Showing papers by "Université catholique de Louvain published in 2021"

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)

Abstract: In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.

Population Properties of Compact Objects from the Second LIGO-Virgo Gravitational-Wave Transient Catalog

Abstract: We report on the population of 47 compact binary mergers detected with a false-alarm rate of 0.01 are dynamically assembled. Third, we estimate merger rates, finding RBBH = 23.9-+8.614.3 Gpc-3 yr-1 for BBHs and RBNS = 320-+240490 Gpc-3 yr-1 for binary neutron stars. We find that the BBH rate likely increases with redshift (85% credibility) but not faster than the star formation rate (86% credibility). Additionally, we examine recent exceptional events in the context of our population models, finding that the asymmetric masses of GW190412 and the high component masses of GW190521 are consistent with our models, but the low secondary mass of GW190814 makes it an outlier.

Observation of Gravitational Waves from Two Neutron Star–Black Hole Coalescences

Abstract: We report the observation of gravitational waves from two compact binary coalescences in LIGO’s and Virgo’s third observing run with properties consistent with neutron star–black hole (NSBH) binaries. The two events are named GW200105_162426 and GW200115_042309, abbreviated as GW200105 and GW200115; the first was observed by LIGO Livingston and Virgo and the second by all three LIGO–Virgo detectors. The source of GW200105 has component masses 8.9−1.5+1.2 and 1.9−0.2+0.3M⊙ , whereas the source of GW200115 has component masses 5.7−2.1+1.8 and 1.5−0.3+0.7M⊙ (all measurements quoted at the 90% credible level). The probability that the secondary’s mass is below the maximal mass of a neutron star is 89%–96% and 87%–98%, respectively, for GW200105 and GW200115, with the ranges arising from different astrophysical assumptions. The source luminosity distances are 280−110+110 and 300−100+150Mpc , respectively. The magnitude of the primary spin of GW200105 is less than 0.23 at the 90% credible level, and its orientation is unconstrained. For GW200115, the primary spin has a negative spin projection onto the orbital angular momentum at 88% probability. We are unable to constrain the spin or tidal deformation of the secondary component for either event. We infer an NSBH merger rate density of 45−33+75Gpc−3yr−1 when assuming that GW200105 and GW200115 are representative of the NSBH population or 130−69+112Gpc−3yr−1 under the assumption of a broader distribution of component masses.

Effect of IBD medications on COVID-19 outcomes: results from an international registry.

Abstract: Objective We sought to evaluate COVID-19 clinical course in patients with IBD treated with different medication classes and combinations. Design Surveillance Epidemiology of Coronavirus Under Research Exclusion for Inflammatory Bowel Disease (SECURE-IBD) is a large, international registry created to monitor outcomes of IBD patients with confirmed COVID-19. We used multivariable regression with a generalised estimating equation accounting for country as a random effect to analyse the association of different medication classes with severe COVID-19, defined as intensive care unit admission, ventilator use and/or death. Results 1439 cases from 47 countries were included (mean age 44.1 years, 51.4% men) of whom 112 patients (7.8%) had severe COVID-19. Compared with tumour necrosis factor (TNF) antagonist monotherapy, thiopurine monotherapy (adjusted OR (aOR) 4.08, 95% CI 1.73 to 9.61) and combination therapy with TNF antagonist and thiopurine (aOR 4.01, 95% CI 1.65 to 9.78) were associated with an increased risk of severe COVID-19. Any mesalamine/sulfasalazine compared with no mesalamine/sulfasalazine use was associated with an increased risk (aOR 1.70, 95% CI 1.26 to 2.29). This risk estimate increased when using TNF antagonist monotherapy as a reference group (aOR 3.52, 95% CI 1.93 to 6.45). Interleukin-12/23 and integrin antagonists were not associated with significantly different risk than TNF antagonist monotherapy (aOR 0.98, 95% CI 0.12 to 8.06 and aOR 2.42, 95% CI 0.59 to 9.96, respectively). Conclusion Combination therapy and thiopurines may be associated with an increased risk of severe COVID-19. No significant differences were observed when comparing classes of biologicals. These findings warrant confirmation in large population-based cohorts. MKH should be changed to MDK for co-last author line

