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FIG. 8 in Des exploitations intensives d'huîtres pendant l'Antiquité et le Moyen Âge sur le littoral atlantique français: l'exemple de Beauvoir-sur-Mer (Vendée)

FIG. 8. — Typologie des stigmates liés à l'ouverture des huîtres: 1, absence de stigmate; 2, impact sous forme d'esquille circulaire ou allongé sans cassure du bord coquillier; 3, échancrure pointue; 4, encoche de largeur égale ou supérieure à 5 mm; 5, cassure rectiligne du bord coquillier; 6, encoche de largeur inférieure à 5 mm plus profonde que large; 7, encoche de largeur inférieure à 5 mm plus large que profonde (l'orientation des stigmates est arbitraire sur cette figure). Échelle: 1 cm (C. Dupont & L. Quesnel, CNRS).

FIG. 7. — Exemples d in Des exploitations intensives d'huîtres pendant l'Antiquité et le Moyen Âge sur le littoral atlantique français: l'exemple de Beauvoir-sur-Mer (Vendée)

FIG. 7. — Exemples d'outils potentiellement utilisés pour exploiter les huîtres (C. Dupont & L. Quesnel, CNRS).

FIG. 6 in Des exploitations intensives d'huîtres pendant l'Antiquité et le Moyen Âge sur le littoral atlantique français: l'exemple de Beauvoir-sur-Mer (Vendée)

FIG. 6. — Mesure de la plus grande dimension des perforations en fonction de la forme du stigmate. Abréviation: N, nombre de valves étudiées (C. Dupont, CNRS).

opencc-by-4.0Jun 2015View details →

FIG. 5 in Exploitation animale à l'Ancien Empire en Égypte: les apports d'Ayn Asil (oasis de Dakhla)

FIG. 5. — Distribution des principales catégories animales selon les différents secteurs du site en nombre de restes: A, Phase I; B, Phase II. Abréviation: N, nombre de restes.

FIG. 2 in Des exploitations intensives d'huîtres pendant l'Antiquité et le Moyen Âge sur le littoral atlantique français: l'exemple de Beauvoir-sur-Mer (Vendée)

FIG. 2. — Localisation des dépôts coquilliers mentionnés dans le texte, d'après Verger 2005 (L. Quesnel, CNRS).

opencc-by-4.0Aug 2017View details →

EAST-WEST and VERTICAL deformation maps of Alto Tiberina Fault supersite: The Post-Proc service in Geohazard Exploitation Platform applied to Sentinel-1 dataset

In the framework of the ESA funded project “MEMpHIS - Multi Scale and Multi Hazard Mapping Space based Solutions ”, the Istituto Nazionale di Geofisica e Vulcanologia (INGV) together with TRE-ALTAMIRA, generated the EAST-WEST and VERTICAL deformation maps of Alto Tiberina Fault supersite. The two maps of ground velocity were derived thanks to the adoption of a specific tool named "Post-Proc", implemented in MEMPHIS and with the support of Terradue, that is able to automatically re-project on the east-west and vertical directions the ascending and descending InSAR time series. In particular, the output refers to the deformation maps calculated by processing with SqueeSAR (TM) method, a large dataset acquired by the ESA Sentinel-1 mission. The Post-Proc tool also calculates the mean accelerations associated to each persistent scatterer in the scenes. Some additional features are also available from this tool: - Change the coherence threshold for selecting a subset of persistent scatterers - Activate a geometrical distortion filter to take into account the layover and foreshortening effects - Change the reference point (position and coherence) - Choose between two types of accelerations: 2nd order model or velocity derivative - Choose among three different projection: east-west, vertical, and downslope. The present dataset is composed of the EAST-WEST and VERTICAL acceleration maps. The data are in shapefile format: for each record (PS) the topography, velocity, acceleration, and InSAR coherence is reported.

opencc-zeroFeb 2024View details →

Decoupling silicon metabolism from carbon and nitrogen assimilation poises diatoms to exploit episodic nutrient pulses in a coastal upwelling system

