Technical note: Seamless extraction and analysis of river networks in R

Spatially explicit mathematical models are key to a mechanistic understanding of environmental processes in rivers. Such models necessitate extended information on networks' morphology, which is often retrieved from geographic information system (GIS) software, thus hindering the establishment of replicable script-based workflows. Here I present rivnet, an R package for GIS-free extraction and analysis of river networks based on digital elevation models (DEMs). The package exploits TauDEM's flow direction algorithm in user-provided or online accessible DEMs, and allows for computing covariate values and assigning hydraulic variables across any network node. The package is designed so as to require minimal user input while allowing for customization for experienced users. It is specifically intended for application in models of ecohydrological, ecological or biogeochemical processes in rivers. As such, rivnet aims to make river network analysis accessible to users unfamiliar with GIS-based and geomorphological methods and therefore enhance the use of spatially explicit models in rivers.</p

Topological fundamental group and enriched monodromy equivalence

The theory of covering spaces is well-behaved when the base spaceis locally path connected and semilocally 1-connected. Following works of Brazas, by generalizing the notion of covering to that of semicovering, by defining a topological fundamental group and enriching over Top the usual monodromy functor, we get an extended theory which is well-behaved with respect to a wider class of spaces, namely locally wep-connected topological spaces.ope

Growth performance, carcass traits and meat quality of growing pigs on different feeding regimes slaughtered at 145\u2009kg BW

This study investigated the effects of feeding regime on growth performance, carcass traits and meat quality of pigs slaughtered at around 145 kg BW. A total of 96 barrows housed in eight pens were allotted to three groups in each pen. One group was fed ad libitum (AL) and the others were fed according to two quasi AL feeding regimes adjusting feed allowances with increasing BW. At slaughterhouse, the weights of the main lean and fat cuts were recorded, and a sample of longissimus lumborum (LL) was taken for physical and chemical analyses. Average daily gain (ADG) approached 940 g d1, and gain to feed ratio (G:F) was close to 0.38. Compared with the AL-feeding regime, the feed restriction reduced the pigs\u2019 ADG (3.5%), feed intake (7.4%) and carcass weight (3%) (p<0.01), but improved their G:F (\ufe4%, p<0.01). Feeding regime did not affect meat quality traits and exerted only minor effects on the weight of primal cuts and on the fatty acid composition of the intramuscular fat of the LL. However, AL-fed pigs tended to yield heavier fat cuts and showed a greater proportion of saturated fatty acid in the LL when compared to restricted feed barrows. In conclusion, moderate restriction in the feeding of medium\u2013heavy pigs seems advisable, as it improves feed efficiency and could cut feed costs compared with the AL-feeding regime without affecting carcass and meat characteristics

Body and milk quality traits of purebred Holstein and three-generation crossbred cows from Viking Red, Montbéliarde, and Holstein sires

The objective of this study was to investigate the effects of 3-way rotational crossbreeding scheme of Holstein (HO) cows with Montbéliarde (MO), Viking Red (VR) and HO sires on body and milk quality traits. Cows were purebred HO; F1:(MO × HO; VR × HO); F2: [MO × (VR × HO); VR × (MO × HO)]; F3: {HO ×[MO ×(VR ×HO)]}; HO ×[VR x (MO ×HO)]}. Data were collected on 745 cows kept in a commercial farm located in Northern Italy. Milk data were acquired from official milk recording and body condition score (BCS) and conformation traits were measured once by trained evaluator. Data were analyzed using a linear model including fixed effects of parity, DIM class and breed combinations. Average body traits: height at withers (HW), body length (BL) and heart girth (HG) of cows were 139, 162 and 207 cm respectively. Crossbred cows had shorter HW, BL and HG than pure HO but greater BCS. Milk yield averaged 31.5 kg/d, with fat and protein content close to 3.8 and 3.75%, respectively. Purebred HO produced greater volume of milk than crossbreds but milk from HO had lower protein content. Different combinations of crossbred cows showed similar performance in terms of milk yield traits, but evidenced different body size. The trial is currently in progress to increase cow sample size and widen the number of herds involved

La causalità della colpa. Evitabilità e comportamento alternativo lecito nelle fattispecie colpose causalmente orientate

