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  • 2020-2024  (32)
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  • 1
    Publication Date: 2024-03-31
    Description: The combinatorial number of possible methylomes in biological time and space is astronomical. Consequently, the computational analysis of methylomes needs to cater for a variety of data, throughput and resolution. Here, we review recent advances in 2nd generation sequencing (2GS) with a focus on the different methods used for the analysis of MeDIP-seq data. The challenges and opportunities presented by the integration of methylation data with other genomic data types are discussed as is the potential impact of emerging 3rd generation sequencing (3GS) based technologies on methylation analysis.
    Keywords: DNA methylation, methylome, immuno precipitation, analysis pipeline ; thema EDItEUR::M Medicine and Nursing::MF Pre-clinical medicine: basic sciences::MFN Medical genetics
    Language: English
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  • 2
    Publication Date: 2024-04-11
    Description: In 1982 the International Association on Water Pollution Research and Control (IAWPRC), as it was then called, established a Task Group on Mathematical Modelling for Design and Operation of Activated Sludge Processes. The aim of the Task Group was to create a common platform that could be used for the future development of models for COD and N removal with a minimum of complexity. As the collaborative result of the work of several modelling groups, the Activated Sludge Model No. 1 (ASM1) was published in 1987, exactly 25 years ago. The ASM1 can be considered as the reference model, since this model triggered the general acceptance of wastewater treatment modelling, first in the research community and later on also in practice. ASM1 has become a reference for many scientific and practical projects, and has been implemented (in some cases with modifications) in most of the commercial software available for modelling and simulation of plants for N removal. The models have grown more complex over the years, from ASM1, including N removal processes, to ASM2 (and its variations) including P removal processes, and ASM3 that corrects the deficiencies of ASM1 and is based on a metabolic approach to modelling. So far, ASM1 is the most widely applied. Applications of Activated Sludge Models has been prepared in celebration of 25 years of ASM1 and in tribute to the activated sludge modelling pioneer, the late Professor G.v.R. Marrais. It consists of a dozen of practical applications for ASM models to model development, plant optimization, extension, upgrade, retrofit and troubleshooting, carried out by the members of the Delft modelling group over the last two decades.
    Keywords: Technology & Engineering ; Environmental ; Water Supply ; thema EDItEUR::T Technology, Engineering, Agriculture, Industrial processes::TQ Environmental science, engineering and technology::TQS Sanitary and municipal engineering::TQSW Water supply and treatment
    Language: English
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  • 3
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    El Colegio de México
    Publication Date: 2022-07-15
    Description: El propósito del presente estudio es hacer una revisión, con ojo crítico y prestando atención a sus claroscuros, de las relaciones entre México y el Banco Mundial desde la creación de éste a mediados de los cuarenta en Bretton Woods. En particular, debido a que el apogeo de tales nexos se remonta apenas al final de los ochenta, casi la mitad del texto está dedicado a hacer una revisión del periodo que empieza con la administración del presidente Carlos Salinas de Gortari y culmina con la crisis que estalló a fines de 1994.
    Keywords: Banking ; bic Book Industry Communication::K Economics, finance, business & management::KF Finance & accounting::KFF Finance::KFFK Banking
    Language: Spanish
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  • 4
    Publication Date: 2024-03-15
    Description: Coral reefs are constructed by calcifiers that precipitate calcium carbonate to build their shells or skeletons through the process of calcification. Accurately assessing coral calcification rates is crucial to determine the health of these ecosystems and their response to major environmental changes such as ocean warming and acidification. Several approaches have been used to assess rates of coral calcification but there is a real need to compare these approaches in order to ascertain that high quality and intercomparable results can be produced. Here, we assessed four methods (total alkalinity anomaly, calcium anomaly, 45Ca incorporation and 13C incorporation) to determine coral calcification of the reef-building coral Stylophora pistillata. Given the importance of environmental conditions on this process, the study was performed under two pH (ambient and low level) and two light (light and dark) conditions. Under all conditions, calcification rates estimated using the alkalinity and calcium anomaly techniques as well as 45Ca incorporation were highly correlated. Such a strong correlation between the alkalinity anomaly and 45Ca incorporation techniques has not been observed in previous studies and most probably results from improvements described in the present paper. The only method which provided calcification rates significantly different from the other three techniques was 13C incorporation. Calcification rates based on this method were consistently higher than those measured using the other techniques. Although reasons for these discrepancies remain unclear, the use of this technique for assessing calcification rates in corals is not recommended without further investigations.
