Relation extraction (RE) is one of the tasks behind many relevant natural language processing (NLP) applications. Exploiting the information hidden in millions of scholarly articles by leveraging NLP, specifically RE, systems could benefit studies in specialized domains, e.g. biomedicine and biodiversity. Although deep learning (DL)-based methods have shown state-of-the-art performance in many NLP tasks including RE, DL for domain-specific RE systems has been hindered by the lack of expert labeled datasets which are typically required to train such methods. In this paper, we take advantage of the zero-shot (i.e., not requiring any labeled data) capability of pattern-based methods for RE using a rule-based approach, combined
with templates for natural language inference (NLI) transformer models. We present our hybrid method for RE that exploits the advantages of both methods, i.e., interpretability of rules and transferability of transformers. Evaluated on a corpus of biodiversity literature with annotated relations, our hybrid method demonstrated
an improvement of up to 15 percentage points in recall and best performance over solely rule-based and transformer-based methods with F1-scores ranging from 89.61% to 96.75% for reproductive condition - temporal expression relations, and ranging from 85.39% to 89.90% for habitat - geographic location relations.

A Hybrid of Rule-based and Transformer-based Approaches for Relation Extraction in Biodiversity Literature

Climate change poses a significant threat to biodiversity, so there is a 
pressing need to understand the capacity of populations to respond and 
adapt to increasing temperatures. Ectotherms are particularly vulnerable 
to changes in ambient temperature, because this directly influences 
their body temperature. Ectotherms are therefore expected to adapt to 
climate change through plastic and/or evolutionary changes in a wide 
range of physiological traits. To better understand these plastic and 
evolutionary responses to temperature, we are using a novel approach of comparing populations of threespine sticklebacks (Gasterosteus 
aculeatus) found in geothermally warmed waters (‘hot springs’) 
and adjacent ambient-temperature lakes in Iceland. This unique 
natural experiment provides repeated and independent examples 
of populations experiencing contrasting thermal environments for 
many generations over a small geographic scale, thereby avoiding 
the confounding factors associated with latitudinal or elevational 
comparisons. We are taking advantage of this study system to study 
(i) plastic responses by looking at within-population variation at 
different temperatures and (ii) evolutionary responses by comparing 
warm- and cold-adapted populations at a common temperature. Some 
of the physiological traits we have examined include metabolic rate, fat 
storage, insulin resistance, and starvation resistance. We have found 
strong divergence in these traits between warm- and cold-adapted 
fish, providing valuable insights into how fishes and other ectotherms 
may adapt in a warming world.

Studying hot-spring fish to understand physiological adaptation to high temperature

On coral reefs, oxygen supersaturation during the day and particularly
hypoxic conditions during the night may be critical in explaining
life history strategies for reef inhabitants. These extreme oxygen
conditions have been mostly overlooked when investigating the
evolutionary ecology in corals reefs. Our main hypothesis is that
late-night hypoxia on tropical coral reefs is a daily bottleneck that
structures physiology, life history, behaviour, and biodiversity
in corals and reef-dwelling fishes. Within the lagoon in Moorea,
French Polynesia, we have explored this hypothesis by measuring
the daily oxygen fluctuations, filming the behaviour of damselfish
at night, and measuring how oxygen affects the fishes’ metabolic
rates under laboratory conditions. How and when does hypoxia
happen on coral reefs? What are the ensuing trade-offs and how
does hypoxia affect predator-prey interactions? Here we present our
field and laboratory results and discuss the insights we have gained.
(*Note: both first authors will present this talk together).

In the heat of the night: hypoxia shapes the physiology and ecology of coral reefs.

