Belgium

One goal of musculoskeletal modelling is to explain dynamic behaviour in terms of fundamental muscle properties, such as the force-velocity (FV) relationship.  However, this is challenging because the complexity of anatomically realistic models (namely, their high degrees of freedom, DOF) often prohibits detailed analysis; the number of mechanical interactions is too large for thorough investigation.  Consequently, we may struggle to explain “high-level” behaviours such as joint kinematics and forces in terms of muscle-level dynamics.  To address this, we developed a descriptive and visual framework for presenting intricate musculoskeletal modelling data.  We computed a “joint-fv” curve as the activation weighted sum of instantaneous FV states of all muscles within a total “joint-FV space”.  We applied our framework to two previously published models: 1) A low-DOF human arm during reaching and 2) a high-DOF human knee during walking.  In both cases, we found that the instantaneous shape of the joint-fv curve morphs depending on synergistic and antagonistic co-contraction.  Additionally, we found broad similarities in joint-fv trajectories, despite the biomechanical, behavioural and anatomical differences between reaching/walking.  Specifically, joints followed a clockwise trajectory through joint-FV space, except when in the presence of non-contractile forces (i.e. contacts or cross-joint interaction forces).  Hence, we propose that joint-fv trajectories communicate not only how mechanical energy flows through joints, but also how this flow is governed by interactions among intrinsic muscle properties (activation, FV) and extrinsic properties (multibody dynamics and contact forces) during dynamic activity.

SEB Conference 2025

Joint-level force-velocity properties for arbitrarily complex musculoskeletal models

musculoskeletal modelling

force-velocity

muscle

simulation

### Welcome to IJCNLP-AACL 2023!
I am honored and happy to welcome you to IJCNLP-AACL 2023! The conference hosts both the 13th
International Joint Conference on Natural Language Processing (IJCNLP) and the 3rd Conference of
the Asia-Pacific Chapter of the Association for Computational Linguistics (AACL). 
The joint conferences of IJCNLP and AACL have been organized by alternating leadership in the
Asia-Pacific region, in odd years by Asian Federation of Natural Language Processing (AFNLP) and
in even years by AACL. The conference is organized by AFNLP this year. 

Considering the current situation that we are not yet fully over the coronavirus pandemic, the
conference is offered in a hybrid mode, off-line in Nusa Dua, Bali, Indonesia, and on-line with the help
of Underline, during November 1-4, 2023. For those attending off-line, I hope that you will find time to
explore the exciting local area, which remains quite warm and pleasant at this time of the year. For
those attending on-line, I hope that the attendance is not much hampered, sometimes even enhanced
and comfortable, though the on-line arrangements have been made without ample time. 

Message from Jong C. Park, Korea Advanced Institute of Science and Technology (KAIST) 
IJCNLP-AACL 2023 General Chair 
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IJCNLP-AACL 2023

The 13th International Joint Conference on Natural Language Processing and the 3rd Conference of the Asia-Pacific Chapter of the Association for Computational Linguistics

technical paper

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SEB’s Annual Conference is celebrated for creating the perfect composition of research, new discoveries and collaborative connections. Be creative and innovative by exchanging ideas and knowledge with masters of biology from all over the world.

Over-fishing is a consequential anthropogenic driver of demographic and phenotypic changes in aquatic fish populations. In Lake Malombe, Malawi, over the past 40 years, intense fishing pressure has led to local extinctions, dramatic population declines, and rapid life history shifts in several commercially important benthic cichlid species. In some of these species, size at maturation has decreased by approximately 50% within only 20 generations, suggesting a strong effect of either fisheries-induced evolution or phenotypic plasticity in response to human induced harvest pressure.
To disentangle the genetic and plastic components of this life history shift, we conducted a common garden experiment using offspring from populations experiencing contrasting fishing pressures. Juveniles from heavily fished and weakly fished populations were reared under standardised laboratory conditions to control for environmental effects and isolate genetic differences. We observed an accelerated growth, earlier maturation, but reduced reproductive investment in offspring from heavily fished populations, consistent with a rapid evolutionary responses to fisheries pressure. Importantly, because of the non-size selective fisheries in Lake Malombe these shifts in life history traits are driven by biotic interactions such as competition for mates and reproductive opportunities, with smaller, faster-maturing individuals potentially gaining an advantage in heavily fished populations.
This work and evolutionary genomic investigations we have carried out highlight how human-induced pressures reshape the genetic determination of life history strategies, with cascading consequences for intra- and interspecific interactions, population stability, and the long-term resilience of biodiversity hotspots like Lake Malawi.

