3,351 research outputs found
MENGA: a new comprehensive tool for the integration of neuroimaging data and the Allen human brain transcriptome atlas
Brain-wide mRNA mappings offer a great potential for neuroscience research as they can provide information about system proteomics. In a previous work we have correlated mRNA maps with the binding patterns of radioligands targeting specific molecular systems and imaged with positron emission tomography (PET) in unrelated control groups. This approach is potentially applicable to any imaging modality as long as an efficient procedure of imaging-genomic matching is provided. In the original work we considered mRNA brain maps of the whole human genome derived from the Allen human brain database (ABA) and we performed the analysis with a specific region-based segmentation with a resolution that was limited by the PET data parcellation. There we identified the need for a platform for imaging-genomic integration that should be usable with any imaging modalities and fully exploit the high resolution mapping of ABA dataset.In this work we present MENGA (Multimodal Environment for Neuroimaging and Genomic Analysis), a software platform that allows the investigation of the correlation patterns between neuroimaging data of any sort (both functional and structural) with mRNA gene expression profiles derived from the ABA database at high resolution.We applied MENGA to six different imaging datasets from three modalities (PET, single photon emission tomography and magnetic resonance imaging) targeting the dopamine and serotonin receptor systems and the myelin molecular structure. We further investigated imaging-genomic correlations in the case of mismatch between selected proteins and imaging targets
Generalised Sandpile Dynamics on Artificial and Real-World Directed Networks
The main finding of this paper is a novel avalanche-size exponent τ ≈ 1.87 when the generalised sandpile dynamics evolves on the real-world Japanese inter-firm network. The topology of this network is non-layered and directed, displaying the typical bow tie structure found in real-world directed networks, with cycles and triangles. We show that one can move from a strictly layered regular lattice to a more fluid structure of the inter-firm network in a few simple steps. Relaxing the regular lattice structure by introducing an interlayer distribution for the interactions, forces the scaling exponent of the avalanche-size probability density function τ out of the two-dimensional directed sandpile universality class τ = 4/3, into the mean field universality class τ = 3/2. Numerical investigation shows that these two classes are the only that exist on the directed sandpile, regardless of the underlying topology, as long as it is strictly layered. Randomly adding a small proportion of links connecting non adjacent layers in an otherwise layered network takes the system out of the mean field regime to produce non-trivial avalanche-size probability density function. Although these do not display proper scaling, they closely reproduce the behaviour observed on the Japanese inter-firm network
Iron Deficiency Induced by Chrysobactin in Saintpaulia Leaves Inoculated with Erwinia chrysanthemi
Self-similar correlation function in brain resting-state fMRI
Adaptive behavior, cognition and emotion are the result of a bewildering
variety of brain spatiotemporal activity patterns. An important problem in
neuroscience is to understand the mechanism by which the human brain's 100
billion neurons and 100 trillion synapses manage to produce this large
repertoire of cortical configurations in a flexible manner. In addition, it is
recognized that temporal correlations across such configurations cannot be
arbitrary, but they need to meet two conflicting demands: while diverse
cortical areas should remain functionally segregated from each other, they must
still perform as a collective, i.e., they are functionally integrated. Here, we
investigate these large-scale dynamical properties by inspecting the character
of the spatiotemporal correlations of brain resting-state activity. In physical
systems, these correlations in space and time are captured by measuring the
correlation coefficient between a signal recorded at two different points in
space at two different times. We show that this two-point correlation function
extracted from resting-state fMRI data exhibits self-similarity in space and
time. In space, self-similarity is revealed by considering three successive
spatial coarse-graining steps while in time it is revealed by the 1/f frequency
behavior of the power spectrum. The uncovered dynamical self-similarity implies
that the brain is spontaneously at a continuously changing (in space and time)
intermediate state between two extremes, one of excessive cortical integration
and the other of complete segregation. This dynamical property may be seen as
an important marker of brain well-being both in health and disease.Comment: 14 pages 13 figures; published online before print September 2
Challenges and recommendations for high quality research using electronic health records
Harnessing Real World Data is vital to improve health care in the 21st Century. Data from Electronic Health Records (EHRs) are a rich source of patient centred data, including information on the patient's clinical condition, laboratory results, diagnoses and treatments. They thus reflect the true state of health systems. However, access and utilisation of EHR data for research presents specific challenges. We assert that using data from EHRs effectively is dependent on synergy between researchers, clinicians and health informaticians, and only this will allow state of the art methods to be used to answer urgent and vital questions for patient care. We propose that there needs to be a paradigm shift in the way this research is conducted - appreciating that the research process is iterative rather than linear. We also make specific recommendations for organisations, based on our experience of developing and using EHR data in trusted research environments
A universal model for mobility and migration patterns
Introduced in its contemporary form by George Kingsley Zipf in 1946, but with
roots that go back to the work of Gaspard Monge in the 18th century, the
gravity law is the prevailing framework to predict population movement, cargo
shipping volume, inter-city phone calls, as well as bilateral trade flows
between nations. Despite its widespread use, it relies on adjustable parameters
that vary from region to region and suffers from known analytic
inconsistencies. Here we introduce a stochastic process capturing local
mobility decisions that helps us analytically derive commuting and mobility
fluxes that require as input only information on the population distribution.