Diatoms serve as the major link between the marine carbon (C) and silicon (Si) biogeochemical cycles through their contributions to primary productivity and requirement for Si during cell wall formation. Although several culture-based studies have investigated the molecular response of diatoms to Si and nitrogen (N) starvation and replenishment, diatom silicon metabolism has been understudied in natural populations. A series of deckboard Si-amendment incubations were conducted using surface water collected in the California Upwelling Zone near Monterey Bay. Steep concentration gradients in macronutrients in the surface ocean coupled with substantial N and Si utilization led to communities with distinctly different macronutrient states: replete ('healthy'), low N ('N-stressed'), and low N and Si ('N- and Si-stressed'). Biogeochemical measurements of Si uptake combined with metatranscriptomic analysis of communities incubated with and without added Si were used to explore the underlying molecular response of diatom communities to different macronutrient availability. Metatranscriptomic analysis revealed that N-stressed communities exhibited dynamic shifts in N and C transcriptional patterns suggestive of compromised metabolism. Expression patterns in communities experiencing both N and Si stress imply that the presence of Si stress may partially ameliorate N stress and dampen the impact on organic matter metabolism. This response builds upon previous observations that the regulation of C and N metabolism is decoupled from Si limitation status, where Si stress allows the cell to optimize the metabolic machinery necessary to respond to episodic pulses of nutrients. Several well-characterized Si-metabolism associated genes were found to be poor molecular markers of Si physiological status; however, several uncharacterized Si-responsive genes were revealed to be potential indicators of Si stress or silica production.

opencc-by-4.0Nov 2023View details →

F I G U R E 1 in Echinorhinus brucus (Bonnaterre, 1788) in the Caribbean Sea: A recurrent visitor, or are the artisanal fisheries exploiting deeper waters?

F I G U R E 1 Confirmed georeferenced records (indicated by black dots) and fishing polygon boundaries (represented by dashed black lines) for the bramble shark Echinorhinus brucus (Bonnaterre, 1788) across the western Atlantic (a). A detailed view of the Caribbean Sea region is provided, highlighting the capture locations of bramble sharks, including our specimen (marked by a black star) (b). Key phenotypic diagnostic characteristics are depicted, showcasing the absence of an anal fin, two closely positioned unpinned dorsal fins near the caudal region, and a flat head and snout (c). An image of the specimen's open mouth, revealing its teeth (d). Additionally, a close-up photograph of an extracted tooth (e). Notations for countries: Colombia (Col), the Dominican Republic (D.R.), Mexico (Mex), Nicaragua (Nic), and Venezuela (Ven).

opencc-by-4.0Nov 2024View details →

Replication Package of "Exploiting Vision-Language Models in GUI Reuse"

This replication package is for the paper entitled "Exploiting Vision-Language Models in GUI Reuse". The authors remain anonymous for double-blind review purposes. The package contains six files. If the paper is accepted, then the authors will move the replication package to a public repository hosted by an institution.

opencc-zeroApr 2022View details →

Data and Rscripts from: An integrated experimental and mathematical approach to inferring the role of food exploitation and interference interactions in shaping life history

