| 1. |
- Layton, K. K. S., et al.
(author)
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Predicting the future of our oceans : Evaluating genomic forecasting approaches in marine species
- 2024
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In: Global Change Biology. - : John Wiley & Sons. - 1354-1013 .- 1365-2486. ; 30:3
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Research review (peer-reviewed)abstract
- Climate change is restructuring biodiversity on multiple scales and there is a pressing need to understand the downstream ecological and genomic consequences of this change. Recent advancements in the field of eco-evolutionary genomics have sought to include evolutionary processes in forecasting species' responses to climate change (e.g., genomic offset), but to date, much of this work has focused on terrestrial species. Coastal and offshore species, and the fisheries they support, may be even more vulnerable to climate change than their terrestrial counterparts, warranting a critical appraisal of these approaches in marine systems. First, we synthesize knowledge about the genomic basis of adaptation in marine species, and then we discuss the few examples where genomic forecasting has been applied in marine systems. Next, we identify the key challenges in validating genomic offset estimates in marine species, and we advocate for the inclusion of historical sampling data and hindcasting in the validation phase. Lastly, we describe a workflow to guide marine managers in incorporating these predictions into the decision-making process. Predicting climate change impacts is of central importance in marine ecosystems that provide a major source of nutrition to global communities and this work must be based on a sound understanding of both ecological and genomic impacts. This opinion synthesizes knowledge about the genomic basis of adaptation in marine species, highlights the few examples where genomic forecasting has been applied in marine systems, identifies the key challenges in validating genomic offset estimates in marine species, and provides a workflow to guide marine managers in incorporating these predictions into the decision-making process.
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| 2. |
- Niimi, Jun, et al.
(author)
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Prediction of wine sensory properties using mid-infrared spectra of Cabernet Sauvignon and Chardonnay grape berries and wines
- 2021
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In: Food Chemistry. - : Elsevier Ltd. - 0308-8146 .- 1873-7072. ; 344
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Journal article (peer-reviewed)abstract
- The study determined optimal parameters to four preprocessing techniques for mid-infrared (MIR) spectra of wines and grape berry homogenates and tested MIR's ability to model sensory properties of research Cabernet Sauvignon and Chardonnay wines. Savitsky-Golay (SG) derivative, smoothing points, and polynomial order, and extended multiplicative signal correction (EMSC) polynomial were investigated as preprocessing techniques at 2, 2, 5, and 3 levels, respectively, all in combination. Preprocessed data were analysed with partial least squares regression (PLS) to model the wine sensory data and the regression coefficients of PLS calibration models (R2) were further analysed with multivariate analysis of variance (MANOVA). SG transformations were significant factors from the MANOVA that influenced R2, while EMSC did not. Overall, PLSR models that predicted wine sensory characteristics gave a poor to moderate R2. Consistently predicting wine sensory attributes within a variety and across vintages is challenging, regardless of using grape or wine spectra as predictors.
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| 3. |
- Desvignes, Thomas, et al.
(author)
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Unification of miRNA and isomiR research : the mirGFF3 format and the mirtop API
- 2020
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In: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 36:3, s. 698-703
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Journal article (peer-reviewed)abstract
- Motivation: MicroRNAs (miRNAs) are small RNA molecules (similar to 22 nucleotide long) involved in post-transcriptional gene regulation. Advances in high-throughput sequencing technologies led to the discovery of isomiRs, which are miRNA sequence variants. While many miRNA-seq analysis tools exist, the diversity of output formats hinders accurate comparisons between tools and precludes data sharing and the development of common downstream analysis methods. Results: To overcome this situation, we present here a community-based project, miRNA Transcriptomic Open Project (miRTOP) working towards the optimization of miRNA analyses. The aim of miRTOP is to promote the development of downstream isomiR analysis tools that are compatible with existing detection and quantification tools. Based on the existing GFF3 format, we first created a new standard format, mirGFF3, for the output of miRNA/isomiR detection and quantification results from small RNA-seq data. Additionally, we developed a command line Python tool, mirtop, to create and manage the mirGFF3 format. Currently, mirtop can convert into mirGFF3 the outputs of commonly used pipelines, such as seqbuster, isomiR-SEA, sRNAbench, Prost! as well as BAM files. Some tools have also incorporated the mirGFF3 format directly into their code, such as, miRge2.0, IsoMIRmap and OptimiR. Its open architecture enables any tool or pipeline to output or convert results into mirGFF3. Collectively, this isomiR categorization system, along with the accompanying mirGFF3 and mirtop API, provide a comprehensive solution for the standardization of miRNA and isomiR annotation, enabling data sharing, reporting, comparative analyses and benchmarking, while promoting the development of common miRNA methods focusing on downstream steps of miRNA detection, annotation and quantification.
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| 4. |
- Im, Annie, et al.
(author)
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Risk Factors for Graft-versus-Host Disease in Haploidentical Hematopoietic Cell Transplantation Using Post-Transplant Cyclophosphamide
- 2020
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In: Biology of blood and marrow transplantation. - : Elsevier BV. - 1083-8791 .- 1523-6536. ; 26:8, s. 1459-1468
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Journal article (peer-reviewed)abstract
- Post-transplant cyclophosphamide (PTCy) has significantly increased the successful use of haploidentical donors with a relatively low incidence of graft-versus-host disease (GVHD). Given its increasing use, we sought to determine risk factors for GVHD after haploidentical hematopoietic cell transplantation (haplo-HCT) using PTCy. Data from the Center for International Blood and Marrow Transplant Research on adult patients with acute myeloid leukemia, acute lymphoblastic leukemia, myelodysplastic syndrome, or chronic myeloid leukemia who underwent PTCy-based haplo-HCT (2013 to 2016) were analyzed and categorized into 4 groups based on myeloablative (MA) or reduced-intensity conditioning (RIC) and bone marrow (BM) or peripheral blood (PB) graft source. In total, 646 patients were identified (MA-BM = 79, MA-PB = 183, RIC-BM = 192, RIC-PB = 192). The incidence of grade 2 to 4 acute GVHD at 6 months was highest in MA-PB (44%), followed by RIC-PB (36%), MA-BM (36%), and RIC-BM (30%) (P = .002). The incidence of chronic GVHD at 1 year was 40%, 34%, 24%, and 20%, respectively (P < .001). In multivariable analysis, there was no impact of stem cell source or conditioning regimen on grade 2 to 4 acute GVHD; however, older donor age (30 to 49 versus <29 years) was significantly associated with higher rates of grade 2 to 4 acute GVHD (hazard ratio [HR], 1.53; 95% confidence interval [CI], 1.11 to 2.12; P = .01). In contrast, PB compared to BM as a stem cell source was a significant risk factor for the development of chronic GVHD (HR, 1.70; 95% CI, 1.11 to 2.62; P = .01) in the RIC setting. There were no differences in relapse or overall survival between groups. Donor age and graft source are risk factors for acute and chronic GVHD, respectively, after PTCy-based haplo-HCT. Our results indicate that in RIC haplo-HCT, the risk of chronic GVHD is higher with PB stem cells, without any difference in relapse or overall survival.
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| 5. |
- Kahn, Justine M., et al.
(author)
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Subsequent neoplasms and late mortality in children undergoing allogeneic transplantation for nonmalignant diseases
- 2020
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In: Blood Advances. - : AMER SOC HEMATOLOGY. - 2473-9529 .- 2473-9537. ; 4:9, s. 2084-2094
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Journal article (peer-reviewed)abstract
- We examined the risk of subsequent neoplasms (SNs) and late mortality in children and adolescents undergoing allogeneic hematopoietic cell transplantation (HCT) for nonmalignant diseases (NMDs). Weincluded 6028 patients (median age, 6 years; interquartile range, 1-11; range, <1 to 20) from the Center for International Blood and Marrow Transplant Research (1995-2012) registry. Standardized mortality ratios (SMRs) in 2-year survivors and standardized incidence ratios (SIRs) were calculated to compare mortality and SN rates with expected rates in the general population. Median follow-up of survivors was 7.8 years. Diagnoses included severe aplastic anemia (SAA; 24%), Fanconi anemia (FA; 10%), other marrow failure (6%), hemoglobinopathy (15%), immunodeficiency (23%), and metabolic/leukodystrophy syndrome (22%). Ten-year survival was 93% (95% confidence interval [95% CI], 92% to 94%; SMR, 4.2; 95% CI, 3.7-4.8). Seventy-one patients developed SNs (1.2%). