HIV Infection: Time from Diagnosis to Initiation of Antiretroviral Therapy in Portugal, a Multicentric Study.

The benefits of antiretroviral therapy (ART) for persons living with HIV (PLWH) are well established. Rapid ART initiation can lead to improved clinical outcomes. Portugal has one of the highest rates of new HIV diagnoses in the European Union, and an average time until ART initiation above the recommendations established by the national guideline according to data from the first two years after its implementation in 2015, with no more recent data available after that. This study aimed to evaluate time from the first hospital appointment until ART initiation among newly diagnosed HIV patients in Portugal between 2017 and 2018, to investigate differences between hospitals, and to understand the experience of patient associations in supporting the navigation of PLWH throughout referral and linkage to the therapeutic process. To answer to these objectives, a twofold design was followed: a quantitative approach, with an analysis of records from five Portuguese hospitals, and a qualitative approach, with individual interviews with three representatives of patient associations. Overall, 847 and 840 PLWH initiated ART in 2017 and in 2018, respectively, 21 days (median of the two years) after the first appointment, with nearly half coming outside the mainstream service for hospital referral, and with observed differences between hospitals. In 2017-2018, only 38.0% of PLWH initiated ART in less than 14 days after the first hospital appointment. From the interviews, barriers of administrative and psychosocial nature were identified that may hinder access to ART. Patient associations work to offer a tailored support to patients' navigation within the health system, which can help to reduce or overcome those potential barriers. Indicators related to time until ART initiation can be used to monitor and improve access to specialized care of PLWH.

Impact of anthropogenic pressures on wild mammals of Northern Portugal.

BACKGROUND AND AIM: Wild mammals are among the most threatened species of the world in large part due to human activity. In this work, we used the method of partial least squares-path modeling associated with a geographic information system to analyze the impact of anthropogenic pressures on the mortality of wild mammals. MATERIALS AND METHODS: We collected the data related to the cause of death of native wild mammals admitted to the Wildlife Rehabilitation Centre of Parque Biológico de Gaia in Northern Portugal, during 10 years (2008-2017). RESULTS: A total of 359 animals from 42 municipalities (rural and urban areas) were included in the study. The main cause of death was of traumatic origin. From the anthropogenic pressures included in the study, water reservoirs, small companies, and residential buildings were the ones that contributed the most to increase the mortality of traumatic and non-traumatic origin. This relation of cause-effect (mortality-anthropogenic pressures) was supported by the high coefficients of determination obtained (R2 > 0.8). CONCLUSION: The present results allow a general view on the reality of mammal's mortality in Northern Portugal. Furthermore, it could also constitute a valuable tool for the conservation of wild mammals in those areas.

Development of a Hydrologic and Water Allocation Model to Assess Water Availability in the Sabor River Basin (Portugal).

The Sabor River basin is a large basin (3170 km2) located in the northeast of Portugal and used mostly for agroforestry. One problem this basin faces is a lack of water during the dry season, when there is a higher demand for water to irrigate crops. To solve this problem, the Portuguese government created a National Irrigation Program to finance new irrigation areas and improve existing ones. Consequently, it is necessary to evaluate the past and future water availability for agricultural and domestic consumption in the basin. This was done through the development of a hydrological and water allocation model. The Soil and Water Assessment Tool (SWAT) was used to model the hydrological processes that took place in the catchment between 1960 and 2008. The MIKE HYDRO Basin was used to simulate water allocation (irrigation and domestic consumption) in a historical view and under two scenarios. The historical view used the time period 1960-2008, and the two scenarios used the same time period but with an increase in the irrigated area. The first scenario simulated the irrigation of the total irrigable area that exists in the basin. The second scenario simulated a 29% increase in the olive grove area and a 24% decrease in the resident population, according to the projection for 2060. The results show that, in the historical view, the average annual water demand deficit was 31% for domestic consumption and 70% for irrigation, which represent 1372 × 103 m3 and 94 × 106 m3 of water, respectively. In the two scenarios, the water demand deficit increased to 37% for domestic consumption and 77% for irrigation. In the first scenario, the average annual water demand deficit was 183 × 106 m3 of water for irrigation. In the second scenario, the average annual water demand deficit was 385 × 103 m3 of water for domestic consumption, and 106 × 106 m3 of water for irrigating the expanded olive grove area. These results demonstrate that Portuguese farmers can use our model as a decision support tool to determine how much water needs to be stored to meet the present and future water demand.