Diet and depression: exploring the biological mechanisms of action

Abstract: The field of nutritional psychiatry has generated observational and efficacy data supporting a role for healthy dietary patterns in depression onset and symptom management. To guide future clinical trials and targeted dietary therapies, this review provides an overview of what is currently known regarding underlying mechanisms of action by which diet may influence mental and brain health. The mechanisms of action associating diet with health outcomes are complex, multifaceted, interacting, and not restricted to any one biological pathway. Numerous pathways were identified through which diet could plausibly affect mental health. These include modulation of pathways involved in inflammation, oxidative stress, epigenetics, mitochondrial dysfunction, the gut microbiota, tryptophan-kynurenine metabolism, the HPA axis, neurogenesis and BDNF, epigenetics, and obesity. However, the nascent nature of the nutritional psychiatry field to date means that the existing literature identified in this review is largely comprised of preclinical animal studies. To fully identify and elucidate complex mechanisms of action, intervention studies that assess markers related to these pathways within clinically diagnosed human populations are needed.

Dynabench: Rethinking Benchmarking in NLP.

Abstract: We introduce Dynabench, an open-source platform for dynamic dataset creation and model benchmarking. Dynabench runs in a web browser and supports human-and-model-in-the-loop dataset creation: annotators seek to create examples that a target model will misclassify, but that another person will not. In this paper, we argue that Dynabench addresses a critical need in our community: contemporary models quickly achieve outstanding performance on benchmark tasks but nonetheless fail on simple challenge examples and falter in real-world scenarios. With Dynabench, dataset creation, model development, and model assessment can directly inform each other, leading to more robust and informative benchmarks. We report on four initial NLP tasks, illustrating these concepts and highlighting the promise of the platform, and address potential objections to dynamic benchmarking as a new standard for the field.

An experimental and modeling study of ammonia with enriched oxygen content and ammonia/hydrogen laminar flame speed at elevated pressure and temperature

Abstract: Laminar flame speeds of ammonia with oxygen-enriched air (oxygen content varying from 21 to 30 vol.%) and ammonia-hydrogen-air mixtures (fuel hydrogen content varying from 0 to 30 vol.%) at elevated pressure (1–10 bar) and temperature (298–473 K) were determined experimentally using a constant volume combustion chamber. Moreover, ammonia laminar flame speeds with helium as an inert were measured for the first time. Using these experimental data along with published ones, we have developed a newly compiled kinetic model for the prediction of the oxidation of ammonia and ammonia-hydrogen blends in freely propagating and burner stabilized premixed flames, as well as in shock tubes, rapid compression machines and a jet-stirred reactor. The reaction mechanism also considers the formation of nitrogen oxides, as well as the reduction of nitrogen oxides depending on the conditions of the surrounding gas phase. The experimental results from the present work and the literature are interpreted with the help of the kinetic model derived here. The experiments show that increasing the initial temperature, fuel hydrogen content, or oxidizer oxygen content causes the laminar flame speed to increase, while it decreases when increasing the initial pressure. The proposed kinetic model predicts the same trends than experiments and a good agreement is found with measurements for a wide range of conditions. The model suggests that under rich conditions the N2H2 formation path is favored compared to stoichiometric condition. The most important reactions under rich conditions are: NH2+NH=N2H2+H, NH2+NH2=N2H2+H2, N2H2+H=NNH+H2 and N2H2+M=NNH+H+M. These reactions were also found to be among the most sensitive reactions for predicting the laminar flame speed for all the cases investigated.

Upper limits on the isotropic gravitational-wave background from Advanced LIGO and Advanced Virgo’s third observing run

