bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dissipative structures in biological systems: bistability, oscillations, spatial patterns and waves
Authors: Goldbeter Albert 
Published: June 2018

The goal of this review article is to assess how relevant is the concept of dissipative structure for understanding the dynamical bases of non-equilibrium self-organization in biological systems, and to see where it has been applied in the five decades since it was initially proposed by Ilya Prigogine. Dissipative structures can be classified into four types, which will be considered, in turn, and illustrated by biological examples: (i) multistability, in the form of bistability and tristability, which involve the coexistence of two or three stable steady states, or in the form of birhythmicity, which involves the coexistence between two stable rhythms; (ii) temporal dissipative structures in the form of sustained oscillations, illustrated by biological rhythms; (iii) spatial dissipative structures, known as Turing patterns; and (iv) spatio-temporal structures in the form of propagating waves. Rhythms occur with widely different periods at all levels of biological organization, from neural, cardiac and metabolic oscillations to circadian clocks and the cell cycle; they play key roles in physiology and in many disorders. New rhythms are being uncovered while artificial ones are produced by synthetic biology. Rhythms provide the richest source of examples of dissipative structures in biological systems. Bistability has been observed experimentally, but has primarily been investigated in theoretical models in an increasingly wide range of biological contexts, from the genetic to the cell and animal population levels, both in physiological conditions and in disease. Bistable transitions have been implicated in the progression between the different phases of the cell cycle and, more generally, in the process of cell fate specification in the developing embryo. Turing patterns are exemplified by the formation of some periodic structures in the course of development and by skin stripe patterns in animals. Spatio-temporal patterns in the form of propagating waves are observed within cells as well as in intercellular communication. This review illustrates how dissipative structures of all sorts abound in biological systems.This article is part of the theme issue ‘Dissipative structures in matter out of equilibrium: from chemistry, photonics and biology (part 1)’.
Early models of chemical oscillations failed to provide bounded solutions
Authors: Erneux Thomas 
Published: June 2018

Before the development of the Brusselator, the Sel’kov and Turing models were considered as possible prototype models of chemical oscillations. We first analyse their Hopf bifurcation branches and show that they become vertical past a critical value of the control parameter. We explain this phenomenon by the emergence of canard orbits. Second, we analyse all solutions in the phase plane and show that some initial conditions lead to unbounded trajectories even if there exists a locally stable attractor. Our findings mathematically explain why these too simple two-variable models fail to account for the emergence of chemical oscillations. They support the conclusion that the Brusselator is the first minimal two-variable model explaining the onset of stable oscillations in a way fully compatible with thermodynamics and the law of mass action.
This article is part of the theme issue ‘Dissipative structures in matter out of equilibrium: from chemistry, photonics and biology (part 1)’.
A taxonomy of optical dissipative structures in whispering-gallery mode resonators with Kerr nonlinearity
Authors: Balakireva Irina V. , Chembo Yanne K. 
Published: June 2018

In this paper, the research related to the formation of optical dissipative structures in Kerr-nonlinear whispering-gallery mode resonators pumped with continuous-wave lasers is reviewed. Pattern formation in these systems can be analysed using the paradigmatic Lugiato–Lefever model, which is a partial differential equation ruling the dynamics of the intra-cavity laser field. Various dissipative structures such as Turing rolls, solitons, breathers and spatio-temporal chaos can emerge in the resonator depending on the laser power and frequency. The bifurcation analysis enables a classification of these patterns, and also permits identification of their basins of attraction.
This article is part of the theme issue ‘Dissipative structures in matter out of equilibrium: from chemistry, photonics and biology (part 1)’.
Reducing nonlinear dynamical systems to canonical forms
Authors: Brenig Léon 
Published: June 2018

