| 1. |
- Aquilante, Francesco, et al.
(author)
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Modern quantum chemistry with [Open]Molcas
- 2020
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In: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 152:21
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Journal article (peer-reviewed)abstract
- MOLCAS/OpenMolcas is an ab initio electronic structure program providing a large set of computational methods from Hartree-Fock and density functional theory to various implementations of multiconfigurational theory. This article provides a comprehensive overview of the main features of the code, specifically reviewing the use of the code in previously reported chemical applications as well as more recent applications including the calculation of magnetic properties from optimized density matrix renormalization group wave functions.
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| 2. |
- Fuso Nerini, Francesco, et al.
(author)
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The Energy and Water Emergency Module : A containerized solution for meeting the energy and water needs in protracted displacement situations
- 2015
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In: Energy Conversion and Management. - : Elsevier BV. - 0196-8904 .- 1879-2227. ; 93, s. 205-214
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Journal article (peer-reviewed)abstract
- The world has faced many natural and man-made disasters in the past few years, resulting in millions of people living in temporary camps across the globe. The energy and clean water needs of the relief operators in such emergency situations are primarily satisfied by diesel engine based generators and importing clean water to the site, in certain cases even for several years after the emergency. This approach results in problems such as low security of supply and high costs. Especially targeting the prolonged displacement situations, this paper presents an alternative solution - the Energy and Water Emergency Module. The proposed solution aims towards reducing the dependency on fossil fuel in prolonged emergency situations to a minimum while including local energy sources in the energy supply in a flexible and reliable way. The proposed module is built in a standard 20 ft container, and encompasses hybrid generation from solar, wind and biomass, with the possibility of using fossil sources too thanks to a dual fuel gas engine. The module can work both in grid connected and stand-alone mode. In addition the module includes a water purification unit to meet the water needs of displaced population. A demonstration unit was assembled at the Royal Institute of Technology in Stockholm during the year 2012 as a 'concept proof, and is now being tested and optimized for future deployment on the field. Preliminary testing and modelling shows that the proposed solution can reliably support emergency situations, and is already cost competitive with the current water and energy supply solutions for emergency situations.
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| 3. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 4. |
- Kowal-Bielecka, Otylia, et al.
(author)
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Update of EULAR recommendations for the treatment of systemic sclerosis
- 2017
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In: Annals of the Rheumatic Diseases. - : BMJ. - 0003-4967 .- 1468-2060. ; 76, s. 1327-1339
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Journal article (peer-reviewed)abstract
- The aim was to update the 2009 European League against Rheumatism (EULAR) recommendations for the treatment of systemic sclerosis (SSc), with attention to new therapeutic questions. Update of the previous treatment recommendations was performed according to EULAR standard operating procedures. The task force consisted of 32 SSc clinical experts from Europe and the USA, 2 patients nominated by the pan-European patient association for SSc (Federation of European Scleroderma Associations (FESCA)), a clinical epidemiologist and 2 research fellows. All centres from the EULAR Scleroderma Trials and Research group were invited to submit and select clinical questions concerning SSc treatment using a Delphi approach. Accordingly, 46 clinical questions addressing 26 different interventions were selected for systematic literature review. The new recommendations were based on the available evidence and developed in a consensus meeting with clinical experts and patients. The procedure resulted in 16 recommendations being developed (instead of 14 in 2009) that address treatment of several SSc-related organ complications: Raynaud's phenomenon (RP), digital ulcers (DUs), pulmonary arterial hypertension (PAH), skin and lung disease, scleroderma renal crisis and gastrointestinal involvement. Compared with the 2009 recommendations, the 2016 recommendations include phosphodiesterase type 5 (PDE-5) inhibitors for the treatment of SSc-related RP and DUs, riociguat, new aspects for endothelin receptor antagonists, prostacyclin analogues and PDE-5 inhibitors for SSc-related PAH. New recommendations regarding the use of fluoxetine for SSc-related RP and haematopoietic stem cell transplantation for selected patients with rapidly progressive SSc were also added. In addition, several comments regarding other treatments addressed in clinical questions and suggestions for the SSc research agenda were formulated. These updated data-derived and consensus-derived recommendations will help rheumatologists to manage patients with SSc in an evidence-based way. These recommendations also give directions for future clinical research in SSc.
