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Superare le sfide nella caratterizzazione delle popolazioni cellulari nei dati omici a cellula singola
No full textLe tecnologie omiche a singola cellula hanno rivoluzionato l’analisi dei tessuti, permettendo una classificazione dettagliata dei tipi cellulari. In particolare, il sequenziamento dell’RNA a singola cellula (scRNA-seq) è stato applicato su larga scala per studiare i profili trascrizionali delle cellule con una risoluzione mai vista prima. L’identificazione accurata delle identità cellulari è cruciale per la corretta interpretazione delle analisi seguenti (per esempio la ricerca di comunicazioni tra cellule o di reti di regolazione genica). Tuttavia, rimane una sfida a causa di artefatti tecnici, della variabilità biologica e della grande dimensionalità dei dati.
Un controllo qualità rigoroso e processi di filtraggio sono essenziali per mitigare tali fattori confondenti e assicurare risultati affidabili. Metriche robuste associate ai controlli qualità sono quindi fondamentali per migliorare l’interpretazione dei dati omici a singola cellula. Abbiamo sviluppato popsicleR, uno pacchetto di R flessibile e facile da applicare per l’analisi di dati di scRNA-seq, proprio con lo scopo di aiutare i ricercatori in queste operazioni.
Una sfida ulteriore è rappresentata nel distinguere i fattori fondamentali associati all’identità cellulare. Nonostante esistano diverse soluzioni, l’elevato livello di rumore e la sparsità dei fattori misurati (ad esempio i livelli di espressione genica in scRNA-seq) rimangono ostacoli significativi. Introduciamo scPleiades, una nuova procedura in R disegnata per migliorare la classificazione delle cellule per scRNA-seq e altre tecnologie omiche, con lo scopo di affrontare queste problematiche. scPleiades sfrutta una nuova metrica che migliora la resilienza nei confronti del rumore e migliora l’identificazione delle distinte popolazioni cellulari. Tramite l’applicazione del nostro strumento a dataset pubblici umani di scRNa-seq, scATAC-seq e multiomici, abbiamo dimostrato la sua abilità nel generare raggruppamenti cellualri più definiti e migliorare l’interpretabilità biologica rispetto ad altri approcci esistenti. Inoltre, la nostra applicazione può essere facilmente applicata a differenti dati omici e può gestire in un unico passaggio anche dati multiomici.
Nonostante scPleiades affronti problematiche chiave nelle tradizionali tecnologie omiche a singola cellula, la crescente complessità dei dati omici spaziali richiede approcci ulteriormente sofisticati. I miglioramenti nelle tecnologie trascrizionali risolte spazialmente permettono di mantenere l’informazione spaziale associata con i dati trascrizionali, offrendo una risoluzione senza precedenti sull’architettura spaziale dei tessuti. Nonostante ciò, queste tecnologie richiedono anche controlli qualità robusti e processi di segmentazione per filtrare correttamente vari artefatti. In particolare, il processo di segmentazione è uno delle più importanti fonti di artefatti nelle tecnologie basate sull’acquisizione di immagini e la sua qualità è fondamentale per tutte le seguenti analisi. Abbiamo valutato la bontà di diversi algoritmi di segmentazione nella trascrittomica spaziale per mettere in luce il loro ruolo nel determinare la qualità dei risultati per gli approcci spaziali a singola cellula.
Questo lavoro sottolinea l’importanza dei controlli qualità e del filtraggio degli artefatti come approccio generale nelle analisi di dati a singola cellula per assicurare una corretta interpretazione dei risultati, concentrandosi sia su tecnologie non spaziali che spaziali.Single-cell omics have revolutionized tissue analysis, enabling detailed classification of cell types. In particular, single-cell RNA sequencing (scRNA-seq) has been widely employed to study cell transcriptomic profiles with unprecedent resolution. Accurate identification of cell identities is crucial for the correct interpretation of downstream analyses – e.g., cell-cell interactions and gene regulatory networks discovery – but remains challenging due to technical artifacts, biological variability, and the high dimensionality of the data.