A global framework for treating nonlinear differential dynamical systems is presented. It rests on the fact that most systems can be transformed into the quasi-polynomial format. Any system in this format belongs to an infinite equivalence class characterized by two canonical forms, the Lotka–Volterra (LV) and the monomial systems. Both forms allow for finding total or partial integrability conditions, invariants and dimension reductions of the original systems. The LV form also provides Lyapunov functions and systematic tools for stability analysis. An abstract Lie algebra is shown to underlie the whole formalism. This abstract algebra can be expressed in several realizations among which are the bosonic creation–destruction operators. One of these representations allows one to obtain the analytic form of the general coefficient of the Taylor series representing the solution of the original system. This generates a new class of special functions that are solutions of these nonlinear dynamical systems. From the monomial canonical form, one can prove an equivalence relationship between urn processes and dynamical systems. This establishes a new link between nonlinear dynamics and stochastic processes.This article is part of the theme issue ‘Dissipative structures in matter out of equilibrium: from chemistry, photonics and biology (part 1)’.
Role of biofilm-specific antibiotic resistance genes PA0756-0757, PA5033 and PA2070 inPseudomonas aeruginosa
Authors: Manohar Prasanth , Shanthini Thamaraiselvan , Philip Reethu Ann , Ramkumar Subramani , Kale Manali , Ramesh Nachimuthu 
Published: June 2018

AbstractTo evaluate the presence of biofilm-specific antibiotic-resistant genes, PA0756-0757, PA5033 and PA2070 inPseudomonas aeruginosaisolated from clinical samples in Tamil Nadu. For this cross-sectional study, 24 clinical isolates (included pus, urine, wound, and blood) were collected from two diagnostic centers in Chennai from May 2015 to February 2016. Biofilm formation was assessed using microtiter dish biofilm formation assay and minimal inhibitory concentration (MIC) and minimal bactericidal concentrations (MBC) were determined for planktonic and biofilm cells (MBC assay). Further, PCR amplification of biofilm-specific antibiotic resistance genes PA0756-0757, PA5033 and PA2070 were performed. Biofilm formation was found to be moderate/strong in 16 strains. MBC for planktonic cells showed that 4, 7, 10 and 14 strains were susceptible to gentamicin, ciprofloxacin, meropenem and colistin respectively. In MBC assay for biofilm cells (MBC-B), all the 16 biofilm producing strains were resistant to ciprofloxacin and gentamicin whereas nine and four were resistant to meropenem, and colistin respectively. The biofilm-specific antibiotic-resistant genes PA0756-0757 was found in 10 strains, 6 strains with PA5033 and 9 strains with PA2070 that were found to be resistant phenotypically. This study highlighted the importance of biofilm-specific antibiotic resistance genes PA0756-0757, PA5033, and PA2070 in biofilm-formingP. aeruginosa.
Topconfects: a package for confident effect sizes in differential expression analysis provides improved usability ranking genes of interest
Authors: Harrison Paul F. , Pattison Andrew D. , Powell David R. , Beilharz Traude H. 
Published: June 2018

AbstractBackgroundA differential gene expression analysis may produce a set of significantly differentially expressed genes that is too large to easily investigate, so that a means of ranking genes by their biological interest level is desirable. The life-sciences have grappled with the abuse of p-values to rank genes for this purpose. As an alternative, a lower confidence bound on the magnitude of Log Fold Change (LFC) could be used to rank genes, but it has been unclear how to reconcile this with the need to perform False Discovery Rate (FDR) correction. The TREAT test of McCarthy and Smyth is a step in this direction, finding genes significantly exceeding a specified LFC threshold. Here we describe the use of test inversion on TREAT to present genes ranked by a confidence bound on the LFC, while still controlling FDR.ResultsTesting the Topconfects R package with simulated gene expression data shows the method outperforming current statistical approaches across a wide range of experiment sizes in the identification of genes with largest LFCs. Applying the method to a TCGA breast cancer data-set shows the method ranks some genes with large LFC higher than would traditional ranking by p-value. Importantly these two ranking methods lead to a different biological emphasis, in terms both of specific highly ranked genes and gene-set enrichment.ConclusionsThe choice of ranking method in differential expression analysis can affect the biological interpretation. The common default of ranking by p-value is implicitly by an effect size in which each gene is standardized to its own variability, rather than comparing genes on a common scale, which may not be appropriate. The Topconfects approach of presenting genes ranked by confident LFC effect size is a variation on the TREAT method with improved usability, removing the need to fine-tune a threshold parameter and removing the temptation to abuse p-values as a de-facto effect size.
Whole-genome analysis of introgression between the spotted owl and barred owl (Strix occidentalisandStrix varia, respectively; Aves: Strigidae) in western North America
Authors: Hanna Zachary R. , Dumbacher John P. , Bowie Rauri C.K. , Henderson James B. , Wall Jeffrey D. 
Published: June 2018