Disentangling evolutionary and plastic responses to over-fishing of Malawi Cichlid fish in a common garden experiment

Plant hydraulics is a growing field that investigates links between the structure and the hydrodynamic function of plants, from cellular to ecosystem scales. Recently, a collaboration of plant hydraulic physiologists and palaeobotanists began re-examining the fossil record to identify the function of key elements of plant vascular structure at the time of their origin.Xylem conduits, which mediate water transport in vascular plants, are subject to blockage by vapour-phase embolism. Under drought, the uncontrolled spread of embolism through the xylem results in mortality through hydraulic failure. Vascular anatomy and morphology can facilitate or constrain embolism spread by affecting the connectivity of the xylem conduit network. Insofar as vascular structure affects the risk of hydraulic failure, it must be subject to selection by drought.Network analysis suggests that drought selection shaped the well-known trend of increasing vascular complexity with plant or organ size. Selection by hydraulic failure would thus have promoted the early diversification of primary vascular forms during the Silurian-Devonian Radiation of plant life onto land. The early Devonian emergence of secondary xylem (wood) conferred resistance to hydraulic failure on par with increasingly complex contemporaneous primary vascular anatomies. Woody growth was particularly effective at maintaining embolism resistance with increasing plant size, although the earliest known woods could not support hydraulically safe arborescent habit without further anatomical innovations. The ongoing reanalysis of the fossil record aims to reinterpret the function of emerging vascular structures with respect to hydraulic safety, ultimately setting the hydraulics of extant plants in a revised evolutionary perspective.

Selection by drought in the early evolution of plant vascular networks

Jumping represent one of the most widely used modes of locomotion in the animal kingdom. However, this does not mean that the characteristics of jumps are universal; there are many different ways in which jumps are powered (actuated). In orthopterans there are two main methods of actuation; direct muscle actuation and latch mediated spring actuation. It has previously been suggested that spring actuated systems provide propulsive power to an animal, which in turn generates incredibly fast jumps. Clown hoppers (Eumastacidae) are a group of south American grasshopper which use their spring actuated laterally projected legs to achieve jump speeds of up to 3.1 m/s. Similar to the muscle actuated group of arboreal orthopterans (Phlugidini), the clown hopper will perform targeted jumps, although the level of control which they employ is less fine tuned. When clown hoppers are presented with 3 different overhead target heights (50 mm, 75 mm and 100 mm), there was a significant difference between the linear velocity (m/s) at take-off with jump speed increasing as target height increases. However, whilst there was a generalised decrease in angular velocity (rad/s), this was not significant suggesting that whilst the hoppers can control the extent to which the spring in their legs powers the jumps (represented by the proportionate change in speed of the jumps), the ability to control jump rotation at different heights remains obscure.

Introducing the Monkey Grasshopper, a spring-powered jumper with the ability to control its linear velocity

Human activities release increasing amounts of chemical contaminants into aquatic environments, raising concerns about their impact on wildlife. Many pollutants act as endocrine disruptors, interfering with hormone-regulated processes essential for growth, reproduction, and development. In fish, such disruptions affect skeletal formation, muscle function, and neural signaling, all of which also affect behaviour. While chemical exposure is indeed known to alter fish behaviour, such as reducing responses to light-dark stimuli, it remains unclear whether these effects stem from skeletal changes or physiological disruptions. To address this, we study how altered skeletal mineralization affects zebrafish swimming behaviour. Using larval zebrafish (Danio rerio), a well-described animal model for skeletal development, we first manipulated calcium availability during early development to induce either increased or decreased bone mineralization. Larvae raised in low-calcium conditions lacked bone mineralization and moved less in 24-hour observations. In light-dark transition assays, they also failed to respond properly. Since calcium is critical for bone formation, muscle contraction, and neural signaling, we extended our study to F0 knockout larvae. F0 knock-outs of enpp1 (promotes mineralization by generating inorganic pyrophosphate) and entpd5a (inhibits mineralization by hydrolyzing nucleotide triphosphates) were generated and validated using genotyping, skeletal staining, and elemental analysis. Swimming behaviour was quantified at 5 days post-fertilization using automated tracking. Even at this early stage, altered mineralization resulted in reduced locomotion. We anticipate that a better understanding of the effect of skeletal mineralization on behaviour will allow for a more thorough understanding of the effect chemical pollutants have on fish behaviour.