Rigorous quality control (QC) and filtering processes are essential to mitigate these confounding factors and ensure reliable results. Robust QC measures are therefore critical for improving single-cell omic data interpretation. In order to help researchers in these tasks, we developed popsicleR, a flexible and user-friendly R package for scRNA-seq data preprocessing.
A further challenge is distinguishing the key features associated with cell identity. Despite existing solutions, the high noise level and sparsity of measured features – such as gene expression levels in scRNA-seq – remain significant obstacles. To address these issues, we introduce scPleiades, a novel R pipeline designed to improve cell classification for scRNA-seq and other single-cell omics. scPleiades employs a novel metric that improves resilience to noise and enhances the identification of distinct cell populations. By applying our tool to publicly available scRNA-seq, scATAC-seq, and multiomic datasets from human cells, we demonstrate its ability to achieve more refined clustering and improved biological interpretability compared to existing methods. Furthermore, our pipeline can be easily applied to different omic data and can handle multiomic assays at once.
While scPleiades addresses key challenges in traditional single-cell omics, the rising complexity of spatial transcriptomics requires even more sophisticated approaches. Advances in spatially resolved single-cell transcriptomic data retain spatial information alongside transcriptomic data, offering unprecedented insights into tissue architecture. However, these technologies also demand robust QC pipelines and segmentation methods to effectively filter artifacts. In particular, segmentation step is one of the most important sources of artifacts in imaging-based spatial technologies and its quality is crucial for all downstream analysis. We evaluated the quality of different segmentation algorithms in spatial transcriptomic to highlight their impact in determining the results quality for spatial single-cell approaches.
This work underscores the importance of QC and artifacts filtering as a general approach in single-cell analysis to assure a correct interpretation of the results, focusing on both non-spatial and spatial technologies
Liquid CO2 and Liquid Air Energy Storage Systems: A Thermodynamic Analysis
Full text linkEnergy storage is a key factor to confer a technological foundation to the concept of energy transition from fossil fuels to renewables. Their solar dependency (direct radiation, wind, biomass, hydro, etc. …) makes storage a requirement to match the supply and demand, with fulfillment being another key factor. Recently, the most attention is directed toward the direct electrical storage inside batteries, probably driven by interest in the transportation sector, which today is the main focus in the transition path. On the contrary, for the generation of electrical energy and, more generally, for industrial sectors whose CO2 emissions are defined as hard-to-abate, electrical storage is not a feasible answer to many political and non-technological concerns. Therefore, other storage methods must be considered to address excess electricity, the most characteristics of which being both the capacity and rate of charging/delivering. Among the efforts under consideration, the liquid storage of gases at ambient conditions is certainly an interesting option. This is the case with air and CO2. The paper focused on the storage of CO2 in liquid form, comparing its performance with those of air liquefaction, which well-studied in the literature. The paper proposed a novel plant layout design for a liquid CO2 energy storage system that can improve the round-trip efficiency by up to 57%. The system was also compared to a liquid air energy storage unit considering a state-of-the-art level of technology for components, showing better efficiency but lower energy density. Finally, a sensitivity analysis was used to discuss the most relevant variables for a plant design. Particular focus was devoted to the discharging time of the plant, one of the most relevant variables that matches the energy demand
Dynamics of SCO2 heat to power units equipped with dual tank inventory control system
