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Immunity in the ABM-DSGE framework for preventing and controlling epidemics - validation of results
No full textThe COVID-19 pandemic has raised many questions on how to manage an epidemiological and economic crisis around the world. Since the beginning of the COVID-19 pandemic, scientists and policy makers have been asking how effective lockdowns are in preventing and controlling the spread of the virus. In the absence of vaccines, the regulators lacked any plausible alternatives. Nevertheless, after the introduction of vaccinations, to what extent the conclusions of these analyses are still valid should be considered. In this paper, we present a study on the effect of vaccinations within the dynamic stochastic general equilibrium model with an agent-based epidemic component. Thus, we validated the results regarding the need to use lockdowns as an efficient tool for preventing and controlling epidemics that were obtained in November 2020
Dynamic Runx1 chromatin boundaries affect gene expression in hematopoietic development
No full textThe transcription factor RUNX1 is a critical regulator of developmental hematopoiesis and is frequently disrupted in leukemia. Runx1 is a large, complex gene that is expressed from two alternative promoters under the spatiotemporal control of multiple hematopoietic enhancers. To dissect the dynamic regulation of Runx1 in hematopoietic development, we analyzed its three-dimensional chromatin conformation in mouse embryonic stem cell (ESC) differentiation cultures. Runx1 resides in a 1.1 Mb topologically associating domain (TAD) demarcated by convergent CTCF motifs. As ESCs differentiate to mesoderm, chromatin accessibility, Runx1 enhancer-promoter (E-P) interactions, and CTCF-CTCF interactions increase in the TAD, along with initiation of Runx1 expression from the P2 promoter. Differentiation to hematopoietic progenitor cells is associated with the formation of tissue-specific sub-TADs over Runx1, a shift in E-P interactions, P1 promoter demethylation, and robust expression from both Runx1 promoters. Deletion of promoter-proximal CTCF sites at the sub-TAD boundaries has no obvious effects on E-P interactions but leads to partial loss of domain structure, mildly affects gene expression, and delays hematopoietic development. Together, our analysis of gene regulation at a large multi-promoter developmental gene reveals that dynamic sub-TAD chromatin boundaries play a role in establishing TAD structure and coordinated gene expression
Robust passage phenomenology probably does not explain future-bias
No full textPeople are ‘biased toward the future’: all else being equal, we typically prefer to have positive experiences in the future, and negative experiences in the past. Several explanations have been suggested for this pattern of preferences. Adjudicating among these explanations can, among other things, shed light on the rationality of future-bias: For instance, if our preferences are explained by unjustified beliefs or an illusory phenomenology, we might conclude that they are irrational. This paper investigates one hypothesis, according to which future-bias is (at least partially) explained by our having a phenomenology that we describe, or conceive of, as being as of time robustly passing. We empirically tested this hypothesis and found no evidence in its favour. Our results present a puzzle, however, when compared with the results of an earlier study. We conclude that although robust passage phenomenology on its own probably does not explain future-bias, having this phenomenology and taking it to be veridical may contribute to future-bias
Is academia becoming more localised? The growth of regional knowledge networks within international research collaboration
No full textIt is well-established that the process of learning and capability building is core to economic development and structural transformation. Since knowledge is ‘sticky’, a key component of this process is learning-by-doing, which can be achieved via a variety of mechanisms including international research collaboration. Uncovering significant inter-country research ties using Scopus co-authorship data, we show that within-region collaboration has increased over the past five decades relative to international collaboration. Further supporting this insight, we find that while communities present in the global collaboration network before 2000 were often based on historical geopolitical or colonial lines, in more recent years they increasingly align with a simple partition of countries by regions. These findings are unexpected in light of a presumed continual increase in globalisation, and have significant implications for the design of programmes aimed at promoting international research collaboration and knowledge diffusion
Measuring time-dependent induced quantum coherences via two-dimensional coherence spectroscopy
No full textWe propose a two-dimensional spectroscopic protocol for measuring the timedependent coherences between the stationary states of a system induced by a timedependent system-bath interaction. We also investigate the role of temporallycorrelated noise on coherence dephasing. This protocol enables dynamical information about the system and its coupling to the environment to be determined.
