Littérature scientifique sur le sujet « Few clusters »

In linear regression analysis, the estimator of the variance of the estimator of the regression coefficients should take into account the clustered nature of the data, if present, since using the standard textbook formula will in that case lead to a severe downward bias in the standard errors. This idea of a cluster-robust variance estimator (CRVE) generalizes to clusters the classical heteroskedasticity-robust estimator. Its justification is asymptotic in the number of clusters. Although an improvement, a considerable bias could remain when the number of clusters is low, the more so when regressors are correlated within cluster. In order to address these issues, two improved methods were proposed; one method, which we call CR2VE, was based on biased reduced linearization, while the other, CR3VE, can be seen as a jackknife estimator. The latter is unbiased under very strict conditions, in particular equal cluster size. To relax this condition, we introduce in this paper CR3VE-λ, a generalization of CR3VE where the cluster size is allowed to vary freely between clusters. We illustrate the performance of CR3VE-λ through simulations and we show that, especially when cluster sizes vary widely, it can outperform the other commonly used estimators.

Background Post-acute sequelae of COVID-19 (PASC) includes a heterogeneous group of patients with variable symptomatology, who may respond to different therapeutic interventions. Identifying phenotypes of PASC and therapeutic strategies for different subgroups would be a major step forward in management. Methods In a prospective cohort study of patients hospitalized with COVID-19, 12-month symptoms and quantitative outcome metrics were collected. Unsupervised hierarchical cluster analyses were performed to identify patients with: (1) similar symptoms lasting ≥4 weeks after acute SARS-CoV-2 infection, and (2) similar therapeutic interventions. Logistic regression analyses were used to evaluate the association of these symptom and therapy clusters with quantitative 12-month outcome metrics (modified Rankin Scale, Barthel Index, NIH NeuroQoL). Results Among 242 patients, 122 (50%) reported ≥1 PASC symptom (median 3, IQR 1–5) lasting a median of 12-months (range 1–15) post-COVID diagnosis. Cluster analysis generated three symptom groups: Cluster1 had few symptoms (most commonly headache); Cluster2 had many symptoms including high levels of anxiety and depression; and Cluster3 primarily included shortness of breath, headache and cognitive symptoms. Cluster1 received few therapeutic interventions (OR 2.6, 95% CI 1.1–5.9), Cluster2 received several interventions, including antidepressants, anti-anxiety medications and psychological therapy (OR 15.7, 95% CI 4.1–59.7) and Cluster3 primarily received physical and occupational therapy (OR 3.1, 95%CI 1.3–7.1). The most severely affected patients (Symptom Cluster 2) had higher rates of disability (worse modified Rankin scores), worse NeuroQoL measures of anxiety, depression, fatigue and sleep disorder, and a higher number of stressors (all P<0.05). 100% of those who received a treatment strategy that included psychiatric therapies reported symptom improvement, compared to 97% who received primarily physical/occupational therapy, and 83% who received few interventions (P = 0.042). Conclusions We identified three clinically relevant PASC symptom-based phenotypes, which received different therapeutic interventions with varying response rates. These data may be helpful in tailoring individual treatment programs.

ABSTRACT The initial sizes and masses of massive star clusters provide information about the cluster formation process and also determine how cluster populations are modified and destroyed, which have implications for using clusters as tracers of galaxy assembly. Young massive cluster populations are often assumed to be unchanged since cluster formation; therefore, their distributions of masses and radii are used as the initial values. However, the first few hundred million years of cluster evolution does change both cluster mass and cluster radius, through both internal and external processes. In this paper, we use a large suite of N-body cluster simulations in an appropriate tidal field to determine the best initial mass and initial size distributions of young clusters in the nearby galaxy M83. We find that the initial masses follow a power-law distribution with a slope of −2.7 ± 0.4 , and the half-mass radii follow a lognormal distribution with a mean of 2.57 ± 0.04 pc and a dispersion of 1.59 ± 0.01 pc. The corresponding initial projected half-light radius function has a mean of 2.7 ± 0.3 pc and a dispersion of 1.7 ± 0.2 pc. The evolution of the initial mass and size distribution functions is consistent with mass-loss and expansion due to stellar evolution, independent of the external tidal field and the cluster’s initial density profile. Observed cluster sizes and masses should not be used as the initial values, even when clusters are only a few hundred million years old.

Cluster randomized trials involving participants nested within intact treatment and control groups are commonly performed in various educational, psychological, and biomedical studies. However, recruiting and retaining intact groups present various practical, financial, and logistical challenges to evaluators and often, cluster randomized trials are performed with a low number of clusters (~20 groups). Although multilevel models are often used to analyze nested data, researchers may be concerned of potentially biased results due to having only a few groups under study. Cluster bootstrapping has been suggested as an alternative procedure when analyzing clustered data though it has seen very little use in educational and psychological studies. Using a Monte Carlo simulation that varied the number of clusters, average cluster size, and intraclass correlations, we compared standard errors using cluster bootstrapping with those derived using ordinary least squares regression and multilevel models. Results indicate that cluster bootstrapping, though more computationally demanding, can be used as an alternative procedure for the analysis of clustered data when treatment effects at the group level are of primary interest. Supplementary material showing how to perform cluster bootstrapped regressions using R is also provided.

Industrial clusters have received considerable attention as a regional development strategy. While their efficacy has been debated by academics, clusters have become popular among practitioners. Despite clusters’ acceptance, there have been few attempts to measure their success or their impact on constituent firms. This paper outlines and discusses the metrics developed to evaluate the success of the northwest Ohio greenhouse cluster. The cluster was launched in 2004 to help the industry become more competitive though collaborative problem solving. In identifying success metrics, the authors were cognizant of the fact that they had to reflect the cluster’s objectives and goals. Thus metrics that measured the impact of branding and marketing efforts, reducing energy costs, and increasing collaboration among cluster stakeholders were developed. The work reported in this paper is only the beginning phases of a longer-term, on-going effort to track the progress and success of the northwest Ohio greenhouse cluster.

Highly-densified Fe cluster-assembled films were obtained at room temperature by an energetic cluster deposition. Fe clusters were produced using a plasma-gas-condensation (PGC)-type cluster deposition apparatus with a high cluster productivity. Ionized clusters in a cluster beam were electrically accelerated and directly deposited onto a substrate together with neutral clusters from the same cluster source. By increasing the impact energy of the ionized clusters up to about 1 eV/atom, the obtained cluster-assemblies have packing fractions higher than 0.8 without any serious size change, and result in a soft magnetic behavior up to a frequency range of few hundred MHz.

