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The interplay between disease spreading and personal risk perception is of key importance for modelling the spread of infectious diseases. We propose a planar system of ordinary differential equations (ODEs) to describe the co-evolution of a spreading phenomenon and the average link density in the personal contact network. Contrary to standard epidemic models, we assume that the contact network changes based on the current prevalence of the disease in the population, i.e. the network adapts to the current state of the epidemic. We assume that personal risk perception is described using two functional responses: one for link-breaking and one for link-creation. The focus is on applying the model to epidemics, but we also highlight other possible fields of application. We derive an explicit form for the basic reproduction number and guarantee the existence of at least one endemic equilibrium, for all possible functional responses. Moreover, we show that for all functional responses, limit cycles do not exist. This means that our minimal model is not able to reproduce consequent waves of an epidemic, and more complex disease or behavioural dynamics are required to reproduce epidemic waves., Network Architectures and Services

Hydrogenases are enzymes that catalyze the oxidation and production of molecular hydrogen. For about fifteen years, there have been many reports about the successful connection of these enzymes to photosensitizers with the aim of designing H2 photoproduction systems, but relatively little attention has been paid to whether and why illumination may affect the catalytic properties of the enzyme. In all hydrogenases, hydrogen activation occurs at an inorganic active site that includes at least one Fe-carbonyl motif, which may make it sensitive to irradiation. Here we review the evidence that hydrogenases are indeed photosensitive. We focus mainly on the so-called FeFe hydrogenases; their active site, called the H-cluster, consists of a [4Fe4S] cluster that is bound by a cysteine sulfur to a diiron site. The iron atoms of the binuclear cluster are coordinated by carbonyl and cyanide ligands and an azadithiolate group. We describe the effects of UV-visible light irradiation on the enzyme under cryogenic or turnover conditions and the photoreactivity of model complexes that mimic the diiron site. We emphasize the dependence of the photochemical processes on wavelength, and warn about FeFe hydrogenase photoinhibition, which should probably be considered when attempts are made to use FeFe hydrogenases for the artificial photosynthesis of solar fuels. We also underline the relevance of studies of synthetic mimics of the H-cluster for understanding at atomistic level the photochemical processes observed in the enzyme.

Background: Targeted therapy with BRAF and MEK inhibitors has improved the survival of patients with BRAF-mutated metastatic melanoma, but most patients relapse upon the onset of drug resistance induced by mechanisms including genetic and epigenetic events. Among the epigenetic alterations, microRNA perturbation is associated with the development of kinase inhibitor resistance. Here, we identified and studied the role of miR-146a-5p dysregulation in melanoma drug resistance. Methods: The miR-146a-5p-regulated NFkB signaling network was identified in drug-resistant cell lines and melanoma tumor samples by expression profiling and knock-in and knock-out studies. A bioinformatic data analysis identified COX2 as a central gene regulated by miR-146a-5p and NFkB. The effects of miR-146a-5p/COX2 manipulation were studied in vitro in cell lines and with 3D cultures of treatment-resistant tumor explants from patients progressing during therapy. Results: miR-146a-5p expression was inversely correlated with drug sensitivity and COX2 expression and was reduced in BRAF and MEK inhibitor-resistant melanoma cells and tissues. Forced miR-146a-5p expression reduced COX2 activity and significantly increased drug sensitivity by hampering prosurvival NFkB signaling, leading to reduced proliferation and enhanced apoptosis. Similar effects were obtained by inhibiting COX2 by celecoxib, a clinically approved COX2 inhibitor. Conclusions: Deregulation of the miR-146a-5p/COX2 axis occurs in the development of melanoma resistance to targeted drugs in melanoma patients. This finding reveals novel targets for more effective combination treatment. [MediaObject not available: see fulltext.] Graphical Abstract: [Figure not available: see fulltext.]