Acoustic barriers as an acoustic deterrent for native potamodromous migratory fish species.

This study focused on the use of sound playbacks as acoustic deterrents to direct native potamodromous migratory species away from all kind of traps. The effects of two acoustic treatments, a repeated sine sweep up to 2 kHz (sweep-up stimulus) and an intermittent 140 Hz tone, were tested in three fish species native to Iberia: Salmo trutta, Pseudochondrostoma duriense and Luciobarbus bocagei. In contrast with S. trutta, the endemic cyprinids P. duriense and L. bocagei exhibited a strong repulse reaction to the frequency sweep-up sound. The 140 Hz stimulus did not seem to alter significantly the behaviour of any of the studied species. These results highlight the potential of acoustic stimuli as fish behavioural barriers and their application to in situ conservation measures of native Iberian fish populations, to protect them from hydropower dams. In addition, this study shows that acoustic deterrents can be used selectively on target species.

Preservation of wild bird species in northern Portugal - Effects of anthropogenic pressures in wild bird populations (2008-2017).

In this study we aim to obtain a holistic view over the consequences of human-induced threats to the wild bird populations in the study area, based on data collected from a Wildlife Rehabilitation Centre (WRC) through the method of Partial Least Squares-Path Modelling (PLS-PM). The study area comprised 76 rural and urban municipalities located in northern Portugal. Within PLS-PM the threats ("anthropogenic pressures") are termed exogenous latent variables, while the final environmental consequence (wild bird mortality) is termed endogenous latent variable. Latent variables are concepts assessed by numerical parameters. The PLS-PM results identified as most significant pressures, the number of small and medium companies in the municipalities, both in traumatic and non-traumatic deaths. Although the pattern of weights is similar regardless of the general cause of death, traumatic causes seem to play a more prominent role given the larger weights in the relevant specific causes (number of companies). The high coefficients of determination (R2 > 0,8) reveal that the variance of wild bird mortality is largely explained by the variance of the pressures, which indicates a cause-effect relationship between the independent (pressures) and dependent (mortality) variables. The ample coverage of northern Portugal with a huge dataset suggests that this cause-effect relationship is typical from this region. The use of a sophisticated statistical method PLS-PM and its incorporation into a Geographic Information System (GIS) revealed to be an important tool for analysing wildlife impacts of environmental and human factors. The results obtained with this model indicate that there is a substantial negative impact of human activity on wild bird mortality.

Fulfilling spawning flow requirements for potamodromous cyprinids in a restored river segment.

The Baixo Sabor hydroelectric scheme was recently constructed (began operating in 2015), blocking fish migration immediately at the river mouth. As a compensation measure for spawning habitat loss the Vilariça River which confluences with Sabor River, immediately downstream from the Baixo Sabor scheme, was chosen for rehabilitation site as an attempt to replace the spawning grounds lost in Sabor River for the potamodromous cyprinid Iberian barbel (Luciobarbus bocagei). Restoration activities included: placement of submerged weirs with fish ramps to increase the lotic/lentic sequence, bank reinforcement, boulder placement and river water profile increase. Water from the nearest reservoir was channeled underground to the lower Vilariça River in order to increase the water flow. The most appropriate volume of water was determined by means of a 1D model coupled with the CASiMiR to determine the weighted usable area for barbel spawners. Nine spawning grounds were identified. Fish migrations began in mid-April when water temperature increased (c. 16°C) and water flow decreased. Barbel tend to spawn in coarse substrate with shallow water and moderate current. Ontogenetic differences in habitat use were reported, with barbel juveniles preferring weaker currents and deeper zones when compared to spawners. Females also display different preferences, which are more apparent after spawning. Both life-stages exhibit the maximum habitat suitability at c. 1.5m3/s. The habitat model used in this study was able to accurately predict the occurrence of spawning grounds, representing, therefore, a valuable decision-making support tool for river managers.