Few-atom silver clusters are fluorophores with a set of attractive properties including sub-nanometer size, high quantum yield and large Stokes shift. Sharing high photostability with semiconductor quantum dots but being of much smaller size, lacking blinking and with expected lack of toxicity, they are especially attractive for biological imaging, down to single molecules. No less promising are their applications in chemical sensing and biosensing as well as for molecular optic and electronic devices on a single molecular level. We demonstrate that it is not a unique property of water that can provide the formation and stability of silver clusters. They can be produced on photoreduction in different organic solvents using the same polymeric template. Unique photophysical properties of these clusters share both similarities and differences to that of organic dyes. When you are citing the document, use the following link http://essuir.sumdu.edu.ua/handle/123456789/35122

Differents clusters mixtes trinucleaires a un ou deux ligands bis(diphenyl)phosphinomethane (dppm) de curs fer-bis platine, platine-bis fer ou palladium-bis fer, sont obtenus par reaction de complexes mononucleaires du platine ou du palladium au degre d'oxydation deux avec des mono- ou dianons carbonylates du fer. Ces reactions ont egalement ete etudiees avec certaines phosphines tertiaires monodentes. Le tetracarbonylferrate disodique reagit avec les composes dinucleaires a deux ligands dppm, palladium-palladium ou platine-palladium pour former selectivement le cluster trinucleaire correspondant a deux ligands dppm. Parmi ceux-ci, le cluster de cur fer-palladium-platine presente une isomerisation remarquable due a la migration d'un ligand dppm autour du squelette metallique. Les structures moleculaires de trois clusters ont ete determinees par diffraction des rayons x (collaboration prof. Y. Dusausoy (nancy), prof. H. Vahrenkamp et dr. R. Planalp (fribourg, all. )

In this thesis we present the results of our simulation studies of iron sulphide minerals, with focus on bulk, surface and cluster chemistry. DFT+U calculations were employed to study the mineral greigite (Fe3S4), which has important implications in Origin of Life theories. Using a combination of DFT and Monte Carlo methods, we were able to explore the probable cation distribution of Ni-doped greigite over the two available lattice sites (tetrahedral and octahedral) at varying concentrations, as well as calculate the enthalpy of mixing and thus deduce at what concentration of Ni this mineral would be most stable. Results showed that within the lattice, site occupation by Ni will be concentration-dependent, whilst violarite, FeNi2S4, is likely to be the most stable (Fe,Ni)S phase. The (001), (011), and (111) surfaces of violarite, both naked and in the presence of water, were investigated next, using a combination of DFT-D2+U methods. The (001) was found to be the most stable surface, whilst the (011) the most reactive with respect to water. The adsorption and dissociation of water on the surfaces also revealed a synergistic effect, whereby the adsorption of one water has a conducive effect on the adsorption of the next. CPMD simulations were then conducted on the following hydrated ions: Fe2+, Fe3+ and S2-, and on the following systems, FexSy (x,y≤ 4), to investigate the structural and dynamical properties in water. Calculation of the Gibbs free energies (ΔGaq) revealed that the formation of FexSy clusters with x,y ≤2 will not only be in competition with the formation of iron hydroxides, but is also temperature-dependent.

Reactivite des complexes fe::(3)(co)::(9)(cch::(3))(coc::(2)h::(5)) ou fe::(3)(co)::(10)(cch::(3))(h). Les reactions de couplage des groupes alkylidynes avec les algues sont faciles. L'action de co a mis en evidence le couplage reversible dans des conditions douces de 2 fragments alkylidynes. En general, la presence du coordinat hydruro rend les reactions plus complexes