    Keywords: Alkalinity, total; Alkalinity, total, standard deviation; Animalia; Aragonite saturation state; Aragonite saturation state, standard deviation; Benthic animals; Bicarbonate ion; Bicarbonate ion, standard deviation; Bottles or small containers/Aquaria (〈20 L); Calcification/Dissolution; Calcification rate, standard error; Calcification rate of calcium carbonate; Calcite saturation state; Calcite saturation state, standard deviation; Calcium; Calcium-45 activity; Calcium-45 activity, standard deviation; Calcium ion, standard deviation; Calculated using seacarb after Nisumaa et al. (2010); Calculated using seacarb after Orr et al. (2018); Carbon, inorganic, dissolved; Carbon, inorganic, dissolved, standard deviation; Carbonate ion; Carbonate ion, standard deviation; Carbonate system computation flag; Carbon dioxide; Carbon dioxide, standard deviation; Cnidaria; Date/time end; Date/time start; Dry mass; Experiment; Fugacity of carbon dioxide (water) at sea surface temperature (wet air); Fugacity of carbon dioxide in seawater, standard deviation; Identification; Incubation duration; Laboratory experiment; Laboratory strains; Light; Mass; Not applicable; OA-ICC; Ocean Acidification International Coordination Centre; Partial pressure of carbon dioxide, standard deviation; Partial pressure of carbon dioxide (water) at sea surface temperature (wet air); pH; Potentiometric; Potentiometric titration; Registration number of species; Salinity; Single species; Size; Species; Stylophora pistillata; Temperature, water; Temperature, water, standard deviation; Treatment; Type; Uniform resource locator/link to reference; δ13C; δ13C, standard deviation
    Type: Dataset
    Format: text/tab-separated-values, 2610 data points
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  • 5
    Publication Date: 2024-03-15
    Description: Tritia reticulata (L.) is a neogastropod ubiquitous in the coastal communities of the NE Atlantic. Its life cycle relies on the swimming performance of planktonic early life stages, whose sensitivity to the climate conditions projected for the near future, namely of ocean acidification (OA) and warming (W), is, to our best knowledge, unknown. To examine the resilience of larval stages to future environmental conditions, this work investigates the effect of OA-W on the swimming performance of T. reticulata veligers under a range of experimental conditions, based on the end-of-century projections of the Intergovernmental Panel on Climate Change. Veligers were exposed to six experimental scenarios for 14 days, employing a full factorial design with three temperatures (T°C: 18, 20 and 22 °C) and two pH levels (pHtarget: 8.1 and 7.8). Mortality was assessed throughout the trial, after which swimming behaviour – characterised by the activity, speed and the distance travelled by veligers – was analysed by automated video recordings in a Zebrabox device. Mortality increased with OA-W and, although more active, larvae travelled shorter distances revealing reduced swimming speed under acidic and warmer conditions, with the interaction of the tested stressors – pH and T°C – being highly significant. Results motivated the morpho-histological analysis of larvae preserved at the end of the trial, to check for the integrity of the organs involved in veligers' motion: statocysts, velum and foot. Statocyst and velar morpho-structure were conserved but histological damage of metapodial epithelia was evident under acidity, namely an apparent hypertrophy and protrusion of the secretory cells, with dispersed pigmented granules and, at 22 °C, less cilia, with potential functional implications. Negative consequences of the OA-W scenarios tested on veligers' competence are unveiled, pointing towards the eminent threat these phenomena constitute to T. reticulata perpetuation in case no mitigation measures are taken, and projections become effective.