The study of “culpability causation” as a dogmatic category underlines the complex logical and juridical connection between the offender’s behavior and the occurrence of a criminal event, particularly when the perpetration of a crime is determined by the mere occurrence of such criminal event and the offence is committed without intent. Indeed, the said legal principle is one of the most debated among today’s criminal law scholars and touches upon some grey areas in the analysis of causality vs. attribution of the crime to the offender, as well as culpability vs. omitting conduct. This paper follows the same methodology throughout, and carefully distinguishes between the static-dogmatic approach and the dynamic-court based approach. With this in mind, the author examines in depth the so-called “second stage” of the culpability causation test, i.e. whether the offender could have prevented the occurrence of a criminal event by keeping a proper conduct (which is commonly regarded as the benchmark analysis for this particular category of crimes). The issue of evitability of the criminal event is discussed both in an ex ante perspective (i.e. how criminal policy should deal with the breach of preventative rules of conduct), and in an ex post perspective (i.e. the court determination of whether keeping a proper conduct would have prevented the occurrence of the event). The paper then focuses on the different way of implementing the aforementioned test in offences committed by action as opposed to those committed by omission, by reviewing the applicable case law as well as scholarly opinions. In this regard, the main theories that have propelled the debate in this field of study are put to test and constructively debated. Following an analysis of the fallacies inherent with the principles of objective attribution of a criminal event to the offender and conditional causality based on the application of scientific rules, the paper proposes an alternative theory based on a different interpretation of crime-constituting elements, which values the heuristic potential of culpability causation in its genuine sense. Whilst culpability causation in principle may be regarded as part of the culpability assessment, at least judging from the consolidated case law (i.e. the objective element of evitability), the effect of this qualification on court practice (inevitably certain criminal actions would go unpunished) compels the author to find a different approach based on a more balanced application of the rules examined in the paper. Considering the need for retrieving a more dynamic concept of criminal action, which is nevertheless able to capture the many actual connotations of human behavior, the author suggests that culpability causation should find its place in the hermeneutics of the principle of harm, as an element embedded in the same which gives significance to the concept of criminal offence as a whole. Such qualification – which the paper puts forth by highlighting the impending need for a review of the general theory of criminal offence – seems to be the right balance between the conflicting souls of culpability causation, in addition to being grounded on solid philosophical and scholarly foundations, rather than on the deductive study of human action alone

Ecohydrological and Metacommunity Studies of Proliferative Kidney Disease Spread in Freshwater Salmonid Fish

Proliferative kidney disease (PKD) is a high-mortality pathology affecting freshwater salmonid populations in Europe and North America. Its causative agent, the myxozoan Tetracapsuloides bryosalmonae, has a complex life-cycle exploiting freshwater bryozoans (mainly Fredericella sultana) and salmonids as hosts. PKD has recently increased in incidence and severity, causing remarkable declines in fish catches. In addition, environmental change is feared to cause PKD outbreaks in regions at higher latitude and altitude, as warmer water temperatures exacerbate disease development and fish mortality. In this perspective, this Thesis develops an integrated approach, involving field and modelling work, for the prediction of the incidence of PKD in river basins. In particular, the Thesis develops a novel spatially-explicit model of PKD epidemiology in riverine host metacommunities. The model, summarizing the current knowledge on disease transmission modes and parasite's life-cycle, accounts for both local population and disease dynamics of bryozoans and fish, as well as hydrodynamic dispersion of parasite spores and hosts along the river network. Model validation was attained through an integrated study of PKD in a prealpine Swiss river, where data on fish abundance, disease prevalence, concentration of primary hosts' and parasite's DNA in environmental samples (eDNA) and water temperatures were gathered at multiple locations within the catchment. In this context, a new method for predicting the spatial distribution of bryozoan density based on eDNA samples was developed. As water temperature is crucial to PKD severity, a deterministic, spatially-explicit water temperature model was formulated and tested on the case-study basin. The model, based on water and energy budgets at the reach scale, considers the effects of the spatial heterogeneity in environmental drivers, allowing the evaluation of gradients of daily mean water temperature along the river network. Stability and sensitivity analyses performed on the local epidemiological model proved that the introduction of T. bryosalmonae in a disease-free community is very likely to trigger a PKD outbreak. Simulation experiments conducted on synthetic river network replicas showed that network connectivity engenders high PKD prevalence at downstream sites, while the speed of invasion fronts in disease-free environments is amplified by climate change. Moreover, patchily located bryozoan hotspots proved able to sustain the infection at the whole river scale. Validation on the case study confirmed the reliability of the epidemiological model, and identified the prediction of bryozoan distribution as a key direction for future research. In this regard, the developed eDNA transport model possibly opens avenues for the modeling of species distributions in freshwater ecosystems, also beyond the case of PKD. The spatially-explicit temperature model was shown to outperform traditional models based on local heat budgets. Such a tool is instrumental to several ecohydrological applications, from the identification of river reaches at highest PKD-related risk, to the assessment of habitat suitability of fish or other freshwater species. Overall, this Thesis bridges the fields of ecology, epidemiology, hydrology and mathematical modelling in order to produce an integrated study of PKD, in the perspective of grasping the factors allowing disease persistence and devising mitigation strategies