FeS clusters are ancient prosthetic groups, widely diffused in almost all living beings in which they are involved in several fundamental metabolic pathways, including redox reactions, electron transfer, enzyme catalysis and many other functions. This assortment is reflected in the presence of several FeS clusters with different structures, from the simple rhombic 2Fe2S and cubic 4Fe4S clusters, to the highly complex 2Fe[4Fe4S] H-cluster (metal cofactor of [FeFe]-hydrogenases). Distinct biosynthetic pathways for the assembly of different FeS clusters exist, in both prokaryotic and eukaryotic microorganisms. In general, these are rather complex processes carried out by many proteins interacting with each other. While keeping some key peculiarities, these systems are highly conserved in terms of action strategy, which can be generally divided in two main steps: the assembly of the metal cofactor on a scaffold protein, and the subsequent transfer of the de novo generated FeS cluster from the scaffold to the acceptor apoprotein, which is eventually converted into the mature active holoprotein. Both steps require key scaffold proteins, that must be able to dynamically interact with the biosynthetic partners as well as with a combination of several chaperones and co-chaperones which participate into the final transfer of the prosthetic group to the recipient FeS protein. Thus, the structural features of scaffold proteins allowing their interactions with all the functional partners are key points. However, for many of these fundamental proteins a clear structure-function relationship characterization is missing, and a complete characterization of the whole complex multistep molecular pathways in which they are functionally involved need a deeper investigation. In this PhD thesis, two different FeS clusters biosynthetic systems have been studied: in Chapter 1), the [FeFe]-hydrogenases maturation system and in Chapter 2), the human mitochondrial FeS clusters biosynthetic system. Chapter 1) [FeFe]-hydrogenases are FeS proteins that in several prokaryotes as well as in unicellular green algae catalyze the reversible reduction of protons to hydrogen gas. Thus, they received an increasing attention for potential technological applications in the field of biological production of clean and renewable fuel. A specific and highly conserved biosynthetic system is required to assemble the complex [FeFe]-hydrogenases FeS cluster, the so-called H-cluster, which is composed by a 4Fe4S center linked to a 2Fe subcluster coordinated by CO and CN- ligands as well as to a bridging dithiolate. Despite the high complexity of this cofactor, its biosynthesis and transfer is carried out by only three specific proteins, working in combination with the FeS cluster housekeeping biogenesis machinery: HydE and HydG assemble the H-cluster on the scaffold protein HydF, a small GTPase which also drives the delivery of the complete cluster to the target apohydrogenase. Thus, HydF plays a central double role of FeS cluster scaffold and carrier protein in [FeFe]-hydrogenases maturation. Although several molecular and functional data have been obtained since the discovery of the HydE/HydF/HydG machinery, the whole biosynthetic process is still not completely characterized. The crystal structure of a recombinant HydF apoprotein was solved in my laboratory and suggested useful molecular insights into the protein function. On the other hand, several open issues remained, including the specific role of the HydF GTPase domain, which is essential for the [FeFe]-hydrogenase maturation and activation. Chapter 2). In mammals, FeS clusters are mainly present and synthetized in mitochondria. Their assembly is performed by a complex and highly conserved system involving several proteins. Among them, ISCU is the scaffold upon which FeS clusters are assembled at the so called SDU, which also includes the desulfurase NFS1, the accessory protein ISD11, and frataxin (FXN). FXN is an iron-binding protein (Fe2+ and Fe3+) whose specific role in this biosynthetic pathway is still controversial, as it was first proposed to be the iron donor of the process, and then an allosteric activator of the SDU complex. In humans, defects of both ISCU or FXN lead to diseases with distinct clinical phenotypes but similar cellular and biochemical features. Decreased levels of ISCU mitochondrial isoform caused by a point mutation of the ISCU gene lead to a rare myopathy with lactic acidosis (ISCU myopathy); decreased levels of FXN, due to an abnormal expansion of GAA trinucleotide repeat in the FXN gene, cause Friedreich’s Ataxia (FRDA), a neurodegenerative disorder. Cellular hallmarks of both diseases are compromised respiration, mitochondrial iron overload and increased sensitivity to oxidative stress, and for both a specific therapy is still missing. This may be due, at least in part, to an incomplete characterization of the pathway(s) in which these proteins are involved, and in particular it is worth to note that FXN is a protein still looking for a function. Based on these premises, I focused the work of my PhD on these two open issues by taking advantage, in both cases, of a combination of biochemical and spectroscopic approaches to assess structural features of 1) HydF GTPase domain and 2) FXN, both alone and in binary complex with the scaffold ISCU. In particular, to explore the HydF protein and its structural response to GTP binding, in collaboration with Prof. Carbonera (Department of Chemical Sciences Padova, University of Padova), I exploited an advanced spectroscopic technique, EPR (Electron Paramagnetic Resonance), that is the ultimate technique for the study of FeS proteins; to characterize into detail the FXN-ISCU direct interaction, I applied the two-dimensional NMR (Nuclear Magnetic Resonance) technique, in collaboration with Prof. Bellanda (Department of Chemical Sciences, University of Padova). Chapter 1). I carried out in vitro spectroscopic studies to characterize the HydF GTPase domain. The obtained results allowed me to conclude that HydF can be considered as a novel member of the K+-dependent GTPases. Thus, these proteins may have a larger spread of functions than supposed before. HydF could be a molecular switch undergoing significant structural modifications upon GTP binding, as other members of the same family. Moreover, diffuse conformational changes due to GTP binding were detected, and this could be pivotal for dynamic structural and functional interactions with the other proteins involved in [FeFe]-hydrogenase maturation and activation. Starting from this discovery, it will be possible to model the GTP-bound state of HydF, an important structural information which was missing in the X-ray structure of the apoprotein previously solved in our laboratory. Chapter 2). I performed biochemical and spectroscopic analysis of human FXN, alone and in complex with ISCU, that allowed me to identify in FXN the residues involved in the binding of Fe3+/2+ and in its interaction with ISCU, which a confirmed to be iron-dependent. Then, since many FXN residues that I found to be involved in the direct interaction with ISCU are mutated in patients with variants of FRDA, I evaluated if and how these mutations can interfere with ISCU-FXN direct interaction and with its capability to bind iron. I found that FRDA-related frataxin variants in which mutations are located in ISCU-binding region do not affect frataxin iron-binding properties, while impairing both the interaction with ISCU and the ability to activate the SDU complex. Other FRDA related frataxin variants, instead, in which mutations are located in the iron-binding region or between the latter and ISCU-binding region, affect, as expected, the capability of FXN to bind iron while not completely impairing its interaction with ISCU. Moreover, these FXN variants keep a partial capability to activate SDU complex. Taken together, these results open new perspectives in the study of the mechanisms leading to FRDA variants, and give additional hints useful to clarify the physiological role of FXN as well as its contribution to the pathogenesis of Friedreich’s ataxia.
I gruppi di FeS sono gruppi protesici ancestrali, ampiamente diffusi in quasi tutti gli esseri viventi in cui sono coinvolti in diverse vie metaboliche fondamentali, tra cui reazioni redox, trasferimento di elettroni, catalisi enzimatica e molte altre funzioni. Questo assortimento si riflette nella presenza di numerosi cluster FeS con diverse strutture, dai semplici cluster rombici 2Fe2S e 4Fe4S cubici, al complesso cluster 2Fe [4Fe4S] H (cofattore metallico di [FeFe] -idrogenasi). Esistono percorsi biosintetici distinti per l'assemblaggio di diversi gruppi di FeS, sia nei microrganismi procarioti che negli eucarioti. In generale, questi sono processi piuttosto complessi realizzati da molte proteine ​​che interagiscono tra loro. Pur mantenendo alcune peculiarità chiave, questi sistemi sono altamente conservati in termini di strategia d'azione, che può essere generalmente suddivisa in due fasi principali: l'assemblaggio del cofattore metallico su una proteina scaffold e il successivo trasferimento del cluster FeS de novo generato da l'impalcatura dell'apoproteina dell'accettore, che alla fine viene convertita nell'oloproteina attiva matura. Entrambi i passaggi richiedono proteine ​​chiave dello scaffold, che devono essere in grado di interagire dinamicamente con i partner biosintetici e con una combinazione di diversi chaperon e co-chaperon che partecipano al trasferimento finale del gruppo protesico alla proteina FeS ricevente. Pertanto, le caratteristiche strutturali delle proteine ​​dello scaffold che consentono le loro interazioni con tutti i partner funzionali sono punti chiave. Tuttavia, per molte di queste proteine ​​fondamentali manca una chiara caratterizzazione delle relazioni struttura-funzione, e una caratterizzazione completa dell'intero complesso percorso molecolare multistep in cui sono coinvolte funzionalmente necessita di un'indagine più approfondita. In questa tesi di dottorato, sono stati studiati due diversi sistemi di biosintesi di cluster FeS: nel Capitolo 1, il sistema di maturazione [FeFe] -idrogenasi e nel Capitolo 2), il FeS mitocondriale umano raggruppa il sistema biosintetico. Capitolo 1) [FeFe] -idrogenasi sono proteine ​​FeS che in diversi procarioti e in alghe verdi unicellulari catalizzano la riduzione reversibile dei protoni al gas idrogeno. Pertanto, hanno ricevuto una crescente attenzione per le potenziali applicazioni tecnologiche nel campo della produzione biologica di carburante pulito e rinnovabile. È necessario un sistema biosintetico specifico e altamente conservato per assemblare il cluster FeS (FeFe) -idrogenasi complesso, il cosiddetto cluster H, composto da un centro 4Fe4S collegato a un subcluster 2Fe coordinato da CO e ligandi CN quanto a un ponte ditiolato. Nonostante l'elevata complessità di questo cofattore, la sua biosintesi e trasferimento sono effettuati da sole tre proteine ​​specifiche, che funzionano in combinazione con il meccanismo di biogenesi del cluster FeS: HydE e HydG assemblano l'H-cluster sulla proteina scaffold HydF, una piccola GTPase che guida anche la consegna del cluster completo alla apoidrogenasi bersaglio. Pertanto, HydF svolge un duplice ruolo centrale nello scaffold di cluster FeS e nella proteina carrier nella maturazione di [FeFe] -idrogenasi. Sebbene diversi dati molecolari e funzionali siano stati ottenuti dalla scoperta dei macchinari HydE / HydF / HydG, l'intero processo biosintetico non è ancora completamente caratterizzato. La struttura cristallina dell' apoproteina ricombinante HydF è stata risolta nel mio laboratorio e ha suggerito utili informazioni molecolari sulla funzione proteica. D'altra parte, sono rimasti alcune questioni aperte, incluso il ruolo specifico del dominio GTPasico di HydF, che è essenziale per la maturazione e l'attivazione di [FeFe] -idrogenasi. Capitolo 2). Nei mammiferi, i cluster di FeS sono principalmente presenti e sintetizzati nei mitocondri. Il loro assemblaggio viene eseguito da un sistema complesso e altamente conservato che coinvolge diverse proteine. Tra questi, l'ISCU è lo scaffold su cui sono sintetizzati i cluster FeS nel cosiddetto SDU, che include anche la desulfurase NFS1, la proteina accessoria ISD11 e la fratassina (FXN). FXN è una proteina legante il ferro (Fe2 + e Fe3 +) il cui ruolo specifico in questo percorso biosintetico è ancora controverso, in quanto è stato inizialmente proposto come donatore di ferro del processo e quindi attivatore allosterico del complesso SDU. Negli esseri umani, i difetti di ISCU o FXN portano a malattie con fenotipi clinici distinti ma caratteristiche cellulari e biochimiche simili. Diminuzione dei livelli di isoforme mitocondriale ISCU causata da una mutazione puntiforme del gene ISCU portano a una rara miopatia con acidosi lattica (miopatia ISCU); livelli diminuiti di FXN, a causa di un'anomala espansione della ripetizione del trinucleotide GAA nel gene FXN, causano l'atassia di Friedreich (FRDA), una malattia neurodegenerativa. Le caratteristiche cellulari di entrambe le malattie sono la respirazione compromessa, il sovraccarico di ferro mitocondriale e l'aumento della sensibilità allo stress ossidativo, e per entrambi una terapia specifica è ancora mancante. Ciò può essere dovuto, almeno in parte, a una caratterizzazione incompleta del / i percorso / i in cui sono coinvolte queste proteine, e in particolare vale la pena notare che FXN è una proteina che sta ancora cercando una funzione. Sulla base di queste premesse, ho focalizzato il lavoro del mio dottorato su questi due problemi aperti sfruttando, in entrambi i casi, una combinazione di approcci biochimici e spettroscopici per valutare le caratteristiche strutturali di 1) dominio GTPase di HydF e 2) FXN, entrambi soli e nel complesso binario con l'impalcatura ISCU. In particolare, per esplorare la proteina HydF e la sua risposta strutturale al legame GTP, in collaborazione con il Prof. Carbonera (Dipartimento di Scienze Chimiche di Padova, Università di Padova), ho sfruttato una tecnica spettroscopica avanzata, EPR (Electron Paramagnetic Resonance), cioè la tecnica definitiva per lo studio delle proteine ​​FeS; per caratterizzare in dettaglio l'interazione diretta FXN-ISCU, ho applicato la tecnica bidimensionale NMR (Nuclear Magnetic Resonance), in collaborazione con il Prof. Bellanda (Dipartimento di Scienze Chimiche, Università di Padova). Capitolo 1). Ho effettuato studi spettroscopici in vitro per caratterizzare il dominio GTPasico di HydF. I risultati ottenuti mi hanno permesso di concludere che HydF può essere considerato un nuovo membro delle GTPasi dipendenti da K +. Pertanto, queste proteine ​​potrebbero avere una più ampia diffusione di funzioni rispetto a quanto supposto prima. HydF potrebbe essere un interruttore molecolare sottoposto a significative modifiche strutturali sul legame GTP, come altri membri della stessa famiglia. Inoltre, sono stati rilevati cambiamenti conformazionali diffusi dovuti al legame GTP, e questo potrebbe essere cruciale per interazioni strutturali e funzionali dinamiche con le altre proteine ​​coinvolte nella maturazione e attivazione di [FeFe] -idrogenasi. A partire da questa scoperta, sarà possibile modellare lo stato di HydF legato a GTP, un'importante informazione strutturale che mancava nella struttura a raggi X dell'apoproteina precedentemente risolta nel nostro laboratorio. Capitolo 2). Ho eseguito analisi biochimiche e spettroscopiche di FXN umana, da solo e in complesso con ISCU, che mi ha permesso di identificare in FXN i residui coinvolti nel legame di Fe3 + / 2 + e nella sua interazione con ISCU, che è confermato essere dipendente dal ferro . Quindi, poiché molti residui di FXN che ho trovato coinvolti nell'interazione diretta con ISCU sono mutati in pazienti con varianti di FRDA, ho valutato se e come queste mutazioni possono interferire con l'interazione diretta ISCU-FXN e con la sua capacità di legare il ferro. Ho trovato che le varianti di fratassina FRDA-correlate in cui le mutazioni si trovano nella regione di legame ISCU non influenzano le proprietà di legame con ferro di fratassina, mentre compromettono sia l'interazione con ISCU e la capacità di attivare il complesso SDU. Altre varianti di fratassina legate a FRDA, invece, in cui le mutazioni sono localizzate nella regione di legame del ferro o tra quest'ultima e la regione legante ISCU, influenzano, come previsto, la capacità di FXN di legare il ferro senza compromettere completamente la sua interazione con ISCU. Inoltre, queste varianti FXN mantengono una capacità parziale di attivare il complesso SDU. Presi insieme, questi risultati aprono nuove prospettive nello studio dei meccanismi che portano alle varianti FRDA e forniscono ulteriori suggerimenti utili a chiarire il ruolo fisiologico di FXN e il suo contributo alla patogenesi dell'atassia di Friedreich.

