University of Aveiro

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. For example, a key point that needs to be emphasized is thatthere 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 versus those that measure flux through the autophagy pathway (i.e., the completeprocess including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defined as increasedautophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost 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 manycases, 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. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. 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 forreviewers 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 multipleassays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation, it is imperative to target by gene knockout or RNA interference more than one autophagyrelated protein. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways implying that not all Atg proteins can be used as a specific marker for an autophagic process. 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 assays, we hope to encourage technical innovation in the field.

Identifying a maximum independent set is a fundamental NP-hard problem. This problem has several real-world applications and requires finding the largest possible set of vertices not adjacent to each other in an undirected graph. Over the past few years, branch-and-bound and branch-and-reduce algorithms have emerged as some of the most effective methods for solving the problem exactly. Specifically, the branch-and-reduce approach, which combines branch-and-bound principles with reduction rules, has proven particularly successful in tackling previously unmanageable real-world instances. This progress was largely made possible by the development of more effective reduction rules. Nevertheless, other key components that can impact the efficiency of these algorithms have not received the same level of interest. Among these is the branching strategy, which determines which vertex to branch on next. Until recently, the most widely used strategy was to choose the vertex of the highest degree. In this work, we present a graph neural network approach for selecting the next branching vertex. The intricate nature of current branch-and-bound solvers makes supervised and reinforcement learning difficult. Therefore, we use a population-based genetic algorithm to evolve the model’s parameters instead. Our proposed approach results in a speedup on 73% of the benchmark instances with a median speedup of 24%.

We present here a new solution for the astronomical computation of the insolation quantities on Earth spanning from -250 Myr to 250 Myr. This solution has been improved with respect to La93 (Laskar et al. [CITE]) by using a direct integration of the gravitational equations for the orbital motion, and by improving the dissipative contributions, in particular in the evolution of the Earth–Moon System. The orbital solution has been used for the calibration of the Neogene period (Lourens et al. [CITE]), and is expected to be used for age calibrations of paleoclimatic data over 40 to 50 Myr, eventually over the full Palaeogene period (65 Myr) with caution. Beyond this time span, the chaotic evolution of the orbits prevents a precise determination of the Earth's motion. However, the most regular components of the orbital solution could still be used over a much longer time span, which is why we provide here the solution over 250 Myr. Over this time interval, the most striking feature of the obliquity solution, apart from a secular global increase due to tidal dissipation, is a strong decrease of about 0.38 degree in the next few millions of years, due to the crossing of the resonance (Laskar et al. [CITE]). For the calibration of the Mesozoic time scale (about 65 to 250 Myr), we propose to use the term of largest amplitude in the eccentricity, related to , with a fixed frequency of /yr, corresponding to a period of 405 000 yr. The uncertainty of this time scale over 100 Myr should be about , and over the full Mesozoic era.

autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.

The combination of the compactness of networks, featuring small diameters, and their complex architectures results in a variety of critical effects dramatically different from those in cooperative systems on lattices. In the last few years, important steps have been made toward understanding the qualitatively new critical phenomena in complex networks. The results, concepts, and methods of this rapidly developing field are reviewed. Two closely related classes of these critical phenomena are considered, namely, structural phase transitions in the network architectures and transitions in cooperative models on networks as substrates. Systems where a network and interacting agents on it influence each other are also discussed. A wide range of critical phenomena in equilibrium and growing networks including the birth of the giant connected component, percolation, $k$-core percolation, phenomena near epidemic thresholds, condensation transitions, critical phenomena in spin models placed on networks, synchronization, and self-organized criticality effects in interacting systems on networks are mentioned. Strong finite-size effects in these systems and open problems and perspectives are also discussed.

"Data Envelopment Analysis: A Comprehensive Text with Models, Applications, References and DEA-Solver Software." Journal of the Operational Research Society, 52(12), pp. 1408–1409

Metal-organic frameworks based on trivalent lanthanides (LnMOFs) are a very promising class of materials for addressing the challenges in engineering of luminescent centres. Lanthanide-bearing phosphors find numerous applications in lighting, optical communications, photonics and biomedical devices. In this critical review we discuss the potential of LnMOFs as multifunctional systems, which combine light emission with properties such as microporosity, magnetism, chirality, molecule and ion sensing, catalysis and activity as multimodal imaging contrast agents. We argue that these materials present a unique chance of observing synergy between several of these properties, such as the coupling between photoluminescence and magnetism. Moreover, an integrated approach towards the design of efficient, stable, cheap, environmentally-friendly and multifunctional luminescent LnMOFs is still missing. Although research into LnMOFs is at its early stage and much basic knowledge is still needed, the field is ripe for new ideas, which will enable sensor devices and photonic prototypes to become a commercial reality (81 references).