Behaviour to the bone: linking skeletal mineralization to behaviour in larval zebrafish (Danio rerio)

Historically relatively sheltered from human disturbance, Arctic regions now face increasing threats from expanding maritime routes and industrial activities. These pressures add to existing environmental stressors, raising concerns about the conservation of fragile polar ecosystems, which are particularly vulnerable to cumulative impacts such as ocean acidification (OA) and widespread pollution. Combined stressors may cause unpredictable non-additive effects on marine ectotherms. Furthermore, by using traditional approaches limited to whole-organism levels, such as metabolic rates and mortality, we have overlooked sublethal, early-signals of physiological failure occurring at the cellular level. Therefore, we aimed at exploring the molecular responses of a key Arctic zooplankton species to different environmentally-realistic doses of a toxic polycyclic aromatic hydrocarbon under an OA scenario. For this purpose, the metabolome and lipidome of field-collected copepodid IV specimens of the copepod Calanus glacialis were profiled after two and ten days of exposure within an orthogonal design of four pyrene concentrations (0, 10, 100 and 200 nM) and two levels of OA (ambient and low pH). Multivariate analyses evidence an interaction between OA and pyrene contamination over time, albeit pyrene is a major driver. OA seemingly shifts the metabolomic dose response to pyrene compared to ambient pH. Further integrative analyses will help to decipher the functional consequences of such molecular alterations, to identify early-signals of physiological failure. Implementing multilayer knowledge from such multifactorial experimental approaches will be critical in improving our ability to predict the fate of Arctic species in future, more disturbed polar oceans.

In the Search of Sublethal Biomarkers: Metabolomic and Lipidomic Profiling of Arctic Copepods Facing Ocean Acidification and Pyrene Pollution

The ecological success of scleractinian reef-building corals is often attributed to the high growth rates of their calcium carbonate skeletons through the process of calcification. However, this capacity is increasingly threatened by multiple environmental stressors, including ocean acidification and thermal stress. Light plays a crucial role in enhancing coral calcification rates, a phenomenon known as light-enhanced calcification (LEC), which has been widely observed in both laboratory and field studies. Certain research suggests that LEC may provide resilience to coral calcification under unfavorable environmental conditions, such as reduced seawater pH.
The physiological mechanisms underlying LEC remain debated, but many hypotheses focus on the symbiotic relationship between scleractinian corals and dinoflagellate algae of the family Symbiodiniaceae, which influence calcification through their photosynthetic activity. Our research investigates the link between light and coral calcification by examining how symbiont photosynthesis affects trans-epithelial pH regulation, from the growing front of the coral skeleton, through the coral tissues, and into the surrounding seawater.
To achieve this, we employ a combination of live tissue imaging using confocal microscopy and pH-sensitive microelectrodes to measure both intracellular and extracellular pH across the complex spatial structure of coral tissues. Our findings reveal that Symbiodiniaceae photosynthetic activity drives pH gradients within coral tissues, which correlate with enhanced calcification rates and mitigate the effects of ocean acidification. In contrast, the impacts of acidification are more pronounced in darkness or in coral tissue regions lacking symbionts. However, energy-dependent pH regulation mechanisms enable corals to sustain calcification even under these challenging conditions.

From Light to Limestone: physiological links between reef coral photosynthesis and calcification via pH regulation

Autochthonous landraces or local varieties are plant genetic resources characterized by high genetic variability, specific adaptation to environmental growth condition, and the presence of health-promoting specialized metabolites. However, these varieties are at risk of extinction due to their replacement by genetically uniform modern varieties. Untargeted metabolomics, based on liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS), is a powerful tool to explore metabolite diversity, promote the valorization, and support the conservation of these landraces. This study investigated the metabolite diversity of three autochthonous lentil landraces from Molise region (Italy) — Capracotta (CA), Rionero Sannitico (RS), and Agnone (A) — compared to one landrace from Umbria region (Italy) — Castelluccio di Norcia (CS) — and three bean landraces from Molise (Ciliegino, CI), and Basilicata (San Spanish Ciliegino, CI SP), respectively. Untargeted metabolomics allowed the detection of 662 and 344 differentially accumulated metabolic features (DAMfs) in lentil (Le) and bean (Be) landraces, respectively. Metabolite annotation, supported by molecular network analysis, assigned 53% and 54% of DAMfs to different metabolic categories, with flavonoids, amino acids, and cinnamic acids as the most represented. Multivariate statistical analyses (PCA, PLS-DA, and HCA) highlighted the distinctiveness of each landrace. The antioxidant, and antibacterial activities of legume seed extracts were evaluated, correlating bioactivity with their metabolic profiles. Ongoing enrichment analysis will further define landrace-specific metabolic features, enhancing the understanding of their health-promoting potential and supporting conservation efforts of traditional varieties.

