Preventing Atomicity Violations with Contracts

Software developers are expected to protect concurrent accesses to shared regions of memory with some mutual exclusion primitive that ensures atomicity properties to a sequence of program statements. This approach prevents data races but may fail to provide all necessary correctness properties.The composition of correlated atomic operations without further synchronization may cause atomicity violations. Atomic violations may be avoided by grouping the correlated atomic regions in a single larger atomic scope. Concurrent programs are particularly prone to atomicity violations when they use services provided by third party packages or modules, since the programmer may fail to identify which services are correlated. In this paper we propose to use contracts for concurrency, where the developer of a module writes a set of contract terms that specify which methods are correlated and must be executed in the same atomic scope. These contracts are then used to verify the correctness of the main program with respect to the usage of the module(s). If a contract is well defined and complete, and the main program respects it, then the program is safe from atomicity violations with respect to that module. We also propose a static analysis based methodology to verify contracts for concurrency that we applied to some real-world software packages. The bug we found in Tomcat 6.0 was immediately acknowledged and corrected by its development team

Neural stem cells and cannabinoids in the spotlight as potential therapy for epilepsy

© 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).Epilepsy is one of the most common brain diseases worldwide, having a huge burden in society. The main hallmark of epilepsy is the occurrence of spontaneous recurrent seizures, having a tremendous impact on the lives of the patients and of their relatives. Currently, the therapeutic strategies are mostly based on the use of antiepileptic drugs, and because several types of epilepsies are of unknown origin, a high percentage of patients are resistant to the available pharmacotherapy, continuing to experience seizures overtime. Therefore, the search for new drugs and therapeutic targets is highly important. One key aspect to be targeted is the aberrant adult hippocampal neurogenesis (AHN) derived from Neural Stem Cells (NSCs). Indeed, targeting seizure-induced AHN may reduce recurrent seizures and shed some light on the mechanisms of disease. The endocannabinoid system is a known modulator of AHN, and due to the known endogenous antiepileptic properties, it is an interesting candidate for the generation of new antiepileptic drugs. However, further studies and clinical trials are required to investigate the putative mechanisms by which cannabinoids can be used to treat epilepsy. In this manuscript, we will review how cannabinoid-induced modulation of NSCs may promote neural plasticity and whether these drugs can be used as putative antiepileptic treatment.This work was supported by IF/01227/2015 and UID/BIM/50005/2019, projeto financiado pela Fundação para a Ciência e a Tecnologia (FCT)/Ministério da Ciência, Tecnologia e Ensino Superior (MCTES) através de Fundos do Orçamento de Estado. D.M.L. (PD/BD/141784/2018) and L.R.-R. (PD/BD/150344/2019) were in receipt of a fellowship from FCT. The authors are in hold of a H2020 Twinning Action from EU (EpiEpiNet).info:eu-repo/semantics/publishedVersio

Chemical and Microbiological Contamination in Limpet (Patella spp.) of the Portuguese Coast

Coastal production areas can be impacted by anthropogenic contamination from urban, agro-industrial and leisure activities. Some contaminants, such as chemical substances might also have a telluric origin. Non filter feeding univalve mollusks, such as limpets, which are collected in rocky shores either for sale or for auto-consumption, are very appreciated in Portugal, but have been excluded from provisions on the classification of production areas, although can present relevant contamination. Thus, the aim of this study was to assess the microbiological and toxic metal contaminations in limpets (Patella spp) of the Portuguese coast, taking into account the production area and seasonal variation, and comparing their contamination levels with those occurring in bivalve mollusk indicator species, mussel (Mytilus edulis). The risks associated to the consumption of limpet meals were also assessed. For that, microbial total and fecal levels and cadmium, lead and mercury contents in limpets and mussels samples from three coastal areas over several months were analyzed based on standard methodologies. Contents of mercury and lead in limpets from the three areas studied, were always below the limits of 0.50 mg kg-1 and 1.5 mg kg-1 allowed by the EU, respectively. Regarding cadmium, levels in limpet were always above the limit of 1.0 mg kg-1, reaching about 3.0 mg kg-1 in some samples. These values probably indicate contamination from telluric origin (soil or rocks) in the coastal studied areas. Results indicated that microbiological contamination of fecal origin was low and in general below the detection level. Contamination levels did not show a clear seasonal pattern. The two mollusk species, limpets and mussels, differed statistically in all contaminants analyzed, being cadmium the most of concern, and always higher in limpets than in mussel samples. Thus, the potential risk associated with limpet consumption, taking into account the cadmium tolerable weekly intake (TWI), was investigated, being possible to reach a reliable recommendation of less than a monthly meal of 160 g. As recreational picking of limpets is common in Portugal, official 4recommendations of maximum periodic human consumption should be published and enforcement increased in forbidden areasinfo:eu-repo/semantics/acceptedVersio

