69 research outputs found
Transkingdom Networks: A Systems Biology Approach to Identify Causal Members of Host-Microbiota Interactions
Improvements in sequencing technologies and reduced experimental costs have
resulted in a vast number of studies generating high-throughput data. Although
the number of methods to analyze these "omics" data has also increased,
computational complexity and lack of documentation hinder researchers from
analyzing their high-throughput data to its true potential. In this chapter we
detail our data-driven, transkingdom network (TransNet) analysis protocol to
integrate and interrogate multi-omics data. This systems biology approach has
allowed us to successfully identify important causal relationships between
different taxonomic kingdoms (e.g. mammals and microbes) using diverse types of
data
The impact of bars on the mid-infrared dust emission of spiral galaxies: global and circumnuclear properties
We study the mid-infrared properties of a sample of 69 nearby spiral
galaxies, selected to avoid Seyfert activity contributing a significant
fraction of the central energetics, or strong tidal interaction, and to have
normal infrared luminosities. These observations were obtained with ISOCAM,
which provides an angular resolution of the order of 10 arcsec (half-power
diameter of the point spread function) and low-resolution spectro-imaging
information. Between 5 and 18 microns, we mainly observe two dust phases,
aromatic infrared bands and very small grains, both out of thermal equilibrium.
On this sample, we show that the global F15/F7 colors of galaxies are very
uniform, the only increase being found in early-type strongly barred galaxies,
consistent with previous IRAS studies. The F15/F7 excesses are unambiguously
due to galactic central regions where bar-induced starbursts occur. However,
the existence of strongly barred early-type galaxies with normal circumnuclear
colors indicates that the relationship between a distortion of the
gravitational potential and a central starburst is not straightforward. As the
physical processes at work in central regions are in principle identical in
barred and unbarred galaxies, and since this is where the mid-infrared activity
is mainly located, we investigate the mid-infrared circumnuclear properties of
all the galaxies in our sample. We show how surface brightnesses and colors are
related to both the available molecular gas content and the mean age of stellar
populations contributing to dust heating. Therefore, the star formation history
in galactic central regions can be constrained by their position in a
color-surface brightness mid-infrared diagram.Comment: 22 pages, 25 figures, accepted for publication in A&A ; small errors
corrected and references update
Global effects of non-native tree species on multiple ecosystem services
Non-native tree (NNT) species have been transported worldwide to create or enhance services that are fundamental
for human well-being, such as timber provision, erosion control or ornamental value; yet NNTs can also produce
undesired effects, such as fire proneness or pollen allergenicity. Despite the variety of effects that NNTs have on multiple
ecosystem services, a global quantitative assessment of their costs and benefits is still lacking. Such information is critical
for decision-making, management and sustainable exploitation of NNTs. We present here a global assessment of NNT
effects on the three main categories of ecosystem services, including regulating (RES), provisioning (PES) and cultural
services (CES), and on an ecosystem disservice (EDS), i.e. pollen allergenicity. By searching the scientific literature,
country forestry reports, and social media, we compiled a global data set of 1683 case studies from over 125 NNT
species, covering 44 countries, all continents but Antarctica, and seven biomes. Using differentmeta-analysis techniques,
we found that, while NNTs increase most RES (e.g. climate regulation, soil erosion control, fertility and formation),
they decrease PES (e.g. NNTs contribute less than native trees to global timber provision). Also, they have different
effects on CES (e.g. increase aesthetic values but decrease scientific interest), and no effect on the EDS considered.
NNT effects on each ecosystem (dis)service showed a strong context dependency, varying across NNT types, biomes
and socio-economic conditions. For instance, some RES are increased more by NNTs able to fix atmospheric nitrogen,
and when the ecosystem is located in low-latitude biomes; some CES are increased more by NNTs in less-wealthy
countries or in countries with higher gross domestic products. The effects of NNTs on several ecosystem (dis)services
exhibited some synergies (e.g. among soil fertility, soil formation and climate regulation or between aesthetic values
and pollen allergenicity), but also trade-offs (e.g. between fire regulation and soil erosion control). Our analyses provide
a quantitative understanding of the complex synergies, trade-offs and context dependencies involved for the effects of
NNTs that is essential for attaining a sustained provision of ecosystem servicesinfo:eu-repo/semantics/publishedVersio
The SAURON project. II. Sample and early results
Early results are reported from the SAURON survey of the kinematics and
stellar populations of a representative sample of nearby E, S0 and Sa galaxies.