The aim of this work was to unravel the molecular basis of the connection of mitochondrial and cytosolic FeS assembly. Following on from previous work showing that the mitochondrial ABC-transporter ATM3 is required for cytosolic FeS assembly (Bernard et al., 2009), one part of my project was to provide in-vivo evidence for the substrate of ATM3. I found that the mitochondrial glutathione pool in atm3 seedlings is shifted towards oxidation, indicating accumulation of oxidised glutathione. Furthermore I showed that ATM3 genetically interacts with two enzymes involved in persulfide metabolism (ETHE1, NFS1). This complemented invitro studies by Dr. Schaedler (Schaedler et al., 2014) who showed that oxidised glutathione is a preferred substrate and glutathione carrying additional S0 can be transported by yeast Atm1. To gather further insight into biosynthesis of the ATM3 substrate I investigated the role of a cytosolic and a mitochondrial glutaredoxin (GRXS17, GRXS15). Mutants had minor but specific effects on FeS enzymes and I concluded that the glutaredoxins are not generally involved in de-novo cluster assembly. Another approach was to identify unknown components of mitochondrial-cytosolic persulfide transport. I characterised two mutants with phenotypic resemblance to atm3 mutants. For one, I located a point mutation in the sequence of ATM3 leading to an amino acid exchange in the 6th transmembrane domain and showed that the ATM3 protein was lacking. The second line was a mutant of CNX2, a mitochondrial enzyme necessary for generation of the first MoCo intermediate cPMP. I found ATM3 protein breakdown in cnx2-2 and in a mutant of CNX5 which is involved in MoCo assembly and t-RNA thiomodification. ATM3 was previously suggested to export cPMP (Teschner et al., 2010). My findings give new evidence for a link between ATM3 and MoCo assembly.

