Data intensive scientific analysis with grid computing

At the end of September 2009, a new Italian GPS receiver for radio occultation was launched from the Satish Dhawan Space Center (Sriharikota, India) on the Indian Remote Sensing OCEANSAT-2 satellite. The Italian Space Agency has established a set of Italian universities and research centers to implement the overall processing radio occultation chain. After a brief description of the adopted algorithms, which can be used to characterize the temperature, pressure and humidity, the contribution will focus on a method for automatic processing these data, based on the use of a distributed architecture. This paper aims at being a possible application of grid computing for scientific research

Carotid beta stiffness association with thyroid function

Background: Thyroid hormone modulation of cardiovascular function has been associated with cardiovascular disease. Recent evidence suggests that free thyroxine (FT4) levels are associated with an increase in systemic arterial stiffness, but little is known about the effects of FT4 at the local level of the common carotid artery. β-stiffness index is a local elastic parameter usually determined by carotid ultrasound imaging. Methods: We conducted a cross-sectional analysis in the ProgeNIA cohort, including 4846 subjects across a broad age range. For the purpose of this study, we excluded subjects with increased thyrotropin (TSH) levels and those treated with levothyroxine or thyrostatic. We assessed β stiffness, strain, wall–lumen ratio, carotid cross-sectional area (CSA), and stress and flow in the right common carotid artery. We tested whether FT4, heart rate, and their interactions were associated with carotid parameters. Results: FT4 was positively and independently associated with β stiffness index (β = 0.026, p = 0.041), and had a negative association with strain (β = −0.025, p = 0.009). After adding heart rate and the interaction between FT4 and heart rate to the model, FT4 was still associated with the β stiffness index (β = 0.186, p = 0.06), heart rate was positively associated with the stiffness index (β = 0.389, p < 0.001) as well as their interaction (β = 0.271, p = 0.007). Conclusion: This study suggests that higher FT4 levels increase arterial stiffness at the common carotid level, consistent with a detrimental effect on elastic arteries. The effect of FT4 is likely to be primarily attributable to its effect on heart rate

Software Defined Radio system for GNSS-Refectometry: activities performed at the Politecnico of Turin (Italy)

The GNSS signals are an important active source for Earth’s remote sensing in L band. Experiments performed over sea and land surfaces demonstrated the capability of GNSS-Reflected signals (GNSS-R) for remote sensing purposes. Presently, many research groups are focusing their efforts in developing GNSS-R sensors for soil moisture, sea, sea-ice, and snow cover monitoring. Applications like drought monitoring, farm production, irrigation planning, flood protection, fire prevention, and meteorological forecasts can take advantage from retrieved soil moisture content. Detected sea-surface winds could help to identify adverse meteorological conditions far from coastal zones. Sea altimetry measurements could be used to monitor tides and to identify natural hazards (i.e. tsunamis). Sea-ice topographic changes in the Arctic and Antarctic regions and dry ice stratification could be monitored in order to improve polar climatology knowledge. Recently the Remote Sensing Group of Politecnico of Turin and NavSAS laboratory of ISMB (Istituto Superiore Mario Boella) starts the design and implementation of a fully reconfigurable GNSS-R instrument for research activities, following a Software Defined Radio approach. Using this solution, the hardware is reduced to the RF stages only (i.e. antennas, demodulation, sampling) and the processing starts from the IF (Intermediate Frequency) samples of the raw signal. This is a low-cost portable observing system, designed to be easily placed for example also on board small aircrafts (also unmanned). In this sense, the system components were carefully chosen to minimize size and weight of the complete observing system. Together with the system definition, a user interface is started to be developed. Actually the interface allows a quasi real time control of the received signal. The correct estimation of the whole correlation function profile (in range and frequency space) is achieved by keeping the noise level as low as possible and increasing the SNR. Therefore, it is important to optimally process signals even when long - non coherent integration time is necessary. The interface we developed is able to process such signals using FFT (Fast Fourier Transform) based acquisition algorithms. In addition, an optimized procedure is implemented to compensate for a residual code delay, enhancing the detection of weak signals. The interface allows also experimental activities planning, since it shows specular reflection points and isorange lines (inside receiver antenna’s footprint), computed knowing estimated or predicted satellite positions. All the information are georeferenced using UTM (Universal Transverse Mercator) coordinate system and projected on Google© static maps. Thus, this user friendly interface is a helpful tool able to generate all the necessary output for the geophysical applications performed exploiting GNSS-R signals. In order to test instrument and interface, some experimental activities were recently done by placing the instrument on a high cliff to collect some looks from the sea surface and on board an aircraft to collects measurements from soil reflections (rice fields water flooding, soil moisture, altimetry). Another important activity is to adapt our GNSS-R system for space-based measurements in the framework of an educational project which is being carried out by students belonging to the Aerospace and ICT Engineering faculties of Politecnico of Turin. This student project is going to be developed in the framework of an initiative offered by the Education Office of the European Space Agency. We are trying to design and develop on a system level a space-based test bed for an Earth’s Remote Sensing payload to be placed on-board a small Cubesat. This is the P-GRESSION payload (Payload for GNSS REmote Sensing and Signal detectION). It will try to demonstrate the feasibility of existing applications based on observations normally carried out by costly and operative space receivers. Two concepts will be tested. The first one is a twofold GNSS Remote Sensing experiment: 1) the GNSS Radio Occultation experiment, for the profiling of atmospheric refractivity, temperature, water vapour and electron density, which are very important for climate and meteorological purposes, and 2) The GNSS-R experiment for the land and sea surface parameters sensing. It is worth noting that, for both these GNSS-based experiments, global world coverage of observations is assured in all weather conditions. Finally, the current development/improvement of future global GNSS systems will enlarge the number of offered GNSS signals, improving consequently the resolution in time and space of the remote sensing observables. The second concept is based on signal identification. In particular P-GRESSION will acquire signals coming from ground-based radars, in C and/or X frequency bands, both for detection and for calibration purposes. All the experiments will be based on the same Software Defined Radio approach, since after standard radio acquisition with low cost front ends and antennas, all operations will be performed by softwar

