Comparative evaluation of image reconstruction methods for the siemens PET-MR scanner using the stir library

With the introduction of Positron Emission Tomography - Magnetic Resonance (PET-MR) scanners the development of new algorithms and the comparison of the performance of different iterative reconstruction algorithms and the characteristics of the reconstructed images data is relevant. In this work, we perform a quantitative assessment of the currently used ordered subset (OS) algorithms for low-counts PET-MR data taken from a Siemens Biograph mMR scanner using the Software for Tomographic Image Reconstruction (STIR, stir.sf.net). A comparison has been performed in terms of bias and coefficient of variation (CoV). Within the STIR library different algorithms are available, such as Order Subsets Expectation Maximization (OSEM), OS Maximum A Posteriori One Step Late (OSMAPOSL) with Quadratic Prior (QP) and with Median Root Prior (MRP), OS Separable Paraboloidal Surrogate (OSSPS) with QP and Filtered Back-Projection (FBP). In addition, List Mode (LM) reconstruction is available. Corrections for attenuation, scatter and random events are performed using STIR instead of using the scanner. Data from the Hoffman brain phantom are acquired, processed and reconstructed. Clinical data from the thorax of a patient have also been reconstructed with the same algorithms. The number of subsets does not appreciably affect the bias nor the coefficient of variation (CoV=11%) at a fixed sub-iteration number. The percentage relative bias and CoV maximum values for OSMAPOSL-MRP are 10% and 15% at 360 s acquisition and 12% and 15% for the 36 s, whilst for OSMAPOSL-QP they are 6% and 16% for 360 s acquisition and 11% and 23% at 36 s and for OSEM 6% and 11% for the 360 s acquisition and 10% and 15% for the 36 s. Our findings demonstrate that when it comes to low-counts, noise and bias become significant. The methodology for reconstructing Siemens mMR data with STIR is included in the CCP-PET-MR website

Modelling the mutual interactions between hydrology, society and water supply systems

We developed a simple conceptual socio-hydrological model to explore the mutual interactions between water management systems and society. We examined the feedback among climate, population, wealth and water availability and capital investment. Given the focus on the interplay among these multiple variables, some simple schemes were designated in order to simulate rainfall inputs, surface and aquifer hydrology and to mimic economic and social mechanisms. The proposed model is applied to synthetic cases in order to explore the dynamics of the water demand, water availability and water deficit that in turn influence the capital invested in water infrastructures. The results show how societal wealth, the number of people living in a given area and the local climate can determine societal efforts in exploiting water resources, the frequency of water deficits and the amount of money invested overall in infrastructures

EFFECT of PRIOR SMOOTHING on the CONVERGENCE of PROXIMAL ALGORITHMS for PET and SPECT RECONSTRUCTION

Proximal-based optimisation algorithms have been developed to be able to handle nondifferentiable functions. They have been widely studied for image reconstruction and denoising with priors such as the popular Total Variation (TV). Relatively little work has been done in evaluating their convergence performance with smooth priors that are more commonly used in emission tomography. We investigated the effect of varying the magnitude of a smoothing parameter for one image-based and one anatomical-based TV-like prior on the convergence rate of two proximal and two gradient-based algorithms for PET and SPECT reconstruction. The results suggest that the smoothness of a prior has less effect on the convergence rate for proximal algorithms than gradient-based algorithms. As expected, a smoother function results in faster convergence for gradient-based algorithms. A smoother function results in a slightly decreased convergence rate for proximal algorithms. Over-smoothing of the function resulted in under-regularisation and the breakdown of convergence observations

Geological and chemical controls in ore shoot mineralization of polymetallic veins: insights from the five-elements Ni-Co-As-Ag-Bi hydrothermal veins of SW Sardinia