Les complexes carbeniques fe#2(co)#7c(r)c(net#2) reagissent avec des ligands organiques insatures. Les complexes formes avec les alcynes rccr(r=net#2; c#2r) resultant d'une insertion dans la fonction fe=c, presentent une structure pyramide pentagonale nido qui peut conduire a des complexes closo de type tripledecker par ajout d'un fragment fe(co)#2. Le passage nido-closo se fait sans modification du couplage. Dans le cas r=c#2r, la triple liaison libre permet de construire des complexes tetranucleaires. Le phosphaalcyne rcp conduit a un couplage c-p par insertion dans le carbene pontant. Avec les heterocumulenes x=c=y, deux types de comportement sont observes, soit une addition de la molecule intacte sur le complexe pour donner des derives de type metallacycle, soit une fragmentation de cette molecule suivie de l'insertion de l'un des fragments dans l'une des fonctions carbeniques. Lorsque, x=y=nc#6h#4me, ces deux possibilites ont ete mises en evidence. Dans le cas rn=c=y, le comportement depend de la nature de l'atome y. Si y=o, aucune fragmentation n'a ete observee. Si y=s ou se, les produits majoritaires resultent de la rupture de la liaison c=y suivie de l'insertion de l'atome y. Phn=s=o subit une double fragmentation, le fragment nitrene phn s'insere dans le carbene terminal, l'atome de souffre s'insere dans le carbene pontant. Ces differentes reactions conduisent a un ensemble de complexes qui tous sont decrits par la theorie psep. Ils s'inscrivent dans des deltaedres a n sommets. La disponibilite du doublet de l'azote du groupe net#2 modifie la geometrie attendue du complexe

Dans le cadre de ce travail de thèse, la polymérisation de type RAFT a été exploitée pour synthétiser des particules de latex magnétiques décorées de polymères stimulables. Cinq (co)polymères hydrophiles ont tout d'abord été préparés via la (co)polymérisation RAFT en solution d'acide acrylique (AA) et de méthacrylate de 2-diméthylaminoéthyle (MADAME). Les agents macromoléculaires obtenus (macroRAFT) : des homopolymères de PAA ou PMADAME ainsi que des copolymères P(AA-co-MADAME), présentent une sensibilité au pH et à la température. Ces macroRAFT hydrophiles ont ensuite été utilisés dans des réactions d’extension de chaîne avec du styrène conduisant à la formation de copolymères à blocs amphiphiles bien définis. Puis, des dispersions aqueuses d’agrégats (clusters) de nanoparticules d’oxyde de fer (OF) ont ensuite été préparées via un procédé de mini-émulsification/évaporation de solvant, en utilisant les copolymères à blocs comme stabilisants. Après optimisation des conditions expérimentales (sonication, concentration de macroRAFT, pH), des agrégats de taille contrôlée (45 à 300 nm) ont pu être obtenus. Ces clusters ont ensuite été utilisés comme semence lors de la polymérisation en émulsion du styrène, conduite en présence d’un agent de réticulation. Les clusters d'OF ont été individuellement encapsulés par une couche de polymère, formant des particules magnétiques stabilisées par le segment hydrophile des copolymères à blocs. Enfin, les particules magnétiques décorées de copolymères de P(AA-co-MADAME) ont été utilisées avec succès pour la capture et le relargage de bactéries grâce à la modulation de leurs propriétés de surface en fonction du pH
In this work reversible addition-fragmentation chain transfer (RAFT) polymerization was exploited to synthesize magnetic latex particles decorated with stimuli-responsive polymer brushes. First, five hydrophilic (co)polymers with various compositions were successfully prepared by RAFT solution (co)polymerization of acrylic acid (AA) and 2-dimethylaminoethyl methacrylate (DMAEMA) for different AA to DMAEMA molar ratios. The obtained macromolecular RAFT agents (macroRAFTs), PAA or PDMAEMA homopolymers and P(AA-co-DMAEMA) copolymers, displayed interesting pH- and thermo-responsive properties. These hydrophilic macroRAFTs were then chain extended with styrene leading to the formation of well-defined amphiphilic block copolymers. An aqueous dispersion of iron oxide clusters was next prepared using a strategy based on emulsification/solvent evaporation in which the block copolymers were used as stabilizers. By varying the experimental conditions (sonication power, macroRAFT concentration and pH of the medium), the cluster size could be controlled from 45 up to 300 nm. These clusters were then used as seeds in styrene emulsion polymerization in the presence of a crosslinker. The iron oxide clusters were individually encapsulated into a polymer shell generating latex particles, stabilized by the hydrophilic segment of the block copolymers, and displaying interesting magnetic properties. At last, these magnetic beads were evaluated as carriers in the magnetic separation of bacteria. The magnetic latex particles decorated with P(AA-co-DMAEMA) copolymers were successfully employed for the capture and trigger release of bacteria, allowing their concentration in a biological sample

