Causality Analysis: Identifying the Leading Element in a Coupled Dynamical System

Physical systems with time-varying internal couplings are abundant in nature. While the full governing equations of these systems are typically unknown due to insufficient understanding of their internal mechanisms, there is often interest in determining the leading element. Here, the leading element is defined as the sub-system with the largest coupling coefficient averaged over a selected time span. Previously, the Convergent Cross Mapping (CCM) method has been employed to determine causality and dominant component in weakly coupled systems with constant coupling coefficients. In this study, CCM is applied to a pair of coupled Lorenz systems with time-varying coupling coefficients, exhibiting switching between dominant sub-systems in different periods. Four sets of numerical experiments are carried out. The first three cases consist of different coupling coefficient schemes: I) Periodic–constant, II) Normal, and III) Mixed Normal/Non-normal. In case IV, numerical experiment of cases II and III are repeated with imposed temporal uncertainties as well as additive normal noise. Our results show that, through detecting directional interactions, CCM identifies the leading sub-system in all cases except when the average coupling coefficients are approximately equal, i.e., when the dominant sub-system is not well defined.     

Where Empathy in Psychotherapy Originated: C. Rogers,His Psychoanalytic Predecessors and Followers

This article presents a historical-psychological analysis of how the concept of empathy appeared and became established in psychotherapy. It examines in detail the early psychoanalytic approaches of S. Ferenczi and O. Rank and their possible influence on C. Rogers’s laying the groundwork for the role of empathy. For the first time in Russian psychology, the article illuminates certain aspects of the biographies of Rogers and H. Kohut as the founders of new schools in psychotherapy, of which empathy is the paramount feature. Kohut’s self-psychology is analyzed from the standpoint of his postulation of the “threefold” status of empathy as a method of psychology, a tool of the analyst, and the subject of a universal requirement of development. It briefly considers the development of the views of Rogers and Kohut in the latest “experiential” schools in the person-centered approach and intersubjective psychoanalysis.     

Losing the beat: deficits in temporal coordination

Tapping or clapping to an auditory beat, an easy task for most individuals, reveals precise temporal synchronization with auditory patterns such as music, even in the presence of temporal fluctuations. Most models of beat-tracking rely on the theoretical concept of pulse: a perceived regular beat generated by an internal oscillation that forms the foundation of entrainment abilities. Although tapping to the beat is a natural sensorimotor activity for most individuals, not everyone can track an auditory beat. Recently, the case of Mathieu was documented (Phillips-Silver et al. 2011 Neuropsychologia 49, 961–969. (doi:10.1016/j.neuropsychologia.2011.02.002)). Mathieu presented himself as having difficulty following a beat and exhibited synchronization failures. We examined beat-tracking in normal control participants, Mathieu, and a second beat-deaf individual, who tapped with an auditory metronome in which unpredictable perturbations were introduced to disrupt entrainment. Both beat-deaf cases exhibited failures in error correction in response to the perturbation task while exhibiting normal spontaneous motor tempi (in the absence of an auditory stimulus), supporting a deficit specific to perception–action coupling. A damped harmonic oscillator model was applied to the temporal adaptation responses; the model''s parameters of relaxation time and endogenous frequency accounted for differences between the beat-deaf cases as well as the control group individuals.     

Leaders in social networks, the Delicious case

Finding pertinent information is not limited to search engines. Online communities can amplify the influence of a small number of power users for the benefit of all other users. Users' information foraging in depth and breadth can be greatly enhanced by choosing suitable leaders. For instance in delicious.com, users subscribe to leaders' collection which lead to a deeper and wider reach not achievable with search engines. To consolidate such collective search, it is essential to utilize the leadership topology and identify influential users. Google's PageRank, as a successful search algorithm in the World Wide Web, turns out to be less effective in networks of people. We thus devise an adaptive and parameter-free algorithm, the LeaderRank, to quantify user influence. We show that LeaderRank outperforms PageRank in terms of ranking effectiveness, as well as robustness against manipulations and noisy data. These results suggest that leaders who are aware of their clout may reinforce the development of social networks, and thus the power of collective search.     

Invasion Is a Community Affair: Clandestine Followers in the Bacterial Community Associated to Green Algae,Caulerpa racemosa,Track the Invasion Source

Biological invasions rank amongst the most deleterious components of global change inducing alterations from genes to ecosystems. The genetic characteristics of introduced pools of individuals greatly influence the capacity of introduced species to establish and expand. The recently demonstrated heritability of microbial communities associated to individual genotypes of primary producers makes them a potentially essential element of the evolution and adaptability of their hosts. Here, we characterized the bacterial communities associated to native and non-native populations of the marine green macroalga Caulerpa racemosa through pyrosequencing, and explored their potential role on the strikingly invasive trajectory of their host in the Mediterranean. The similarity of endophytic bacterial communities from the native Australian range and several Mediterranean locations confirmed the origin of invasion and revealed distinct communities associated to a second Mediterranean variety of C . racemosa long reported in the Mediterranean. Comparative analysis of these two groups demonstrated the stability of the composition of bacterial communities through the successive steps of introduction and invasion and suggested the vertical transmission of some major bacterial OTUs. Indirect inferences on the taxonomic identity and associated metabolism of bacterial lineages showed a striking consistency with sediment upheaval conditions associated to the expansion of their invasive host and to the decline of native species. These results demonstrate that bacterial communities can be an effective tracer of the origin of invasion and support their potential role in their eukaryotic host’s adaptation to new environments. They put forward the critical need to consider the ''meta-organism'' encompassing both the host and associated micro-organisms, to unravel the origins, causes and mechanisms underlying biological invasions.     