We study an SAIRS-type epidemic model with vaccination, where the role of asymptomatic and symptomatic infectious individuals is explicitly considered in the transmission patterns of the disease. We provide a global stability analysis for the model. We determine the value of the basic reproduction number R0 and prove that the disease-free equilibrium is globally asymptotically stable if R0<1. If R0>1, the disease free equilibrium is unstable and a unique endemic equilibrium exists. We investigate the global stability of the endemic equilibrium for some variations of the original model under study and answer an open problem proposed in Ansumali et al. (2020). In the case of the SAIRS model without vaccination, we prove the global asymptotic stability of the disease-free equilibrium also when R0=1. We provide a thorough numerical exploration of our model to illustrate our analytical results., Network Architectures and Services

We introduce a Markov Modulated Process (MMP) to describe human mobility. We represent the mobility process as a time-varying graph, where a link specifies a connection between two nodes (humans) at any discrete time step. Each state of the Markov chain encodes a certain modification to the original graph. We show that our MMP model successfully captures the main features of a random mobility simulator, in which nodes moves in a square region. We apply our MMP model to human mobility, measured in a library., Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public., Network Architectures and Services, Transport and Planning

Background: Safinamide modulates both dopaminergic and glutamatergic systems with positive effects on motor and non-motor symptoms of Parkinson's disease (PD). The drug utilization study SYNAPSES was designed to investigate the use of safinamide in routine clinical practice, as recommended by the European Medicines Agency. Objective: To describe the occurrence of adverse events in PD patients treated with safinamide in real-life conditions. Methods: The SYNAPSES trial is an observational, European, multicenter, retrospective-prospective cohort study. Patients were followed up to 12 months with analyses performed in the overall population and in patients aged >75 years, with relevant comorbidities and with psychiatric conditions. Results: Of the 1610 patients included, 82.4% were evaluable after 12 months with 25.1% of patients >75 years, 70.8% with relevant comorbidities and 42.4% with psychiatric conditions. During observation 45.8% patients experienced adverse events, 27.7% patients had adverse drug reactions and 9.2% patients had serious adverse events. The adverse events were those already described in the patients' information leaflet. The majority were mild or moderate and completely resolved and no differences were detected between the subgroup of patients. Clinically significant improvements were seen in the UPDRS motor score and in the UPDRS total score in ≥40% of patients, according to the criteria developed by Shulman et al. Conclusion: The SYNAPSES study confirms the good safety profile of safinamide even in special groups of patients. Motor complications and motor scores improved with clinically significant results in the UPDRS scale maintained in the long-term.

In view of the depletion of fossil fuel reserves and climatic effects of greenhouse gas emissions, Ni,Fe-containing carbon monoxide dehydrogenase (Ni-CODH) enzymes have attracted increasing interest in recent years for their capability to selectively catalyze the reversible reduction of CO2 to CO (CO2 + 2H+ + 2e-⇌ CO + H2O). The possibility of converting the greenhouse gas CO2 into useful materials that can be used as synthetic building blocks or, remarkably, as carbon fuels makes Ni-CODH a very promising target for reverse-engineering studies. In this context, in order to provide insights into the chemical principles underlying the biological catalysis of CO2 activation and reduction, quantum mechanics calculations have been carried out in the framework of density functional theory (DFT) on different-sized models of the Ni-CODH active site. With the aim of uncovering which stereoelectronic properties of the active site (known as the C-cluster) are crucial for the efficient binding and release of CO2, different coordination modes of CO2 to different forms and redox states of the C-cluster have been investigated. The results obtained from this study highlight the key role of the protein environment in tuning the reactivity and the geometry of the C-cluster. In particular, the protonation state of His93 is found to be crucial for promoting the binding or the dissociation of CO2. The oxidation state of the C-cluster is also shown to be critical. CO2 binds to Cred2 according to a dissociative mechanism (i.e., CO2 binds to the C-cluster after the release of possible ligands from Feu) when His93 is doubly protonated. CO2 can also bind noncatalytically to Cred1 according to an associative mechanism (i.e., CO2 binding is preceded by the binding of H2O to Feu). Conversely, CO2 dissociates when His93 is singly protonated and the C-cluster is oxidized at least to the Cint redox state.