Several studies on polymetallic hydrothermal veins of western Europe recently highlighted the role of physicochemical controls in determining and enhancing mineralizing processes in structurally defined, spatially limited environments (vein “ore shoots”). Host rocks have critical roles: a) the development and geometry of the structures and veins depend on their rheological features; b) they may act as sources of elements and c) regulate the type and kinetics of chemical reactions after fluid-rock interaction. An excellent example is provided in SW Sardinia by the five-elements (Ni-Co-As-Ag-Bi) veins of the Arburèse District. These late- to post-Variscan low-temperature veins are hosted in Ordovician-Silurian very low-grade metamorphic siliciclastic rocks outcropping between the Arbus granitoid (304±1 Ma) and the Mt. Linas granite (289±1 Ma). Ordovician host rocks mostly include sandstones and siltstones, while Silurian rocks are dominated by carbonaceous argillites (black shales). The distinct competence of these host rocks resulted in different geometries of spaces opened to fluid circulation, leading to the formation of orebodies with different shapes: large veins mainly occur in Ordovician sandstones and siltstones (e.g., Pira Inferida mine), while thinner, often anastomosed veins occur in Silurian black shales (e.g. Acqua Is Prunas mine). Vein formation is triggered by seismic cycles in faults at shallow crustal levels, as testified by widespread breccia and cockade textures. The ore shoots display complex mineral assemblages: native Bi; Ni-Co-Fe arsenides and antimonides (nickeline, breithauptite, rammelsbergite, safflorite, skutterudite, loellingite); Ni-Co-Fe sulfarsenides-sulfantimonides (gersdorffite, cobaltite, ullmannite, arsenopyrite); and Pb-Zn-Cu-Fe sulfides (galena, sphalerite, chalcopyrite, pyrite); Ag-Sb-As and Se sulfosalts. Carbonates (mainly siderite, minor ankerite, dolomite-calcite) and quartz are the main gangue minerals. Field, textural and analytical data support an overall rapid formation of ore minerals under multiple and distinct mineralizing pulses, starting with native elements and arsenides, followed by sulfarsenides and sulfides. Ore shoots must have formed in relatively restricted environments chemically marked by the abundant redox agents (carbonaceous matter, pyrite and, possibly, hydrocarbons) provided by Silurian black shales, which may have supplied sulfur and other elements (e.g., Se) for mineralization. Thus, differences in host rock geochemistry may explain local differences in ore shoots composition and paragenetic sequences. A further control at the district scale is represented by the repeated intersections of the five-elements vein system with earlier Mt. Linas granite-related Sn-As and W-Bi-Te-Au veins, documented in several ore shoots of the district (Pira Inferida, Acqua is Prunas and Sa Menga mines). Such intersections formed preferred pathways for fluid circulation and wider spaces for mineral precipitation during ore-forming processes; moreover, main components of five-elements ores (e.g., As, Bi) appear to be inherited by remobilization from granite-related veins. In summary, ore shoot mineralization in the studied vein system may have been controlled by multiple factors (host structures; host rock rheology and composition; intersections with other vein systems) that may be assumed as key prospection guidelines for further mineral exploration in the area; until now this vein system has only been explored in its shallower parts, and it is possible that much of the ore shoots has yet to be discovered

Bi-minerals occurrence in various ore deposits of Southern Sardinia: a short review