Helium clusters containing a few thousand monomers, formed from a sonic nozzle at 15 K, are doped with SF6 molecules that they pick up in a scattering box containing this gas at partial pressures of 10−5 to 10−4 Torr. The IR spectrum of the doped clusters is obtained by line tunable CO2 laser excitation of the SF6 and bolometric detection of the photoevaporated helium atoms. If the clusters contain a single SF6 molecule, the spectrum shows two absorptions located at 945.8 cm−1 and 946.1 cm−1, which indicates that the SF6 molecule is located in an anisotropic environment, i.e., near the surface of the cluster. If the cluster contains two SF6 molecules, the spectrum of the SF6 dimer is recovered and found to be very narrow, as appropriate to the very low temperature of the medium in which the spectrum is taken (~0.4 K). The linear and quadratic dependence of the spectral intensities of, respectively, the monomer and the dimer features allows for an independent confirmation of the average cluster size.

The emission process of polyatomic species, in particular the sputtering of metal-adsorbate molecules and metal clusters, has very recently been studied to an increasing extent theoretically and experimentally [1-5]. However, due to the small fraction of sputttered clusters, relatively few experimental data are available at present. The interest in metal clusters arises primarily because metal clusters exhibit a strong potential as catalysts and they represent an intermediate state between atoms and metals. Often already metal clusters, build up of relatively few constituents, show features close to metals.

In this paper, we propose a statistical model for relevance-dependent biclustering to analyze relational data. The proposed model factorizes relational data into bicluster structure with two features: (1) each object in a cluster has a relevance value, which indicates how strongly the object relates to the cluster and (2) all clusters are related to at least one dense block. These features simplify the task of understanding the meaning of each cluster because only a few highly relevant objects need to be inspected. We introduced the Relevance-Dependent Bernoulli Distribution (R-BD) as a prior for relevance-dependent binary matrices and proposed the novel Relevance-Dependent Infinite Biclustering (R-IB) model, which automatically estimates the number of clusters. Posterior inference can be performed efficiently using a collapsed Gibbs sampler because the parameters of the R-IB model can be fully marginalized out. Experimental results show that the R-IB extracts more essential bicluster structure with better computational efficiency than conventional models. We further observed that the biclustering results obtained by R-IB facilitate interpretation of the meaning of each cluster.

Abstract The last few years have witnessed researches concerned by vertical axis wind turbine (VAWT) performance considering its advantages compared to the horizontal axis wind turbines, as it can be operated in urban areas without producing noise, ease of maintenance and simple construction, in addition to its low cost. More interest is growing in developing efficient clusters of VAWT in order to increase power generation at specific sites by using multiple turbines. In the present work, the performance of various configurations of Darrieus type VAWT clusters is examined using computational fluid dynamics (CFD) simulations. The objective of this work is to increase the overall power coefficient of the turbines cluster compared to single rotor performance. This objective shall be achieved by examining mutual interactions between rotors arranged in close proximity and examining the effect of oblique angle between rotors on overall performance of the cluster of rotors. The performance is assessed by observing the overall power coefficient of the cluster. Also, the velocity wake of the simulated three rotors turbine cases was analyzed and compared to the that of the single rotor.

As clusters of state-of-the-art instruments and research enablement services, research cores are not only the cornerstone of research activities at university campuses but also critical assets that provide competitive differentiation for their host institutions. However, these research cores are highly expensive for academic institutions to manage. Despite the growing recognition and impact of these research cores, there are few studies that describe the business models for sustaining and funding research cores or their increasing significance to the larger academic community.

In road mitigation systems characterized by multiple wildlife crossing structures (CS) and multiple-focal species, these species-specific design criteria are important to meeting management goals. CS types and locations are fixed in place and cannot be manipulated experimentally; long term studies may offer the best chance to inform evidence-based designs for new CS projects in the future. Long-term data from Banff National Park are uniquely posed to answer these critical questions. More recently, highway mitigation along US93 in Montana provides an additional case study with which to understand the responses of large animals to different CS designs. The purpose of this study is to identify factors affecting movement of large mammals through CS using data sets from both mitigation projects. Year-round monitoring of CS use was used in an analytical framework to address questions regarding species-specific and community level use of CS; design and habitat factors that best explain species-specific variation; and whether importance of design parameters changes over time. Over the 17 years of the Banff study, and the six years of the Montana study, CS facilitated over 200,000 crossing events at 55 locations. There were significant changes in annual crossing events over time. Variables associated with CS passage rates were species specific, but aligned with a few clusters of preference. With the exception of coyotes, all large carnivore species preferred open span bridges or overpasses to other CS types. In Montana, fencing was positively associated with passage rates for black bears and cougars. We found that wider CS tend to be preferred by most species, irrespective of their location. We also found that wider CS tend to have shorter ‘adaptation’ curves than narrower ones for grizzly bears, coyotes, cougars, and moose. Depending on the heterogeneity of the landscape near the highway, more CS may not create more crossing opportunities if local habitat conditions do not favor animals’ access to the road. At the scale of ecological communities, the flows of mass and energy are likely enough to alter the distribution of ecological processes in the Banff and Montana ecosystems. Our results highlight the value of long-term monitoring for assessing the effectiveness of mitigation measures. Our work confirms the species-specific nature of measure CS performance, leading to our primary recommendation that a diversity of CS designs be considered an essential part of a well-designed mitigation system for the large mammals of western North America. Short-term monitoring efforts may fail to accurately portray the ecological benefits of mitigation for populations and ecological communities. Our results will help to inform design and aid in the establishment of robust, long-term performance measures.