Abstract: We report results of a search for an isotropic gravitational-wave background (GWB) using data from Advanced LIGO’s and Advanced Virgo’s third observing run (O3) combined with upper limits from the earlier O1 and O2 runs. Unlike in previous observing runs in the advanced detector era, we include Virgo in the search for the GWB. The results of the search are consistent with uncorrelated noise, and therefore we place upper limits on the strength of the GWB. We find that the dimensionless energy density Ω GW ≤ 5.8 × 10 − 9 at the 95% credible level for a flat (frequency-independent) GWB, using a prior which is uniform in the log of the strength of the GWB, with 99% of the sensitivity coming from the band 20–76.6 Hz; Ω GW ( f ) ≤ 3.4 × 10 − 9 at 25 Hz for a power-law GWB with a spectral index of 2 / 3 (consistent with expectations for compact binary coalescences), in the band 20–90.6 Hz; and Ω GW ( f ) ≤ 3.9 × 10 − 10 at 25 Hz for a spectral index of 3, in the band 20–291.6 Hz. These upper limits improve over our previous results by a factor of 6.0 for a flat GWB, 8.8 for a spectral index of 2 / 3 , and 13.1 for a spectral index of 3. We also search for a GWB arising from scalar and vector modes, which are predicted by alternative theories of gravity; we do not find evidence of these, and place upper limits on the strength of GWBs with these polarizations. We demonstrate that there is no evidence of correlated noise of magnetic origin by performing a Bayesian analysis that allows for the presence of both a GWB and an effective magnetic background arising from geophysical Schumann resonances. We compare our upper limits to a fiducial model for the GWB from the merger of compact binaries, updating the model to use the most recent data-driven population inference from the systems detected during O3a. Finally, we combine our results with observations of individual mergers and show that, at design sensitivity, this joint approach may yield stronger constraints on the merger rate of binary black holes at z ≳ 2 than can be achieved with individually resolved mergers alone.

Immune-mediated neurological syndromes in SARS-CoV-2-infected patients.

Abstract: Evidence of immune-mediated neurological syndromes associated with the severe acute respiratory syndrome coronavirus (SARS-CoV-2) infection is limited. We therefore investigated clinical, serological and CSF features of coronavirus disease 2019 (COVID-19) patients with neurological manifestations. Consecutive COVID-19 patients with neurological manifestations other than isolated anosmia and/or non-severe headache, and with no previous neurological or psychiatric disorders were prospectively included. Neurological examination was performed in all patients and lumbar puncture with CSF examination was performed when not contraindicated. Serum anti-gangliosides antibodies were tested when clinically indicated. Of the 349 COVID-19 admitted to our center between March 23rd and April 24th 2020, 15 patients (4.3%) had neurological manifestations and fulfilled the study inclusion/exclusion criteria. CSF examination was available in 13 patients and showed lymphocytic pleocytosis in 2 patients: 1 with anti-contactin-associated protein 2 (anti-Caspr2) antibody encephalitis and 1 with meningo-polyradiculitis. Increased serum titer of anti-GD1b antibodies was found in three patients and was associated with variable clinical presentations, including cranial neuropathy with meningo-polyradiculitis, brainstem encephalitis and delirium. CSF PCR for SARS-CoV-2 was negative in all patients. In SARS-Cov-2 infected patients with neurological manifestations, CSF pleocytosis is associated with para- or post-infectious encephalitis and polyradiculitis. Anti-GD1b and anti-Caspr2 autoantibodies can be identified in certain cases, raising the question of SARS-CoV-2-induced secondary autoimmunity.

The decline of butterflies in Europe: Problems, significance, and possible solutions.

Abstract: We review changes in the status of butterflies in Europe, focusing on long-running population data available for the United Kingdom, the Netherlands, and Belgium, based on standardized monitoring transects. In the United Kingdom, 8% of resident species have become extinct, and since 1976 overall numbers declined by around 50%. In the Netherlands, 20% of species have become extinct, and since 1990 overall numbers in the country declined by 50%. Distribution trends showed that butterfly distributions began decreasing long ago, and between 1890 and 1940, distributions declined by 80%. In Flanders (Belgium), 20 butterflies have become extinct (29%), and between 1992 and 2007 overall numbers declined by around 30%. A European Grassland Butterfly Indicator from 16 European countries shows there has been a 39% decline of grassland butterflies since 1990. The 2010 Red List of European butterflies listed 38 of the 482 European species (8%) as threatened and 44 species (10%) as near threatened (note that 47 species were not assessed). A country level analysis indicates that the average Red List rating is highest in central and mid-Western Europe and lowest in the far north of Europe and around the Mediterranean. The causes of the decline of butterflies are thought to be similar in most countries, mainly habitat loss and degradation and chemical pollution. Climate change is allowing many species to spread northward while bringing new threats to susceptible species. We describe examples of possible conservation solutions and a summary of policy changes needed to conserve butterflies and other insects.