AbstractAs the barred owl (Strix varia; Aves: Strigiformes: Strigidae) expands throughout western North America, hybridization between barred and spotted owls (Strix variaandS. occidentalis, respectively), if abundant, may lead to genetic swamping of the endangered spotted owl. We analyzed low-coverage, whole-genome sequence data from fifty-one barred and spotted owls to investigate recent introgression between these two species. Although we obtained genomic confirmation that these species can and do hybridize and backcross, we found no evidence of widespread introgression. Plumage characteristics of westernS. variathat suggested admixture withS. occidentalisappear unrelated toS. occidentalisancestry and may instead reflect local selection.
Weighted Network Density Predicts Range of Latent Variable Model Accuracy
Authors: Palmerston Jeremiah B. , She Qi , Chan Rosa H. M. 
Published: June 2018

AbstractCurrent experimental techniques impose spatial limits on the number of neuronal units that can be recorded in-vivo. To model the neural dynamics utilizing these sampled data, Latent Variable Models (LVMs) have been proposed to study the common unobserved processes within the system that drives neural activities, through an implicit network with hidden states. Yet, relationships between these latent variable models and widely-studied network connectivity measures remained unclear. In this paper, a biologically plausible latent variable model was first fit to neural activity recorded via 2-photon microscopic calcium imaging in the murine primary visual cortex. Graph theoretic measures were then applied to quantify network properties in the recorded sub-regions. Comparison of weighted network measures with LVM prediction accuracy shows some network measures having a strong relationship with LVM prediction accuracy, while other measures do not have a robust relationship with LVM prediction accuracy. Results show LVM will achieve high accuracy in dense networks.
Bagging Improves Reproducibility of Functional Parcellation of the Human Brain
Authors: Nikolaidis Aki , Heinsfeld Anibal Solon , Xu Ting , Bellec Pierre , Vogelstein Joshua , Milham Michael 
Published: June 2018

AbstractIncreasing the reproducibility of neuroimaging measurement addresses a central impediment to the advancement of human neuroscience and its clinical applications. Recent efforts demonstrating variance in functional brain organization within and between individuals shows a need for improving reproducibility of functional parcellations without long scan times. We apply bootstrap aggregation, or bagging, to the problem of improving reproducibility in functional parcellation. We use two large datasets to demonstrate that compared to a standard clustering framework, bagging improves the reproducibility and test-retest reliability of both cortical and subcortical functional parcellations across a range of sites, scanners, samples, scan lengths, clustering algorithms, and clustering parameters (e.g., number of clusters, spatial constraints). With as little as six minutes of scan time, bagging creates more reproducible group and individual level parcellations than standard approaches with twice as much data. This suggests that regardless of the specific parcellation strategy employed, bagging may be a key method for improving functional parcellation and bringing functional neuroimaging-based measurement closer to clinical impact.
Oxytocin facilitates empathic- and self-embarrassment ratings by attenuating amygdala and anterior insula responses
Authors: Geng YaYuan , Zhao Weihua , Zhou Feng , Ma Xiaole , Yao Shuxia , Becker Benjamin , Kendrick Keith M. 
Published: June 2018