experimental methods for quantifying effects of water content and other dynamic environmental factors on bacterial growth in partially-saturated soils. Towards this end we reviewed critically the relevant scientific literature and performed theoretical and experimental studies of bacterial growth and activity in modeled, idealized and real unsaturated soils. The natural wetting-drying cycles common to agricultural soils affect water content and liquid organization resulting in fragmentation of aquatic habitats and limit hydraulic connections. Consequently, substrate diffusion pathways to soil microbial communities become limiting and reduce nutrient fluxes, microbial growth, and mobility. Key elements that govern the extent and manifestation of such ubiquitous interactions include characteristics of diffusion pathways and pore space, the timing, duration, and extent of environmental perturbations, the nature of microbiological adjustments (short-term and longterm), and spatial distribution and properties of EPS clusters (microcolonies). Of these key elements we have chosen to focus on a manageable subset namely on modeling microbial growth and coexistence on simple rough surfaces, and experiments on bacterial growth in variably saturated sand samples and columns. Our extensive review paper providing a definitive “snap-shot” of present scientific understanding of microbial behavior in unsaturated soils revealed a lack of modeling tools that are essential for enhanced predictability of microbial processes in soils. We therefore embarked on two pronged approach of development of simple microbial growth models based on diffusion-reaction principles to incorporate key controls for microbial activity in soils such as diffusion coefficients and temporal variations in soil water content (and related substrate diffusion rates), and development of new methodologies in support of experiments on microbial growth in simple and observable porous media under controlled water status conditions. Experimental efforts led to a series of microbial growth experiments in granular media under variable saturation and ambient conditions, and introduction of atomic force microscopy (AFM) and confocal scanning laser microscopy (CSLM) to study cell size, morphology and multi-cell arrangement at a high resolution from growth experiments in various porous media. The modeling efforts elucidated important links between unsaturated conditions and microbial coexistence which is believed to support the unparallel diversity found in soils. We examined the role of spatial and temporal variation in hydration conditions (such as exist in agricultural soils) on local growth rates and on interactions between two competing microbial species. Interestingly, the complexity of soil spaces and aquatic niches are necessary for supporting a rich microbial diversity and the wide array of microbial functions in unsaturated soils. This project supported collaboration between soil physicists and soil microbiologist that is absolutely essential for making progress in both disciplines. It provided a few basic tools (models, parameterization) for guiding future experiments and for gathering key information necessary for prediction of biological processes in agricultural soils. The project sparked a series of ongoing studies (at DTU and EPFL and in the ARO) into effects of soil hydration dynamics on microbial survival strategy under short term and prolonged desiccation (important for general scientific and agricultural applications).

Five stocks of tilapia [oreochromis niloticus (on), red O. niloticus (ROn), O. aureus (Oa), O. mossambicus (Om), and Sarotherodon galilaeus (Sg)] were used to produce two-way (F1), three-way (3WC) and four-way crosses (4WC). Three 4WC groups, containing equal representation of all four species, formed the base population for a new synthetic stock, called an "artificial center of origin" (ACO). Four genomic maps were created using microsatellite and AFLP markers, two from a 3WC family [Om female and (Oa x ROn) male] and two from a 4WC family [(Om x Oas) females and (Sg x On) male]. Sixty-two loci segregating from the female parent of the 3WC mapped to 14 linkage groups while 214 loci from the male parent mapped to 24 linkage groups. Similarly, 131 loci segregating from the female parent of the 4WC mapped to 26 linkage groups and 118 loci from the male parent mapped to 25 linkage groups. Preliminary screening of an F2 and a 4WC family identified a number of loci associated with cold tolerance and body weight. These loci were clustered in a few linkage groups, suggesting they may be indicative of quantitative trait loci.

We built a collector to filter interplanetary dust particles (IDPs) larger than 5 µm from the clean air at the Amundsen Scott South Pole station. Our sampling strategy used long duration, continuous dry filtering of near-surface air in place of short duration, high-speed impact collection on flags flown in the stratosphere. We filtered ~107 m³ of clean Antarctic air through 20 cm diameter, 3 µm filters coupled to a suction blower of modest power consumption (5–6 kW). Our collector ran continuously for 2 years and yielded 41 filters for analyses. Based on stratospheric concentrations, we predicted that each month’s collection would provide 300–900 IDPs for analysis. We identified 19 extraterrestrial (ET) particles on the 66 cm² of filter examined, which represented ~0.5% of the exposed filter surfaces. The 11 ET particles larger than 5 µm yield about a fifth of the expected flux based on >5 µm stratospheric ET particle flux. Of the 19 ET particles identified, four were chondritic porous IDPs, seven were FeNiS beads, two were FeNi grains, and six were chondritic material with FeNiS components. Most were <10 µm in diameter and none were cluster particles. Additionally, a carbon-rich candidate particle was found to have a small ¹⁵N isotopic enrichment, supporting an ET origin. Many other candidate grains, including chondritic glasses and C-rich particles with Mg and Si and FeS grains, require further analysis to determine if they are ET. The vast majority of exposed filter surfaces remain to be examined.

