Fe Ka line emission from the Arches cluster region - evidence for ongoing particle bombardment?

We present the results of eight years of XMM-Newton observations of the region surrounding the Arches cluster in the Galactic Center. We study the spatial distribution and temporal behaviour of the Fe-Ka line emission with the objective of identifying the likely source of the excitation. We investigate the variability of the 6.4-keV line emission of four clouds through spectral fitting of the EPIC MOS data with the use of a modelled background, which avoids many of the systematics inherent in local background subtraction. We also employ spectral stacking of both EPIC PN and MOS data to search for evidence of an Fe-K edge feature imprinted on the underlying X-ray continuum. The lightcurves of the Fe-Ka line from three bright molecular knots close to the Arches cluster are found to be constant over the 8-year observation window. West of the cluster, however, we found a bright cloud exhibiting the fastest Fe-Ka variability yet seen in a molecular cloud in the Galactic Center region. The time-averaged spectra of the molecular clouds reveal no convincing evidence of the 7.1-keV edge feature. The EW of the 6.4-keV line emitted by the clouds near the cluster is found to be ~1.0 keV. The observed Fe-Ka line flux and the high EW suggest the fluorescence has a photoionization origin, although excitation by cosmic-ray particles is not specifically excluded. For the three clouds nearest to the cluster, an identification of the source of photo-ionizing photons with an earlier outburst of Sgr A* is however at best tentative. The hardness of the nonthermal component associated with the 6.4-keV line emission might be best explained in terms of bombardment by cosmic-ray particles from the Arches cluster itself. The relatively short-timescale variability seen in the 6.4-keV line emission from the cloud to the West of the cluster is most likely the result of illumination by a nearby transient X-ray source.Comment: 13 pages, 6 figures, accepted for publication in Astronomy and Astrophysic

Effectiveness of the spot-on combination of moxidectin and imidacloprid (Advocate®) in the treatment of ocular thelaziosis by Thelazia callipaeda in naturally infected cats

Background: The present study evaluated the therapeutic effectiveness of moxidectin 1.0% (w/v) and imidacloprid 10% (w/v) (Advocate® spot-on solution for cats, Bayer Animal Health) against natural infections with the eyeworm Thelazia callipaeda in cats. This study was conducted as a GCP, negative-controlled, blinded and randomised field study in privately owned cats living in an area in southern Italy where T. callipaeda is enzootic. Methods: The study was carried out in 30 cats (19 females and 11 males, aged from 8 months to 5 years, weighing 1.2-5.2 kg) of different breeds, naturally infected by T. callipaeda. At study inclusion (Day 0), animals were physically examined and the infection level was assessed by examination of both eyes for clinical score and live adult T. callipaeda count. Each cat was weighed and randomly assigned to one of the treatment groups (G1: Advocate, G2: untreated control). Clinical assessments and T. callipaeda adult counts were performed on Day 14. At the study completion visit on Day 28, clinical assessments and counts of T. callipaeda adults and larvae were performed. All cats were daily observed by their owners and general health conditions were recorded during the entire period of the study. Results: The primary effectiveness variable was the percentage of animals in G1 group (Advocate) showing a complete elimination (parasitological cure) of adult eye worms at Day 14 and Day 28. The effectiveness of the treatment in the G1 group was 93.3 and 100% at Day 14 and Day 28, respectively, when compared to group G2. Total worm count reduction from both eyes for Advocate was 96.3% on Day 14 and 100% on Day 28. Clinical data were confirmed by the examination of conjunctival pouch flushing. An overall reduction in the number of cats with lacrimation and conjunctivitis was observed following treatment despite the fact that in a few cats treated with Advocate clinical signs persisted due to the chronic nature of the disease. Conclusions: Based on the results of the present trial, a single dose of Advocate was found to be safe and highly effective in the treatment of natural T. callipaeda infection in cats

Evolution of frustrated and stabilising contacts in reconstructed ancient proteins

Energetic properties of a protein are a major determinant of its evolutionary fitness. Using a reconstruction algorithm, dating the reconstructed proteins and calculating the interaction network between their amino acids through a coevolutionary approach, we studied how the interactions that stabilise 890 proteins, belonging to five families, evolved for billions of years. In particular, we focused our attention on the network of most strongly attractive contacts and on that of poorly optimised, frustrated contacts. Our results support the idea that the cluster of most attractive interactions extends its size along evolutionary time, but from the data, we cannot conclude that protein stability or that the degree of frustration tends always to decrease