Intraspecific interactions can occur through many ways but the mechanisms can be broadly categorized as food exploitation and interference interactions. Identifying how intraspecific interactions impact life history is crucial to accurately predict how population density and structure influence dynamics. However, disentangling the effects of interference interactions from exploitation using experiments, is challenging for most biological systems. Here we propose an approach that combines experiments with modeling to infer the pathways of intraspecific interactions in a system. First, a consumer-resource model is built without intraspecific interactions. Then, the model is parameterized by fitting it to life-history data from a first experiment in which food abundance was varied. Next, hypothesized scenarios of intraspecific interactions are incorporated into the model which is then used to predict life histories with increasing competitor density. Lastly, model predictions are compared against data from a second experiment which raised groups of competitors of different densities. This comparison allows us to infer the role of interference and exploitation in shaping life history. We demonstrated the approach using the smaller tea tortrix Adoxophyes honmai across a range of temperature. We investigated five scenarios of interactions that included exploitation and three pathways for interference through some effects either on energetics to represent changes in ingestion or activity, or on mortality to model deadly interactions, or on mortality and ingestion to model cannibalism. Overall, intraspecific interactions in tea tortrix are best explained by a high level of deadly interactions along with some level of interference that acts on energy such as escaping and blocking access to food. Deadly interactions increase with temperature while interference that acts on energy is strongest close to the optimal temperature for reproduction. Interestingly, exploitation is more important than interference at low competitor density. The combination of mathematical modeling and experimentation allowed us to mechanistically characterize the intraspecific interactions in tea tortrix in a way that is readily incorporated into population-level mathematical models. The primary value of this approach, however, is that it can be applied to a much wider range of taxa than is possible with pure experimental approaches.

opencc-zeroApr 2022View details →

Negotiating mutualism: a locus for exploitation by rhizobia has a broad effect size distribution and context-dependent effects on legume hosts

In mutualisms, variation at genes determining partner fitness provides the raw material upon which coevolutionary selection acts, setting the dynamics and pace of coevolution. However, we know little about variation in the effects of genes that underlie symbiotic fitness in natural mutualist populations. In some species of legumes that form root nodule symbioses with nitrogen-fixing rhizobial bacteria, hosts secrete nodule-specific cysteine-rich (NCR) peptides that cause rhizobia to differentiate in the nodule environment. However, rhizobia can cleave NCR peptides through the expression of genes like the plasmid-borne Host range restriction peptidase (hrrP), whose product degrades target NCR peptides. Although hrrP activity can confer host exploitation by depressing host fitness and enhancing symbiont fitness, the effects of hrrP on symbiosis phenotypes depend strongly on the genotypes of the interacting partners. However, the effects of hrrP have yet to be characterized in a natural population context, so its contribution to variation in wild mutualist populations is unknown. To understand the distribution of effects of hrrP in wild rhizobia, we measured mutualism phenotypes conferred by hrrP in 12 wild Ensifer medicae strains. To evaluate context dependency of hrrP effects, we compared hrrP effects across two Medicago polymorpha host genotypes and across two experimental years for five E. medicae strains. We show for the first time in a natural population context that hrrP has a wide distribution of effect sizes for many mutualism traits, ranging from strongly positive to strongly negative. Furthermore, we show that hrrP effect size varies across both host genotype and experiment year, suggesting that researchers should be cautious about extrapolating the role of genes in natural populations from controlled laboratory studies of single genetic variants.

opencc-zeroMay 2022View details →

Data and R code used for the GLMM and NBDA analyses in 'Captive Asian short-clawed otters (Aonyx cinereus) learn to exploit unfamiliar natural prey'

Foraging plays a vital role in animal life histories, learning whether unfamiliar food items are palatable is a key part of this process. Animals that engage in extractive foraging must also learn how to overcome the protective measures of their prey. While otters (subfamily Lutrinae) are a taxon known for their extractive foraging behaviour, how they learn about prey palatability and acquire extractive foraging techniques remains poorly understood. Here we investigated: (i) how captive Asian short-clawed otters (Aonyx cinereus) learned to interact with, and extract meat from, unfamiliar natural prey, and (ii) how their exploitation of such prey compared to their ability to overcome artificial foraging tasks containing familiar food rewards. Network-based diffusion analysis showed that otters learned to interact with unfamiliar natural prey by observing their group mates. However, once interacting with the prey, they learned to extract the meat mainly asocially. In addition, otters took longer to overcome the protective measures of unfamiliar natural prey than those of extractive food puzzles. Asian short-clawed otter populations are declining in the wild. Increasing our understanding of how they learn to overcome novel foraging challenges could help develop pre-release training procedures as part of reintroduction programmes for otter conservation.