Population history from the Neolithic to present on the Mediterranean island of Sardinia: an ancient DNA perspective

Recent ancient DNA studies of western Eurasia have revealed a dynamic history of admixture, with evidence for major migrations during the Neolithic and Bronze Age. The population of the Mediterranean island of Sardinia has been notable in these studies –} Neolithic individuals from mainland Europe cluster more closely with Sardinian individuals than with all other present-day Europeans. The current model to explain this result is that Sardinia received an initial influx of Neolithic ancestry and then remained relatively isolated from expansions in the later Neolithic and Bronze Age that took place in continental Europe. To test this model, we generated genome-wide capture data (approximately 1.2 million variants) for 43 ancient Sardinian individuals spanning the Neolithic through the Bronze Age, including individuals from Sardinia{’}s Nuragic culture, which is known for the construction of numerous large stone towers throughout the island. We analyze these new samples in the context of previously generated genome-wide ancient DNA data from 972 ancient individuals across western Eurasia and whole-genome sequence data from approximately 1,500 modern individuals from Sardinia. The ancient Sardinian individuals show a strong affinity to western Mediterranean Neolithic populations and we infer a high degree of genetic continuity on the island from the Neolithic (around fifth millennium BCE) through the Nuragic period (second millennium BCE). In particular, during the Bronze Age in Sardinia, we do not find significant levels of the {“}Steppe{” ancestry that was spreading in many other parts of Europe at that time. We also characterize subsequent genetic influx between the Nuragic period and the present. We detect novel, modest signals of admixture between 1,000 BCE and present-day, from ancestry sources in the eastern and northern Mediterranean. Within Sardinia, we confirm that populations from the more geographically isolated mountainous provinces have experienced elevated levels of genetic drift and that northern and southwestern regions of the island received more gene flow from outside Sardinia. Overall, our genetic analysis sheds new light on the origin of Neolithic settlement on Sardinia, reinforces models of genetic continuity on the island, and provides enhanced power to detect post-Bronze-Age gene flow. Together, these findings offer a refined demographic model for future medical genetic studies in Sardinia

Facing the urgency of therapies for progressive MS — a Progressive MS Alliance proposal

Therapies for infiltrative inflammation in multiple sclerosis (MS) have advanced greatly, but neurodegeneration and compartmentalized inflammation remain virtually untargeted as in other diseases of the nervous system. Consequently, many therapies are available for the relapsing–remitting form of MS, but the progressive forms remain essentially untreated. The objective of the International Progressive MS Alliance is to expedite the development of effective therapies for progressive MS through new initiatives that foster innovative thinking and concrete advancements. Based on these principles, the Alliance is developing a new funding programme that will focus on experimental medicine trials. Here, we discuss the reasons behind the focus on experimental medicine trials, the strengths and weaknesses of these approaches and of the programme, and why we hope to advance therapies while improving the understanding of progression in MS. We are soliciting public and academic feedback, which will help shape the programme and future strategies of the Alliance

An in vivo Comparison Study Between Strontium Nanoparticles and rhBMP2

The osteoinductive property of strontium was repeatedly proven in the last decades. Compelling in vitro data demonstrated that strontium hydroxyapatite nanoparticles exert a dual action, by promoting osteoblasts-driven matrix secretion and inhibiting osteoclasts-driven matrix resorption. Recombinant human bone morphogenetic protein 2 (rhBMP2) is a powerful osteoinductive biologic, used for the treatment of vertebral fractures and critically-sized bone defects. Although effective, the use of rhBMP2 has limitations due its recombinant morphogen nature. In this study, we examined the comparison between two osteoinductive agents: rhBMP2 and the innovative strontium-substituted hydroxyapatite nanoparticles. To test their effectiveness, we independently loaded Gelfoam sponges with the two osteoinductive agents and used the sponges as agent-carriers. Gelfoam are FDA-approved biodegradable medical devices used as delivery system for musculoskeletal defects. Their porous structure and spongy morphology make them attractive in orthopedic field. The abiotic characterization of the loaded sponges, involving ion release pattern and structure investigation, was followed by in vivo implantation onto the periosteum of healthy mice and comparison of the effects induced by each implant was performed. Abiotic analysis demonstrated that strontium was continuously released from the sponges over 28 days with a pattern similar to rhBMP2. Histological observations and gene expression analysis showed stronger endochondral ossification elicited by strontium compared to rhBMP2. Osteoclast activity was more inhibited by strontium than by rhBMP2. These results demonstrated the use of sponges loaded with strontium nanoparticles as potential bone grafts might provide better outcomes for complex fractures. Strontium nanoparticles are a novel and effective non-biologic treatment for bone injuries and can be used as novel powerful therapeutics for bone regeneration

Art therapy for Parkinson's disease.

