20 research outputs found
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Prostaglandin E2 promotes survival of naive UCB T cells via the Wnt/β-catenin pathway and alters immune reconstitution after UCBT
The outcome of umbilical cord blood transplantation (UCBT) is compromised by low hematopoietic stem cell (HSC) doses leading to prolonged time to engraftment, delayed immunological reconstitution and late memory T-cell skewing. Exposure of UCB to dimethyl-prostaglandin E2 (dmPGE2) increases HSC in vivo. We determined that exposure of UCB T lymphocytes to dmPGE2 modified Wnt signaling resulting in T cell factor (TCF)-mediated transcription. Wnt signaling upregulated interleukin (IL)-7R and IL-2Rβ, resulting in enhanced survival mediated by the homeostatic cytokines IL-7 and IL-15. dmPGE2 also induced components of the Wnt pathway and Wnt receptors, thereby priming UCB T cells to receive signals via Wnt ligands in vivo. We observed that the Wnt transcription factor TCF7 and its target EOMES were elevated in the T cells of patients who received PGE2-treated UCBs. Consistent with the role of Wnt/β-catenin signaling to induce and maintain naive, memory precursors and long-lived central memory CD8+ cells, these patients also had increased fractions of CD8+CD45RO-CD62L+ plus CD8+CD45RO+CD62L+ subsets encompassing these T-cell populations. These effects of the PGE2/Wnt/β-catenin axis may have significant implications for harnessing immunity in the context of UCBT, where impaired immune reconstitution is associated with late memory T-cell skewing
Machine learning in marine ecology: an overview of techniques and applications
Machine learning covers a large set of algorithms that can be trained to identify patterns in data. Thanks to the increase in the amount of data and computing power available, it has become pervasive across scientific disciplines. We first highlight why machine learning is needed in marine ecology. Then we provide a quick primer on machine learning techniques and vocabulary. We built a database of ∼1000 publications that implement such techniques to analyse marine ecology data. For various data types (images, optical spectra, acoustics, omics, geolocations, biogeochemical profiles, and satellite imagery), we present a historical perspective on applications that proved influential, can serve as templates for new work, or represent the diversity of approaches. Then, we illustrate how machine learning can be used to better understand ecological systems, by combining various sources of marine data. Through this coverage of the literature, we demonstrate an increase in the proportion of marine ecology studies that use machine learning, the pervasiveness of images as a data source, the dominance of machine learning for classification-type problems, and a shift towards deep learning for all data types. This overview is meant to guide researchers who wish to apply machine learning methods to their marine datasets
CD4+ T cells in aged or thymectomized recipients of allogeneic stem cell transplantations
Application of a bioenergetics growth model for European anchovy (Engraulis encrasicolus) linked with a lower trophic level ecosystem model
Machine learning in marine ecology: an overview of techniques and applications
International audienceMachine learning covers a large set of algorithms that can be trained to identify patterns in data. Thanks to the increase in the amount of data and computing power available, it has become pervasive across scientific disciplines. We first highlight why machine learning is needed in marine ecology. Then we provide a quick primer on machine learning techniques and vocabulary. We built a database of ∼1000 publications that implement such techniques to analyse marine ecology data. For various data types (images, optical spectra, acoustics, omics, geolocations, biogeochemical profiles, and satellite imagery), we present a historical perspective on applications that proved influential, can serve as templates for new work, or represent the diversity of approaches. Then, we illustrate how machine learning can be used to better understand ecological systems, by combining various sources of marine data. Through this coverage of the literature, we demonstrate an increase in the proportion of marine ecology studies that use machine learning, the pervasiveness of images as a data source, the dominance of machine learning for classification-type problems, and a shift towards deep learning for all data types. This overview is meant to guide researchers who wish to apply machine learning methods to their marine datasets
IL-7 and SCF Levels Inversely Correlate with T Cell Reconstitution and Clinical Outcomes after Cord Blood Transplantation in Adults
Infection Rates among Acute Leukemia Patients Receiving Alternative Donor Hematopoietic Cell Transplantation
Alternative graft sources (umbilical cord blood [UCB], matched unrelated donors [MUD], or mismatched unrelated donors [MMUD]) enable patients without a matched sibling donor to receive potentially curative hematopoietic cell transplantation (HCT). Retrospective studies demonstrate comparable outcomes among different graft sources. However, the risk and types of infections have not been compared among graft sources. Such information may influence the choice of a particular graft source. We compared the incidence of bacterial, viral, and fungal infections in 1781 adults with acute leukemia who received alternative donor HCT (UCB, n= 568; MUD, n = 930; MMUD, n = 283) between 2008 and 2011. The incidences of bacterial infection at 1 year were 72%, 59%, and 65% (P < .0001) for UCB, MUD, and MMUD, respectively. Incidences of viral infection at 1 year were 68%, 45%, and 53% (P < .0001) for UCB, MUD, and MMUD, respectively. In multivariable analysis, bacterial, fungal, and viral infections were more common after either UCB or MMUD than after MUD (P < .0001). Bacterial and viral but not fungal infections were more common after UCB than MMUD (P = .0009 and <.0001, respectively). The presence of viral infection was not associated with an increased mortality. Overall survival (OS) was comparable among UCB and MMUD patients with Karnofsky performance status (KPS) ≥ 90% but was inferior for UCB for patients with KPS < 90%. Bacterial and fungal infections were associated with poorer OS. Future strategies focusing on infection prevention and treatment are indicated to improve HCT outcomes
SEAwise Report on improved predictive models of growth, production and stock quality.
