Showing papers by "Université catholique de Louvain published in 2018"

Minimal information for studies of extracellular vesicles 2018 (MISEV2018) : a position statement of the International Society for Extracellular Vesicles and update of the MISEV2014 guidelines

Abstract: The last decade has seen a sharp increase in the number of scientific publications describing physiological and pathological functions of extracellular vesicles (EVs), a collective term covering various subtypes of cell-released, membranous structures, called exosomes, microvesicles, microparticles, ectosomes, oncosomes, apoptotic bodies, and many other names. However, specific issues arise when working with these entities, whose size and amount often make them difficult to obtain as relatively pure preparations, and to characterize properly. The International Society for Extracellular Vesicles (ISEV) proposed Minimal Information for Studies of Extracellular Vesicles (“MISEV”) guidelines for the field in 2014. We now update these “MISEV2014” guidelines based on evolution of the collective knowledge in the last four years. An important point to consider is that ascribing a specific function to EVs in general, or to subtypes of EVs, requires reporting of specific information beyond mere description of function in a crude, potentially contaminated, and heterogeneous preparation. For example, claims that exosomes are endowed with exquisite and specific activities remain difficult to support experimentally, given our still limited knowledge of their specific molecular machineries of biogenesis and release, as compared with other biophysically similar EVs. The MISEV2018 guidelines include tables and outlines of suggested protocols and steps to follow to document specific EV-associated functional activities. Finally, a checklist is provided with summaries of key points.

Trajectories of the Earth System in the Anthropocene.

Abstract: We explore the risk that self-reinforcing feedbacks could push the Earth System toward a planetary threshold that, if crossed, could prevent stabilization of the climate at intermediate temperature rises and cause continued warming on a "Hothouse Earth" pathway even as human emissions are reduced. Crossing the threshold would lead to a much higher global average temperature than any interglacial in the past 1.2 million years and to sea levels significantly higher than at any time in the Holocene. We examine the evidence that such a threshold might exist and where it might be. If the threshold is crossed, the resulting trajectory would likely cause serious disruptions to ecosystems, society, and economies. Collective human action is required to steer the Earth System away from a potential threshold and stabilize it in a habitable interglacial-like state. Such action entails stewardship of the entire Earth System-biosphere, climate, and societies-and could include decarbonization of the global economy, enhancement of biosphere carbon sinks, behavioral changes, technological innovations, new governance arrangements, and transformed social values.

Human gut microbiome: hopes, threats and promises

Abstract: The microbiome has received increasing attention over the last 15 years. Although gut microbes have been explored for several decades, investigations of the role of microorganisms that reside in the human gut has attracted much attention beyond classical infectious diseases. For example, numerous studies have reported changes in the gut microbiota during not only obesity, diabetes, and liver diseases but also cancer and even neurodegenerative diseases. The human gut microbiota is viewed as a potential source of novel therapeutics. Between 2013 and 2017, the number of publications focusing on the gut microbiota was, remarkably, 12 900, which represents four-fifths of the total number of publications over the last 40 years that investigated this topic. This review discusses recent evidence of the impact of the gut microbiota on metabolic disorders and focus on selected key mechanisms. This review also aims to provide a critical analysis of the current knowledge in this field, identify putative key issues or problems and discuss misinterpretations. The abundance of metagenomic data generated on comparing diseased and healthy subjects can lead to the erroneous claim that a bacterium is causally linked with the protection or the onset of a disease. In fact, environmental factors such as dietary habits, drug treatments, intestinal motility and stool frequency and consistency are all factors that influence the composition of the microbiota and should be considered. The cases of the bacteria Prevotella copri and Akkermansia muciniphila will be discussed as key examples.

Color Balance and Fusion for Underwater Image Enhancement

Abstract: We introduce an effective technique to enhance the images captured underwater and degraded due to the medium scattering and absorption. Our method is a single image approach that does not require specialized hardware or knowledge about the underwater conditions or scene structure. It builds on the blending of two images that are directly derived from a color-compensated and white-balanced version of the original degraded image. The two images to fusion, as well as their associated weight maps, are defined to promote the transfer of edges and color contrast to the output image. To avoid that the sharp weight map transitions create artifacts in the low frequency components of the reconstructed image, we also adapt a multiscale fusion strategy. Our extensive qualitative and quantitative evaluation reveals that our enhanced images and videos are characterized by better exposedness of the dark regions, improved global contrast, and edges sharpness. Our validation also proves that our algorithm is reasonably independent of the camera settings, and improves the accuracy of several image processing applications, such as image segmentation and keypoint matching.

