Model Revision of Logical Regulatory Networks Using Logic-Based Tools

Recently, biological data has been increasingly produced calling for the existence of computational models able to organize and computationally reproduce existing observations. In particular, biological regulatory networks have been modeled relying on the Sign Consistency Model or the logical formalism. However, their construction still completely relies on a domain expert to choose the best functions for every network component. Due to the number of possible functions for k arguments, this is typically a process prone to error. Here, we propose to assist the modeler using logic-based tools to verify the model, identifying crucial network components responsible for model inconsistency. We intend to obtain a model building procedure capable of providing the modeler with repaired models satisfying a set of pre-defined criteria, therefore minimizing possible modeling errors

Quantification of reachable attractors in asynchronous discrete dynamics

Motivation: Models of discrete concurrent systems often lead to huge and complex state transition graphs that represent their dynamics. This makes difficult to analyse dynamical properties. In particular, for logical models of biological regulatory networks, it is of real interest to study attractors and their reachability from specific initial conditions, i.e. to assess the potential asymptotical behaviours of the system. Beyond the identification of the reachable attractors, we propose to quantify this reachability. Results: Relying on the structure of the state transition graph, we estimate the probability of each attractor reachable from a given initial condition or from a portion of the state space. First, we present a quasi-exact solution with an original algorithm called Firefront, based on the exhaustive exploration of the reachable state space. Then, we introduce an adapted version of Monte Carlo simulation algorithm, termed Avatar, better suited to larger models. Firefront and Avatar methods are validated and compared to other related approaches, using as test cases logical models of synthetic and biological networks. Availability: Both algorithms are implemented as Perl scripts that can be freely downloaded from http://compbio.igc.gulbenkian.pt/nmd/node/59 along with Supplementary Material.Comment: 19 pages, 2 figures, 2 algorithms and 2 table

Partial Order on the set of Boolean Regulatory Functions

Logical models have been successfully used to describe regulatory and signaling networks without requiring quantitative data. However, existing data is insufficient to adequately define a unique model, rendering the parametrization of a given model a difficult task. Here, we focus on the characterization of the set of Boolean functions compatible with a given regulatory structure, i.e. the set of all monotone nondegenerate Boolean functions. We then propose an original set of rules to locally explore the direct neighboring functions of any function in this set, without explicitly generating the whole set. Also, we provide relationships between the regulatory functions and their corresponding dynamics. Finally, we illustrate the usefulness of this approach by revisiting Probabilistic Boolean Networks with the model of T helper cell differentiation from Mendoza & Xenarios

The landscape and plant communities of Serra da Arrábida

The field trip takes place in the biogeographic territories of the Sadensean-Dividing Portuguese Subprovince (Coastal Lusitan- Andalusian Province, Mediterranean Region), throughout the upper thermomediterranean thermotype and subhumid ombrotype

Climate change impacts on water supply: implications for reservoir management in upper Sabor, northeast Portugal

