Memory distribution in complex fitness landscapes

In a co-evolutionary context, the survive probability of individual elements of a system depends on their relation with their neighbors. The natural selection process depends on the whole population, which is determined by local events between individuals. Particular characteristics assigned to each individual, as larger memory, usually improve the individual fitness, but an agent possess also endogenous characteristics that induce to re-evaluate her fitness landscape and choose the best-suited kind of interaction, inducing a non absolute value of the outcomes of the interaction. In this work, a novel model with agents combining memory and rational choice is introduced, where individual choices in a complex fitness landscape induce changes in the distribution of the number of agents as a function of the time. In particular, the tail of this distribution is fat compared with distributions for agents interacting only with memory.Comment: 6 pages, 3 figures, submited to Physica

Computational purification of individual tumor gene expression profiles leads to significant improvements in prognostic prediction.

Tumor heterogeneity is a limiting factor in cancer treatment and in the discovery of biomarkers to personalize it. We describe a computational purification tool, ISOpure, to directly address the effects of variable normal tissue contamination in clinical tumor specimens. ISOpure uses a set of tumor expression profiles and a panel of healthy tissue expression profiles to generate a purified cancer profile for each tumor sample and an estimate of the proportion of RNA originating from cancerous cells. Applying ISOpure before identifying gene signatures leads to significant improvements in the prediction of prognosis and other clinical variables in lung and prostate cancer

Avian Resistance to Campylobacter jejuni Colonization Is Associated with an Intestinal Immunogene Expression Signature Identified by mRNA Sequencing

peer-reviewedThis research was funded by the The Irish Department of Agriculture and Food’s Food Institutional Research Measure (http://www.agriculture.gov.ie/ research/foodinstitutionalresearchmeasurefirm) – Grant No: 06_RDD_486.Campylobacter jejuni is the most common cause of human bacterial gastroenteritis and is associated with several post-infectious manifestations, including onset of the autoimmune neuropathy Guillain-Barré syndrome, causing significant morbidity and mortality. Poorly-cooked chicken meat is the most frequent source of infection as C. jejuni colonizes the avian intestine in a commensal relationship. However, not all chickens are equally colonized and resistance seems to be genetically determined. We hypothesize that differences in immune response may contribute to variation in colonization levels between susceptible and resistant birds. Using high-throughput sequencing in an avian infection model, we investigate gene expression associated with resistance or susceptibility to colonization of the gastrointestinal tract with C. jejuni and find that gut related immune mechanisms are critical for regulating colonization. Amongst a single population of 300 4-week old chickens, there was clear segregation in levels of C. jejuni colonization 48 hours post-exposure. RNAseq analysis of caecal tissue from 14 C. jejuni-susceptible and 14 C. jejuni-resistant birds generated over 363 million short mRNA sequences which were investigated to identify 219 differentially expressed genes. Significantly higher expression of genes involved in the innate immune response, cytokine signaling, B cell and T cell activation and immunoglobulin production, as well as the renin-angiotensin system was observed in resistant birds, suggesting an early active immune response to C. jejuni. Lower expression of these genes in colonized birds suggests suppression or inhibition of a clearing immune response thus facilitating commensal colonization and generating vectors for zoonotic transmission. This study describes biological processes regulating C. jejuni colonization of the avian intestine and gives insight into the differential immune mechanisms incited in response to commensal bacteria in general within vertebrate populations. The results reported here illustrate how an exaggerated immune response may be elicited in a subset of the population, which alters host-microbe interactions and inhibits the commensal state, therefore having wider relevance with regard to inflammatory and autoimmune disease

A systematic review of horticultural therapy’s influence on Chinese older adults’ psychosocial wellbeing

Aim: This systematic review aims to evaluate changes in Chinese older adults’ psychosocial wellbeing after receiving horticultural therapy, and examine existing evidence regarding horticultural therapy’s effectiveness in a Chinese setting. Method: Intervention studies measuring relevant outcomes amongst older adults and conducted in China were identified from ASSIA, CIHAHL Plus, PsycINFO, EMBASE, MEDLINE, SCOPUS, Web of Science Core Collection and CNKI. Cochrane risk of bias assessment tools were used to appraise study quality. Result: 16 studies were selected, among which four were published in English and 12 in Chinese. Findings suggested that after receiving horticultural therapy, older adults’ psychosocial wellbeing is generally improved, but causal relationships between improvements and horticulture therapy were less clear. Conclusion: Features of horticultural therapy conducted in China is with its cultural and social uniqueness. Existing evidence supports the post-intervention benefits on completion of horticultural therapies, but the limitations in programme design, sample representativeness and methodological robustness limited the quality of the evidence

Inferring the dynamics of ionic currents from recursive piecewise data assimilation of approximate neuron models

We construct neuron models from data by transferring information from an observed time series to the state variables and parameters of Hodgkin-Huxley models. When the learning period completes, the model will predict additional observations and its parameters uniquely characterise the complement of ion channels. However, the assimilation of biological data, as opposed to model data, is complicated by the lack of knowledge of the true neuron equations. Reliance on guessed conductance models is plagued with multi-valued parameter solutions. Here, we report on the distributions of parameters and currents predicted with intentionally erroneous models, over-specified models, and an approximate model fitting hippocampal neuron data. We introduce a recursive piecewise data assimilation (RPDA) algorithm that converges with near-perfect reliability when the model is known. When the model is unknown, we show model error introduces correlations between certain parameters. The ionic currents reconstructed from these parameters are excellent predictors of true currents and carry a higher degree of confidence, >95.5%, than underlying parameters, >53%. Unexpressed ionic currents are correctly filtered out even in the presence of mild model error. When the model is unknown, the covariance eigenvalues of parameter estimates are found to be a good gauge of model error. Our results suggest that biological information may be retrieved from data by focussing on current estimates rather than parameters

New records of Burgess Shale-type taxa from the middle Cambrian of Utah

Cambrian strata of the Laurentian craton contain numerous examples of Burgess Shale-type faunas. Although displaying a more or less concentric distribution around the cratonal margin, most faunal occurrences are in present-day western North America, extending from the Northwest Territories to California. Nevertheless, the soft-bodied and lightly skeletalized fossils in most of these Lagerstätten are highly sporadic. Here, we extend knowledge of such Middle Cambrian occurrences in Utah with reports of four taxa. An arthropod from the Marjum Formation, Dytikosicula desmatae gen. et sp. nov., is a putative megacheiran. It is most similar to Dicranocaris guntherorum, best known from the younger Wheeler Formation, but differs primarily in the arrangement of pleurae and overall size. Along with a specimen of ?Yohoia sp, a new species of Yohoia, Y. utahana sp. nov., is described. It differs from the type and only known species, Y. tenuis, principally in its larger size and shorter exopods; it is the first description of this genus from outside the Burgess Shale. A new species of a stem-group lophotrochozoan from the Spence Shale, Wiwaxia herka sp. nov., possesses a palisade of dorso-lateral spines that are more robust and numerous than the type species of Wiwaxia, W. corrugata. Another notable taxon is Eldonia ludwigi from the Marjum Formation, which is interpreted as a primitive ambulacrarian (assigned to the cambroernids) and a new specimen of the ?cnidarian Cambrorhytium from the Wheeler Shale is illustrated