Introduction The GREENFIELD observational study assessed the effect of levodopa/carbidopa intestinal gel (LCIG) on motor and non-motor symptoms, and the related impact on patient quality of life and caregiver burden up to 8 years. Methods Final results of a large Italian cohort of patients who started LCIG in routine care between 2007 and 2014 are presented. Comparison between baseline (before LCIG) and follow-up visits on yearly basis (visit 2/3) is reported. Primary endpoint was Unified Parkinson's Disease Rating Scale (UPDRS-IV) Item 39; secondary endpoints were UPDRS I and II, dyskinesia items, PD Quality of Life Questionnaire-39, Parkinson's Disease Sleep Scale-2, Gait and Falls Questionnaire, Questionnaire on Impulsive Disorders, and Relative Stress Scale. Results Overall, 145 patients from 14 centers were assessed with a mean time since LCIG start of 2.8 +/- 1.7 years at visit 2. The mean UPDRS-IV item 39 score showed significant reductions compared to baseline (mean score 2.0 +/- 0.81) at visit 2 (mean score 0.9 +/- 0.69; - 55%; p < 0.001) and at visit 3 (mean score 1.0 +/- 0.75; - 50%; p < 0.001). At visit 3, significant reductions were observed for dyskinesia duration score (- 28%; p < 0.001), dyskinesia disability (- 40%; p < 0.001), and painful dyskinesia (- 50%; p < 0.001). Overall, 40 (27.6%) patients experienced 49 serious adverse events which were considered related to PEG/J procedure or to device in 16.3% of the cases. Conclusions The results of this study support the long-term efficacy of LCIG on PD symptoms as well as on activities of daily living. The adverse events were consistent with the established LCIG safety profile.

FeFe hydrogenases catalyze H2 oxidation and production using an "H-cluster", where two Fe ions are bound by an aza-dithiolate (adt) ligand. Various hypotheses have been proposed (by us and others) to explain that the enzyme reversibly inactivates under oxidizing, anaerobic conditions: intramolecular binding of the N atom of adt, formation of the so-called "Hox/inact" state or nonproductive binding of H2 to isomers of the H-cluster. Here, we show that none of the above explains the new finding that the anaerobic, oxidative, H2-dependent reversible inactivation is strictly dependent on the presence of Cl- or Br-. We provide experimental evidence that chloride uncompetitively inhibits the enzyme: it reversibly binds to catalytic intermediates of H2 oxidation (but not to the resting "Hox" state), after which oxidation locks the active site into a stable, saturated, inactive form, the structure of which is proposed here based on DFT calculations. The halides interact with the amine group of the H-cluster but do not directly bind to iron. It should be possible to stabilize the inhibited state in amounts compatible with spectroscopic investigations to explore further this unexpected reactivity of the H-cluster of hydrogenase.

Conspectus Many enzymes that produce or transform small molecules such as O2, H2, and CO2 embed inorganic cofactors based on transition metals. Their active site, where the chemical reaction occurs, is buried in and protected by the protein matrix, and connected to the solvent in several ways: chains of redox cofactors mediate long-range electron transfer; static or dynamic tunnels guide the substrate, product and inhibitors; amino acids and water molecules transfer protons. The catalytic mechanism of these enzymes is therefore delocalized over the protein and involves many different steps, some of which determine the response of the enzyme under conditions of stress (extreme redox conditions, presence of inhibitors, light), the catalytic rates in the two directions of the reaction and their ratio (the "catalytic bias"). Understanding all the steps in the catalytic cycle, including those that occur on sites of the protein that are remote from the active site, requires a combination of biochemical, structural, spectroscopic, theoretical, and kinetic methods. Here we argue that kinetics should be used to the fullest extent, by extracting quantitative information from the comparison of data and kinetic models and by exploring the combination of experimental kinetics and theoretical chemistry. In studies of these catalytic mechanisms, direct electrochemistry, the technique which we use and contribute to develop, has become unescapable. It simply consists in monitoring the changes in activity of an enzyme that is wired to an electrode by recording an electric current. We have described kinetic models that can be used to make sense of these data and to learn about various aspects of the mechanism that are difficult to probe using more conventional methods: long-range electron transfer, diffusion along gas channels, redox-driven (in)activations, active site chemistry and photoreactivity under conditions of turnover. In this Account, we highlight a few results that illustra