AbstractThe hypothalamic neuropeptide oxytocin has been reported to enhance emotional empathy in association with reduced amygdala activation, although to date studies have not investigated empathy for individuals expressing self-conscious, moral emotions which engage mentalizing as well as emotion processing networks. In the current randomized, double-blind placebo controlled functional MRI experiment on 70 male and female subjects we have therefore investigated the effects of intranasal oxytocin (40 IU) on behavioral and neural responses to embarrassment experienced by others or by self. Results showed that oxytocin significantly increased ratings of both empathic and self-embarrassment and concomitantly decreased skin conductance response and activation in the right amygdala and insula but not in the medial prefrontal cortex. The amygdala effects of oxytocin were associated with the magnitude of the skin conductance response and trait anxiety scores. Overall our results demonstrate that oxytocin increases ratings of self- and other embarrassment and that this is associated with reduced physiological arousal and activity in neural circuitry involved in emotional arousal. The neural effects of oxytocin are also stronger in individuals with high trait anxiety suggesting that it may particularly reduce their anxiety in embarrassing situations.
Neuronal thresholds and correlations in the peripheral vestibular system during rotation discrimination
Authors: Garcia Courtney D. , Liu Sheng , Laurens Jean , DeAngelis Gregory C. , Dickman J. David , Angelaki Dora E. 
Published: June 2018

ABSTRACTNeuronal and behavioral thresholds were measured simultaneously as trained male macaques performed a yaw rotation discrimination task in darkness. When corrected to account for variations in neuronal direction preferences, neurons in the vestibular nuclei and semicircular canal afferents had discrimination thresholds that were only two-fold smaller than behavioral thresholds. There was no significant trial-by-trial correlation between neuronal activity and perceptual decisions, despite the presence of significant pair-wise noise correlations. The lack of choice-related activity during rotation discrimination contrasts with the robust correlations observed previously between brainstem neurons and choices during translation perception. These results suggest task-dependent differences in subcortical processing of vestibular signals, as well as how signals related to perceptual decisions may propagate back to early stages of sensory processing.SIGNIFICANCE STATEMENTThis is the first ever simultaneous recordings of neural and behavioral thresholds during rotation discrimination. Its importance lies on the fact that the vestibular system provides an excellent model to probe origins of perception because directional selectivity signals are similar at many levels of processing, from afferents to cortex. The findings of similar neuronal and behavioral discrimination thresholds, significant inter-neuronal correlations, but lack of correlations between behavior and neuronal activity of both afferents and central brainstem neurons are intriguing and suggest task-dependent organization of early sensory areas.
Decoding Hierarchical Control of Sequential Behavior in Oscillatory EEG Activity
Authors: Kikumoto Atsushi , Mayr Ulrich 
Published: June 2018

AbstractDespite strong theoretical reasons for assuming that abstract representations organize complex action sequences in terms of subplans (chunks) and sequential positions, we lack methods to directly track such content-independent, hierarchical representations in humans. We applied time-resolved, multivariate decoding analysis to the pattern of rhythmic EEG activity that was registered while participants planned and executed individual elements from pre-learned, structured sequences. Across three experiments, the theta and alpha-band activity independently coded basic elements and abstract control representations, in particular the ordinal position of basic elements, but also the identity and position of chunks. Further, a robust representation of higher-level, chunk identity information was only found in individuals with above-median working memory capacity, potentially providing a neural-level explanation for working-memory differences in sequential performance. Our results suggest that by decoding oscillations we can track how the cognitive system traverses through the states of a hierarchical control structure.
Repetition of deliberate self-poisoning in rural Sri Lanka
Authors: Pushpakumara PHGJ , Thennakoon SUB , Rajapakse TN , Abeysinghe Ranil , Dawson AH 
Published: June 2018