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| 5. |
- Sacchetto, Daniela, et al.
(author)
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Mammographic density : Comparison of visual assessment with fully automatic calculation on a multivendor dataset
- 2016
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In: European Radiology. - : Springer. - 0938-7994 .- 1432-1084. ; 26:1, s. 175-183
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Journal article (peer-reviewed)abstract
- To compare breast density (BD) assessment provided by an automated BD evaluator (ABDE) with that provided by a panel of experienced breast radiologists, on a multivendor dataset. Twenty-one radiologists assessed 613 screening/diagnostic digital mammograms from nine centers and six different vendors, using the BI-RADS a, b, c, and d density classification. The same mammograms were also evaluated by an ABDE providing the ratio between fibroglandular and total breast area on a continuous scale and, automatically, the BI-RADS score. A panel majority report (PMR) was used as reference standard. Agreement (kappa) and accuracy (proportion of cases correctly classified) were calculated for binary (BI-RADS a-b versus c-d) and 4-class classification. While the agreement of individual radiologists with the PMR ranged from kappa = 0.483 to kappa = 0.885, the ABDE correctly classified 563/613 mammograms (92 %). A substantial agreement for binary classification was found for individual reader pairs (kappa = 0.620, standard deviation [SD] = 0.140), individual versus PMR (kappa = 0.736, SD = 0.117), and individual versus ABDE (kappa = 0.674, SD = 0.095). Agreement between ABDE and PMR was almost perfect (kappa = 0.831). The ABDE showed an almost perfect agreement with a 21-radiologist panel in binary BD classification on a multivendor dataset, earning a chance as a reproducible alternative to visual evaluation. aEuro cent Individual BD assessment differs from PMR with kappa as low as 0.483. aEuro cent An ABDE correctly classified 92 % of mammograms with almost perfect agreement (kappa = 0.831). aEuro cent An ABDE can be a valid alternative to subjective BD assessment.
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| 6. |
- Sorriso-Valvo, Luca, et al.
(author)
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Turbulence-Driven Ion Beams in the Magnetospheric Kelvin-Helmholtz Instability
- 2019
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In: Physical Review Letters. - : AMER PHYSICAL SOC. - 0031-9007 .- 1079-7114. ; 122:3
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Journal article (peer-reviewed)abstract
- The description of the local turbulent energy transfer and the high-resolution ion distributions measured by the Magnetospheric Multiscale mission together provide a formidable tool to explore the cross-scale connection between the fluid-scale energy cascade and plasma processes at subion scales. When the small-scale energy transfer is dominated by Alfvenic, correlated velocity, and magnetic field fluctuations, beams of accelerated particles are more likely observed. Here, for the first time, we report observations suggesting the nonlinear wave-particle interaction as one possible mechanism for the energy dissipation in space plasmas.
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| 7. |
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The Seventeenth Data Release of the Sloan Digital Sky Surveys : Complete Release of MaNGA, MaStar, and APOGEE-2 Data
- 2022
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In: Astrophysical Journal Supplement Series. - : Institute of Physics (IOP). - 0067-0049 .- 1538-4365. ; 259:2
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Journal article (peer-reviewed)abstract
- This paper documents the seventeenth data release (DR17) from the Sloan Digital Sky Surveys; the fifth and final release from the fourth phase (SDSS-IV). DR17 contains the complete release of the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey, which reached its goal of surveying over 10,000 nearby galaxies. The complete release of the MaNGA Stellar Library accompanies this data, providing observations of almost 30,000 stars through the MaNGA instrument during bright time. DR17 also contains the complete release of the Apache Point Observatory Galactic Evolution Experiment 2 survey that publicly releases infrared spectra of over 650,000 stars. The main sample from the Extended Baryon Oscillation Spectroscopic Survey (eBOSS), as well as the subsurvey Time Domain Spectroscopic Survey data were fully released in DR16. New single-fiber optical spectroscopy released in DR17 is from the SPectroscipic IDentification of ERosita Survey subsurvey and the eBOSS-RM program. Along with the primary data sets, DR17 includes 25 new or updated value-added catalogs. This paper concludes the release of SDSS-IV survey data. SDSS continues into its fifth phase with observations already underway for the Milky Way Mapper, Local Volume Mapper, and Black Hole Mapper surveys.