Le FeFe idrogenasi sono metalloenzimi che catalizzano l’ossidazione e la produzione di H2. Il ciclo catalitico e vari aspetti di questi enzimi, come l’inattivazione in condizioni aerobiche e anaerobiche, sono tutt’ora oggetto di studio. Per ottenere informazioni sulla struttura elettronica del sito attivo delle FeFe idrogenasi vengono abitualmente impiegate tecniche spettroscopiche, grazie alle quali viene determinato l’assorbimento di luce a diverse lunghezze d’onda da parte dell’enzima. In questa tesi, invece, abbiamo sviluppato una nuova tecnica, detta “fotoelettrochimica diretta”, in cui l’enzima è direttamente collegato ad un elettrodo, che può essere illuminato da una sorgente luminosa, e la frequenza di turnover viene direttamente misurata sotto forma di corrente elettrica. Monitorando le variazioni dell’attività dell’enzima in presenza di irraggiamento, possiamo determinare l’assorbimento del sito attivo in funzione della lunghezza d’onda e della potenza della sorgente luminosa. Concentrandoci sulle variazioni della frequenza di turnover, siamo certi che stiamo indagando l’effetto della luce localizzato sul sito attivo. Abbiamo utilizzato la fotoelettrochimica diretta per studiare l’effetto dell'irraggiamento, per mezzo di laser monocromatici, sulla cinetica di inibizione da CO in tre distinte FeFe idrogenasi. Abbiamo determinato lo spettro d’azione della fotodissociazione del CO inibitore e abbiamo descritto il processo a livello QM per la prima volta, ottenendo un buon accordo tra dati sperimentali e teorici. Ci siamo poi focalizzati sullo studio della fotoinibizione dell’enzima. Tramite esperimenti di fotoelettrochimica, in cui la proteina è stata illuminata per mezzo di laser monocromatici, una lampada alogena o una lampada allo xeno, abbiamo determinato che le FeFe idrogenasi di C. reinhardtii e C. acetobutylicum sono inattivate irreversibilmente dai raggi UVB. Utilizzando DFT e TDDFT, abbiamo concluso che le fasi iniziali della fotoinibizione consi, FeFe hydrogenases are metalloenzymes that catalyze the oxidation and production of H2. The catalytic cycle and many aspects of the reactivity of these enzymes, including their aerobic and anaerobic inactivation, are still the subjects of intense investigations. Spectroscopy is commonly used to obtain information on the electronic structure of the active site of FeFe hydrogenases, by determining the absorption of the enzyme at different wavelengths. In contrast, in this thesis, I propose to use in this context a new technique which we have called "direct photoelectrochemistry", whereby the enzyme is directly wired to an electrode which can be irradiated with a light source, and the turnover frequency is measured as a current. We can detect the absorption of the active site as a function of light wavelength and power by monitoring changes in reactivity upon irradiation. Focusing on the variations of turnover rate, we are sure that we are studying the effect of light on catalytic intermediates. I used direct photo-electrochemistry to study the effect of monochromatic irradiation in the visible range on the kinetics of inhibition by CO of three distinct FeFe hydrogenases. I determined the action spectrum of the photo-dissociation of the inhibitor CO and I described the process at the QM level for the first time, obtaining good agreement between experiments and theory. I also studied the photoinhibition of the enzyme. I carried out photoelectrochemistry experiments irradiating the protein with monochromatic visible light laser diodes, a halogen lamp or a xenon lamp, and I observed that the FeFe hydrogenases from C. reinhardtii and C. acetobutylicum are irreversibly inactivated by UVB light. Using DFT and TDDFT, I concluded that the initial steps of photoinhibition consist in the photodissociation of one carbonyl intrinsic ligand of the active site, followed by the formation of a stable inactive species. I also performed preliminary experiments to examine the effect of li

In the enzyme FeFe hydrogenase, hydrogen oxidation and production occur at the H-cluster, a Fe6S6 active site that bears intrinsic carbonyl and cyanide ligands. This enzyme has been coupled to photosensitizers to design H2 photoproduction systems, and yet, according to earlier reports, the enzyme from Desulfovibrio desulfuricans is "easily destroyed" in "normal laboratory light". Here we report direct electrochemistry measurements of the effect of light on the activity of the enzymes from Chlamydomonas reinhardtii and Clostridium acetobutylicum, together with TDDFT and DFT calculations of the reactivity of the excited states of the H-cluster. We conclude that visible light does not inhibit these enzymes, but absorption of UV-B (280-315 nm) irreversibly damages the H-cluster by triggering the release of an intrinsic CO ligand; the resulting unsaturated species rearranges and protonates to form a stable, inactive dead-end. Answering the question of which particular hydrogenase can resist which particular wavelengths is important regarding solar H2 production, and our results show that some but not all FeFe hydrogenases can actually be combined with photosensitizers that utilise the solar spectrum, provided a UV screen is used. We suggest that further investigations of the compatibility of hydrogenases or hydrogenase mimics with light-harvesting systems should also consider the possibility of irreversible photoinhibition