opencc-by-4.0Jul 2022View details →

Exploiting Pretrained Biochemical Language Models for Targeted Drug Design

This repository contains materials for the paper, Exploiting Pretrained Biochemical Language Models for Targeted Drug Design, which has been accepted for publication in Bioinformatics Published by Oxford University Press. data.zip contains vocabulary files for the pretrained models, additional information regarding proteins (PFAM family, protein similarity) and interactions filtered from <a href="https://www.bindingdb.org/bind/index.jsp">BindingDB</a> which are further split into train, validation and test sets and used to train target specific molecule generation models.  models.zip includes files for the models trained in this study.      predictions.zip comprises the compounds generated with the targeted models and the result of their evaluation with respect to benchmarking metrics.  docking.zip contains targets/ including PDB files of the test proteins selected for docking evaluation, ligands/ including SDF files for molecules generated with the targeted models and two decoding strategies (i.e. beam search and sampling) and complex/ including docking outputs.

opencc-by-4.0Oct 2021View details →

"Chirality and accurate structure models by exploiting dynamical effects in continuous-rotation 3D ED data". Raw data and JANA refinement files.

Chirality and accurate structure models by exploiting dynamical effects in continuous-rotation 3D ED data 3D ED data sets of 5 compounds and JANA refinement files of 12 compounds Relevant tools: <ul> <li>PETS2: data reduction and analysis of electron diffraction patterns <ul> <li>Download program and access step-by-step tutorials at <a href="http://pets.fzu.cz/">http://pets.fzu.cz/</a></li> <li>Palatinus, L. et al. Specifics of the data processing of precession electron diffraction tomography data and their implementation in the program PETS2.0. Acta Cryst. B75, 512–522 (2019). <a href="https://doi.org/10.1107/S2052520619007534">DOI: 10.1107/S2052520619007534</a></li> </ul> </li> <li>JANA2006: crystal structure model refinement program <ul> <li>Download program from <a href="http://jana.fzu.cz/">http://jana.fzu.cz/</a> and access step-by-step tutorials at <a href="http://pets.fzu.cz/">http://pets.fzu.cz/</a></li> <li>Results here were obtained with JANA2006. We recommend using JANA2020.</li> <li>Petricek, V., Dusek, M. & Palatinus, L. Crystallographic Computing System JANA2006: General features. Z. Kristallogr. 229, 345–352 (2014). <a href="https://doi.org/10.1515/zkri-2014-1737">DOI: 10.1515/zkri-2014-1737</a></li> </ul> </li> <li>DYNGO: Bloch wave program, calculates dynamical diffraction intensities and derivatives <ul> <li>Program automatically included in JANA2006/JANA2020</li> <li>Palatinus, L., Petříček, V. & Corrêa, C. A. Structure refinement using precession electron diffraction tomography and dynamical diffraction: theory and implementation. Acta Cryst. A71, 235–244 (2015). <a href="https://doi.org/10.1107/S2053273315001266">DOI: 10.1107/S2053273315001266</a></li> </ul> </li> </ul> 3D ED data sets: STW_HPM-1 (RT) was measured on a JEOL JEM-2100-LaB6 and diffraction patterns were recorded with an ASI Timepix detector. Another sample of STW_HPM-1 was measured at a temperature of 100 K after cryotransfer with a Titan Krios (CETA-D detector). The other data sets were measured on an FEI Tecnai G2 20 (Olympus SIS Veleta, CCD). Each data set contains the raw diffraction patterns (*.tif) and the basic input files needed to reproduce the data reduction with PETS2 as used in the associated publication (*.pts2, *.celllist, *.cenloc). Step-by-step tutorials are provided for quartz and glycine (and selected steps for abiraterone acetate) at <a href="http://pets.fzu.cz/">http://pets.fzu.cz/</a>. <ul> <li>α-quartz, stepwise continuous-rotation and precession-assisted (2 data sets from the same crystal)</li> <li>natrolite, stepwise continuous-rotation and precession-assisted (2 data sets from the same crystal)</li> <li>cobalt aluminophosphate (CAP), static ED patterns recorded in 0.1° steps (3 data sets from 2 crystals)</li> <li>abiraterone acetate, stepwise continous-rotation (5 data sets from 5 crystals)</li> <li>STW_HPM-1, continuous-rotation (1 data set, room temperature)</li> <li>STW_HPM-1, continuous-rotation (1 data set, T = 100 K, cryotransfer)</li> </ul> JANA refinement and CIF files: CIF (Crystallographic Information Framework) files include two data items. The first is related to the dynamical and the second to the kinematical refinement. Relevant parameters and statistics specific for dynamical refinement are found in the field _refine_special_details. JANA files are provided for the dynamical and kinematical refinement at the stage after the final refinement cycle together with the original input files generated by PETS2. For quartz and natrolite, relevant files for the refinements against precession-assisted 3D ED data are included. For abiraterone acetate and limaspermidine, relevant files for the absolute structure determination are included. <ul> <li>α-quartz</li> <li>albite</li> <li>mordenite</li> <li>natrolite</li> <li>STW_HPM-1</li> <li>cobalt aluminophosphate (CAP)</li> <li>CAU-36</li> <li>α-glycine</li> <li>carbamazepine</li> <li>(+)-limaspermidine</li> <li>abiraterone acetate</li> <li>MBBF4</li> </ul> For the kinematical refinements based on more than one data set, the self-written tool "CompInt" (unpublished) was used. The tool can be found in the file "tool_scalehkl_compint.zip". Input (*.hkl, *.compint) and output files (*.scalehkl) are provided in the respective folder with the JANA files. Raw data sources of other data sets relevant for the associated publication are given in the SI of the associated publication.