Bismuth is recognized as a Critical Raw Material by the EU Commission and it is found in many ore deposits across the world. In Southwestern (SWS) and Southeastern (SES) Sardinia, Bi-minerals are commonly found in two main groups of ore deposit: 1) late Variscan granite-related orebodies including greisens, W-Mo(-Sn) HT hydrothermal veins, skarns and hornfelses; and 2) late- to post- Variscan five-element (Ni-Co-As-Bi-Ag) LT hydrothermal veins. In the first group, greisens (Flumini Binu prospect, SWS) and HT hydrothermal W-Mo(-Sn) veins (Perd’e Pibera mine and Togoro prospect, SWS; Perda Majori-Bruncu Spangas prospects, SES) tipically host native Bi, bismuthinite and, subordinately, Pb-Ag-Bi-sulfosalts interstitial to molybdenite and/or scattered in the quartz-feldspar(-fluorite-topaz) gangue. Locally, maldonite (Au2Bi), Bi-tellurides (hedleyite Bi7Te3, and Bi2Te) and probable russellite (Bi2WO6) are abundant in wolframite-rich veins (Togoro prospect), associated with native Au. Small grains of native Bi have also been found in some poorly mineralized garnet-vesuvianite-epidote calc-silicate hornfelses (Domus De Maria, SWS). Besides native Bi and bismuthinite, skarn orebodies frequently host wider assemblages consisting of Bi-Pb-Ag-Cu-sulfosalts intergrowths, once again associated with wolframates (scheelite at Monte Tamara prospect and Sa Marchesa mine, SWS) and molybdenite (Monte Tamara, Sa Marchesa and Morettu prospect, SWS). As a reference, the Monte Tamara assemblage includes “phase 88.6” (Cu0.33Pb0.33Bi7.67S12), pekoite (PbCuBi11S16Se2), salzburgite-paarite (Cu1.58-1.67Fe2+ 0.03-0.01Pb1.65-1.72Bi6.38-6.3S12-12.06), gustavite (PbAgBi3S6) xilingolite-lillianite (Pb3Bi2S6), cosalite (Pb2Bi2S6), berryite (Cu3Ag2Pb3Bi7S16), ourayite (Pb4Ag3Bi5S13) and cupropavonite (Cu0.9Ag0.5Pb0.6Bi2.5S5), identified by means of EPMA analyses. Moreover, since high Bi(-Ag-Te) contents have been detected in sulfides (sphalerite, galena, arsenopyrite), micro-inclusions of -sulfosalts and/or -tellurides may also occur. In the same area, wittichenite ((Bi,Cu)2S3) and hammariite (Pb2Cu2Bi4S9) have been previously identified, while schapbachite (AgBiS2) has been reported at the Sa Marchesa mine. The second group of Bi-bearing orebodies includes the five-element veins of the Arburèse district (Pira Inferìda, Acqua Is Prunas and Sa Menga mines, SWS), where native Bi and bismuthinite tipically occur at the core of Ni-Co arsenides-sulfarsenides (e.g. nickeline and gersdorffite-cobaltite) concentric growths. Therefore, the strong affinity of bismuth for granite-related W-Mo(-Sn) deposits of Southern Sardinia indicates that the late-Variscan (Early Permian) granites represent its main metallogenic source. However, the formation of such diverse Bi-minerals assemblages is seemingly controlled by local-scale conditions. In skarn ores, the Bi-Pb-Ag-Cu-sulfosalts intergrowths formed during the sulfide stages, apparently after the interaction between primary Bi-phases and Pb-Ag-Cu-bearing hydrothermal fluids and under oscillatory variations of metals availability and stability. Conversely, in W-Mo(-Sn) hydrothermal veins and greisens, where sulfides are apparently more scarce, the array of Bi-phases is usually more limited. Furthermore, field and analytical data point towards a selective remobilization of bismuth from the primary native and -tellurides assemblage of HT wolframite-quartz veins (Togoro, SWS) by late cross-cutting LT five-element veins, suggesting that multiple, spaced over time hydrothermal-veining events occurred in the same area. In conclusion, bismuth and related mineral phases could serve as important markers, providing useful qualitative indications regarding the source of metals, the ore-forming processes and the relationships between different ore deposits at the district-scale

Factors affecting adherence to guidelines for antithrombotic therapy in elderly patients with atrial fibrillation admitted to internal medicine wards