COMPUTATIONAL MODELING OF PROTEINS: FROM STATISTICAL MECHANICS TO IMMUNOLOGY

One of the biggest revolutions occurred during the second half of the 20th century in physics was the introduction of computers in research. In particular, the use of fast computing machines opened the possibility to study complex systems by simulating their dynamics, without the need to pursue analytical solutions, otherwise impossible to tackle. The consequences of this breakthrough were huge both in the study of equilibrium and non-equilibrium many-body problems, with the strong limitation given by the number of atoms involved in the calculation. The first technique used in biology-related problems was the Monte Carlo Method, and some years later Molecular Dynamics (MD) was formalized. In MD, for each atom of the system one can solve its Newton equations of motion, obtaining a trajectory in the phase space for the entire system, and study its behavior in equilibrium and non-equilibrium conditions. The constant rise in computational power gave the possibility to scientists to study larger and larger systems, while the advances in experimental techniques enhanced the possibility for direct comparisons between wet and in silico data at similar levels of resolution. Despite the validity of Moore\u2019s Law (i.e., the exponential growth of the computing power due to transistors miniaturization) until now, the timescale of the events that can be simulated has an upper limit of the millisecond with tailor-made computers, which is not enough to study all the biologically-relevant phenomena. Since the birth of computational chemistry, a huge number of different statistical mechanics-based methods has been implemented to permit, given the computing power limit, an effective reliable use of MD simulations in biochemistry. One of the most relevant problems tackled by MD is the calculation of free energy differences, both in conformational changes and in sequence mutations of a protein. The main reason of this difficulty is represented by the frustrated nature of interactions in proteins and the size of these systems: this leads to a complex energy landscape which in principle needs very long sampling times to overcome all possible energy barriers. In the present thesis, we studied and improved a path-independent and system-independent free energy calculation technique, called Simplified Confinement Method. We describe this work in Chapter 1. Although MD has been successful in most of its applications, there are still many open problems: as mentioned before, the available parametrizations of interaction potentials (called force fields) are not completely reliable. In particular, the choice of force field parameters is performed comparing experimental data on a fixed set of (usually small) molecules with computed data on the same molecules. This raises a significant problem: large molecules can have a more complex behavior, and using these potentials can lead to a systematic error; furthermore, the timescale in which the force field is tested needs to be limited. Another strong limitation of MD depends on the equilibrium experiments used for parametrization: the kinetic properties of a system are not considered. Given the impossibility to reparametrize a general force field with non-equilibrium experimental data, we implemented a technique that uses equilibrium-based force fields, adding a potential term based on time series resulting from kinetic experiments. This approach, based on the principle of Maximum Caliber, restrains the system with an experimental-based bias, returning a more realistic behavior of the simulation in condition where the usual force fields show their limitations. We describe this work in Chapter 2. The application of computational methods in the study of proteins confirms its efficacy in other fields of life sciences: an actual and emerging topic is represented by vaccinology. With techniques developed by Louis Pasteur at the end of the 19 th century (isolation of the pathogen, its inactivation and subsequent inoculation in the host), various scientists developed vaccines for deadly diseases like poliomyelitis, diphterite and measles. None of the mentioned was developed with molecular biology-based approaches. Almost 50 years after the birth of molecular biology, the Human Genome Project decoded human DNA and, at the same time, the genome of the most dangerous pathogen was screened. This has laid the foundation of Reverse Vaccinology (RV), where the proteins responsible for immune reaction can be identified from the pathogen DNA and tested directly on animal models, obtaining a new vaccine candidate with little or no risk for the host, having removed the pathogen itself. At the beginning of the 21st century the first vaccine against Meningococcus B, responsible for the 50% of the meningococcal meningitis, was developed using this protocol. Since then, crystallographic data was inserted in RV workflow to exploit conformational data, creating the so-called Structural Vaccinology (SV). To enhance its efficacy, SV exploits all the aspects of molecular modeling like computer-aided drug/protein design and MD to integrate information that come from experimental sources. One of the most promising technique in this field is the grafting of an immunogenic sequence (i.e., a portion of a protein recognized by the immune system) on a foreign protein; this approach could lead to a new vaccine component which have no risk for the patient. To date, the grafting technique has been carried out by human-driven workflows. Motivated by this reason, we studied immunogenic peptides from a family of pathogens involved in respiratory diseases, exploiting Structural Vaccinology principles with both computational and experimental approach. Furthermore, we developed and implemented an unsupervisionated automated tool to design grafted protein sequences. We describe this work in Chapter 3

The X-ray lightcurve of Sgr A* over the past 150 years inferred from Fe-Ka line reverberation in Galactic Centre molecular clouds

We examine the temporal and spectral properties of nine Fe-Ka bright molecular clouds within about 30 pc of Sgr A*, in order to understand and constrain the primary energising source of the Fe fluorescence. Significant Fe-Ka variability was detected, with a spatial and temporal pattern consistent with that reported in previous studies. The main breakthrough that sets our paper apart from earlier contributions on this topic is the direct measurement of the column density and the Fe abundance of the MCs in our sample. We used the EW measurements to infer the average Fe abundance within the clouds to be 1.6$\pm$0.1 times solar. The cloud column densities derived from the spectral analysis were typically of the order of 10$^{23}$ cm$^{-2}$, which is significantly higher than previous estimates. This in turn has a significant impact on the inferred geometry and time delays within the cloud system. Past X-ray activity of Sgr A* is the most likely source of ionisation within the molecular clouds in the innermost 30 pc of the Galaxy. In this scenario, the X-ray luminosity required to excite these reflection nebulae is of the order of 10$^{37}-10^{38}$ erg s$^{-1}$, significantly lower than that estimated for the Sgr B2 molecular cloud. Moreover, the inferred Sgr A* lightcurve over the past 150 years shows a long-term downwards trend punctuated by occasional counter-trend brightening episodes of at least 5 years duration. Finally, we found that contributions to the Fe fluorescence by X-ray transient binaries and cosmic-ray bombardment are very likely, and suggest possible ways to study this latter phenomenon in the near future.Comment: 23 pages, 14 figures, accepted for publication in Astronomy & Astrophysic