Many Labs 2: Investigating Variation in Replicability Across Samples and Settings

Abstract: We conducted preregistered replications of 28 classic and contemporary published findings, with protocols that were peer reviewed in advance, to examine variation in effect magnitudes across samples and settings. Each protocol was administered to approximately half of 125 samples that comprised 15,305 participants from 36 countries and territories. Using the conventional criterion of statistical significance (p < .05), we found that 15 (54%) of the replications provided evidence of a statistically significant effect in the same direction as the original finding. With a strict significance criterion (p < .0001), 14 (50%) of the replications still provided such evidence, a reflection of the extremely high-powered design. Seven (25%) of the replications yielded effect sizes larger than the original ones, and 21 (75%) yielded effect sizes smaller than the original ones. The median comparable Cohen’s ds were 0.60 for the original findings and 0.15 for the replications. The effect sizes were small (< 0.20) in 16 of the replications (57%), and 9 effects (32%) were in the direction opposite the direction of the original effect. Across settings, the Q statistic indicated significant heterogeneity in 11 (39%) of the replication effects, and most of those were among the findings with the largest overall effect sizes; only 1 effect that was near zero in the aggregate showed significant heterogeneity according to this measure. Only 1 effect had a tau value greater than .20, an indication of moderate heterogeneity. Eight others had tau values near or slightly above .10, an indication of slight heterogeneity. Moderation tests indicated that very little heterogeneity was attributable to the order in which the tasks were performed or whether the tasks were administered in lab versus online. Exploratory comparisons revealed little heterogeneity between Western, educated, industrialized, rich, and democratic (WEIRD) cultures and less WEIRD cultures (i.e., cultures with relatively high and low WEIRDness scores, respectively). Cumulatively, variability in the observed effect sizes was attributable more to the effect being studied than to the sample or setting in which it was studied.

Identification of heavy-flavour jets with the CMS detector in pp collisions at 13 TeV

Abstract: Many measurements and searches for physics beyond the standard model at the LHC rely on the efficient identification of heavy-flavour jets, i.e. jets originating from bottom or charm quarks. In this paper, the discriminating variables and the algorithms used for heavy-flavour jet identification during the first years of operation of the CMS experiment in proton-proton collisions at a centre-of-mass energy of 13 TeV, are presented. Heavy-flavour jet identification algorithms have been improved compared to those used previously at centre-of-mass energies of 7 and 8 TeV. For jets with transverse momenta in the range expected in simulated events, these new developments result in an efficiency of 68% for the correct identification of a b jet for a probability of 1% of misidentifying a light-flavour jet. The improvement in relative efficiency at this misidentification probability is about 15%, compared to previous CMS algorithms. In addition, for the first time algorithms have been developed to identify jets containing two b hadrons in Lorentz-boosted event topologies, as well as to tag c jets. The large data sample recorded in 2016 at a centre-of-mass energy of 13 TeV has also allowed the development of new methods to measure the efficiency and misidentification probability of heavy-flavour jet identification algorithms. The b jet identification efficiency is measured with a precision of a few per cent at moderate jet transverse momenta (between 30 and 300 GeV) and about 5% at the highest jet transverse momenta (between 500 and 1000 GeV).

O-HAZE: A Dehazing Benchmark with Real Hazy and Haze-Free Outdoor Images

Abstract: Haze removal or dehazing is a challenging ill-posed problem that has drawn a significant attention in the last few years. Despite this growing interest, the scientific community is still lacking a reference dataset to evaluate objectively and quantitatively the performance of proposed dehazing methods. The few datasets that are currently considered, both for assessment and training of learning-based dehazing techniques, exclusively rely on synthetic hazy images. To address this limitation, we introduce the first outdoor scenes database (named O-HAZE) composed of pairs of real hazy and corresponding haze-free images. In practice, hazy images have been captured in presence of real haze, generated by professional haze machines, and O-HAZE contains 45 different outdoor scenes depicting the same visual content recorded in haze-free and hazy conditions, under the same illumination parameters. To illustrate its usefulness, O-HAZE is used to compare a representative set of state-of-the-art dehazing techniques, using traditional image quality metrics such as PSNR, SSIM and CIEDE2000. This reveals the limitations of current techniques, and questions some of their underlying assumptions.