White bread made with high-amylose wheat flour has potential to 
be low-glycaemic compared to bread made with conventional wheat 
flour, however, the effects of using high-amylose wheat flour on 
starch characteristics of white bread and its glycaemic response in 
people still require investigation. In this study we report the impact 
of a high-amylose starch branching enzyme II (sbeII) mutant wheat 
flour on starch characteristics (including in vitro starch digestibility) 
of white bread made with different processing methods and stored 
in different conditions. We also report the impact of breads made 
with high-amylosesbeIIwheat flour on postprandial glycaemia in vivo 
compared to an isoglucidic wild-type control in two acute dietary 
intervention studies. Overall, we found that white bread made with 
high-amylosesbeIIwheat flour leads to lower starch digestibility in 
vitro, and has a tendency towards lower glycaemic responses in vivo. 
These results will greatly support the rational design of new wheat 
varieties using mutant wheat flours to deliver healthier bread with 
lower glycaemic impact.

Delivering low-glycaemic white bread using high-amylose wheat flour

Metabolic scaling theory: New Insights in Scaling Form, Function & Diversity

Species Distribution Modelling (SDM) is used for biodiversity preservation and wildlife management. In order to apply it, a large and reliable
dataset about the species occurrence is required. However, in some cases, this
can be difficult when there are only a few occurrence records. In this context,
uncertainty handling techniques can be applied. Thus, Bayesian inference was
used in this study to perform SDM in the Amazon Basin region near Manaus
(AM) with data collected by the GoAmazon 2014/15 project. The results were
compared with those obtained in statistical models and were similar.

Handling uncertainty through Bayesian inference for Species Distribution Modelling in the Amazon Basin region

Ethnobotanical survey & Covid 19 pandemic: A case study of Fumaria in Iran

Geological mapping of the Longobucco Basin (NE Calabria) revealed the multifaceted nature of the Paludi Formation, an unconformity-bounded, syn-orogenic, turbiditic/megaclastic unit. Sedimentology and lithostratigraphy were merged with nannoplancton and macroforams analysis. The Longobucco Basin belongs to the Calabria Peloritani Arc, an exotic crustal fragment, scraped off from its original paleogeographic position along with other continental ribbons (Kabilie, Alboran, Rif) and accreted to the Apennines during the southeastwards retreat of the Adria-Ionian slab. The Longobucco Basin hosts a Meso-Cenozoic succession overlying the Hercynian basement, and it records polyphase deformation: i) two extensional phases in the Early Jurassic, related to opening of the W Tethys, ii) a compressive phase in the ?late Oligocene/early Miocene followed by a poorly constrained extensional event. The Mesozoic succession ends with Hauterivian Maiolica-like deposits and is unconformably overlain by the Paludi Fm, which exhibits three lithofacies: a) reddish marls and shales (“Scaglia” facies), b) turbiditic sandstones and hybrid arenites, and c) clast- to matrix-supported breccias. The reddish marls are locally cannibalized by megaclastic and turbiditic deposits. Lithofacies (c) includes two mass transport deposits (MTD), >100m thick in the depocentres and with a lateral continuity of 6km. The basal megaclastic interval rests on the basement through a basin-wide SW-dipping onlap surface. Lithofacies (b) bears chaotic intervals, slumped megabeds to debrites, and calcarenites/hybrid arenites bearing macroforams in the form of resedimented loose grains forming biostratigraphically coherent assemblages, suggesting they are penecontemporaneous with the turbidites and thus provide reliable ages. Nannoplancton from the hemipelagites served for cross-checking the ages derived from benthic forams. Both methods produced an early Eocene age (Ypresian) for the basal Paludi and a late Oligocene/?Aquitanian age for the top. The style of basal interaction of the MTD with the substrate varies, with two main modes: i) deep plastic deformation of the substrate paired with sand injections, and ii) erosion, with scours and grooves. Clasts pertain to the Mesozoic succession or to the basement (phyllites, granitoids), ranging in size from pebbles to megablocks (longer axis up to 220m). Semi-consolidated clasts and bedstacks display common ductile/brittle features (asymmetric rootless folds, pseudo sigma structures, boudinage, shear zones). As sedimentation of the Paludi Fm is mainly the product of mass wasting processes, the unit as a whole can be referred to as a Mass Transport Complex. Clast composition, paired with biostratigraphic ages, suggests the Paludi Fm was sedimented in a foredeep setting, receiving the products of the dismantling of an Alpine orogen. This was followed by shortening during a proto-Apenninic phase, and eventually by accretion to the Apenninic orogen.