AbstractRepetition of deliberate self harm is an important predictor of subsequent suicide. Repetition rates in Asian countries appear to be significantly lower than in western high income countries. The reason for these reported differences is not clear and has been suggested to due methodological differences or the impact of access to more lethal means of self harm. This prospective study determines the rates and demographic pattern of deliberate self-poisoning, suicide and fatal and non fatal repeated deliberate self-poisoning in rural Sri Lanka.Details of deliberate self poisoning admission in all hospitals (n=46) and suicides reported to all the police stations (n=28) of a rural district were collected for 3 years, 2011-2013. Demographic details of the cohort of deliberate self-poisoning patients admitted to all hospitals in 2011 (N=4022), were screened to link with patient records and police reports of successive two years with high sensitivity using a computer program and manual matching was performed with higher specificity. Life time repetition was assessed in a randomly selected subset of DSP patients (n=438).There were 15,914 DSP admissions and 1078 suicides during the study period. Within the study area the deliberate self poisoning and suicide population incidences were, 248.3/100,000 and 20.7/100,000 in 2012. Repetition rate for four weeks, one-year and two-years were 1.9% (95% CI 1.5-2.3%), 5.7% (95% CI 5.0 to 6.4) and 7.9% (95% CI 7.1 to 8.8) respectively. The median interval between two attempts were 92 (IQR 10 - 238) and 191 (IQR 29 - 419.5) days for the one and two-year repetition groups. The majority of patients used the same poison in the repeat attempt. Age and hospital stay of individuals with repetitive events were not significantly different from those who had no repetitive events. The two-year rate for suicide following DSP was 0.7% (95% CI 0.4-0.9%). Reported life time history of deliberate self harm attempts was 9.5% (95% CI 6.7-12.2%).The low comparative repetition rates in rural Sri Lanka was not explained by higher rates of suicide or access to more lethal means or differences in methodology.
Evaluating the integrated reporting journey: insights, gaps and agendas for future research
Authors: Rinaldi Leonardo , Unerman Jeffrey , de Villiers Charl 
Published: June 2018

Purpose
The purpose of this paper is to identify key challenges, opportunities, strengths and weaknesses experienced by the integrated reporting (IR) idea since the International Integrated Reporting Council (IIRC)’s Discussion Paper was published in late 2011. It provides insights into the phases of the IR journey as investigated by accounting researchers, identifies important gaps in the literature and sketches an agenda for future research.

Design/methodology/approach
The paper develops a theoretically informed analysis of published IR research articles using the idea journey theoretical framework. The paper draws upon academic analysis and insights published in 65 IR-related articles across 83 accounting journals listed in the Scopus database.

Findings
A key insight of the paper is that the academic literature has not yet covered all stages of the IR idea journey. The highest proportion of articles provide insights in the generation and production phases of this journey, while there is relatively little research into the impact phase of the IR idea. Furthermore, the locus of research covered by the current IR literature is situated at macro- and meso-levels. This reveals opportunities for future research to explore, at a more detailed level, interactions between single individuals or small groups in implementing or understanding the IR idea.

Research limitations/implications
This paper focuses on the idea journey of the IIRC’s version of IR. It identifies gaps regarding the stages of the IR idea journey that have not been covered by the extant academic literature and suggests some research areas that need to be addressed to help inform improvements in policy and practice. A key limitation is that it draws on a single communication channel, namely, academic articles published in accounting journals, but it provides opportunities for considerable further developments.

Originality/value
The paper extends IR research by reconciling insights from an understandably fragmented emerging literature. It provides a multi-dimensional perspective on IR, highlighting the dynamics and interrelationships in the literature. It also helps inform improvements in research, policy and practice by identifying gaps regarding the stages of the IR idea journey that have not been covered by the extant academic literature. Lastly, the paper builds on the work of innovation and creativity scholars showing how the idea journey framework can be used to shape and add coherence to accounting research.