Current guidelines for ischemic stroke prevention in atrial fibrillation or flutter (AFF) recommend Vitamin K antagonists (VKAs) for patients at high-intermediate risk and aspirin for those at intermediate-low risk. The cost-effectiveness of these treatments was demonstrated also in elderly patients. However, there are several reports that emphasize the underuse of pharmacological prophylaxis of cardio-embolism in patients with AFF in different health care settings. AIMS: To evaluate the adherence to current guidelines on cardio-embolic prophylaxis in elderly (> 65 years old) patients admitted with an established diagnosis of AFF to the Italian internal medicine wards participating in REPOSI registry, a project on polypathologies/polytherapies stemming from the collaboration between the Italian Society of Internal Medicine and the Mario Negri Institute of Pharmacological Research; to investigate whether or not hospitalization had an impact on guidelines adherence; to test the role of possible modifiers of VKAs prescription. METHODS: We retrospectively analyzed registry data collected from January to December 2008 and assessed the prevalence of patients with AFF at admission and the prevalence of risk factors for cardio-embolism. After stratifying the patients according to their CHADS(2) score the percentage of appropriateness of antithrombotic therapy prescription was evaluated both at admission and at discharge. Univariable and multivariable logistic regression models were employed to verify whether or not socio-demographic (age >80years, living alone) and clinical features (previous or recent bleeding, cranio-facial trauma, cancer, dementia) modified the frequency and modalities of antithrombotic drugs prescription at admission and discharge. RESULTS: Among the 1332 REPOSI patients, 247 were admitted with AFF. At admission, CHADS(2) score was ≥ 2 in 68.4% of patients, at discharge in 75.9%. Among patients with AFF 26.5% at admission and 32.8% at discharge were not on any antithrombotic therapy, and 43.7% at admission and 40.9% at discharge were not taking an appropriate therapy according to the CHADS(2) score. The higher the level of cardio-embolic risk the higher was the percentage of antiplatelet- but not of VKAs-treated patients. At admission or at discharge, both at univariable and at multivariable logistic regression, only an age >80 years and a diagnosis of cancer, previous or active, had a statistically significant negative effect on VKAs prescription. Moreover, only a positive history of bleeding events (past or present) was independently associated to no VKA prescription at discharge in patients who were on VKA therapy at admission. If heparin was considered as an appropriate therapy for patients with indication for VKAs, the percentage of patients admitted or discharged on appropriate therapy became respectively 43.7% and 53.4%. CONCLUSION: Among elderly patients admitted with a diagnosis of AFF to internal medicine wards, an appropriate antithrombotic prophylaxis was taken by less than 50%, with an underuse of VKAs prescription independently of the level of cardio-embolic risk. Hospitalization did not improve the adherence to guideline

Importance of plants with extremely small populations (Psesps) in endemic-rich areas, elements often forgotten in conservation strategies

The distribution of the threatened fern Ophioglossum vulgatum L., a plant with extremely small populations (PSESPs) in Sardinia, is characterized by small disjunct populations with only a few individuals, and little is known about its status in the wild. To provide information for the conservation of O. vulgatum and with the aim to develop an in situ conservation strategy, we investigated its distribution, population size, and habitat. Field surveys confirmed that the species grows in only five localities. Two representative populations were selected for this study (Funtanamela and Gedili), and in each population, all plants were mapped and monitored monthly from April to August over an 8-year period. During the study, the populations had a very low number of reproductive plants and the populations appeared to be in decline, with the total number of plants per population slightly decreased in Gedili while a sharp reduction was recorded in Funtanamela due to wild boar threat. A fence was built in order to protect the site from further damage, but no noticeable signals of recovery were observed. The most urgent conservation requirement for this species is to preserve the threatened habitat of the remnant populations. Further field surveys and research are also required for an improved understanding of the species’ status

Analysis of rainfall seasonality from observations and climate models

Two new indicators of rainfall seasonality based on information entropy, the relative entropy (RE) and the dimensionless seasonality index (DSI), together with the mean annual rainfall, are evaluated on a global scale for recently updated precipitation gridded datasets and for historical simulations from coupled atmosphere--ocean general circulation models. The RE provides a measure of the number of wet months and, for precipitation regimes featuring a distinct wet and dry season, it is directly related to the duration of the wet season. The DSI combines the rainfall intensity with its degree of seasonality and it is an indicator of the extent of the global monsoon region. We show that the RE and the DSI are fairly independent of the time resolution of the precipitation data, thereby allowing objective metrics for model intercomparison and ranking. Regions with different precipitation regimes are classified and characterized in terms of RE and DSI. Comparison of different land observational datasets reveals substantial difference in their local representation of seasonality. It is shown that two-dimensional maps of RE provide an easy way to compare rainfall seasonality from various datasets and to determine areas of interest. Models participating to the Coupled Model Intercomparison Project platform, Phase 5, consistently overestimate the RE over tropical Latin America and underestimate it in West Africa, western Mexico and East Asia. It is demonstrated that positive RE biases in a general circulation model are associated with excessively peaked monthly precipitation fractions, too large during the wet months and too small in the months preceding and following the wet season; negative biases are instead due, in most cases, to an excess of rainfall during the premonsoonal months