The role of calcium concentration in the invasive capacity of Corbicula fluminea in crystalline basins.

The natural variation of environmental factors in freshwater basins determines their biodiversity. Among them, calcium is a key physiological compound for freshwater invertebrates. It is required for shell formation, muscle contraction, it mediates gene expression and allows counteracting acidosis during stress periods, among other functions. Although the distribution of different freshwater species has been suggested to be linked with the environmental calcium concentration, as yet, no research studies have confirmed this. Identifying whether environmental calcium concentrations might determine the invasion success of alien species would be critical in developing and implementing effective management strategies to control them. Here, a multidisciplinary approach integrating field surveys, analytical chemistry techniques, molecular biology analyses and a lab-scale experiment was taken to decipher whether the environmental calcium concentration might hamper the establishment of Corbicula fluminea in northwestern Iberian rivers. A Principal Component Analysis on water chemistry variables from 13 water bodies identified environmental calcium concentration, among others, as one key factor that best characterized the distribution area of C. fluminea. The calcium content in animals' bodies from two representative rivers was dependent on the environmental calcium concentration of freshwater basins; the lower the concentration, the lower the body's content. The expression of stress- and calcium homeostasis-related genes was higher in C. fluminea from low calcium concentration environments than in those from calcium-rich freshwater basins. Finally, under experimental conditions, lower water calcium concentrations decreased C. fluminea growth rates. The present data suggest, for the first time, that environmental calcium concentration may act as a determinant factor on the invasion success of C. fluminea in freshwater environments. Our results provide new clues for the identification of basins with increased risk of potential invasion by C. fluminea based on environmental calcium levels.

A multiple index integrating different levels of organization.

Many methods in freshwater biomonitoring tend to be restricted to a few levels of biological organization, limiting the potential spectrum of measurable of cause-effect responses to different anthropogenic impacts. We combined distinct organisational levels, covering biological biomarkers (histopathological and biochemical reactions in liver and fish gills), community based bioindicators (fish guilds, invertebrate metrics/traits and chironomid pupal exuviae) and ecosystem functional indicators (decomposition rates) to assess ecological status at designated Water Framework Directive monitoring sites, covering a gradient of human impact across several rivers in northern Portugal. We used Random Forest to rank the variables that contributed more significantly to successfully predict the different classes of ecological status and also to provide specific cut levels to discriminate each WFD class based on reference condition. A total of 59 Biological Quality Elements and functional indicators were determined using this procedure and subsequently applied to develop the integrated Multiple Ecological Level Index (MELI Index), a potentially powerful bioassessment tool.

A stochastic dynamic model to assess land use change scenarios on the ecological status of fluvial water bodies under the Water Framework Directive.

This method development paper outlines an integrative stochastic dynamic methodology (StDM) framework to anticipate land use (LU) change effects on the ecological status of monitored and non-monitored lotic surface waters under the Water Framework Directive (WFD). Tested in the Alto Minho River Basin District in North West Portugal, the model is an innovative step towards developing a decision-making and planning tool to assess the influence impacts such as LU change and climate change on these complex systems. Comprising a series of sequential steps, a Generalized Linear Model based, competing model Multi Model Inference (MMI) approach was used for parameter estimation to identify principal land use types (distal factors) driving change in biological and physicochemical support elements (proximal factors) in monitored water bodies. The framework integrated MMI constants and coefficients of selected LU categories in the StDM simulations and spatial projections to simulate the ecological status of monitored and non-monitored lotic waterbodies in the test area under 2 scenarios of (1) LU intensification and (2) LU extensification. A total of 100 simulations were run for a 50year period for each scenario. Spatially dynamic projections of WFD metrics were obtained, taking into account the occurrence of stochastic wildfire events which typically occur in the study region and are exacerbated by LU change. A marked projected decline to "Moderate" ecological status for most waterbodies was detected under intensification but little change under extensification; only a few waterbodies fell to "moderate" status. The latter scenario describes the actual regional socio-economic situation of agricultural abandonment due to rural poverty, partly explaining the projected lack of change in ecological status. Based on the WFD "one out all out" criterion, projected downward shifts in ecological status were due to physicochemical support elements, namely increased phosphorus levels. Little or no change in status was driven by Intercalibrated Biological Quality Elements, indicating innate resilience and raising questions concerning uncertainty, the effect of pressures other than land use and metric redundancy and the WFD classification process.