Full text linkCopyright © 2021 The Author(s). A key aspect in upscaling the technology readiness level of supercritical CO2 (sCO2) power generation systems is the control of the main cycle parameters (i.e. temperature at the turbine or compressor inlet) at off-design conditions and during transient operation. A further challenge in small scale (<0.5MWe) systems is the limited number of control variables due to the streamlined configuration of the power units. Among the possible control strategies, is the regulation of the system inventory, which consists of the variation of the CO2 fluid mass (or charge) in the power loop to achieve a given control target. Such strategy, which relies on different storage tanks for injections/withdrawals of the working fluid into/from the system, poses several technical challenges that are still not fully understood. To fill the gap, this work presents an analysis of inventory control systems. The impact of this control approach is investigated using a high-fidelity one-dimensional simulation platform calibrated on a 50 kW simple regenerative High Temperature Heat to Power sCO2 test facility being commissioned at Brunel University London. Transient simulations are carried out to assess the dynamics of the main thermodynamic variables in the power loop and the inventory tanks. Stability implications (e.g. pressure gradients in the loop) as well as the effects of size of the inventory tanks are discussed. Inventory tanks with a volume 3 times higher than the one of the power loop (including the receiver) can lead to a higher controllability range (±30% of the nominal turbine inlet temperature) and an extended availability of the control action (slower tank discharge).European Union’s Horizon 2020 research and innovation program under grant agreement No. 680599; EPSRC (UK) research grants (i) EP/V001752/1; (ii) EP/P004636/1; (iii) EP/K011820/1
Integration of Floating Photovoltaics and Pumped Hydro Energy Storage with Water Electrolysis for Combined Power and Hydrogen Generation
Full text linkThis study proposes a floating photovoltaic - pumped hydro energy storage system integrated with a water electrolyzer for combined power and hydrogen generation. Compared to solutions without electrolyzers, this integrated system is able to further mitigate the non-programmable photovoltaic generation and simultaneously decarbonize hard-to-abate sectors. The performance of the integrated system is herein studied on daily, monthly, and yearly bases using a mathematical model with a 1-hour time resolution for a real case represented by a pumped hydroelectric energy storage system in Sardinia. The study considers integrating the existing system with a 11 MW floating photovoltaic system and a 4 MW PEM electrolyzer, appropriately sized to achieve a hydrogen production target of 100 tonnes per year and a photovoltaic self-consumption not below 95%. The power used for pumping water and producing hydrogen is 100% renewable, as it is supplied solely by the floating photovoltaic plant, and the electricity is fed in the grid at night, aiming to increase the share of renewables in the nighttime energy mix of the Sardinia region. Results show that the integration provides significant benefits to the grid, with 8.5 GWh/year of nighttime inertial feed-ins. Moreover, since the integrated plant is characterized by annual self-consumption values of photovoltaic generation around 97% and monthly values never below 93%, the negative impact caused by its non-programmable feed-ins on the grid is minimal. Hydrogen production, capable of replacing approximately 0.1% of the current yearly fossil fuel-based thermal demand of the regional industrial sector, exhibits strong seasonality, with daily production averaging 65 kg/day during winter months and over 7 times more (465 kg/day) during summer months, suggesting the opportunity for a seasonal storage
An analysis of EU power system flexibility: storage capacity needs under increasing variable renewable energy sources (VRES) penetration
No full textThe increasing penetration of variable renewable energy sources in the energy mix plays a key role in
the energy transition but it also poses serious challenges in terms of grid scheduling, regulation,
management, and resilience. To cope with the non-programmable nature of renewables, increased
generation reserves, ramp rates and curtailments are required to meet the electricity demand with an
increasingly uncertain supply and to provide flexibility services to the grid. To avoid excessive
operational costs and mounting inefficiencies, the grid calls for higher flexibility requirements from the
electricity system. Currently, this can be provided only by conventional generators (such as thermoelectric
or hydro-electric), by demand shifting (mainly by industrial loads) or by energy storage systems,
whose current limited adoption is still insufficient for such objective. The definition of such flexibility
requirements is still an open topic in the literature, with few analyses available targeting the problem in
a quantitative fashion, especially when future energy scenarios are considered.
For these reasons, this study provides insights into the historical trends of flexibility parameters in three
representative EU members (Italy, Germany and Hungary). These parameters are discussed separately
for each country and compared among countries through a novel visualization mode which traces their
temporal evolution and seasonal patterns and allows comparison between electrical grids with varying
power levels.