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| 8. |
- Aquilante, Francesco, et al.
(author)
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Molcas 8 : New capabilities for multiconfigurational quantum chemical calculations across the periodic table
- 2016
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In: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 37:5, s. 506-541
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Journal article (peer-reviewed)abstract
- In this report, we summarize and describe the recent unique updates and additions to the Molcas quantum chemistry program suite as contained in release version 8. These updates include natural and spin orbitals for studies of magnetic properties, local and linear scaling methods for the Douglas-Kroll-Hess transformation, the generalized active space concept in MCSCF methods, a combination of multiconfigurational wave functions with density functional theory in the MC-PDFT method, additional methods for computation of magnetic properties, methods for diabatization, analytical gradients of state average complete active space SCF in association with density fitting, methods for constrained fragment optimization, large-scale parallel multireference configuration interaction including analytic gradients via the interface to the Columbus package, and approximations of the CASPT2 method to be used for computations of large systems. In addition, the report includes the description of a computational machinery for nonlinear optical spectroscopy through an interface to the QM/MM package Cobramm. Further, a module to run molecular dynamics simulations is added, two surface hopping algorithms are included to enable nonadiabatic calculations, and the DQ method for diabatization is added. Finally, we report on the subject of improvements with respects to alternative file options and parallelization.
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| 9. |
- Balador, Ali, et al.
(author)
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Survey on decentralized congestion control methods for vehicular communication
- 2022
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In: Vehicular Communications. - : Elsevier BV. - 2214-2096 .- 2214-210X. ; 33
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Journal article (peer-reviewed)abstract
- Vehicular communications have grown in interest over the years and are nowadays recognized as a pillar for the Intelligent Transportation Systems (ITSs) in order to ensure an efficient management of the road traffic and to achieve a reduction in the number of traffic accidents. To support the safety applications, both the ETSI ITS-G5 and IEEE 1609 standard families require each vehicle to deliver periodic awareness messages throughout the neighborhood. As the vehicles density grows, the scenario dynamics may require a high message exchange that can easily lead to a radio channel congestion issue and then to a degradation on safety critical services. ETSI has defined a Decentralized Congestion Control (DCC) mechanism to mitigate the channel congestion acting on the transmission parameters (i.e., message rate, transmit power and data-rate) with performances that vary according to the specific algorithm. In this paper, a review of the DCC standardization activities is proposed as well as an analysis of the existing methods and algorithms for the congestion mitigation. Also, some applied machine learning techniques for DCC are addressed.
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| 10. |
- Benella, Simone, et al.
(author)
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Linking the Langevin equation to scaling properties of space plasma turbulence at sub-ion scales
- 2023
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In: Physical Review Research. - : American Physical Society. - 2643-1564. ; 5:4
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Journal article (peer-reviewed)abstract
- Current understanding of the kinetic-scale turbulence in weakly collisional plasmas still remains elusive. We employ a general framework in which the turbulent energy transfer is envisioned as a scale-to-scale Langevin process. Fluctuations in the sub-ion range show a global scale invariance, thus suggesting a homogeneous energy repartition. In this Letter, we interpret such a feature by linking the drift term of the Langevin equation to scaling properties of fluctuations. Theoretical expectations are verified on solar wind observations and numerical simulations, thus giving relevance to the proposed framework for understanding kinetic-scale turbulence in space plasmas.
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