Causal Consistency Verification in Restful Systems

Replicated systems cannot maintain both availability and (strong) consistency when exposed to network partitions. Strong consistency requires every read to return the last written value, which can lead clients to experience high latency or even timeout errors. Replicated applications usually rely on weak consistency, since clients can perform operations contacting a single replica, leading to decreased latency and increased availability. Causal consistency is a weak consistency model, however, it is the strongest one for highly available systems. Many applications are switching to this particular consistency model, since it ensures users never observe data items before they observe the ones that influenced their creation. Verifying if applications satisfy the consistency they claim to provide is no easy task. In this dissertation, we propose an algorithm to verify causal consistency in RESTful applications. Our approach adopts a black box testing, where multiple concurrent clients execute operations in a service and records the log of interactions. This log of interactions is then processed to verify if the results respect causal consistency. The key challenge is to infer causal dependencies among operations executed in different clients without adding any additional metadata to the data maintained by the service. When considering a particular operation, the algorithm builds a new dependency graph that considers one of the possible justifications the operation might have, but if this justification results in failure further ahead in the processing, it is necessary to build another graph considering another justification of that same operation. The algorithm relies on recursion in order to achieve this backtracking behaviour. If the algorithm is able to build a graph containing every operation present in the log, where the chosen justifications remain valid until the end of the processing, it outputs that the execution corresponding to that log satisfies causal consistency. The evaluation confirms that the algorithm is able to detect violations when feeding either small or large logs representing executions of RESTful applications that do not satisfy causal consistency.Os sistemas replicados não podem manter a disponibilidade e a consistência (forte) quando expostos a partições de rede. A consistência forte exige que cada leitura retorne o último valor escrito, o que pode levar os clientes a experienciar alta latência ou até mesmo erros de tempo limite. As aplicações replicados geralmente usam consistência fraca, pois os clientes podem realizar operações contactando uma única réplica, levando a latências baixas e maior disponibilidade. A consistência causal é um modelo de consistência fraco, mas é o mais forte para sistemas altamente disponíveis. Muitas aplicações usam este modelo, pois garante que os clientes nunca observem dados antes de observar os que influenciaram a sua criação. Verificar se as aplicações satisfazem a consistência que alegam fornecer não é fácil. Nesta dissertação, propomos um algoritmo para verificar a consistência causal em aplicações RESTful. A nossa abordagem adota um teste de caixa negra, onde vários clientes concurrentes executam operações num serviço, onde as interações são documentadas num ficheiro. Este ficheiro é processado para verificar se os resultados respeitam a consistência causal. O principal desafio é inferir as dependências causais entre as operações executadas em diferentes clientes sem adicionar metadados adicionais aos dados mantidos pelo serviço. Ao considerar uma determinada operação, o algoritmo constrói um novo grafo de dependências que considera uma das possíveis justificações que a operação possa ter, mas se esta justificação resultar em erro mais tarde no processamento, é necessário construir outro grafo considerando outra justificação dessa mesma operação. O algoritmo é recursivo de modo a alcançar esse comportamento de retrocesso. Se o algoritmo conseguir construir um grafo que contém todas as operações presentes no ficheiro, onde as justificações escolhidas permanecem válidas até o final do processamento, indica que a execução correspondente a este ficheiro satisfaz a consistência causal. Aavaliação confirma que o algoritmo é capaz de detectar violações ao fornecer ficheiros pequenos ou grandes representando execuções de aplicações RESTful que não satisfazem a consistência causal

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

Mitochondrial physiology

As the knowledge base and importance of mitochondrial physiology to evolution, health and disease expands, the necessity for harmonizing the terminology concerning mitochondrial respiratory states and rates has become increasingly apparent. The chemiosmotic theory establishes the mechanism of energy transformation and coupling in oxidative phosphorylation. The unifying concept of the protonmotive force provides the framework for developing a consistent theoretical foundation of mitochondrial physiology and bioenergetics. We follow the latest SI guidelines and those of the International Union of Pure and Applied Chemistry (IUPAC) on terminology in physical chemistry, extended by considerations of open systems and thermodynamics of irreversible processes. The concept-driven constructive terminology incorporates the meaning of each quantity and aligns concepts and symbols with the nomenclature of classical bioenergetics. We endeavour to provide a balanced view of mitochondrial respiratory control and a critical discussion on reporting data of mitochondrial respiration in terms of metabolic flows and fluxes. Uniform standards for evaluation of respiratory states and rates will ultimately contribute to reproducibility between laboratories and thus support the development of data repositories of mitochondrial respiratory function in species, tissues, and cells. Clarity of concept and consistency of nomenclature facilitate effective transdisciplinary communication, education, and ultimately further discovery

Mitochondrial physiology

As the knowledge base and importance of mitochondrial physiology to evolution, health and disease expands, the necessity for harmonizing the terminology concerning mitochondrial respiratory states and rates has become increasingly apparent. The chemiosmotic theory establishes the mechanism of energy transformation and coupling in oxidative phosphorylation. The unifying concept of the protonmotive force provides the framework for developing a consistent theoretical foundation of mitochondrial physiology and bioenergetics. We follow the latest SI guidelines and those of the International Union of Pure and Applied Chemistry (IUPAC) on terminology in physical chemistry, extended by considerations of open systems and thermodynamics of irreversible processes. The concept-driven constructive terminology incorporates the meaning of each quantity and aligns concepts and symbols with the nomenclature of classical bioenergetics. We endeavour to provide a balanced view of mitochondrial respiratory control and a critical discussion on reporting data of mitochondrial respiration in terms of metabolic flows and fluxes. Uniform standards for evaluation of respiratory states and rates will ultimately contribute to reproducibility between laboratories and thus support the development of data repositories of mitochondrial respiratory function in species, tissues, and cells. Clarity of concept and consistency of nomenclature facilitate effective transdisciplinary communication, education, and ultimately further discovery

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

Make EU trade with Brazil sustainable

Brazil, home to one of the planet's last great forests, is currently in trade negotiations with its second largest trading partner, the European Union (EU). We urge the EU to seize this critical opportunity to ensure that Brazil protects human rights and the environment