Nitric oxide signalling in cardiovascular health and disease

Abstract: Nitric oxide (NO) signalling has pleiotropic roles in biology and a crucial function in cardiovascular homeostasis. Tremendous knowledge has been accumulated on the mechanisms of the nitric oxide synthase (NOS)-NO pathway, but how this highly reactive, free radical gas signals to specific targets for precise regulation of cardiovascular function remains the focus of much intense research. In this Review, we summarize the updated paradigms on NOS regulation, NO interaction with reactive oxidant species in specific subcellular compartments, and downstream effects of NO in target cardiovascular tissues, while emphasizing the latest developments of molecular tools and biomarkers to modulate and monitor NO production and bioavailability.

Vowel recognition with four coupled spin-torque nano-oscillators

Abstract: In recent years, artificial neural networks have become the flagship algorithm of artificial intelligence1. In these systems, neuron activation functions are static, and computing is achieved through standard arithmetic operations. By contrast, a prominent branch of neuroinspired computing embraces the dynamical nature of the brain and proposes to endow each component of a neural network with dynamical functionality, such as oscillations, and to rely on emergent physical phenomena, such as synchronization2–6, for solving complex problems with small networks7–11. This approach is especially interesting for hardware implementations, because emerging nanoelectronic devices can provide compact and energy-efficient nonlinear auto-oscillators that mimic the periodic spiking activity of biological neurons12–16. The dynamical couplings between oscillators can then be used to mediate the synaptic communication between the artificial neurons. One challenge for using nanodevices in this way is to achieve learning, which requires fine control and tuning of their coupled oscillations17; the dynamical features of nanodevices can be difficult to control and prone to noise and variability18. Here we show that the outstanding tunability of spintronic nano-oscillators—that is, the possibility of accurately controlling their frequency across a wide range, through electrical current and magnetic field—can be used to address this challenge. We successfully train a hardware network of four spin-torque nano-oscillators to recognize spoken vowels by tuning their frequencies according to an automatic real-time learning rule. We show that the high experimental recognition rates stem from the ability of these oscillators to synchronize. Our results demonstrate that non-trivial pattern classification tasks can be achieved with small hardware neural networks by endowing them with nonlinear dynamical features such as oscillations and synchronization. A network of four spin-torque nano-oscillators can be trained in real time to recognize spoken vowels, in a simple and scalable approach that could be exploited for large-scale neural networks.

On the Min-cost Traveling Salesman Problem with Drone

Abstract: Over the past few years, unmanned aerial vehicles (UAV), also known as drones, have been adopted as part of a new logistic method in the commercial sector called “last-mile delivery”. In this novel approach, they are deployed alongside trucks to deliver goods to customers to improve the quality of service and reduce the transportation cost. This approach gives rise to a new variant of the traveling salesman problem (TSP), called TSP with drone (TSP-D). A variant of this problem that aims to minimize the time at which truck and drone finish the service (or, in other words, to maximize the quality of service) was studied in the work of Murray and Chu (2015). In contrast, this paper considers a new variant of TSP-D in which the objective is to minimize operational costs including total transportation cost and one created by waste time a vehicle has to wait for the other. The problem is first formulated mathematically. Then, two algorithms are proposed for the solution. The first algorithm (TSP-LS) was adapted from the approach proposed by Murray and Chu (2015), in which an optimal TSP solution is converted to a feasible TSP-D solution by local searches. The second algorithm, a Greedy Randomized Adaptive Search Procedure (GRASP), is based on a new split procedure that optimally splits any TSP tour into a TSP-D solution. After a TSP-D solution has been generated, it is then improved through local search operators. Numerical results obtained on various instances of both objective functions with different sizes and characteristics are presented. The results show that GRASP outperforms TSP-LS in terms of solution quality under an acceptable running time.