Non-invasive precise thermometers working at the nanoscale with high spatial resolution, where the conventional methods are ineffective, have emerged over the last couple of years as a very active field of research. This has been strongly stimulated by the numerous challenging requests arising from nanotechnology and biomedicine. This critical review offers a general overview of recent examples of luminescent and non-luminescent thermometers working at nanometric scale. Luminescent thermometers encompass organic dyes, QDs and Ln(3+)ions as thermal probes, as well as more complex thermometric systems formed by polymer and organic-inorganic hybrid matrices encapsulating these emitting centres. Non-luminescent thermometers comprise of scanning thermal microscopy, nanolithography thermometry, carbon nanotube thermometry and biomaterials thermometry. Emphasis has been put on ratiometric examples reporting spatial resolution lower than 1 micron, as, for instance, intracellular thermometers based on organic dyes, thermoresponsive polymers, mesoporous silica NPs, QDs, and Ln(3+)-based up-converting NPs and β-diketonate complexes. Finally, we discuss the challenges and opportunities in the development for highly sensitive ratiometric thermometers operating at the physiological temperature range with submicron spatial resolution.

One century after its formulation, Einstein's general relativity has made remarkable predictions and turned out to be compatible with all experimental tests. Most of these tests probe the theory in the weak-field regime, and there are theoretical and experimental reasons to believe that general relativity should be modified when gravitational fields are strong and spacetime curvature is large. The best astrophysical laboratories to probe strong-field gravity are black holes and neutron stars, whether isolated or in binary systems. We review the motivations to consider extensions of general relativity. We present a (necessarily incomplete) catalog of modified theories of gravity for which strong-field predictions have been computed and contrasted to Einstein's theory, and we summarize our current understanding of the structure and dynamics of compact objects in these theories. We discuss current bounds on modified gravity from binary pulsar and cosmological observations, and we highlight the potential of future gravitational wave measurements to inform us on the behavior of gravity in the strong-field regime.

In recent years, more attention has been paid to natural sources of antioxidants. Flavonoids are natural substances synthesized in several parts of plants that exhibit a high antioxidant capacity. They are a large family, presenting several classes based on their basic structure. Flavonoids have the ability to control the accumulation of reactive oxygen species (ROS) via scavenger ROS when they are formed. Therefore, these antioxidant compounds have an important role in plant stress tolerance and a high relevance in human health, mainly due to their anti-inflammatory and antimicrobial properties. In addition, flavonoids have several applications in the food industry as preservatives, pigments, and antioxidants, as well as in other industries such as cosmetics and pharmaceuticals. However, flavonoids application for industrial purposes implies extraction processes with high purity and quality. Several methodologies have been developed aimed at increasing flavonoid extraction yield and being environmentally friendly. This review presents the most abundant natural flavonoids, their structure and chemical characteristics, extraction methods, and biological activity.

The effects of microplastics (MP) on aquatic organisms are currently the subject of intense research. Here, we provide a critical perspective on published studies of MP ingestion by aquatic biota. We summarize the available research on MP presence, behaviour and effects on aquatic organisms monitored in the field and on laboratory studies of the ecotoxicological consequences of MP ingestion. We consider MP polymer type, shape, size as well as group of organisms studied and type of effect reported. Specifically, we evaluate whether or not the available laboratory studies of MP are representative of the types of MPs found in the environment and whether or not they have reported on relevant groups or organisms. Analysis of the available data revealed that 1) despite their widespread detection in field-based studies, polypropylene, polyester and polyamide particles were under-represented in laboratory studies; 2) fibres and fragments (800-1600 μm) are the most common form of MPs reported in animals collected from the field; 3) to date, most studies have been conducted on fish; knowledge is needed about the effects of MPs on other groups of organisms, especially invertebrates. Furthermore, there are significant mismatches between the types of MP most commonly found in the environment or reported in field studies and those used in laboratory experiments. Finally, there is an overarching need to understand the mechanism of action and ecotoxicological effects of environmentally relevant concentrations of MPs on aquatic organism health.