    Keywords: Activity; Activity, standard error; Alkalinity, total; Angle; Animalia; Aragonite saturation state; Behaviour; Bicarbonate ion; Bottles or small containers/Aquaria (〈20 L); Calcite saturation state; Calculated using CO2SYS; Calculated using seacarb after Nisumaa et al. (2010); Carbon, inorganic, dissolved; Carbonate ion; Carbonate system computation flag; Carbon dioxide; Coast and continental shelf; Day of experiment; Development; Distance; Distance, standard error; EXP; Experiment; Fugacity of carbon dioxide (water) at sea surface temperature (wet air); Laboratory experiment; Larvae; Larval stages; Mollusca; Mortality; Mortality/Survival; North Atlantic; OA-ICC; Ocean Acidification International Coordination Centre; Partial pressure of carbon dioxide (water) at sea surface temperature (wet air); Pelagos; Percentage; pH; Potentiometric; Potentiometric titration; Registration number of species; Ria_de_Aveiro; Salinity; Single species; Species; Stage; Temperate; Temperature; Temperature, water; Treatment; Tritia reticulata; Type; Uniform resource locator/link to reference; Zooplankton
    Type: Dataset
    Format: text/tab-separated-values, 3660 data points
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  • 6
    Publication Date: 2024-03-15
    Description: Ocean acidification and warming (OA-W) result mainly from the absorption of carbon dioxide and heat by the oceans, altering its physical and chemical properties and affecting carbonate secretion by marine calcifiers such as gastropods. These processes are ongoing, and the projections of their aggravation are not encouraging. This work assesses the concomitant effect of the predicted pH decrease and temperature rise on early life stages of the neogastropod Tritia reticulata (L.), a common scavenger of high ecological importance on coastal ecosystems of the NE Atlantic. Veligers were exposed for 14 days to 12 OA-W experimental scenarios generated by a factorial design of three pH levels (targeting 8.1, 7.8 and 7.5) at four temperatures (16, 18, 20 and 22 °C). Results reveal effects of both pH and temperature (T °C) on larval development, growth, shell integrity and survival, individually or interactively at different exposure times. All endpoints were initially driven by pH, with impaired development and high mortalities being recorded in the first week, constrained by the most acidic scenarios (pHtarget 7.5). Development was also significantly driven by T °C, and its acceleration with warming was observed for the remaining exposure time. Still, by the end of this 2-weeks trial, larval performance and survival were highly affected by the interaction between pH and T °C: growth under warming was evident but only for T °C ≤ 20 °C and carbonate saturation (pHtarget ≥ 7.8). In fact, carbonate undersaturation rendered critical larval mortality (100%) at 22 °C, and the occurrence of extremely vulnerable, unshelled specimens in all other tested temperatures. As recruitment cohorts are the foundation for future populations, our results point towards the extreme vulnerability of this species in case tested scenarios become effective that, according to the IPCC, are projected for the northern hemisphere, where this species is ubiquitous, by the end of the century. Increased veliger mortality associated with reduced growth rates, shell dissolution and loss under OA-W projected scenarios will reduce larval performance, jeopardizing T. reticulata subsistence.
    Keywords: Alkalinity, total; Animalia; Aragonite saturation state; Bicarbonate ion; Bottles or small containers/Aquaria (〈20 L); Calcification/Dissolution; Calcite saturation state; Calculated using CO2SYS; Calculated using seacarb after Nisumaa et al. (2010); Carbon, inorganic, dissolved; Carbonate ion; Carbonate system computation flag; Carbon dioxide; Coast and continental shelf; Day of experiment; Development; EXP; Experiment; Fugacity of carbon dioxide (water) at sea surface temperature (wet air); Growth/Morphology; Laboratory experiment; Larvae; Larval stages; Mollusca; Mortality; Mortality/Survival; North Atlantic; OA-ICC; Ocean Acidification International Coordination Centre; Partial pressure of carbon dioxide (water) at sea surface temperature (wet air); Pelagos; pH; Potentiometric; Potentiometric titration; Registration number of species; Ria_de_Aveiro; Salinity; Shell length; Shell length, standard deviation; Single species; Species; Stage; Temperate; Temperature; Temperature, water; Treatment; Tritia reticulata; Type; Uniform resource locator/link to reference; Zooplankton
    Type: Dataset
    Format: text/tab-separated-values, 8308 data points
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  • 7
    Publication Date: 2024-01-02
    Description: Global biodiversity loss and mass extinction of species are two of the most critical environmental issues the world is currently facing, resulting in the disruption of various ecosystems central to environmental functions and human health. Microbiome-targeted interventions, such as probiotics and microbiome transplants, are emerging as potential options to reverse deterioration of biodiversity and increase the resilience of wildlife and ecosystems. However, the implementation of these interventions is urgently needed. We summarize the current concepts, bottlenecks and ethical aspects encompassing the careful and responsible management of ecosystem resources using the microbiome (termed microbiome stewardship) to rehabilitate organisms and ecosystem functions. We propose a real-world application framework to guide environmental and wildlife probiotic applications. This framework details steps that must be taken in the upscaling process while weighing risks against the high toll of inaction. In doing so, we draw parallels with other aspects of contemporary science moving swiftly in the face of urgent global challenges.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , peerRev