Sedimentological and biostratigraphic characterization of the Paludi Formation (Longobucco Basin, north-eastern Calabria): proto-Apenninic shortening of an Alpine foredeep?

Shallow landslides susceptibility assessment usually relies on the parametrization of hydraulic and geotechnical features of soils. Among these, saturated hydraulic conductivity (Ks) represents one of the most important soil properties that influences infiltration rates, runoff, groundwater recharge and drainage processes, which makes it of particular concern in the prediction of natural hazards including catastrophic floods and shallow landslides. On the other hand, it is well known that vegetation may play a positive role towards slope stability and over the last decades many efforts have been done in order to quantify the role of the vegetation towards protection from shallow landsliding (Giadrossich et al., 2017). Basically, there are two main vegetation effects: hydrological (e.g., reduction of the water pore pressure through tree rainfall interception) and mechanical ones (increase of the soil strength due to the presence of roots and increase of the soil shear stress due to the vegetation load). Soil Ks is expected to be an important factor that influences plant growth, plant-available water, root system and root biomass and, therefore, this work focuses on the quantitative assessment of the relationship between vegetation characters and hydraulic conductivity. Study areas affected by shallow landslides were chosen in the Garfagnana and Cardoso basin (Northern Apennines, Italy) and in Mt. Amiata volcano (Southern Tuscany, Italy) where field measurements (about 200) of below-ground vegetation (Root Area Ratio - RAR), above-ground vegetation (Leaf Area Index-LAI and vegetation load) and Ks were carried out inside, in the neighbour and far outside shallow landslide locations. Acquisition of data within landslides areas was supported by means of a multi-temporal landslide inventory already available for study areas. Below-ground vegetation data were collected in trench profiles, while above-ground vegetation data were acquired using digital relascope and digital cover photography. Measurements of Ks were carried out by means of both constant and falling head permeameters. Results showed that RAR and soil depth affected Ks, with a decrease of Ks as the depth increases and roots decrease. Moreover, Ks varied for different vegetation types, indicating that shifts in aboveground vegetation features may strongly impact the water dynamics of soil. Above-ground vegetation plays a slight negative role on slope stability. Instead, root reinforcement to soil in terms of a root-related cohesion parameter plays a relevant role for depths involved in shallow landslides.

Influences of vegetation characters on saturated hydraulic conductivity at catchment scale

Life and planet have significantly coevolved over time, influencing each other stability trajectory and ultimately maintaining our planet habitable over most of the last 4 billion years. Elemental cycling plays a vital role in this mechanism, with microbes controlling a large portion of the biogeochemical cycles. The majority of the key reactions that control biogeochemistry are carried out by a small set of microbially encoded proteins containing a redox-sensitive transition metal as core catalytic center. Different metal centers (such as Fe, Co, Ni, Zn, Mo, W, V, Cu) are used by biology to access diverse redox couples, utilizing more oxidized compounds as they became available during the planet's evolution. Despite the importance of this process, the relationship between metal availability and metabolic innovation and diversity has not been investigated in detail. Here I will present recent data that suggest a significant coevolution between the geosphere and biosphere analyzed through the lenses of metal use by biology, and suggest possible implication of different mechanisms of metal delivery to the planetary surface throiugh time on the emergence and evolution of metabolism.

Trace element availability at the interface between planetary evolution and life emergence