Abiotic stresses (such as metals/metalloids, salinity, ozone, UV-B radiation, extreme temperatures, and drought) are among the most challenging threats to agricultural system and economic yield of crop plants. These stresses (in isolation and/or combination) induce numerous adverse effects in plants, impair biochemical/physiological and molecular processes, and eventually cause severe reductions in plant growth, development and overall productivity. Phytohormones have been recognized as a strong tool for sustainably alleviating adverse effects of abiotic stresses in crop plants. In particular, the significance of salicylic acid (SA) has been increasingly recognized in improved plant abiotic stress-tolerance via SA-mediated control of major plant-metabolic processes. However, the basic biochemical/physiological and molecular mechanisms that potentially underpin SA-induced plant-tolerance to major abiotic stresses remain least discussed. Based on recent reports, this paper: (a) overviews historical background and biosynthesis of SA under both optimal and stressful environments in plants; (b) critically appraises the role of SA in plants exposed to major abiotic stresses;

The synthesis and study of so-called “nanoparticles”, particles with diameters in the range of 1−20 nm, has become a major interdisciplinary area of research over the past 10 years. Semiconductor nanoparticles promise to play a major role in several new technologies. The intense interest in this area derives from their unique chemical and electronic properties, which gives rise to their potential use in the fields of nonlinear optics, luminescence, electronics, catalysis, solar energy conversion, and optoelectronics, as well as other areas. The small dimensions of these particles result in different physical properties from those observed in the corresponding macrocrystalline, “bulk”, material. As particle sizes become smaller, the ratio of surface atoms to those in the interior increase, leading to the surface properties playing an important role in the properties of the material. Semiconductor nanoparticles also exhibit a change in their electronic properties relative to that of the bulk material; as the size of the solid becomes smaller, the band gap becomes larger. This allows chemists and material scientists the unique opportunity to change the electronic and chemical properties of a material simply by controlling its particle size. Research has already led to the fabrication of a number of devices. This review aims to highlight recent advances in the synthesis of compound semiconductor nanoparticle materials and their potential use in areas such as catalysis and electronic device fabrication.

Abstract Species occurrence records from online databases are an indispensable resource in ecological, biogeographical and palaeontological research. However, issues with data quality, especially incorrect geo‐referencing or dating, can diminish their usefulness. Manual cleaning is time‐consuming, error prone, difficult to reproduce and limited to known geographical areas and taxonomic groups, making it impractical for datasets with thousands or millions of records. Here, we present CoordinateCleaner , an r ‐package to scan datasets of species occurrence records for geo‐referencing and dating imprecisions and data entry errors in a standardized and reproducible way. CoordinateCleaner is tailored to problems common in biological and palaeontological databases and can handle datasets with millions of records. The software includes (a) functions to flag potentially problematic coordinate records based on geographical gazetteers, (b) a global database of 9,691 geo‐referenced biodiversity institutions to identify records that are likely from horticulture or captivity, (c) novel algorithms to identify datasets with rasterized data, conversion errors and strong decimal rounding and (d) spatio‐temporal tests for fossils. We describe the individual functions available in CoordinateCleaner and demonstrate them on more than 90 million occurrences of flowering plants from the Global Biodiversity Information Facility (GBIF) and 19,000 fossil occurrences from the Palaeobiology Database (PBDB). We find that in GBIF more than 3.4 million records (3.7%) are potentially problematic and that 179 of the tested contributing datasets (18.5%) might be biased by rasterized coordinates. In PBDB, 1205 records (6.3%) are potentially problematic. All cleaning functions and the biodiversity institution database are open‐source and available within the CoordinateCleaner r ‐package.

Abstract Present technological demands in disparate areas, such as microfluidics and nanofluidics, microelectronics and nanoelectronics, photonics and biomedicine, among others, have reached to a development such that conventional contact thermal probes are not accomplished anymore to perform accurate measurements with submicrometric spatial resolution. The development of novel noncontact thermal probes is, then, mandatory, contributing to an expansionary epoch of luminescence thermometry. Luminescence thermometry based on trivalent lanthanide ions has become very popular since 2010 due to the unique versatility, stability, and narrow emission band profiles of the ions that cover the entire electromagnetic spectrum with relatively high emission quantum yields. Here, a perspective overview on the field is given from the beginnings in the 1950s until the most recent cutting‐edge examples. The current movement toward usage of the technique as a new tool for thermal imaging, early tumor detection, and as a tool for unveiling the properties of the thermometers themselves or of their local neighborhoods is also summarized.