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  • 8
    Publication Date: 2023-06-21
    Description: 〈jats:p〉Genes of unknown function are among the biggest challenges in molecular biology, especially in microbial systems, where 40–60% of the predicted genes are unknown. Despite previous attempts, systematic approaches to include the unknown fraction into analytical workflows are still lacking. Here, we present a conceptual framework, its translation into the computational workflow AGNOSTOS and a demonstration on how we can bridge the known-unknown gap in genomes and metagenomes. By analyzing 415,971,742 genes predicted from 1749 metagenomes and 28,941 bacterial and archaeal genomes, we quantify the extent of the unknown fraction, its diversity, and its relevance across multiple organisms and environments. The unknown sequence space is exceptionally diverse, phylogenetically more conserved than the known fraction and predominantly taxonomically restricted at the species level. From the 71 M genes identified to be of unknown function, we compiled a collection of 283,874 lineage-specific genes of unknown function for 〈jats:italic〉Cand〈/jats:italic〉. Patescibacteria (also known as Candidate Phyla Radiation, CPR), which provides a significant resource to expand our understanding of their unusual biology. Finally, by identifying a target gene of unknown function for antibiotic resistance, we demonstrate how we can enable the generation of hypotheses that can be used to augment experimental data.〈/jats:p〉
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , NonPeerReviewed
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  • 9
    Publication Date: 2023-02-08
    Description: Vertebrates are recognized as sentient beings. Consequently, urgent priority is now being given to understanding the needs and maximizing the welfare of animals under human care. The general health of animals is most commonly determined by physiological indices e.g., blood sampling, but may also be assessed by documenting behavior. Physiological health assessments, although powerful, may be stressful for animals, time-consuming and costly, while assessments of behavior can also be time-consuming, subject to bias and suffer from a poorly defined link between behavior and health. However, behavior is recognized as having the potential to code for stress and well-being and could, therefore, be used as an indicator of health, particularly if the process of quantifying behavior could be objective, formalized and streamlined to be time efficient. This study used Daily Diaries (DDs) (motion-sensitive tags containing tri-axial accelerometers and magnetometers), to examine aspects of the behavior of bycaught loggerhead turtles, Caretta caretta in various states of health. Although sample size limited statistical analysis, significant behavioral differences (in terms of activity level and turn rate) were found between “healthy” turtles and those with external injuries to the flippers and carapace. Furthermore, data visualization (spherical plots) clearly showed atypical orientation behavior in individuals suffering gas emboli and intestinal gas, without complex data analysis. Consequently, we propose that the use of motion-sensitive tags could aid diagnosis and inform follow-up treatment, thus facilitating the rehabilitation process. This is particularly relevant given the numerous rehabilitation programs for bycatch sea turtles in operation. In time, tag-derived behavioral biomarkers, TDBBs for health could be established for other species with more complex behavioral repertoires such as cetaceans and pinnipeds which also require rehabilitation and release. Furthermore, motion-sensitive data from animals under human care and wild conspecifics could be compared in order to define a set of objective behavioral states (including activity levels) for numerous species housed in zoos and aquaria and/or wild species to help maximize their welfare.
    Type: Article , PeerReviewed
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  • 10
    Publication Date: 2023-02-08
    Description: It is fundamentally important for many animal ecologists to quantify the costs of animal activities, although it is not straightforward to do so. The recording of triaxial acceleration by animal-attached devices has been proposed as a way forward for this, with the specific suggestion that dynamic body acceleration (DBA) be used as a proxy for movement-based power. Dynamic body acceleration has now been validated frequently, both in the laboratory and in the field, although the literature still shows that some aspects of DBA theory and practice are misunderstood. Here, we examine the theory behind DBA and employ modelling approaches to assess factors that affect the link between DBA and energy expenditure, from the deployment of the tag, through to the calibration of DBA with energy use in laboratory and field settings. Using data from a range of species and movement modes, we illustrate that vectorial and additive DBA metrics are proportional to each other. Either can be used as a proxy for energy and summed to estimate total energy expended over a given period, or divided by time to give a proxy for movement-related metabolic power. Nonetheless, we highlight how the ability of DBA to predict metabolic rate declines as the contribution of non-movement-related factors, such as heat production, increases. Overall, DBA seems to be a substantive proxy for movement-based power but consideration of other movement-related metrics, such as the static body acceleration and the rate of change of body pitch and roll, may enable researchers to refine movement-based metabolic costs, particularly in animals where movement is not characterized by marked changes in body acceleration.
    Type: Article , PeerReviewed , info:eu-repo/semantics/article
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