Furthermore, the study anticipates diverse future scenarios for the Italian power system, considering
increased variable renewables penetration. Each scenario is analyzed for renewable generation
curtailments and seasonal variations in renewable energy supply. The assessment of different storage
needs in terms of capacity and duration provides a quantitative foundation for addressing the evolving
flexibility requirements in the face of future energy scenarios. Particularly, future scenarios for Italy
highlight the potential need for short-term energy storage systems, such as batteries, with a capacity
between 10 and 110 TWh/year to avoid renewable curtailment levels ranging from 5% to 40%.
Alternatively, by expanding the potential for use to sectors other than electricity generation, the same
curtailment levels could be used to generate green hydrogen, between 0.2-1.9 million tons per year. The
results underscore the importance of balanced increases in wind and solar capacities to optimize
flexibility and reduce seasonal storage demands, showcasing the study's relevance in shaping informed
energy transition strategies
popsicleR: a R Package for pre-processing and quality control analysis of single cell RNA-seq data
Full text linkThe advent of single-cell sequencing is providing unprecedented opportunities to disentangle tissue complexity and investigate cell identities and functions. However, the analysis of single cell data is a challenging, multi-step process that requires both advanced computational skills and biological sensibility. When dealing with single cell RNA-seq (scRNA-seq) data, the presence of technical artifacts, noise, and biological biases imposes to first identify, and eventually remove, unreliable signals from low-quality cells and unwanted sources of variation that might affect the efficacy of subsequent downstream modules. Preprocessing and quality control (QC) of scRNA-seq data is a laborious process consisting in the manual combination of different computational strategies to quantify QC-metrics and define optimal sets of preprocessing parameters. Here we present popsicleR, a R package to interactively guide skilled and unskilled command line-users in the pre-processing and QC analysis of scRNA-seq data. The package integrates, into several main wrapper functions, methods derived from widely used pipelines for the estimation of quality-control metrics, filtering of low-quality cells, data normalization, removal of technical and biological biases, and for cell clustering and annotation. popsicleR starts from either the output files of the Cell Ranger pipeline from 10X Genomics or from a feature-barcode matrix of raw counts generated from any scRNA-seq technology. Open-source code, installation instructions, and a case study tutorial are freely available https://github.com/biccialolab/popsicleR . (C) 2022 The Authors. Published by Elsevier Ltd
Comparative analysis of different Rankine PTES system configurations
Full text linkIn this paper, four main configurations of a Rankine-based Pumped Thermal Energy Storage (PTES) system are proposed and compared in terms of achievable electrical and exergy roundtrip efficiency and energy density. The analysis considers a conventional setup employing commercial heat pumps and Organic Rankine Cycle (ORC) systems integrated with a Thermal Energy Storage (TES) unit as reference. The initial findings indicate that off-the-shelf systems result in roundtrip efficiencies lower than 40%, even under optimal high-temperature conditions at the heat pump evaporator inlet. This is primarily due to significant exogenous exergy destructions inherent in the commercial equipment. The study then explores upgraded alternatives to the reference PTES configuration, focusing on optimizing the heat pump layout and selecting non-conventional working fluids. This optimization process includes evaluating various working fluids, where n-hexane is identified as the optimal choice for achieving the highest electrical and exergy roundtrip efficiencies, particularly at evaporator inlet temperatures above 60°C. For lower temperature ranges, acetone emerges as a more suitable fluid due to its favorable thermodynamic properties. Further enhancements are made by optimizing the ORC layout, specifically through the introduction of an additional thermal storage tank and improved heat exchangers. These modifications are aimed at minimizing heat transfer losses and thereby boosting the overall system performance. With these changes, the PTES system's roundtrip efficiency reaches approximately 70%. The most advanced configuration integrates the heat pump and ORC systems into a single assembly, utilizing the working fluid not only for energy transfer but also as a storage medium. This integration reduces the number of required components and further increases efficiency. As a result, roundtrip efficiencies of about 80% are achieved, representing a significant advancement over current commercial systems
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
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