Candida species are the most common cause of opportunistic fungal infection worldwide. Here we report the genome sequences of six Candida species and compare these and related pathogens and non-pathogens. There are significant expansions of cell wall, secreted and transporter gene families in pathogenic species, suggesting adaptations associated with virulence. Large genomic tracts are homozygous in three diploid species, possibly resulting from recent recombination events. Surprisingly, key components of the mating and meiosis pathways are missing from several species. These include major differences at the mating-type loci (MTL); Lodderomyces elongisporus lacks MTL, and components of the a1/α2 cell identity determinant were lost in other species, raising questions about how mating and cell types are controlled. Analysis of the CUG leucine-to-serine genetic-code change reveals that 99% of ancestral CUG codons were erased and new ones arose elsewhere. Lastly, we revise the Candida albicans gene catalogue, identifying many new genes. The genome sequences of six Candida species have been determined, and compared with those of Candida albicans, a marine yeast and baker's yeast. Candida species are the most common cause of opportunistic fungal infection in humans. The genomic comparisons reveal striking gene family expansions associated with pathogenic species. Other aspects of Candida biology, including evolution of the genetic code, and the architecture of mating and meiotic processes, can also be addressed in the interspecies comparisons. Candida species are the most common cause of opportunistic fungal infection worldwide. Here, the genomes of six Candida species are sequenced and compared with each other and with related pathogens and non-pathogens; providing insight into the genetic features that underlie the diversity of Candida biology, including pathogenesis and the architecture of mating and meiotic processes.

This perspective article examines the state of the art regarding the field of polymers from renewable resources and attempts to give a critical appraisal of the situation related to a representative number of specific materials, in terms of their interest, present degree of advancement, and prospective development within short- and medium-term projections. The selected examples include polysaccharides and their derivatives, lignin, suberin, vegetable oils, tannins, natural monomers like terpenes, and monomers derived from sugars, with particular emphasis on furan derivatives and lactic acid, bacterial cellulose, and poly(hydroxyalkanoates), ending with a brief assessment of the potential role of glycerol and ethanol as future precursors to monomers.

Plastics have become a severe transboundary threat to natural ecosystems and human health, with studies predicting a twofold increase in the number of plastic debris (including micro and nano-sized plastics) by 2030. However, such predictions will likely be aggravated by the excessive use and consumption of single-use plastics (including personal protective equipment such as masks and gloves) due to COVID-19 pandemic. This review aimed to provide a comprehensive overview on the effects of COVID-19 on macroplastic pollution and its potential implications on the environment and human health considering short- and long-term scenarios; addressing the main challenges and discussing potential strategies to overcome them. It emphasises that future measures, involved in an emergent health crisis or not, should reflect a balance between public health and environmental safety as they are both undoubtedly connected. Although the use and consumption of plastics significantly improved our quality of life, it is crucial to shift towards sustainable alternatives, such as bio-based plastics. Plastics should remain in the top of the political agenda in Europe and across the world, not only to minimise plastic leakage and pollution, but to promote sustainable growth and to stimulate both green and blue- economies. Discussions on this topic, particularly considering the excessive use of plastic, should start soon with the involvement of the scientific community, plastic producers and politicians in order to be prepared for the near future.

The Multilingual Turn is a ‘plaidoyer’ for an epistemological change in applied linguistics, within three main areas: second language acquisition (SLA), teaching English for speakers of other langu...

Ionic liquids (ILs) have been proposed as promising media for the extraction and separation of bioactive compounds from the most diverse origins. This critical review offers a compilation on the main results achieved by the use of ionic-liquid-based processes in the extraction and separation/purification of a large range of bioactive compounds (including small organic extractable compounds from biomass, lipids, and other hydrophobic compounds, proteins, amino acids, nucleic acids, and pharmaceuticals). ILs have been studied as solvents, cosolvents, cosurfactants, electrolytes, and adjuvants, as well as used in the creation of IL-supported materials for separation purposes. The IL-based processes hitherto reported, such as IL-based solid-liquid extractions, IL-based liquid-liquid extractions, IL-modified materials, and IL-based crystallization approaches, are here reviewed and compared in terms of extraction and separation performance. The key accomplishments and future challenges to the field are discussed, with particular emphasis on the major lacunas found within the IL community dedicated to separation processes and by suggesting some steps to overcome the current limitations.