The ILAE classification of seizures and the epilepsies: Modification for seizures in the neonate. Position paper by the ILAE Task Force on Neonatal Seizures.

Abstract: Seizures are the most common neurological emergency in the neonatal period and in contrast to those in infancy and childhood, are often provoked seizures with an acute cause and may be electrographic-only. Hence, neonatal seizures may not fit easily into classification schemes for seizures and epilepsies primarily developed for older children and adults. A Neonatal Seizures Task Force was established by the International League Against Epilepsy (ILAE) to develop a modification of the 2017 ILAE Classification of Seizures and Epilepsies, relevant to neonates. The neonatal classification framework emphasizes the role of electroencephalography (EEG) in the diagnosis of seizures in the neonate and includes a classification of seizure types relevant to this age group. The seizure type is determined by the predominant clinical feature. Many neonatal seizures are electrographic-only with no evident clinical features; therefore, these are included in the proposed classification. Clinical events without an EEG correlate are not included. Because seizures in the neonatal period have been shown to have a focal onset, a division into focal and generalized is unnecessary. Seizures can have a motor (automatisms, clonic, epileptic spasms, myoclonic, tonic), non-motor (autonomic, behavior arrest), or sequential presentation. The classification allows the user to choose the level of detail when classifying seizures in this age group.

Antibody titres decline 3-month post-vaccination with BNT162b2.

Abstract: Several studies reported on the humoral response in subjects having received the BNT162b2 mRNA COVID-19 vaccine. However, data on the kinetics of antibodies 3 months post-vaccination are currently ...

Electron and photon reconstruction and identification with the CMS experiment at the CERN LHC

Abstract: The performance is presented of the reconstruction and identification algorithms for electrons and photons with the CMS experiment at the LHC. The reported results are based on proton-proton collision data collected at a center-of-mass energy of 13 TeV and recorded in 2016-2018, corresponding to an integrated luminosity of 136 fb$^{-1}$. Results obtained from lead-lead collision data collected at $\sqrt{s_\mathrm{NN}}=$ 5.02 TeV are also presented. Innovative techniques are used to reconstruct the electron and photon signals in the detector and to optimize the energy resolution. Events with electrons and photons in the final state are used to measure the energy resolution and energy scale uncertainty in the recorded events. The measured energy resolution for electrons produced in Z boson decays in proton-proton collision data ranges from 2 to 5%, depending on electron pseudorapidity and energy loss through bremsstrahlung in the detector material. The energy scale in the same range of energies is measured with an uncertainty smaller than 0.1 (0.3)% in the barrel (endcap) region in proton-proton collisions and better than 1 (3)% in the barrel (endcap) region in heavy ion collisions. The timing resolution for electrons from Z boson decays with the full 2016-2018 proton-proton collision data set is measured to be 200 ps.

Beliefs in Conspiracy Theories and Misinformation About COVID-19: Comparative Perspectives on the Role of Anxiety, Depression and Exposure to and Trust in Information Sources

Abstract: While COVID-19 spreads aggressively and rapidly across the globe, many societies have also witnessed the spread of other viral phenomena like misinformation, conspiracy theories, and general mass suspicions about what is really going on. This study investigates how exposure to and trust in information sources, and anxiety and depression, are associated with conspiracy and misinformation beliefs in eight countries/regions (Belgium, Canada, England, Philippines, Hong Kong, New Zealand, United States, Switzerland) during the COVID-19 pandemic. Data were collected in an online survey fielded from May 29, 2020 to June 12, 2020, resulting in a multinational representative sample of 8,806 adult respondents. Results indicate that greater exposure to traditional media (television, radio, newspapers) is associated with lower conspiracy and misinformation beliefs, while exposure to politicians and digital media and personal contacts are associated with greater conspiracy and misinformation beliefs. Exposure to health experts is associated with lower conspiracy beliefs only. Higher feelings of depression are also associated with greater conspiracy and misinformation beliefs. We also found relevant group- and country differences. We discuss the implications of these results.