The Northern Adriatic Sea hosts a rich biodiversity, in both the Italian and Slovenian offshore and nearshore zones. Peculiar habitats, locally known as Trezze and Tegnue, mostly represented by the coralligenous outcrops and colonized by serpulids, red algae, bryozoans, bivalves, and dead corallites of Cladocora caespitosa, Cymodocea nodosa and Zostera marina associated with the presence of Pinna nobilis are investigated in the North Italian offshore, and in marine protected areas of Debeli rtič Natural Monument and the Strunjan Nature Park of Strunjan, in Slovenia. This research is carried out  in the frame of the INTERREG ITA-SLO TRETAMARA Project, which aims to provide an integrated and strengthened management of the Northern Adriatic marine-coastal habitats with high ecological value. They are characterize by a fragile biological equilibrium, due to the slow-growing calcareous organisms considered as non renewable resources, and the dredging and bottom trawling pressure that strongly threatens the physical characteristics of the habitat and negatively affect the associated biota. Here we present the preliminary results of cross-border pilot actions supporting biodiversity of these precious marine-coastal habitats. They consist of high quality seafloor images obtained by Multibeam and Side Scan Sonar surveys, aimed at: (1) mapping the Trezze and Tegnue buildups for better understanding  their origins, which are still debated (e.g., Gordini et al., 2012; Tosi et al., 2017; Donda et al., 2015 and 2019), and the seagrass meadows and Pinna nobilis settlement; 2. Collecting the Management Plans, Conservation Measures, and Regulations actions relating to marine-coastal Natura 2000 areas, aimed at producing a review document for the integrated management of the Northern Adriatic Sea marine habitats with high ecological value. This document will play a key role to promote cross-border sustainability and governance of such fragile environments.

Unveiling the secrets of the Northern Adriatic Sea: the TRETAMARA project for their management, valorization and conservation

A biodiversity crisis was observed in the benthic community from a latest Triassic carbonate platform of western Tethys. The studied succession, i.e. Mt Sparagio section in NW Sicily, consists of a continuous Upper Triassic to Lower Jurassic peritidal carbonate succession organized in shallowing upward cycles. The Upper Triassic horizons can be sub-divided into two informal units on the base of the benthic fossils assemblage: at the base the Unit A (thickness about 111 m) consists of a high diverse fossiliferous assemblage comprising very large megalodontoids specimens (up to 40 cm); Unit B (about 179 m) shows a reduction of biodiversity with the occurrence of rare and small megalodontoids (Conchodon?) up to 15 cm in size. Both units are Rhaetian in age as indicated by the presence of large tested specimens of the benthic foraminifer Triasina hantkeni. The top of Unit B is marked by an oolitic level, and records the total disappearance of the Triassic benthic fossil assemblage. Upward, the subtidal members of peritidal cycles (Unit C) show the presence of an oligotypic assemblage with T. parvovesiculifera, which represents a survival zone, followed in turn by a gradual recovery of the Lower Jurassic benthic community (e.g. Siphovalvulina sp.). A negative excursion of δ18Ocarb, corresponding to an increase in temperature, matches the biodiversity reduction between Unit A and Unit B. This episode correlates the Initial Carbon Isotopic Excursion already individuated in this section and related to the first pulse of the CAMP volcanic activity. A second change in temperature that is characterized by a positive excursion of δ18Ocarb matches the total extinction of the Upper Triassic benthic community. These data well fit with the environmental parameters of the modern tropical shallow water platform (T-factory). In particular, the sea surface temperature (SST) of a T-factory range from 18 °C to 30.5 °C representing respectively the minimum SST for the carbonate factory persistence and the maximum SST that a T-factory can tolerate.

Underline digital video library

A Hybrid of Rule-based and Transformer-based Approaches for Relation Extraction in Biodiversity Literature

Studying hot-spring fish to understand physiological adaptation to high temperature

In the heat of the night: hypoxia shapes the physiology and ecology of coral reefs.

Delivering low-glycaemic white bread using high-amylose wheat flour

Metabolic scaling theory: New Insights in Scaling Form, Function & Diversity

Handling uncertainty through Bayesian inference for Species Distribution Modelling in the Amazon Basin region

Ethnobotanical survey & Covid 19 pandemic: A case study of Fumaria in Iran

Sedimentological and biostratigraphic characterization of the Paludi Formation (Longobucco Basin, north-eastern Calabria): proto-Apenninic shortening of an Alpine foredeep?

Influences of vegetation characters on saturated hydraulic conductivity at catchment scale

Trace element availability at the interface between planetary evolution and life emergence

Unveiling the secrets of the Northern Adriatic Sea: the TRETAMARA project for their management, valorization and conservation

Temperature vs extinction events: the case of Rhaetian peritidal carbonate succession from westernmost Tethys (Sicily)

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