The survey is aimed at determining the intrinsic shape of the galaxies, their
orbital structure, the mass-to-light ratio as a function of radius, the age and
metallicity of the stellar populations, and the frequency of kinematically
decoupled cores and nuclear black holes. The construction of the representative
sample is described, and its properties are illustrated. A comparison with
long-slit spectroscopic data establishes that the SAURON measurements are
comparable to, or better than, the highest-quality determinations. Comparisons
are presented for NGC 3384 and NGC 4365 where stellar velocities and velocity
dispersions are determined to a precision of 6 km/s, and the h3 and h4
parameters of the line-of-sight velocity distribution to a precision of better
than 0.02. Extraction of accurate gas emission-line intensities, velocities and
line widths from the datacubes is illustrated for NGC 5813. Comparisons with
published line-strengths for NGC 3384 and NGC 5813 reveal uncertainties of <
0.1 A on the measurements of the Hbeta, Mgb and Fe5270 indices. Integral-field
mapping uniquely connects measurements of the kinematics and stellar
populations to the galaxy morphology. The maps presented here illustrate the
rich stellar kinematics, gaseous kinematics, and line-strength distributions of
early-type galaxies. The results include the discovery of a thin, edge-on, disk
in NGC 3623, confirm the axisymmetric shape of the central region of M32,
illustrate the LINER nucleus and surrounding counter-rotating star-forming ring
in NGC 7742, and suggest a uniform stellar population in the decoupled core
galaxy NGC 5813.Comment: 20 pages, 17 figures. To be published in MNRAS. Version with full
resolution images available at
http://www.strw.leidenuniv.nl/~dynamics/Instruments/Sauron/pub_list.htm
The re-identification risk of Canadians from longitudinal demographics
<p>Abstract</p> <p>Background</p> <p>The public is less willing to allow their personal health information to be disclosed for research purposes if they do not trust researchers and how researchers manage their data. However, the public is more comfortable with their data being used for research if the risk of re-identification is low. There are few studies on the risk of re-identification of Canadians from their basic demographics, and no studies on their risk from their longitudinal data. Our objective was to estimate the risk of re-identification from the basic cross-sectional and longitudinal demographics of Canadians.</p> <p>Methods</p> <p>Uniqueness is a common measure of re-identification risk. Demographic data on a 25% random sample of the population of Montreal were analyzed to estimate population uniqueness on postal code, date of birth, and gender as well as their generalizations, for periods ranging from 1 year to 11 years.</p> <p>Results</p> <p>Almost 98% of the population was unique on full postal code, date of birth and gender: these three variables are effectively a unique identifier for Montrealers. Uniqueness increased for longitudinal data. Considerable generalization was required to reach acceptably low uniqueness levels, especially for longitudinal data. Detailed guidelines and disclosure policies on how to ensure that the re-identification risk is low are provided.</p> <p>Conclusions</p> <p>A large percentage of Montreal residents are unique on basic demographics. For non-longitudinal data sets, the three character postal code, gender, and month/year of birth represent sufficiently low re-identification risk. Data custodians need to generalize their demographic information further for longitudinal data sets.</p
Psychological resilience in sport performers: a review of stressors and protective factors
Psychological resilience is important in sport because athletes must utilize and optimize a range of mental qualities to withstand the pressures that they experience. In this paper, we discuss psychological resilience in sport performers via a review of the stressors athletes encounter and the protective factors that help them withstand these demands. It is hoped that synthesizing what is known in these areas will help researchers gain a deeper profundity of resilience in sport, and also provide a rigorous and robust foundation for the development of a sport-specific measure of resilience. With these points in mind, we divided the narrative into two main sections. In the first section, we review the different types of stressors encountered by sport performers under three main categories: competitive, organizational, and personal. Based on our recent research examining psychological resilience in Olympics champions (Fletcher & Sarkar, 2012), in the second section we discuss the five main families of psychological factors (viz. positive personality, motivation, confidence, focus, perceived social support) that protect the best athletes from the potential negative effect of stressors. It is anticipated that this review will help sport psychology researchers examine the interplay between stressors and protective factors which will, in turn, focus the analytical lens on the processes underlying psychological resilience in athletes
Next-gen sequencing identifies non-coding variation disrupting miRNA-binding sites in neurological disorders
