of Apps and the speed of touchscreen use also reflected this variability. We suggest that smartphone use affects elementary computations even in tasks not involving a phone and that social activities uniquely reconfigure the thumb to touchscreen use.Impact StatementUnconstrained behavior on a smartphone is a powerful predictor of neuronal functions measured in the laboratory and the details of the smartphone-neuronal association challenges the established ideas of brain plasticity.
Threshold concept in intellectual property law
Authors: Azam Monirul 
Published: July 2016

PurposeThis paper aims to identify the threshold concept in intellectual property (IP) law.Design/methodology/approachIt used doctrinal methods for such identification based on the existing pedagogical scholarship in the field of effective teaching and learning.FindingsIt explained how the use of the threshold concept in IP law education could facilitate understanding of IP law from globalised perspectives and validate use of IP in a balanced way.Research limitations/implicationsIt is yet to be tested for practical curriculum design in different jurisdictions.Practical implicationsThe understanding of threshold concepts in IP law could generate “eureka” moments, when, after a long struggle, students come to a deep understanding of a new concept.Social implicationsThis will facilitate social acceptance of IP for balancing global obligation and national developmental and social goals.Originality/valueTill date, little work has been undertaken on the threshold concepts on IP law. Therefore, this study tried to make a unique contribution by identifying threshold concepts in intellectual property law.
Social capital, networks and interlocked independent directors: a Mexican case
Authors: Avina-Vazquez Carlos Rafael , Uddin Shahzad 
Published: July 2016

Purpose– The purpose of this paper is to investigate whether a pattern of interlocking directorates is emerging following reforms in Mexican corporations, and who, if any, are the powerful actors in this network. Drawing on the Bourdieusian notion of social capital, the paper also analyses theoretically the interlocking directorates, networks and powerful actors, and their influences on and potential implications for corporate governance mechanisms.Design/methodology/approach– The data used in the study consisted of 1,442 internal and external board members of the population of 126 Mexican corporations trading on the Mexican Stock Market as of January 2011. Use of social network analysis (SNA) demonstrates individuals’ links with corporations and allows the production of spatial maps to visualise the network structure of interlocking boards.Findings– Using the measures of SNA developed by Freeman (1979 and Bonacich (1972), the authors identify the most powerful and influential directors in the network structure of board members in Mexico. Board members with the greatest number of connections occupy central positions in the network. The authors also find a catalogue of corporate governance scandals. The inclusion of independent directors seems to have had no influence in ensuring better corporate governance.Research limitations/implications– Mapping out the directors’ links might offer excellent opportunities for policy makers to see how many companies a single director represents, how they share boards, and the implications for minority shareholders of sharing boards, and to understand the workloads of directors in carrying out the monitoring tasks expected of them.Originality/value– This paper makes an important contribution by employing SNA to illustrate interlocking directorates and the positions of powerful and influential actors. Examining networks of directors from a “social capital” point of view also provides an understanding of why the role of independent directors remains toothless in family-dominated corporations.
Satisfaction gap in public sector financial reporting
Authors: Krambia-Kapardis Maria , Clark Colin , Zopiatis Anastasios 
Published: July 2016

Purpose– Public information disclosure is a manifestation of transparency and contributes to governance-by-disclosure. Also, better financial reporting can improve the credibility and integrity of public finances and contribute to a better management of public resources. A survey was carried out in Cyprus of users’ of public financial reports concerning an expectation gap about the types of information included in such reports (information needs expectation gap) as well as the quality of such information (information quality satisfaction gap). The paper aims to discuss these issues.Design/methodology/approach– Two focus groups of users and preparers of public financial reports were used to construct the questionnaire. Users of such reports, who belonged to all three categories of public sector financial reporting identified by IPSASB, were surveyed. The quantitative data obtained was analysed using SPSS and quadrant analysis to answer the research questions posed.Findings– Data from 101 respondents confirmed that each of the information needs identified in the IPSASB Consultation Paper (2008) was rated as being a significant information need. Data analysis also showed that both types of expectation gap exist, especially as far as local authority and semi-public organisations are concerned.Research limitations/implications– The response rate in the self-administered survey was admittedly rather low but it was not unexpected mainly due to the survey’s very specialised nature and the tendency by people in Cyprus not to critique public bodies.Practical implications– Deficient financial public sector reporting means the auditor general is not able to adequately express an opinion on public spending at the local government level. This, in turn, means taxpayers do not get the quality of services they pay for. At the same time, the lack of information transparency means corrupt practices are not eradicated. One answer to the problem would be legislating the content of public financial reports.Social implications– The lack of governance-by-public exposure means that services to the local community cost a lot more, due to corruption and inefficiency. In addition, it contributes to lowering market confidence and eventually contributes to financial crisis at the national level.Originality/value– The survey conducted was the first of its kind in Cyprus to investigate financial public sector reporting and document both manifestations of the expectation gap. In addition, information needs identified in the IPSASB Consultation Paper (2008) was rated as significantly needed and this is the first time it has been done in Eurozone member state and in a country facing a financial crisis.
On the tax-accounting linkage in the European emerging context
Authors: Deaconu Adela , Cuzdriorean Dan Dacian 
Published: July 2016

Purpose
– The purpose of this paper is to investigate stakeholders’ salience on accounting and in particular to assess the magnitude of state influence in Romania, an emerging context.

Design/methodology/approach
– This research integrates stakeholders’ theory and an empirical approach based on a survey administrated to professional accountants as preparers of accounts on the financial reporting market.

Findings
– The findings confirm the hypothesis of Mitchell et al. (1997) that the importance of stakeholders is high if attributes like power, legitimacy and claims urgency are perceived as current. In the Romanian emergent context, for the period 1991-2010, a relatively strong tax-accounting linkage is still identified according to Lamb et al.’s (1998) hierarchy. However, as compared to the absolute dominance observed for the early post-communist stage, the state holds the second position in terms of values of stakeholder attributes, after the shareholders.

Practical implications
– An increased influence of the accounting bodies, academics and business representatives, who should communicate effectively and constructively with the public structures with respect to enforcement of accounting regulations and the type of organizations involved. The higher focus on IFRS in the EU and in Romania and the evolution of Romanian economic and legal structures lead to the reassessment of the usefulness of IFRS, at least in the case of certain types of organizations. This is also due to the fact that the new IASB framework takes into consideration other types of stakeholders than (actual) shareholders along with the providers of finance from the entity and stewardship perspective.

Originality/value
– This paper argues that one of the factors of state influence in accounting is the tax-accounting linkage who is still occurs in this context in present. Also, refers to another factor that caused the watering down of the state’ position, namely, the growing impact of IFRS on Romanian financial reporting.