MAMMALS IN PORTUGAL : A data set of terrestrial, volant, and marine mammal occurrences in P ortugal

Mammals are threatened worldwide, with 26% of all species being includedin the IUCN threatened categories. This overall pattern is primarily associatedwith habitat loss or degradation, and human persecution for terrestrial mam-mals, and pollution, open net fishing, climate change, and prey depletion formarine mammals. Mammals play a key role in maintaining ecosystems func-tionality and resilience, and therefore information on their distribution is cru-cial to delineate and support conservation actions. MAMMALS INPORTUGAL is a publicly available data set compiling unpublishedgeoreferenced occurrence records of 92 terrestrial, volant, and marine mam-mals in mainland Portugal and archipelagos of the Azores and Madeira thatincludes 105,026 data entries between 1873 and 2021 (72% of the data occur-ring in 2000 and 2021). The methods used to collect the data were: live obser-vations/captures (43%), sign surveys (35%), camera trapping (16%),bioacoustics surveys (4%) and radiotracking, and inquiries that represent lessthan 1% of the records. The data set includes 13 types of records: (1) burrowsjsoil moundsjtunnel, (2) capture, (3) colony, (4) dead animaljhairjskullsjjaws, (5) genetic confirmation, (6) inquiries, (7) observation of live animal (8),observation in shelters, (9) photo trappingjvideo, (10) predators dietjpelletsjpine cones/nuts, (11) scatjtrackjditch, (12) telemetry and (13) vocalizationjecholocation. The spatial uncertainty of most records ranges between 0 and100 m (76%). Rodentia (n=31,573) has the highest number of records followedby Chiroptera (n=18,857), Carnivora (n=18,594), Lagomorpha (n=17,496),Cetartiodactyla (n=11,568) and Eulipotyphla (n=7008). The data setincludes records of species classified by the IUCN as threatened(e.g.,Oryctolagus cuniculus[n=12,159],Monachus monachus[n=1,512],andLynx pardinus[n=197]). We believe that this data set may stimulate thepublication of other European countries data sets that would certainly contrib-ute to ecology and conservation-related research, and therefore assisting onthe development of more accurate and tailored conservation managementstrategies for each species. There are no copyright restrictions; please cite thisdata paper when the data are used in publications.info:eu-repo/semantics/publishedVersio

Mammals in Portugal: a data set of terrestrial, volant, and marine mammal occurrences in Portugal

Mammals are threatened worldwide, with ~26% of all species being included in the IUCN threatened categories. This overall pattern is primarily associated with habitat loss or degradation, and human persecution for terrestrial mammals, and pollution, open net fishing, climate change, and prey depletion for marine mammals. Mammals play a key role in maintaining ecosystems functionality and resilience, and therefore information on their distribution is crucial to delineate and support conservation actions. MAMMALS IN PORTUGAL is a publicly available data set compiling unpublished georeferenced occurrence records of 92 terrestrial, volant, and marine mammals in mainland Portugal and archipelagos of the Azores and Madeira that includes 105,026 data entries between 1873 and 2021 (72% of the data occurring in 2000 and 2021). The methods used to collect the data were: live observations/captures (43%), sign surveys (35%), camera trapping (16%), bioacoustics surveys (4%) and radiotracking, and inquiries that represent less than 1% of the records. The data set includes 13 types of records: (1) burrows | soil mounds | tunnel, (2) capture, (3) colony, (4) dead animal | hair | skulls | jaws, (5) genetic confirmation, (6) inquiries, (7) observation of live animal (8), observation in shelters, (9) photo trapping | video, (10) predators diet | pellets | pine cones/nuts, (11) scat | track | ditch, (12) telemetry and (13) vocalization | echolocation. The spatial uncertainty of most records ranges between 0 and 100 m (76%). Rodentia (n =31,573) has the highest number of records followed by Chiroptera (n = 18,857), Carnivora (n = 18,594), Lagomorpha (n = 17,496), Cetartiodactyla (n = 11,568) and Eulipotyphla (n = 7008). The data set includes records of species classified by the IUCN as threatened (e.g., Oryctolagus cuniculus [n = 12,159], Monachus monachus [n = 1,512], and Lynx pardinus [n = 197]). We believe that this data set may stimulate the publication of other European countries data sets that would certainly contribute to ecology and conservation-related research, and therefore assisting on the development of more accurate and tailored conservation management strategies for each species. There are no copyright restrictions; please cite this data paper when the data are used in publications