Understanding the genetic factors underlying neurodevelopmental and neuropsychiatric disorders is a major challenge given their prevalence and potential severity for quality of life. While large-scale genomic screens have made major advances in this area, for many disorders the genetic underpinnings are complex and poorly understood. To date the field has focused predominantly on protein coding variation, but given the importance of tightly controlled gene expression for normal brain development and disorder, variation that affects non-coding regulatory regions of the genome is likely to play an important role in these phenotypes. Herein we show the importance of 3 prime untranslated region (3'UTR) non-coding regulatory variants across neurodevelopmental and neuropsychiatric disorders. We devised a pipeline for identifying and functionally validating putatively pathogenic variants from next generation sequencing (NGS) data. We applied this pipeline to a cohort of children with severe specific language impairment (SLI) and identified a functional, SLI-associated variant affecting gene regulation in cells and post-mortem human brain. This variant and the affected gene (ARHGEF39) represent new putative risk factors for SLI. Furthermore, we identified 3'UTR regulatory variants across autism, schizophrenia and bipolar disorder NGS cohorts demonstrating their impact on neurodevelopmental and neuropsychiatric disorders. Our findings show the importance of investigating non-coding regulatory variants when determining risk factors contributing to neurodevelopmental and neuropsychiatric disorders. In the future, integration of such regulatory variation with protein coding changes will be essential for uncovering the genetic causes of complex neurological disorders and the fundamental mechanisms underlying health and disease
An overview of animal prion diseases
Prion diseases are transmissible neurodegenerative conditions affecting human and a wide range of animal species. The pathogenesis of prion diseases is associated with the accumulation of aggregates of misfolded conformers of host-encoded cellular prion protein (PrPC). Animal prion diseases include scrapie of sheep and goats, bovine spongiform encephalopathy (BSE) or mad cow disease, transmissible mink encephalopathy, feline spongiform encephalopathy, exotic ungulate spongiform encephalopathy, chronic wasting disease of cervids and spongiform encephalopathy of primates. Although some cases of sporadic atypical scrapie and BSE have also been reported, animal prion diseases have basically occurred via the acquisition of infection from contaminated feed or via the exposure to contaminated environment. Scrapie and chronic wasting disease are naturally sustaining epidemics. The transmission of BSE to human has caused more than 200 cases of variant Cruetzfeldt-Jacob disease and has raised serious public health concerns. The present review discusses the epidemiology, clinical neuropathology, transmissibility and genetics of animal prion diseases
The Atlas3D project -- XIII. Mass and morphology of HI in early-type galaxies as a function of environment
We present the Atlas3D HI survey of 166 nearby early-type galaxies (ETGs)
down to M(HI)~10^7 M_sun. We detect HI in ~40% of all ETGs outside the Virgo
cluster and in ~10% of all ETGs inside it. This demonstrates that it is common
for non-cluster ETGs to host HI. The HI morphology varies from regular
discs/rings (the majority of the detections) to unsettled gas distributions.
The former are either small discs (M(HI)<10^8 M_sun) confined within the
stellar body and sharing the same kinematics of the stars, or large discs/rings
(M(HI) up to 5x10^9 M_sun) extending to tens of kpc from the host galaxy and
frequently kinematically decoupled from the stars. Neutral hydrogen provides
material for star formation in ETGs. Galaxies with central HI exhibit
signatures of star formation in ~70% of the cases, ~5 times more frequently
than galaxies without central HI. The central ISM is dominated by molecular
gas. In ETGs with a small gas disc the conversion of HI into H_2 is as
efficient as in spirals. The ETG HI mass function has M*~2x10^9 M_sun and
slope=-0.7. ETGs host much less HI than spirals as a family. However, a
significant fraction of them is as HI-rich as spirals. The main difference
between ETGs and spirals is that the former lack the high-column-density HI
typical of the bright stellar disc of the latter. We find an envelope of
decreasing M(HI) with increasing environment density. The gas-richest ETGs live
in the poorest environments (where star-formation is more common), galaxies in
the centre of Virgo have the lowest HI content, and the cluster outskirts are a
transition region. We find an HI morphology-density relation. At low
environment density HI is mostly distributed on large discs/rings. More
disturbed HI morphologies dominate environment densities typical of rich
groups, confirming the importance of processes occurring on a galaxy-group
scale for the evolution of ETGs.Comment: Accepted for publication on MNRA
RhoGTPase Regulators Orchestrate Distinct Stages of Synaptic Development
Small RhoGTPases regulate changes in post-synaptic spine morphology and density that support learning and memory. They are also major targets of synaptic disorders, including Autism. Here we sought to determine whether upstream RhoGTPase regulators, including GEFs, GAPs, and GDIs, sculpt specific stages of synaptic development. The majority of examined molecules uniquely regulate either early spine precursor formation or later matura- tion. Specifically, an activator of actin polymerization, the Rac1 GEF β-PIX, drives spine pre- cursor formation, whereas both FRABIN, a Cdc42 GEF, and OLIGOPHRENIN-1, a RhoA GAP, regulate spine precursor elongation. However, in later development, a novel Rac1 GAP, ARHGAP23, and RhoGDIs inactivate actomyosin dynamics to stabilize mature synap- ses. Our observations demonstrate that specific combinations of RhoGTPase regulatory pro- teins temporally balance RhoGTPase activity during post-synaptic spine development
- …