The SEAwise project works to deliver a fully operational tool that will allow fishers, managers, and policy makers to easily apply Ecosystem Based Fisheries Management (EBFM) in their fisheries and understanding how ecological drivers impact stock productivity through growth, condition and maturity is essential to this proces. In this SEAwise report, we present the predictive models of fish growth, condition and maturity obtained so far in each of the four regional case studies.The biological processes (fish growth, condition and maturity) were studied in terms of body size (weight-at-age, length-at-age), condition factor, otolith increments and size at first maturity. Underlying data were available at different levels, ranging from individual fish, to sampling haul or stock level. Accordingly, the methods employed varied across case studies to adapt to the specific features of the process under study and the available data.The methodology encompassed statistical models (linear models, generalised additive models, mixed models, Bayesian nested hierarchical models, changepoint models), otolith growth increment analyses and mechanistic models (DEB-IBM model coupled to the environment and mizer model). Some of these models were focused on detecting overall trends, including potential changepoints along the time series or identification of the main intrinsic factors. Other models explored the impact of ecological drivers such as temperature, salinity, food availability or density dependence.In the Baltic Sea, two regimes were identified in the weight-at-age time series of herring in the Gulf of Riga (1961-1988 and 1989-2020). During the first period the main driver of the individual annual growth of the fish was the abundance of the copepod L. macrurus macrurus, while the abundance of the adult stages of E. affinis affinis was the dominating explanatory variable affecting herring growth during the second period. Neither SSB nor summer temperature during the main feeding period were significant drivers of the individual growth in the two distinct ecosystem regimes.In the Mediterranean Sea, the analysis of the impact of the environmental variables on biological parameters like size at first maturity, condition factor and growth in South Adriatic Sea and North-West Ionian Sea showed some significant effects in relation to the different species/area. In most of the cases, the environmental driver was bottom temperature, although some relationships with bottom salinity and primary production were also found. The model outcomes suggested that temperatures prevailing in deeper waters were the most significant factor affecting gonad maturity of hakes, while those in the shallow zone had the main impact on the L50 of red mullets. Condition factor of hake and red mullet in the Eastern Ionian Sea were affected not only by temperature, but also by zooplankton abundance.In the North Sea, mediated length-based growth models, linear mixed models and state-space linear mixed models were applied to four gadoids, two flatfishes and one pelagic stock and their performances were assessed in terms of model fit and predictive capability. For the mediated length-based growth model approach, the best model differed across stocks, but density dependent mediation effects were significant for five out of the seven stocks. Regarding the linear mixed models, the two types of models and the different penalisation procedures led to different models across stocks. Among the additional ecological variables, surface temperature was the most frequently included in the final model, closely followed closely by SSB and to a lesser extent by NAO. Detailed otolith increment analysis was used in the development of multidecadal biochronologies of average annual growth of sole in the North Sea and in the Irish Sea. In the North Sea, the best extrinsic model of sole growth included sea bottom temperature, fishing mortality at age, and stock biomass at maturity stage, and their interactions with age and maturity stage, while in the Irish Sea, the best extrinsic model included sea bottom temperature and fishing mortality at maturity stage and its interaction with maturity stage. These results confirmed the expected positive effect of temperature on adult growth. However, in the North Sea, temperature showed unexpected negative effect on juvenile growth, which might be linked to changes in food availability and/or intraspecific competition and need to be further studied. The mizer model (package for size-spectrum ecological modelling) with environmental forcing was used to study whether warming in the North Sea is responsible for the failure of the cod stock. The simulated fish community response when recruitment and carrying capacity depended on surface temperature fitted better with the assessment data than when the environment was fixed. However, the qualitative differences remain, suggesting that temperature effects were not the main cause of the model-assessment disparity.In the Western Waters, the mediated length-based growth models developed for the North Sea case study were applied to 14 stocks in the Celtic Sea. The best model differed across stocks, but again SSB mediation was significant for most of the stocks. From visual inspection of the plots, however, it was noted that the raw data from certain stock objects showed a reduced growth compared to the model fits, requiring further analyses. The analysis on biological measurements of individuals collected at fish markets, observers at sea or during scientific cruises allowed to study temporal variations in body size and condition factor of benthic, pelagic and demersal species in the Celtic Sea and the Bay of Biscay. The linear models indicated a significant negative monotonic relationship of sizes at all ages for anchovy and pilchard, but variations in size at age were less clear and significant for benthic and demersal species. In contrast, the results of the body condition indices showed a moderate but significant decrease for all the studied 19 species over time. The in-depth analysis for anchovy in the Bay of Biscay based on research surveys confirmed the decline in the length and weight of anchovy in the Bay of Biscay and pointed to a decline in body condition toward slender body shapes. Detected associations between temperature and size became more apparent for adult age classes than for juveniles, whereas the association between anchovy size and the biomass of spawners was more important for juvenile than for adult age classes. Associations between anchovy size and chlorophyll-a concentration were in general weak. Finally, the DEB-IBM model coupled to the environment that is under development for the two main seabass stocks of the North East Atlantic will provide further insights on how growth, condition and maturation can affect the future dynamics and productivity of these stocks.Read more about the project at www.seawiseproject.org</p