Lineage-specific changes in mitochondrial properties during neural stem cell differentiation

© 2024 Soares et al. This article is available under a Creative Commons License (Attribution 4.0 International, as described at https://creativecommons.org/licenses/by/4.0/).Neural stem cells (NSCs) reside in discrete regions of the adult mammalian brain where they can differentiate into neurons, astrocytes, and oligodendrocytes. Several studies suggest that mitochondria have a major role in regulating NSC fate. Here, we evaluated mitochondrial properties throughout NSC differentiation and in lineage-specific cells. For this, we used the neurosphere assay model to isolate, expand, and differentiate mouse subventricular zone postnatal NSCs. We found that the levels of proteins involved in mitochondrial fusion (Mitofusin [Mfn] 1 and Mfn 2) increased, whereas proteins involved in fission (dynamin-related protein 1 [DRP1]) decreased along differentiation. Importantly, changes in mitochondrial dynamics correlated with distinct patterns of mitochondrial morphology in each lineage. Particularly, we found that the number of branched and unbranched mitochondria increased during astroglial and neuronal differentiation, whereas the area occupied by mitochondrial structures significantly reduced with oligodendrocyte maturation. In addition, comparing the three lineages, neurons revealed to be the most energetically flexible, whereas astrocytes presented the highest ATP content. Our work identified putative mitochondrial targets to enhance lineage-directed differentiation of mouse subventricular zone-derived NSCs.This work was supported by the European Molecular Biology Organization (EMBO), IG#3309; Fundação para a Ciência e Tecnologia (FCT) (PTDC/MED-NEU/7976/2020); International Society for Neurochemistry (ISN) Career Development Grant; and International Brain Research Organization (IBRO) Early Career Award. R Soares (PD/BD/128280/2017, COVID/BD/151619/2021, and IMM/BI/8-2021) and DM Lourenço (PD/BD/141784/2018 and COVID/BD/152658/2022) were in receipt of a fellowship from FCT. VA Morais is supported by FCT (IF/01693/2014; IMM/CT/27-2020). This project has received funding from H2020-WIDESPREAD-05-2020-Twinning (EpiEpinet) under grant agreement No 952455. We thank members of the VA Morais and AM Sebastião Labs for fruitful discussions. We would like to thank the BioImaging Facility, with a special thanks to José Rino, António Temudo, and Ana Nascimento and the Rodent Facility of Instituto de Medicina Molecular João Lobo Antunes for their technical support, and we also acknowledge the funding PPBI-POCI-01-0145-FEDER-022122.info:eu-repo/semantics/publishedVersio

The neurosphere assay : an effective in vitro technique to study neural stem cells

© 2021, Wolters Kluwer Medknow Publications. This is an open access journal, and articles are distributed under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 License, which allows others to remix, tweak, and build upon the work non-commercially, as long as appropriate credit is given and the new creations are licensed under the identical termsNeural stem cells (NSCs) are known to be present in the adult mammalian brain where they constitutively differentiate into the neuronal, astroglial, and oligodendroglial lineages, in defined processes termed n e u ro ge n e s i s , a st ro g l i o ge n e s i s a n d oligodendrogenesis, respectively (reviewed in Braun and Jessberger, 2014). During brain development, NSCs are present throughout the brain, becoming progressively restricted to defined brain regions. In the adult brain, NSCs are mainly present in areas classically known as neurogenic niches, i.e. the subventricular zone (SVZ), along the lateral walls of the lateral ventricles, and the subgranular zone, located in the dentate gyrus (DG) of the hippocampus. These areas are particularly enriched with NSCs, which not only are multipotent cells but also proliferative cells with the ability to selfrenew, thus maintaining their own pool of cells. In fact, neurogenesis, astrogliogenesis and oligodendrogenesis are highly intricate processes comprising several steps, including proliferation, differentiation, migration, and functional integration of the newly formed cells in the existing circuitry, which are regulated by a plethora of factors. These newly differentiated adult-born cells have the capacity to continuously modulate brain function and plasticity, by constantly reacting to external or internal stimuli (reviewed in Braun and Jessberger, 2014).This work was supported by IF/01227/2015 and UID/BIM/50005/2019, projeto financiado pela Fundação para a Ciência e a Tecnologia (FCT)/Ministério da Ciência, Tecnologia e Ensino Superior (MCTES) através de Fundos do Orçamento de Estado. RS (SFRH/BD/128280/2017), FFR (IMM/CT/35-2018), DML (PD/BD/141784/2018), and RSR (SFRH/BD/129710/2017) received a fellowship from FCTinfo:eu-repo/semantics/publishedVersio