Our results are based on the quantum-trajectory method, and are obtained from
both approximate, analytical and exact, numerical solutions of the time-dependent
Schr¨odinger equation. As an example, we show how this protocol can be used to investigate exciton dynamics in conjugated polymers induced by the coupling of their
torsional modes with the environment
2-Oxoglutarate derivatives can selectively enhance or inhibit the activity of human oxygenases
No full text2-Oxoglutarate (2OG) oxygenases are validated agrochemical and human drug targets. The potential for modulating their activity with 2OG derivatives has not been explored, possibly due to concerns regarding selectivity. We report proof-of-principle studies demonstrating selective enhancement or inhibition of 2OG oxygenase activity by 2-oxo acids. The human 2OG oxygenases studied, factor inhibiting hypoxia-inducible transcription factor HIF-α (FIH) and aspartate/asparagine-β-hydroxylase (AspH), catalyze C3 hydroxylations of Asp/Asn-residues. Of 35 tested 2OG derivatives, 10 enhance and 17 inhibit FIH activity. Comparison with results for AspH reveals that 2OG derivatives selectively enhance or inhibit FIH or AspH. Comparison of FIH structures complexed with 2OG derivatives to those for AspH provides insight into the basis of the observed selectivity. 2-Oxo acid derivatives have potential as drugs, for use in biomimetic catalysis, and in functional studies. The results suggest that the in vivo activity of 2OG oxygenases may be regulated by natural 2-oxo acids other than 2OG
Development of a novel index to characterise arterial dynamics using ultrasound imaging
No full textAbdominal aortic aneurysms (AAA) are associated with systemic inflammation and endothelial dysfunction. We previously reported flow mediated dilatation (FMD) of the brachial artery as a predictor of AAA growth. We hence hypothesised that other physical characteristics of the brachial artery correlate with AAA growth. Using a prospectively cohort of AAA patients, we devised a 'brachial artery relaxation index' (BARI) and examined its role as a biomarker for AAA growth. However, no correlation between BARI and future aneurysm growth was observed (p = 0.45). Therefore, our investigations did not substantiate the hypothesis that other physical characteristics of the brachial artery predicts AAA growth
Neural ordinary differential equations for ecological and evolutionary time‐series analysis
No full textInferring the functional shape of ecological and evolutionary processes from time-series data can be challenging because processes are often not describable with simple equations. The dynamical coupling between variables in time series further complicates the identification of equations through model selection as the inference of a given process is contingent on the accurate depiction of all other processes.
We present a novel method, neural ordinary differential equations (NODEs), for learning ecological and evolutionary processes from time-series data by modelling dynamical systems as ordinary differential equations and dynamical functions with artificial neural networks (ANNs). Upon successful training, the ANNs converge to functional shapes that best describe the biological processes underlying the dynamics observed, in a way that is robust to mathematical misspecifications of the dynamical model.
We demonstrate NODEs in a population dynamic context and show how they can be used to infer ecological interactions, dynamical causation and equilibrium points. We tested NODEs by analysing well-understood hare and lynx time-series data, which revealed that prey–predator oscillations were mainly driven by the interspecific interaction, as well as intraspecific densitydependence, and characterised by a single equilibrium point at the centre of the oscillation.
Our approach is applicable to any system that can be modelled with differential equations, and particularly suitable for linking ecological, evolutionary and environmental dynamics where parametric approaches are too challenging to implement, opening new avenues for theoretical and empirical investigations
High prevalence of epilepsy in an onchocerciasis-endemic area in Mvolo County, South Sudan: A door-to-door survey
No full textIn June 2020, a door-to-door household survey was conducted in Mvolo County, an onchocerciasis-endemic area in South Sudan. A total of 2357 households containing 15,699 individuals agreed to participate in the study. Of these, 5046 (32.1%, 95% CI: 31.4–32.9%) had skin itching and 445 (2.8%, 95% CI: 2.6–3.1%) were blind. An epilepsy screening questionnaire identified 813 (5.1%) persons suspected of having epilepsy. Of them, 804 (98.9%) were seen by a medical doctor, and in 798 (98.1%) the diagnosis of epilepsy was confirmed. The overall epilepsy prevalence was 50.8/1000 (95% CI: 47.6–54.4/1000), while the prevalence of nodding syndrome was 22.4/1000 (95% CI: 20.1–24.9/1000). Younger age, being male, skin itching, blindness, and living in a neighbourhood or village close to the Naam River were risk factors for epilepsy. The annual incidence of epilepsy was 82.8/100,000 (95% CI: 44.1–141.6/100,000). Among children 7–9 years old without epilepsy, 34% were Ov16 seropositive, suggesting high ongoing Onchocerca volvulus transmission, but only 41.9% of them took ivermectin during the last mass distribution. In conclusion, a high prevalence and incidence of epilepsy was observed in Mvolo, South Sudan. Strengthening of the onchocerciasis elimination programme is urgently needed in order to prevent epilepsy in this region