opencc-by-4.0Mar 2022View details →

SSHOC Training Material Video 2 - How to exploit the Ethnic and Migrant Minorities Survey Registry as an academic and non-academic user - training video in English, French and Spanish

A training video about how to search for and learn about surveys using the EMM Survey Registry, both as an academic and non-academic user. This video has been produced in English, French, Spanish

Fig. 8 in Exploitation status and stock assessment of the smooth clam Callista chione (Linnaeus, 1758) in the northern Alboran Sea (GSA01-W Mediterranean Sea)

Fig. 8: Time trajectories from 2002 to 2015 and forecasting for the next 20 years (2016-2036) of the relative fishing mortality rate (F/Fmsy) and relative population biomass (B/Bmsy) estimated using a non-equilibrium surplus production model, setting maximum sustainable yield (MSY) at a level corresponding to the value of the latest year. The dotted lines represent the upper and lower 80% confidence limits.

Fig. 7 in Exploitation status and stock assessment of the smooth clam Callista chione (Linnaeus, 1758) in the northern Alboran Sea (GSA01-W Mediterranean Sea)

Fig. 7: Trajectories from 2002 to 2015 of relative fishing mortality and biomass for Callista chione in the northern Alboran Sea.

Fig. 3 in Exploitation status and stock assessment of the smooth clam Callista chione (Linnaeus, 1758) in the northern Alboran Sea (GSA01-W Mediterranean Sea)

Fig. 3: Distribution of artisanal fisheries by fishing gear and landing port from March 2013 to March 2014. Values are given as percentage contribution of each fishery in tonnes.

Fig. 4 in Exploitation status and stock assessment of the smooth clam Callista chione (Linnaeus, 1758) in the northern Alboran Sea (GSA01-W Mediterranean Sea)

Fig. 4: Number of vessels by landing port targeting bivalves with mechanised dredges, in the northern Alboran Sea.

Fig. 1 in Exploitation status and stock assessment of the smooth clam Callista chione (Linnaeus, 1758) in the northern Alboran Sea (GSA01-W Mediterranean Sea)

Fig. 1: Geographical subareas of the General Fisheries Commission for the Mediterranean (GFCM) and map of the study area in the northern Alboran Sea (W Mediterranean Sea), showing the locations of the fishing ports.