Electrochemical studies of hydrogenases, the biological catalysts of H2 oxidation and production, have proven wrong the old saying that enzymes do not easily transfer electrons to electrodes in the absence of mediators. Many distinct hydrogenases have actually been directly connected to electrodes or particles, for studying their catalytic mechanism or for designing solar-fuels catalysts. In this review, we list the electrodes that have proved successful for direct electron transfer to hydrogenases, and we discuss recent results which illustrate new directions in this research field: the study of the biosynthesis of FeFe hydrogenase, the electrochemical characterization of non-standard NiFe or FeFe hydrogenases, the general discussion of what makes a catalyst better in one particular direction of the reaction, and the elucidation of the molecular mechanisms of hydrogenase catalysis by combining electrochemistry and theoretical chemistry, spectroscopy or photochemistry. The electrochemical methods described herein will probably prove useful for studying or using other redox enzymes.

FeFe hydrogenases are the most efficient H2-producing enzymes. However, inactivation by O2 remains an obstacle that prevents them being used in many biotechnological devices. Here, we combine electrochemistry, site-directed mutagenesis, molecular dynamics and quantum chemical calculations to uncover the molecular mechanism of O2 diffusion within the enzyme and its reactions at the active site. We propose that the partial reversibility of the reaction with O2 results from the four-electron reduction of O2 to water. The third electron/proton transfer step is the bottleneck for water production, competing with formation of a highly reactive OH radical and hydroxylated cysteine. The rapid delivery of electrons and protons to the active site is therefore crucial to prevent the accumulation of these aggressive species during prolonged O2 exposure. These findings should provide important clues for the design of hydrogenase mutants with increased resistance to oxidative damage

FeFe hydrogenases catalyze H2 oxidation and formation at an inorganic active site (the "H-cluster"), which consists of a [Fe2(CO)3(CN)2(dithiomethylamine)] subcluster covalently attached to a Fe4S4 subcluster. This active site is photosensitive: visible light has been shown to induce the release of exogenous CO (a reversible inhibitor of the enzyme), shuffle the intrinsic CO ligands, and even destroy the H-cluster. These reactions must be understood because they may negatively impact the use of hydrogenase for the photoproduction of H2. Here, we explore in great detail the reactivity of the excited states of the H-cluster under catalytic conditions by examining, both experimentally and using TDDFT calculations, the simplest photochemical reaction: the binding and release of exogenous CO. A simple dyad model can be used to predict which excitations are active. This strategy could be used for probing other aspects of the photoreactivity of the H-cluster.

The SNCA/alpha-synuclein p.A53T mutation segregating in the Contursi kindred was the first mutation ever described in inherited Parkinson’s disease (PD).1,2 We directly examined 10 subjects (4 PD patients and 6 asymptomatic relatives) of a branch of the Contursi kindred. We also collected data on 11 members affected by history, through interviews and inspection of available medical records. Nine had died in the fourth to seventh decade diagnosed with PD (plus psychiatric features in 3), whereas 2 were reported to have severe psychiatric disturbances and were unavailable for examination. After obtaining ethics approval and written informed consent, all subjects underwent a complete neurological examination (see Video 1) and SNCA p.A53T mutation testing. The 4 PD patients (age, 4269.8 years), and 2 unaffected individuals (age, 29.562.1 years) resulted as heterozygous for the mutation. Two affected (III:1, IV:1) and 2 unaffected (IV:2, IV:6) carriers also underwent extensive neuropsychological and psychiatric assessment, olfaction evaluation, and dopamine transporter imaging with single-photon emission computed tomography (DAT-SPECT); 3T brain MRI was performed in 3 subjects (III:1, IV:2, and IV:6; Fig. 1). Although the overall phenotype in the 4 patients was typical of SNCA-related PD with early, asymmetric onset, initial good response to dopaminergic therapy and early motor complications, 3 a relevant variability was observed in the combination and severity of motor symptoms (partially responding to levodopa and DBS in III-9) and nonmotor features (Table 1). Age at onset varied from 26 to 48 years (mean, 32.7610.5), with longer disease duration than previously reported (from 2 to 19 years; mean, 9.268.5). Cognitive deficits were present in all 4 patients, ranging from frank dementia in those with longer disease duration (III-8, III-9) to moderate cognitive impairment (III-1) or slight isolated executive dysfunction (IV-1) in those with a shorter one. Depression and a