Modelling stream-fish functional traits in reference conditions: regional and local environmental correlates.

Identifying the environmental gradients that control the functional structure of biological assemblages in reference conditions is fundamental to help river management and predict the consequences of anthropogenic stressors. Fish metrics (density of ecological guilds, and species richness) from 117 least disturbed stream reaches in several western Iberia river basins were modelled with generalized linear models in order to investigate the importance of regional- and local-scale abiotic gradients to variation in functional structure of fish assemblages. Functional patterns were primarily associated with regional features, such as catchment elevation and slope, rainfall, and drainage area. Spatial variations of fish guilds were thus associated with broad geographic gradients, showing (1) pronounced latitudinal patterns, affected mainly by climatic factors and topography, or (2) at the basin level, strong upstream-downstream patterns related to stream position in the longitudinal gradient. Maximum native species richness was observed in midsize streams in accordance with the river continuum concept. The findings of our study emphasized the need to use a multi-scale approach in order to fully assess the factors that govern the functional organization of biotic assemblages in 'natural' streams, as well as to improve biomonitoring and restoration of fluvial ecosystems.

Evaluation of the ecological status of an impaired watershed by using a multi-index approach.

The objective of this study was to use an integrative approach to assess the ecological status of a small river impacted by multiple sources of disturbance. The River Febros (NW Portugal) is a small and highly impacted non-regulated river; approximately 44% of the watershed area is dedicated to agriculture, but there is also some urbanization. Environmental status was evaluated using a new multi-index approach, combining quality indices for water (Water Quality Index (WQI)), benthic macroinvertebrates (Iberian Biological Monitoring Working Party Index (IBMWP)), and human modification (Riparian Forest Quality Index (QBR)); Ecological Status River Mediterranean Index (ECOSTRIMED); River Habitat Survey (RHS)). Surveys were carried out between October 2002 and 2003, along four stretches of the main course of the river for physicochemical characteristics, as well as water microbiology and macroinvertebrates. Water quality was poor at all sites (WQI averaged 30.4%) and decreased downstream. The RHS (assessment of instream habitats and the river corridor) and the QBR quantification displayed the same trend. Macroinvertebrates diversity was permanently low with only the most tolerant insects taxa present; oligochaetes dominated. The ecological status of River Febros was well represented using the experimental assessment system, where a downstream decrease in condition was noticeable (in spite of a lower water quality upstream). Our results emphasize the importance of assessing several components of disturbed ecosystems in order to ascertain overall quality and the importance of promoting improvement of the riparian gallery as a buffer against multiple agents of disturbance.

Evaluating macroinvertebrate biological metrics for ecological assessment of streams in northern Portugal.

A procedure to select the most relevant metrics for assessing the ecological condition of the Douro basin (north Portugal) was developed based upon a set of 184 benthic community metrics. They were grouped into 16 biological categories selected from literature using data collected over 2 years from 54 sites along 31 rivers covering the whole perceived range of human disturbance. Multivariate analyses were carried out to identify the main trends in the macroinvertebrate data, to select reference versus impaired sites, to avoid multicolinearity between metrics, and to identify those that were clearly independent from natural stream typology. Structural metrics, adaptation metrics, and tolerance measures most effectively responded across a range of human influence. We find these attributes to be ecologically sound for monitoring Portugal's lotic ecosystems and providing information relevant to the Water Framework Directive, which asserts that the definition of water quality depends on its "ecological status", independent of the actual or potential uses of those waters.