Performance of the CMS muon detector and muon reconstruction with proton-proton collisions at s=13 TeV

Abstract: The CMS muon detector system, muon reconstruction software, and high-level trigger underwent significant changes in 2013–2014 in preparation for running at higher LHC collision energy and instantaneous luminosity. The performance of the modified system is studied using proton-proton collision data at center-of-mass energy √s=13 TeV, collected at the LHC in 2015 and 2016. The measured performance parameters, including spatial resolution, efficiency, and timing, are found to meet all design specifications and are well reproduced by simulation. Despite the more challenging running conditions, the modified muon system is found to perform as well as, and in many aspects better than, previously. We dedicate this paper to the memory of Prof. Alberto Benvenuti, whose work was fundamental for the CMS muon detector.

Global distribution data for cattle, buffaloes, horses, sheep, goats, pigs, chickens and ducks in 2010.

Abstract: Global data sets on the geographic distribution of livestock are essential for diverse applications in agricultural socio-economics, food security, environmental impact assessment and epidemiology. We present a new version of the Gridded Livestock of the World (GLW 3) database, reflecting the most recently compiled and harmonized subnational livestock distribution data for 2010. GLW 3 provides global population densities of cattle, buffaloes, horses, sheep, goats, pigs, chickens and ducks in each land pixel at a spatial resolution of 0.083333 decimal degrees (approximately 10 km at the equator). They are accompanied by detailed metadata on the year, spatial resolution and source of the input census data. Two versions of each species distribution are produced. In the first version, livestock numbers are disaggregated within census polygons according to weights established by statistical models using high resolution spatial covariates (dasymetric weighting). In the second version, animal numbers are distributed homogeneously with equal densities within their census polygons (areal weighting) to provide spatial data layers free of any assumptions linking them to other spatial variables. Machine-accessible metadata file describing the reported data (ISA-Tab format)

Middle-range theories of land system change

Abstract: Changes in land systems generate many sustainability challenges Identifying more sustainable land-use alternatives requires solid theoretical foundations on the causes of land-use/cover changes Land system science is a maturing field that has produced a wealth of methodological innovations and empirical observations on land-cover and land-use change, from patterns and processes to causes We take stock of this knowledge by reviewing and synthesizing the theories that explain the causal mechanisms of land-use change, including systemic linkages between distant land-use changes, with a focus on agriculture and forestry processes We first review theories explaining changes in land-use extent, such as agricultural expansion, deforestation, frontier development, and land abandonment, and changes in land-use intensity, such as agricultural intensification and disintensification We then synthesize theories of higher-level land system change processes, focusing on: (i) land-use spillovers, including land sparing and rebound effects with intensification, leakage, indirect land-use change, and land-use displacement, and (ii) land-use transitions, defined as structural non-linear changes in land systems, including forest transitions Theories focusing on the causes of land system changes span theoretically and epistemologically disparate knowledge domains and build from deductive, abductive, and inductive approaches A grand, integrated theory of land system change remains elusive Yet, we show that middle-range theories – defined here as contextual generalizations that describe chains of causal mechanisms explaining a well-bounded range of phenomena, as well as the conditions that trigger, enable, or prevent these causal chains –, provide a path towards generalized knowledge of land systems This knowledge can support progress towards sustainable social-ecological systems

Endoscopic management of acute necrotizing pancreatitis: European Society of Gastrointestinal Endoscopy (ESGE) evidence-based multidisciplinary guidelines