Structural transition in Fe ultrathin epitaxial films grown on Ni(111)

A structural study of Fe ultrathin epitaxial films, grown at room temperature on Ni(111), has been performed in the 1.5-18 ML coverage range by angle-scanned photoelectron diffraction. Both backscattering and forward-scattering energy regimes have been employed, in order to enhance the structural sensitivity at lower and higher film thicknesses, respectively. Modeling of the experimental data has been performed with multiple scattering calculations. We found indications that Fe atoms in the first layer occupy fcc hollow sites and stack with a pseudomorphic fcc structure up to 2 ML. Concerning the growth mode at these early stages, data suggest that a good substrate wetting and a sharp Fe/Ni interface take place. Between 3 and 6 ML, transition to a bcc(110) phase develops. By quantitative R-factor analysis, we found that Nishiyama-Wassermann (NW) in-plane orientation of the bcc(110) cell ((bcc)parallel to(fcc)) is favored over the Kurdjumov-Sachs ((bcc)parallel to(fcc)) orientation. The best-fit vertical interlayer distance between bcc(110) planes is d(NW)=2.11 Angstrom (+3.9% expansion) at 6 ML and relaxes to d(NW)=2.05 Angstrom (+1.0%) at 18 ML, in agreement with the angular shift observed for the forward-focusing features. In the same coverage range, the angle between bcc(110) surface basis vectors changes from 67.7degrees to 69.0degrees, corresponding to -1.7% and -1.0% contractions of the surface cell area, respectively

A neutron scattering study of the interplay between structure and magnetism in Ba(Fe1−x_{1-x}Cox_{x})2_2As2_2

Single crystal neutron diffraction is used to investigate the magnetic and structural phase diagram of the electron doped superconductor Ba(Fe$_{1-x}$Co$_x$)$_2$As$_2$. Heat capacity and resistivity measurements have demonstrated that Co doping this system splits the combined antiferromagnetic and structural transition present in BaFe$_2$As$_2$ into two distinct transitions. For $x$=0.025, we find that the upper transition is between the high-temperature tetragonal and low-temperature orthorhombic structures with ($T_{\mathrm{TO}}=99 \pm 0.5$ K) and the antiferromagnetic transition occurs at $T_{\mathrm{AF}}=93 \pm 0.5$ K. We find that doping rapidly suppresses the antiferromagnetism, with antiferromagnetic order disappearing at $x \approx 0.055$. However, there is a region of co-existence of antiferromagnetism and superconductivity. The effect of the antiferromagnetic transition can be seen in the temperature dependence of the structural Bragg peaks from both neutron scattering and x-ray diffraction. We infer from this that there is strong coupling between the antiferromagnetism and the crystal lattice

Ceramic production and raw materials in the Tuscan-Ligurian region: an archaeological and petrographic approach in a diachronic perspective

This contribute focuses on the history of ceramic production of a large geographic area from the archaeological point of view encompassing Liguria and N-W Tuscany and using a petro-archaeometrical approach ( essentially based on thin-section analyses of more than a thousand of samples)

Design and fabrication of 3D-printed anatomically shaped lumbar cage for intervertebra disc (IVD) degeneration treatment

Spinal fusion is the gold standard surgical procedure for degenerative spinal conditions when conservative therapies have been unsuccessful in rehabilitation of patients. Novel strategies are required to improve biocompatibility and osseointegration of traditionally used materials for lumbar cages. Furthermore, new design and technologies are needed to bridge the gap due to the shortage of optimal implant sizes to fill the intervertebral disc defect. Within this context, additive manufacturing technology presents an excellent opportunity to fabricate ergonomic shape medical implants. The goal of this study is to design and manufacture a 3D-printed lumbar cage for lumbar interbody fusion. Optimisations of the proposed implant design and its printing parameters were achieved via in silico analysis. The final construct was characterised via scanning electron microscopy, contact angle, x-ray micro computed tomography (μCT), atomic force microscopy, and compressive test. Preliminary in vitro cell culture tests such as morphological assessment and metabolic activities were performed to access biocompatibility of 3D-printed constructs. Results of in silico analysis provided a useful platform to test preliminary cage design and to find an optimal value of filling density for 3D printing process. Surface characterisation confirmed a uniform coating of nHAp with nanoscale topography. Mechanical evaluation showed mechanical properties of final cage design similar to that of trabecular bone. Preliminary cell culture results showed promising results in terms of cell growth and activity confirming biocompatibility of constructs. Thus for the first time, design optimisation based on computational and experimental analysis combined with the 3D-printing technique for intervertebral fusion cage has been reported in a single study. 3D-printing is a promising technique for medical applications and this study paves the way for future development of customised implants in spinal surgical applications