Abstract Objective To explore the potential rehabilitative effect of art therapy and its underlying mechanisms in Parkinson's disease (PD). Methods Observational study of eighteen patients with PD, followed in a prospective, open-label, exploratory trial. Before and after twenty sessions of art therapy, PD patients were assessed with the UPDRS, Pegboard Test, Timed Up and Go Test (TUG), Beck Depression Inventory (BDI), Modified Fatigue Impact Scale and PROMIS-Self-Efficacy, Montreal Cognitive Assessment, Rey-Osterrieth Complex Figure Test (RCFT), Benton Visual Recognition Test (BVRT), Navon Test, Visual Search, and Stop Signal Task. Eye movements were recorded during the BVRT. Resting-state functional MRI (rs-fMRI) was also performed to assess functional connectivity (FC) changes within the dorsal attention (DAN), executive control (ECN), fronto-occipital (FOC), salience (SAL), primary and secondary visual (V1, V2) brain networks. We also tested fourteen age-matched healthy controls at baseline. Results At baseline, PD patients showed abnormal visual-cognitive functions and eye movements. Analyses of rs-fMRI showed increased functional connectivity within DAN and ECN in patients compared to controls. Following art therapy, performance improved on Navon test, eye tracking, and UPDRS scores. Rs-fMRI analysis revealed significantly increased FC levels in brain regions within V1 and V2 networks. Interpretation Art therapy improves overall visual-cognitive skills and visual exploration strategies as well as general motor function in patients with PD. The changes in brain connectivity highlight a functional reorganization of visual networks

Visuospatial exploration and art therapy intervention in patients with Parkinson's disease: an exploratory therapeutic protocol

Abstract Though abnormalities of visuospatial function occur in Parkinson's disease, the impact of such deficits on functional independence and psychological wellbeing has been historically under- recognized, and effective treatments for this impairment are unknown. These symptoms can be encountered at any stage of the disease, affecting many activities of daily living, and negatively influencing mood, self-efficacy, independence, and overall quality of life. Furthermore, visuospatial dysfunction has been recently linked to gait impairment and falls, symptoms that are known to be poor prognostic factors. Here, we aim to present an original modality of neurorehabilitation designed to address visuospatial dysfunction and related symptoms in Parkinson's disease, known as "Art Therapy". Art creation relies on sophisticated neurologic mechanisms including shape recognition, motion perception, sensory-motor integration, abstraction, and eye-hand coordination. Furthermore, art therapy may enable subjects with disability to understand their emotions and express them through artistic creation and creative thinking, thus promoting self-awareness, relaxation, confidence and self-efficacy. The potential impact of this intervention on visuospatial dysfunction will be assessed by means of combined clinical, behavioral, gait kinematic, neuroimaging and eye tracking analyses. Potential favorable outcomes may drive further trials validating this novel paradigm of neurorehabilitation

Sex-Specific Parental Effects on Offspring Lipid Levels

Background: Plasma lipid levels are highly heritable traits, but known genetic loci can only explain a small portion of their heritability. Methods and Results: In this study, we analyzed the role of parental levels of total cholesterol (TC), low‐density lipoprotein cholesterol (LDL‐C), high‐density lipoprotein cholesterol (HDL‐C), and triglycerides (TGs) in explaining the values of the corresponding traits in adult offspring. We also evaluated the contribution of nongenetic factors that influence lipid traits (age, body mass index, smoking, medications, and menopause) alone and in combination with variability at the genetic loci known to associate with TC, LDL‐C, HDL‐C, and TG levels. We performed comparisons among different sex‐specific regression models in 416 families from the Framingham Heart Study and 304 from the SardiNIA cohort. Models including parental lipid levels explain significantly more of the trait variation than models without these measures, explaining up to ≈39% of the total trait variation. Of this variation, the parent‐of‐origin effect explains as much as ≈15% and it does so in a sex‐specific way. This observation is not owing to shared environment, given that spouse‐pair correlations were negligible (\u3c1.5% explained variation in all cases) and is distinct from previous genetic and acquired factors that are known to influence serum lipid levels. Conclusions: These findings support the concept that unknown genetic and epigenetic contributors are responsible for most of the heritable component of the plasma lipid phenotype, and that, at present, the clinical utility of knowing age‐matched parental lipid levels in assessing risk of dyslipidemia supersedes individual locus effects. Our results support the clinical utility of knowing parental lipid levels in assessing future risk of dyslipidemia