Modelling environmental DNA transport in rivers reveals highly resolved spatio-temporal biodiversity patterns

The ever-increasing threats to riverine ecosystems call for novel approaches for highly resolved biodiversity assessments across taxonomic groups and spatio-temporal scales. Recent advances in the joint use of environmental DNA (eDNA) data and eDNA transport models in rivers (e.g., eDITH) allow uncovering the full structure of riverine biodiversity, hence elucidating ecosystem processes and supporting conservation measures. We applied eDITH to a metabarcoding dataset covering three taxonomic groups (fish, invertebrates, bacteria) and three seasons for a catchment sampled for eDNA at 73 sites. We upscaled eDNA-based biodiversity predictions to approximately 1900 reaches, and assessed α- and β-diversity patterns across seasons and taxonomic groups over the whole network. Genus richness predicted by eDITH was generally higher than values from direct eDNA analysis. Both predicted α- and β-diversity varied depending on season and taxonomic group. Predicted fish α-diversity increased downstream in all seasons, while invertebrate and bacteria α-diversity either decreased downstream or were unrelated to network position. Spatial β-diversity mostly decreased downstream, especially for bacteria. The eDITH model yielded a more refined assessment of freshwater biodiversity as compared to raw eDNA data, both in terms of spatial coverage, diversity patterns and effect of covariates, thus providing a more complete picture of freshwater biodiversity

Coupled biological and hydrological processes shape spatial food-web structures in riverine metacommunities

IntroductionUnderstanding how species are distributed in space and how they interact with each other is central for scientific and conservation purposes. Species' distributions and interactions result from a complex interplay of local trophic dynamics, dispersal processes, resource availability, and abiotic factors governed by the landscape matrix, which also determines the spatial connectivity for organisms' dispersal and resource fluxes. River networks not only exhibit universal spatial structures, but their dendritic landscape structure is tightly linked to species and metacommunity processes therein.MethodsHere, using a mechanistic model of spatially connected food webs integrating both essential biological and hydrological aspects, we investigate how food-web properties vary in space, and how these patterns are influenced by key model parameters. We then contrast our predictions with a suite of null models, where different aspects (such as spatial structure or trophic interactions) of the spatial food-web model are alternatively relaxed.ResultsWe find that species richness is highest in areas where local nutrient load is maximal (lowland headwaters, according to our default assumption). Overall, species richness is positively associated with link density, modularity and omnivory, and negatively related to connectance, nestedness, and niche overlap. However, for metrics such as connectance and omnivory, stochasticity of trophic interactions is a much stronger predictor than spatial variables such as distance to outlet and drainage area. Remarkably, relationships between species richness and food-web metrics do not generally hold in null models, and are hence the outcome of coupled biological and physical (i.e., hydrological) processes characteristic to river networks.DiscussionOur model generates realistic patterns of species richness and food-web properties, shows that no universal food-web patterns emerge as a result of the riverine landscape structure, and paves the way for future applications aimed at disentangling metacommunity dynamics in river networks

Contribution of natural milk culture to microbiota, safety and hygiene of raw milk cheese produced in alpine malga

Processing of alpine milk in malga farms is carried out under conditions that can favor contamination by coliforms, coagulase-positive staphylococci, or pathogens such as Listeria monocytogenes. With the aim to improve the hygienic characteristics and safety of cheese produced in four malga farms the use of lyophilized Natural Milk Culture prepared with selected strains was tested.. Two cheesemaking tests were carried out in the same day always starting from the same milk: in the first case following the malga recipe that uses either Natural Whey Culture or without the addition of a starter, in the second one using a Natural Milk Culture. Cheesemaking were carried out in four malga farms located in the west area of Trentino region within the same week. For hygienic and safety evaluation, aerobic colony count, coagulase-positive staphylococci, Escherichia coli, staphylococcal toxins, Listeria monocytogenes, and Salmonella spp, pH and aw were determined in raw milk from evening and morning milking, curd in vat, curd after extraction and two months-ripened cheese. Pathogens or toxins, high values of coagulase- positive staphylococci and E. coli were not found in cheese samples. However, in the curd coagulase-positive staphylococci reached values almost of 5 Log CFU/g in the two malga without starter cultures. The use of Natural Milk Culture reduced E. coli counts. In addition, DNA was extracted from cheese samples and from Natural Milk Culture and the composition of the microbial community determined by Next Generation Sequencing method. The determination of cheese microbial communities demonstrated that the use of Natural Milk Culture exerted different effects in the different malga, in any case preserving bacterial biodiversity