European Green Deal – legal and financial challenges of the climate change

Abstract: The European Green Deal announced by the European Commission in December 2019 is a roadmap meant to foster the transition of the European Union towards the climate-neutral economy by reducing carbon emissions towards 55% by 2030 and achieving carbon neutrality by 2050. By putting the EGD in a boarder perspective of evolving, constitutional rationale of environmental protection in the EU legal order, this contribution examines horizontal, legal dimension and financial implications of the green transition. The challenge ahead of the Union is now how to transform the ambitious climate agenda into efficient legal and economic instruments ‘in a fair way, leaving no one behind’. This paper argues that EGD is a great opportunity, but in order to turn it into a success, it must be strongly anchored in the concepts pertaining to the constitutional framework of the EU legal order, in particular, the concepts of solidarity, sustainable development and high level of environmental protection.

Critical knowledge gaps and research priorities in global soil salinity

Abstract: Approximately 1 billion ha of the global land surface is currently salt-affected, representing about 7% of the earth's land surface. Whereas most of it results from natural geochemical processes, an estimated 30% of irrigated lands globally are salt-affected through secondary human-induced salinization. Application of lower quality, alternative irrigation water is further threatening expansion of the areal extent of soil salinity, in addition to climate change causing increases of salt-water intrusion in coastal areas and increasing crop water requirements. The reduced availability of freshwater resources for irrigation, the continued reduction of the world's cultivated agricultural area by land degradation and urbanization, in conjunction with a growing world population further complicates the problem seeking sustainable solutions. This scoping review prioritizes critical knowledge gaps and makes recommendations for 10 priorities in soil salinity research toward a sustainable and productive agricultural system for a food-secure future world. We also include basin-specific case studies that illustrate progress of the world's major irrigated areas in addressing impacts of soil salinization. By identifying research priorities, we seek to accelerate enhanced research funding to bring new knowledge and innovative solutions toward mitigation of soil salinity impacts. We further want to inspire the science community to develop new directions in salinity research.

The EC-Earth3 Earth System Model for the Climate Model Intercomparison Project 6

Abstract: The Earth System Model EC-Earth3 for contributions to CMIP6 is documented here, with its flexible coupling framework, major model configurations, a methodology for ensuring the simulations are comparable across different HPC systems, and with the physical performance of base configurations over the historical period The variety of possible configurations and sub-models reflects the broad interests in the EC-Earth community EC-Earth3 key performance metrics demonstrate physical behaviour and biases well within the frame known from recent CMIP models With improved physical and dynamic features, new ESM components, community tools, and largely improved physical performance compared to the CMIP5 version, EC-Earth3 represents a clear step forward for the only European community ESM We demonstrate here that EC-Earth3 is suited for a range of tasks in CMIP6 and beyond

Localization of lattice dynamics in low-angle twisted bilayer graphene

Abstract: Twisted bilayer graphene is created by slightly rotating the two crystal networks in bilayer graphene with respect to each other. For small twist angles, the material undergoes a self-organized lattice reconstruction, leading to the formation of a periodically repeated domain1-3. The resulting superlattice modulates the vibrational3,4 and electronic5,6 structures within the material, leading to changes in the behaviour of electron-phonon coupling7,8 and to the observation of strong correlations and superconductivity9. However, accessing these modulations and understanding the related effects are challenging, because the modulations are too small for experimental techniques to accurately resolve the relevant energy levels and too large for theoretical models to properly describe the localized effects. Here we report hyperspectral optical images, generated by a nano-Raman spectroscope10, of the crystal superlattice in reconstructed (low-angle) twisted bilayer graphene. Observations of the crystallographic structure with visible light are made possible by the nano-Raman technique, which reveals the localization of lattice dynamics, with the presence of strain solitons and topological points1 causing detectable spectral variations. The results are rationalized by an atomistic model that enables evaluation of the local density of the electronic and vibrational states of the superlattice. This evaluation highlights the relevance of solitons and topological points for the vibrational and electronic properties of the structures, particularly for small twist angles. Our results are an important step towards understanding phonon-related effects at atomic and nanometric scales, such as Jahn-Teller effects11 and electronic Cooper pairing12-14, and may help to improve device characterization15 in the context of the rapidly developing field of twistronics16.