In depth characterization of autochthonous bean (Phaseolus vulgarisL.) and lentil (Lens culinarisMedik) landraces from Apennine Italian regions

Arbuscular mycorrhizal fungi (AM fungi) may facilitate plants during increasingly prevalent extreme stress events such as heatwaves and drought. Heatwaves are commonly characterised by the presence of extreme temperatures and frequently co-occur with droughts or water deficits. The combination of these stressors is deleterious for plants and the role of AM fungi in ameliorating this compound stress event is not fully understood, particularly within threatened communities such as grasslands. This study has investigated the role of field-collected AM fungi in facilitating plant responses to heat and water stress using a simulated heatwave event in a factorial greenhouse experiment to test how native grassland species respond. We found that the impact of heat stress combined with water stress on plant performance was shown to be greater than the additive effects of heat and water stress in isolation. AM fungi was shown to have variable influences on plant growth, fitness, and physiological responses but these influences were commonly at odds with previous publications on AM fungi with agricultural species. Most notably, AM fungi increased the germination success of seeds of one species grown following exposure to climate stress. The results of this study highlight the dynamic role of AM fungi and help us understand grassland responses to heatwave events in the face of increasing extreme climate events. Furthermore, this study emphasises the importance of building ecologically relevant ex-situ experiments to study and understand current global pressures facing natural ecological communities.

Interactions of Arbuscular Mycorrhizal Fungi with Native Grassland Species Under Combined Heat and Water Stress

Harvest-related traits are key agronomic traits for cereal crops. Understanding the influence of abiotic stress on yield and the ability to find the most predictive traits for final yield are important for understanding and characterizing crop resilience strategies. Using a high spatial and temporal phenotyping approach with multiple imaging sensors we monitored the growth dynamics of plants and assessed their physiological responses throughout development until reaching the maturity stage under control and drought conditions. Here we present a dataset comprising 145 traits over 70 time points under two conditions for six barley lines including elite, cultivated, and wild lines. We applied advanced data analysis using machine learning approaches for effective integrative visualisation and subsequent modelling. The main objectives of this study were to identify distinct traits that differentiate drought-stressed from well-watered plants and to accurately predict harvest traits. Using a classification model, we observed an accurate separation between control and drought treatments and ranked the tolerance levels of different lines. For the harvest prediction models, we evaluated all time points under different watering regimes compared with models using only early time points and determined the importance of traits. Finally, we analysed the variance components of highly predictive traits and identified which traits are mostly driven either by genetic, environmental or time components. With the applied modelling approach, we were able to predict the harvest-related traits and pinpoint the most predictive traits at specific time points. Identifying predictive traits early in the developmental stage can help breeders find stress-tolerant traits of interest.

Integrative phenotyping combined with modelling as a tool for predicting harvest-related traits

Traditional plant phenotyping for physiology, morphology, chemical composition and plant or seed biomass is labor-intensive and difficult to scale up. Like other scientific fields, it has benefited from automation, both in controlled environments and in the field. For practical reasons – particularly the need to handle the large numbers of plants required for genetic analysis - choices generally have been to measure plants fast and non-destructively. As a result, the traits being measured have shifted from ‘hard-core variables’ such as CO2  uptake rates or total plant biomass, to proxies like fluorescence or digital biomass. In this talk, I will discuss some of the implications of this shift for interpretating experimental results.
Another challenge is the gap that often exists between results obtained in controlled conditions and those observed in the field. This issue becomes even more pressing when using expensive high-throughput phenotyping equipment.  Addressing this discrepancy requires greater attention from the phenotyping community. We will also explore strategies to bridge this gap.

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Disentangling evolutionary and plastic responses to over-fishing of Malawi Cichlid fish in a common garden experiment

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