Losing balance: the origin and impact of aneuploidy in cancer

Most solid human tumours are aneuploid, that is, they contain an abnormal number of chromosomes. Paradoxically, however, aneuploidy has been reported to induce a stress response that suppresses cellular proliferation in vitro. Here, we review the progress in our understanding of the causes and effects of aneuploidy in cancer and discuss how, in specific contexts, aneuploidy can provide a growth advantage and facilitate cellular transformation. We also explore the emerging possibilities for targeting the cause or consequences of aneuploidy therapeutically.     

Identifying and monitoring pain in farm animals: a review

One important objective for animal welfare is to maintain animals free from pain, injury or disease. Therefore, detecting and evaluating the intensity of animal pain is crucial. As animals cannot directly communicate their feelings, it is necessary to identify sensitive and specific indicators that can be easily used. The aim of the present paper is to review relevant indicators to assess pain in several farm species. The term pain is used for mammals, birds and fish, even though the abilities of the various species to experience the emotional component of pain may be different. Numerous behavioural changes are associated with pain and many of them could be used on farms to assess the degree of pain being experienced by an animal. Pain, as a stressor, is associated with variations in the hypothalamic–pituitary–adrenal axis as well as in the sympathetic and immune systems that can be used to identify the presence of pain rapidly after it started. However, most of these measures need sophisticated equipment for their assessment. Therefore, they are mainly adapted to experimental situations. Injuries and other lesional indicators give information on the sources of pain and are convenient to use in all types of situations. Histopathological analyses can identify sources of pain in experimental studies. When pronounced and/or long lasting, the pain-induced behavioural and physiological changes can decrease production performance. Some indicators are very specific and sensitive to pain, whereas others are more generally related to stressful situations. The latter can be used to indicate that animals are suffering from something, which may be pain. Overall, this literature review shows that several indicators exist to assess pain in mammals, a few in birds and very few in fish. Even if in some cases, a single indicator, usually a behavioural indicator, may be sufficient to detect pain, combining various types of indicators increases sensitivity and specificity of pain assessment. Research is needed to build and validate new indicators and to develop systems of pain assessment adapted to each type of situation and each species.     

Repeated regions in mitochondrial genomes: Distribution, origin and evolutionary significance

All complete or nearly complete mitochondrial genomes of Metazoa (2819) have been subject to bioinformatic analysis to investigate the distribution and features of repeated and palindromic sequences. Repeats are ubiquitous, with 29.9% of genomes containing at least one and 1.95% of total genome length being repeated. Repeat boundaries were tested for the presence of secondary structure motifs, consensus sequences or small repeats, features generally reported as associated with duplications. No significant relationship was detected, suggesting the non ubiquitousness of such features. A mechanism related to gene conversion is proposed to explain the origin of small interspersed repeats.     

Reflections on a Life in Biomedicine: Leading Change

Dr. Elizabeth Nabel delivered the following presentation as the Lee E. Farr Lecturer on May 7, 2013, which served as the culmination of the annual Student Research Day at Yale School of Medicine. Dr. Nabel is President of the Brigham and Women’s Hospital in Boston, Massachusetts, and Professor of Medicine at Harvard Medical School. Her lecture to Yale medical students portrayed her own personal and professional journey through medicine as a series of opportunities. Dr. Nabel focused on the roles and responsibilities of physicians to recognize need and to make change through focused advocacy.     

Redundancy in ribonucleotide excision repair: Competition,compensation, and cooperation

The survival of all living organisms is determined by their ability to reproduce, which in turn depends on accurate duplication of chromosomal DNA. In order to ensure the integrity of genome duplication, DNA polymerases are equipped with stringent mechanisms by which they select and insert correctly paired nucleotides with a deoxyribose sugar ring. However, this process is never 100% accurate. To fix occasional mistakes, cells have evolved highly sophisticated and often redundant mechanisms. A good example is mismatch repair (MMR), which corrects the majority of mispaired bases and which has been extensively studied for many years. On the contrary, pathways leading to the replacement of nucleotides with an incorrect sugar that is embedded in chromosomal DNA have only recently attracted significant attention. This review describes progress made during the last few years in understanding such pathways in both prokaryotes and eukaryotes. Genetic studies in Escherichia coli and Saccharomyces cerevisiae demonstrated that MMR has the capacity to replace errant ribonucleotides, but only when the base is mispaired. In contrast, the major evolutionarily conserved ribonucleotide repair pathway initiated by the ribonuclease activity of type 2 Rnase H has broad specificity. In yeast, this pathway also requires the concerted action of Fen1 and pol δ, while in bacteria it can be successfully completed by DNA polymerase I. Besides these main players, all organisms contain alternative enzymes able to accomplish the same tasks, although with differing efficiency and fidelity. Studies in bacteria have very recently demonstrated that isolated rNMPs can be removed from genomic DNA by error-free nucleotide excision repair (NER), while studies in yeast suggest the involvement of topoisomerase 1 in alternative mutagenic ribonucleotide processing. This review summarizes the most recent progress in understanding the ribonucleotide repair mechanisms in prokaryotes and eukaryotes.