Abstract: 1 ESGE suggests using contrast-enhanced computed tomography (CT) as the first-line imaging modality on admission when indicated and up to the 4th week from onset in the absence of contraindications. Magnetic resonance imaging (MRI) may be used instead of CT in patients with contraindications to contrast-enhanced CT, and after the 4th week from onset when invasive intervention is considered because the contents (liquid vs. solid) of pancreatic collections are better characterized by MRI and evaluation of pancreatic duct integrity is possible. Weak recommendation, low quality evidence. 2 ESGE recommends against routine percutaneous fine needle aspiration (FNA) of (peri)pancreatic collections. Strong recommendation, moderate quality evidence. FNA should be performed only if there is suspicion of infection and clinical/imaging signs are unclear. Weak recommendation, low quality evidence. 3 ESGE recommends initial goal-directed intravenous fluid therapy with Ringer’s lactate (e. g. 5 – 10 mL/kg/h) at onset. Fluid requirements should be patient-tailored and reassessed at frequent intervals. Strong recommendation, moderate quality evidence. 4 ESGE recommends against antibiotic or probiotic prophylaxis of infectious complications in acute necrotizing pancreatitis. Strong recommendation, high quality evidence. 5 ESGE recommends invasive intervention for patients with acute necrotizing pancreatitis and clinically suspected or proven infected necrosis. Strong recommendation, low quality evidence. ESGE suggests that the first intervention for infected necrosis should be delayed for 4 weeks if tolerated by the patient. Weak recommendation, low quality evidence. 6 ESGE recommends performing endoscopic or percutaneous drainage of (suspected) infected walled-off necrosis as the first interventional method, taking into account the location of the walled-off necrosis and local expertise. Strong recommendation, moderate quality evidence. 7 ESGE suggests that, in the absence of improvement following endoscopic transmural drainage of walled-off necrosis, endoscopic necrosectomy or minimally invasive surgery (if percutaneous drainage has already been performed) is to be preferred over open surgery as the next therapeutic step, taking into account the location of the walled-off necrosis and local expertise. Weak recommendation, low quality evidence. 8 ESGE recommends long-term indwelling of transluminal plastic stents in patients with disconnected pancreatic duct syndrome. Strong recommendation, low quality evidence. Lumen-apposing metal stents should be retrieved within 4 weeks to avoid stent-related adverse effects. Strong recommendation, low quality evidence.

The role of supply-chain initiatives in reducing deforestation

Abstract: A major reduction in global deforestation is needed to mitigate climate change and biodiversity loss Recent private sector commitments aim to eliminate deforestation from a company’s operations or supply chain, but they fall short on several fronts Company pledges vary in the degree to which they include time-bound interventions with clear definitions and criteria to achieve verifiable outcomes Zero-deforestation policies by companies may be insufficient to achieve broader impact on their own due to leakage, lack of transparency and traceability, selective adoption and smallholder marginalization Public–private policy mixes are needed to increase the effectiveness of supply-chain initiatives that aim to reduce deforestation We review current supply-chain initiatives, their effectiveness, and the challenges they face, and go on to identify knowledge gaps for complementary public–private policies

Quantifying climate feedbacks in polar regions

Abstract: The concept of feedback is key in assessing whether a perturbation to a system is amplified or damped by mechanisms internal to the system. In polar regions, climate dynamics are controlled by both radiative and non-radiative interactions between the atmosphere, ocean, sea ice, ice sheets and land surfaces. Precisely quantifying polar feedbacks is required for a process-oriented evaluation of climate models, a clear understanding of the processes responsible for polar climate changes, and a reduction in uncertainty associated with model projections. This quantification can be performed using a simple and consistent approach that is valid for a wide range of feedbacks, offering the opportunity for more systematic feedback analyses and a better understanding of polar climate changes.

Akkermansia muciniphila induces gut microbiota remodelling and controls islet autoimmunity in NOD mice

Abstract: Objective Intestinal microbiota is implicated in the pathogenesis of autoimmune type 1 diabetes in humans and in non-obese diabetic (NOD) mice, but evidence on its causality and on the role of individual microbiota members is limited. We investigated if different diabetes incidence in two NOD colonies was due to microbiota differences and aimed to identify individual microbiota members with potential significance. Design We profiled intestinal microbiota between two NOD mouse colonies showing high or low diabetes incidence by 16S ribosomal RNA gene sequencing and colonised the high-incidence colony with the microbiota of the low-incidence colony. Based on unaltered incidence, we identified a few taxa which were not effectively transferred and thereafter, transferred experimentally one of these to test its potential significance. Results Although the high-incidence colony adopted most microbial taxa present in the low-incidence colony, diabetes incidence remained unaltered. Among the few taxa which were not transferred, Akkermansia muciniphila was identified. As A. muciniphila abundancy is inversely correlated to the risk of developing type 1 diabetes-related autoantibodies, we transferred A. muciniphila experimentally to the high-incidence colony. A. muciniphila transfer promoted mucus production and increased expression of antimicrobial peptide Reg3γ , outcompeted Ruminococcus torques from the microbiota, lowered serum endotoxin levels and islet toll-like receptor expression, promoted regulatory immunity and delayed diabetes development. Conclusion Transfer of the whole microbiota may not reduce diabetes incidence despite a major change in gut microbiota, but single symbionts such as A. muciniphila with beneficial metabolic and immune signalling effects may reduce diabetes incidence when administered as a probiotic.