The resulting radiation model predicts mobility patterns in good agreement with
mobility and transport patterns observed in a wide range of phenomena, from
long-term migration patterns to communication volume between different regions.
Given its parameter-free nature, the model can be applied in areas where we
lack previous mobility measurements, significantly improving the predictive
accuracy of most of phenomena affected by mobility and transport processes.Comment: Main text and supplementary informatio
Mesoscopic structure and social aspects of human mobility
The individual movements of large numbers of people are important in many
contexts, from urban planning to disease spreading. Datasets that capture human
mobility are now available and many interesting features have been discovered,
including the ultra-slow spatial growth of individual mobility. However, the
detailed substructures and spatiotemporal flows of mobility - the sets and
sequences of visited locations - have not been well studied. We show that
individual mobility is dominated by small groups of frequently visited,
dynamically close locations, forming primary "habitats" capturing typical daily
activity, along with subsidiary habitats representing additional travel. These
habitats do not correspond to typical contexts such as home or work. The
temporal evolution of mobility within habitats, which constitutes most motion,
is universal across habitats and exhibits scaling patterns both distinct from
all previous observations and unpredicted by current models. The delay to enter
subsidiary habitats is a primary factor in the spatiotemporal growth of human
travel. Interestingly, habitats correlate with non-mobility dynamics such as
communication activity, implying that habitats may influence processes such as
information spreading and revealing new connections between human mobility and
social networks.Comment: 7 pages, 5 figures (main text); 11 pages, 9 figures, 1 table
(supporting information
TREC-Rio trial: a randomised controlled trial for rapid tranquillisation for agitated patients in emergency psychiatric rooms [ISRCTN44153243]
Agitated or violent patients constitute 10% of all emergency psychiatric treatment. Management guidelines, the preferred treatment of clinicians and clinical practice all differ. Systematic reviews show that all relevant studies are small and none are likely to have adequate power to show true differences between treatments. Worldwide, current treatment is not based on evidence from randomised trials. In Brazil, the combination haloperidol-promethazine is frequently used, but no studies involving this mix exist.
TREC-Rio (Tranquilização Rápida-Ensaio ClÃnico [Translation: Rapid Tranquillisation-Clinical Trial]) will compare midazolam with haloperidol-promethazine mix for treatment of agitated patients in emergency psychiatric rooms of Rio de Janeiro, Brazil. TREC-Rio is a randomised, controlled, pragmatic and open study. Primary measure of outcome is tranquillisation at 20 minutes but effects on other measures of morbidity will also be assessed.
TREC-Rio will involve the collaboration of as many health care professionals based in four psychiatric emergency rooms of Rio as possible. Because the design of this trial does not substantially complicate clinical management, and in several aspects simplifies it, the study can be large, and treatments used in everyday practice can be evaluated
Spatial correlations in attribute communities
Community detection is an important tool for exploring and classifying the
properties of large complex networks and should be of great help for spatial
networks. Indeed, in addition to their location, nodes in spatial networks can
have attributes such as the language for individuals, or any other
socio-economical feature that we would like to identify in communities. We
discuss in this paper a crucial aspect which was not considered in previous
studies which is the possible existence of correlations between space and
attributes. Introducing a simple toy model in which both space and node
attributes are considered, we discuss the effect of space-attribute
correlations on the results of various community detection methods proposed for
spatial networks in this paper and in previous studies. When space is
irrelevant, our model is equivalent to the stochastic block model which has
been shown to display a detectability-non detectability transition. In the
regime where space dominates the link formation process, most methods can fail
to recover the communities, an effect which is particularly marked when
space-attributes correlations are strong. In this latter case, community
detection methods which remove the spatial component of the network can miss a
large part of the community structure and can lead to incorrect results.Comment: 10 pages and 7 figure
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