In September 2006 an outbreak of 'Bluetongue like' disease struck the cattle herds in Israel. Over 100 dairy and beef cattle herds were affected. Epizootic hemorrhagic disease virus (EHDV) (an Orbivirusclosely related to bluetongue virus (BTV)), was isolated from samples collected from several herds during the outbreaks. Following are the aims of the study and summary of the results: which up until now were published in 6 articles in peer-reviewed journals. Three more articles are still under preparation: 1. To identify the origin of the virus: The virus identified was fully sequenced and compared with the sequences available in the GenBank. It appeared that while gene segment L2 was clustered with EHDV-7 isolated in Australia, most of the other segments were clustered with EHDV-6 isolates from South-Africa and Bahrain. This may suggest that the strain which affected Israel on 2006 may have been related to similar outbreaks which occurred in north-Africa at the same year and could also be a result of reassortment with an Australian strain (Wilson et al. article in preparation). Analysis of the serological results from Israel demonstrated that cows and calves were similarly positive as opposed to BTV for which seropositivity in cows was significantly higher than in calves. This finding also supports the hypothesis that the 2006 EHD outbreak in Israel was an incursive event and the virus was not present in Israel before this outbreak (Kedmi et al. Veterinary Journal, 2011) 2. To identify the vectors of this virus: In the US, Culicoides sonorensis was found as an efficient vector of EHDV as the virus was transmitted by midges fed on infected white tailed deer (WTD; Odocoileusvirginianus) to susceptible WTD (Ruder et al. Parasites and Vectors, 2012). We also examined the effect of temperature on replication of EHDV-7 in C. sonorensis and demonstrated that the time to detection of potentially competent midges decreased with increasing temperature (Ruder et al. in preparation). Although multiple attempts were made, we failed to evaluate wild-caught Culicoidesinsignisas a potential vector for EHDV-7; however, our finding that C. sonorensis is a competent vector is far more significant because this species is widespread in the U.S. As for Israeli Culicoides spp. the main species caught near farms affected during the outbreaks were C. imicolaand C. oxystoma. The vector competence studies performed in Israel were in a smaller scale than in the US due to lack of a laboratory colony of these species and due to lack of facilities to infect animals with vector borne diseases. However, we found both species to be susceptible for infection by EHDV. For C. oxystoma, 1/3 of the Culicoidesinfected were positive 11 days post feeding. 3. To identify the host and environmental factors influencing the level of exposure to EHDV, its spread and its associated morbidity: Analysis of the cattle morbidity in Israel showed that the disease resulted in an average loss of over 200 kg milk per cow in herds affected during September 2006 and 1.42% excess mortality in heavily infected herds (Kedmi et al. Journal of Dairy Science, 2010). Outbreak investigation showed that winds played a significant role in virus spread during the 2006 outbreak (Kedmi et al. Preventive Veterinary Medicine, 2010). Further studies showed that both sheep (Kedmi et al. Veterinary Microbiology, 2011) and wild ruminants did not play a significant role in virus spread in Israel (Kedmi et al. article in preparation). Clinical studies in WTD showed that this species is highly susceptibile to EHDV-7 infection and disease (Ruder et al. Journal of Wildlife Diseases, 2012). Experimental infection of Holstein cattle (cows and calves) yielded subclinical viremia (Ruder et al. in preparation). The findings of this study, which resulted in 6 articles, published in peer reviewed journals and 4 more articles which are in preparation, contributed to the dairy industry in Israel by defining the main factors associated with disease spread and assessment of disease impact. In the US, we demonstrated that sufficient conditions exist for potential virus establishment if EHDV-7 were introduced. The significant knowledge gained through this study will enable better decision making regarding prevention and control measures for EHDV and similar viruses, such as BTV.

Original objectives The general goal of the project was to utilize the bactericidal potential of curcumin- functionalizednanostructures (CFN) for reinforcement of food safety by developing active antimicrobial food-contact surfaces. In order to reach the goal, the following secondary tasks were pursued: (a) further enhancement of the CFN activity based on understanding their mode of action; (b) preparing efficient antimicrobial surfaces, investigating and optimizing their performance; (c) testing the efficacy of the antimicrobial surfaces in real food trials. Background to the topic The project dealt with reducing microbial food spoilage and safety hazards. Cross-contamination through food-contact surfaces is one of the major safety concerns, aggravated by bacterial biofilm formation. The project implemented nanotech methods to develop novel antimicrobial food-contact materials based on natural compounds. Food-grade phenylpropanoidcurcumin was chosen as the most promising active principle for this research. Major conclusions, solutions, achievements In agreement with the original plan, the following research tasks were performed. Optimization of particles structure and composition. Three types of curcumin-functionalizednanostructures were developed and tested: liposome-type polydiacetylenenanovesicles, surface- stabilized nanoparticles and methyl-β-cyclodextrin inclusion complexes (MBCD). The three types had similar minimal inhibitory concentration but different mode of action. Nanovesicles and inclusion complexes were bactericidal while the nanoparticlesbacteriostatic. The difference might be due to different paths of curcumin penetration into bacterial cell. Enhancing the antimicrobial efficacy of CFN by photosensitization. Light exposure strengthened the bactericidal efficacy of curcumin-MBCD inclusion complexes approximately three-fold and enhanced the bacterial death on curcumin-coated plastic surfaces. Investigating the mode of action of CFN. Toxicoproteomic study revealed oxidative stress in curcumin-treated cells of E. coli. In the dark, this effect was alleviated by cellular adaptive responses. Under light, the enhanced ROS burst overrode the cellular adaptive mechanisms, disrupted the iron metabolism and synthesis of Fe-S clusters, eventually leading to cell death. Developing industrially-feasible methods of binding CFN to food-contact surfaces. CFN binding methods were developed for various substrates: covalent binding (binding nanovesicles to glass, plastic and metal), sonochemical impregnation (binding nanoparticles to plastics) and electrostatic layer-by-layer coating (binding inclusion complexes to glass and plastics). Investigating the performance of CFN-coated surfaces. Flexible and rigid plastic materials and glass coated with CFN demonstrated bactericidal activity towards Gram-negative (E. coli) and Gram-positive (Bac. cereus) bacteria. In addition, CFN-impregnated plastic material inhibited bacterial attachment and biofilm development. Testing the efficacy of CFN in food preservation trials. Efficient cold pasteurization of tender coconut water inoculated with E. coli and Listeriamonocytogeneswas performed by circulation through a column filled with CFN-coated glass beads. Combination of curcumin coating with blue light prevented bacterial cross contamination of fresh-cut melons through plastic surfaces contaminated with E. coli or Bac. licheniformis. Furthermore, coating of strawberries with CFN reduced fruit spoilage during simulated transportation extending the shelf life by 2-3 days. Implications, both scientific and agricultural BARD Report - Project4680 Page 2 of 17 Antimicrobial food-contact nanomaterials based on natural active principles will preserve food quality and ensure safety. Understanding mode of antimicrobial action of curcumin will allow enhancing its dark efficacy, e.g. by targeting the microbial cellular adaptation mechanisms.