Climate change scenarios project warmer temperatures and less precipitation in Mediterranean watersheds. This can aggravate drought conditions, with negative impacts on water supply. Here, reservoirs may play an important role to mitigate these impacts. However, the implications of climate change are not always considered in the reservoir planning and management. This study aimed to address this issue for the Upper Sabor watershed, northeast Portugal. This is a medium watershed (403km2), part of the Sabor river, a tributary of Douro (one of the major rivers in the Iberian Peninsula). It is a mountainous watershed (up to 1500m), characterized by humid Mediterranean climate, with three dry months in summer. Almost 52% of the area is occupied by shrubland and 18% agriculture. Water supply for about 33 000 people has been based almost exclusively in one reservoir, but constant problems of water supply in dry summers, which coincide with a doubling of population due to summer holidays, led to the construction of a new reservoir in 2015. The Soil andWater Assessment Tool (SWAT) model was used for a climate change impact assessment, considering the current water supply regime (single reservoir) and the construction of the new reservoir. SWAT was calibrated and validated against daily-observed discharge and reservoir volume, with a good agreement between model predictions and observations. Results from four GCMs (General Circulation Models) for two scenarios (RCP 4.5 and RCP 8.5) were statistically downscaled and bias-corrected with ground observations; climate scenarios for 2021-2040 and 2041-2060 were compared with a control period in 1981-2000. In the future, a general increase of temperatures is expected in the Upper Sabor watershed, especially in the maximum temperature under RCP 8.5 scenario for 2041-2060 (Tmax: +2.88ºC). The change in precipitation is more uncertain, with larger differences according to the selected climate model. Annual precipitation would slightly decrease in RCP 8.5, less than 1% change compared to 1981-2000. However, seasonal changes would be more significant, with more precipitation in winter (+ 6.8%) and much less in spring and summer (-13.2% and -14.9%, respectively). In turn, an annual increase in precipitation is expected under RCP 4.5 for 2021-2040 (+1.8%) and a higher decrease for 2041-2060 (+6.4%), when compared to RCP 8.5. For hydrological impacts, SWAT results showed a small reduction in river discharge, more pronounced under RCP 8.5 for 2041-2060, for the spring and summer months. Results showed that the existence of two reservoirs will solve the water supply problems in current conditions, but in future conditions the reliability of this solution will decrease, especially under scenario RCP 8.5 for 2041-2060 (reliability of water supply below 80%). Here, the variability given by the different climate models simulated in SWAT brings some uncertainty. The main conclusion of this study is that the solution for water supply in this region, calculated taking only present-day climate into account, will be inefficient for water supply management under future climates. Taking climate change into account would have avoided the need for further investment in the near future. It is a mountainous watershed (up to 1500m), characterized by humid Mediterranean climate, with three dry months in summer. Almost 52% of the area is occupied by shrubland and 18% agriculture. Water supply for about 33 000 people has been based almost exclusively in one reservoir, but constant problems of water supply in dry summers, which coincide with a doubling of population due to summer holidays, led to the construction of a new reservoir in 2015. The Soil andWater Assessment Tool (SWAT) model was used for a climate change impact assessment, considering the current water supply regime (single reservoir) and the construction of the new reservoir. SWAT was calibrated and validated against daily-observed discharge and reservoir volume, with a good agreement between model predictions and observations. Results from four GCMs (General Circulation Models) for two scenarios (RCP 4.5 and RCP 8.5) were statistically downscaled and bias-corrected with ground observations; climate scenarios for 2021-2040 and 2041-2060 were compared with a control period in 1981-2000. In the future, a general increase of temperatures is expected in the Upper Sabor watershed, especially in the maximum temperature under RCP 8.5 scenario for 2041-2060 (Tmax: +2.88ºC). The change in precipitation is more uncertain, with larger differences according to the selected climate model. Annual precipitation would slightly decrease in RCP 8.5, less than 1% change compared to 1981-2000. However, seasonal changes would be more significant, with more precipitation in winter (+ 6.8%) and much less in spring and summer (-13.2% and -14.9%, respectively). In turn, an annual increase in precipitation is expected under RCP 4.5 for 2021-2040 (+1.8%) and a higher decrease for 2041-2060 (+6.4%), when compared to RCP 8.5. For hydrological impacts, SWAT results showed a small reduction in river discharge, more pronounced under RCP 8.5 for 2041-2060, for the spring and summer months. Results showed that the existence of two reservoirs will solve the water supply problems in current conditions, but in future conditions the reliability of this solution will decrease, especially under scenario RCP 8.5 for 2041-2060 (reliability of water supply below 80%). Here, the variability given by the different climate models simulated in SWAT brings some uncertainty. The main conclusion of this study is that the solution for water supply in this region, calculated taking only present-day climate into account, will be inefficient for water supply management under future climates. Taking climate change into account would have avoided the need for further investment in the near future

Sintra vegetation and landscape

The field trip to Sintra region, as part of the 48th IAVS Symposium, aims to illustrate well-preserved and representative plant communities of Sintra municipality. It consists of two short field stops and a 3 km wal

Goat Kidding Dataset

The detection of kidding in production animals is of the utmost importance, given the frequency of problems associated with the process, and the fact that timely human help can be a safeguard for the well-being of the mother and kid. The continuous human monitoring of the process is expensive, given the uncertainty of when it will occur, so the establishment of an autonomous mechanism that does so would allow calling the human responsible who could intervene at the opportune moment. The present dataset consists of data from the sensorization of 16 pregnant and two non-pregnant Charnequeira goats, during a period of four weeks, the kidding period. The data include measurements from neck to floor height, measured by ultrasound and accelerometry data measured by an accelerometer existing at the monitoring collar. Data was continuously sampled throughout the experiment every 10 s. The goats were monitored both in the goat shelter (day and night) and during the grazing period in the pasture. The births of the animals were also registered, both in terms of the time at which they took place, but also with details regarding how they took place and the number of offspring, and notes were also added.info:eu-repo/semantics/publishedVersio

Sheep Nocturnal Activity Dataset

Monitoring sheep’s behavior is of paramount importance, because deviations from normal patterns may indicate nutritional, thermal or social stress, changes in reproductive status, health issues, or predator attacks. The night period, despite being a more restful period in which animals are theoretically sleeping and resting, represents approximately half of the life cycle of animals; therefore, its study is of immense interest. Wearable sensors have become a widely recognized technique for monitoring activity, both for their precision and the ease with which the sensorized data can be analyzed. The present dataset consists of data from the sensorization of 18 Serra da Estrela sheep, during the nocturnal period between 18 November 2021 and 16 February 2022. The data contain measurements taken by ultrasound and accelerometry of the height from neck to ground, as well as measurements taken by an accelerometer in the monitoring collar. Data were collected every 10 s when the animals were in the shelter. With the collection of data from various sensors, active and inactive periods can be identified throughout the night, quantifying the number and average time of those periods.info:eu-repo/semantics/publishedVersio

The application of the Habitats Directive in Portugal

A succinct review of the application of the Habitats Directive in Portugal is presented. Since 1971 until 2000 Portugal has defined approximately 8,8% of its territory as national protected areas. With the application of the Habitats Directive nature conservation policies extended to more than 17,4 % of the territory increasing by 98% and the knowledge on vegetation community’s habitats was certainly deepened. Including special protection areas (Birds Directive) the Portuguese territory under one or more conservation status totals 21,5%. Finally, the support given by the Portuguese Phytosociology Association – ALFA in the detailed description of the Directive habitats is divulged, showing the importance, usefulness and efficacy of phytosociologic studies

Climate change impacts on water resources and reservoir management: uncertainty and adaptation for a mountain catchment in Northeast Portugal

Reservoirs often play an important role in mitigating water supply problems. However, the implications of climate change are not always considered in reservoir planning and management. This study aimed to address this challenge in the Alto Sabor watershed, northeast Portugal. The study analysed whether or not the shortage of water supply can be effectively addressed through the construction of a new reservoir (two-reservoir system) by considering future climate projections. The hydrological model Soil and Water Assessment Tool (SWAT) was calibrated and validated against daily-observed discharge and reservoir volume, with a good agreement between model predictions and observations. Outputs from four General Circulation Models (GCM) for two scenarios (RCP 4.5 and 8.5) were statistically downscaled and bias-corrected with ground observations. A general increase in temperature is expected in the future while the change in precipitation is more uncertain as per the differences among climatic models. In general, annual precipitation would slightly decrease while seasonal changes would be more significant, with more precipitation in winter and much less in spring and summer. SWAT simulations suggest that the existence of two-reservoir will better solve the water supply problems under current climate conditions compared to a single-reservoir system. However in the future, the reliability of this solution will decrease, especially due to the variability of projections from the different climatic models. The solution to water supply problems in this region, adopted taking only present-day climate into account, will likely be inefficient for water supply management under future climate conditions.This work was funded by FEDER funds through the Operational Programme for Competitiveness Factors - COMPETE and by National Funds through FCT - Foundation for Science and Technology under the project PTDC/AAG-MAA/4539/2012 / FCOMP-01-0124-FEDER-027863 (IND_CHANGE). J.P. Nunes was financially supported by FCT (Portuguese Science Foundation), and the European Social Fund through post-doctoral grant (SFRH/BPD/87571/2012). A.T. Monteiro is supported by FEDER funds through the Operational Programme for Competitiveness Factors - COMPETE and by National Funds through FCT - Foundation for Science and Technology under the UID/BIA/50027/2013 and POCI-01-0145-FEDER-006821. The authors would like to thank the Municipality of Bragança for the datasets on water inflows.info:eu-repo/semantics/publishedVersio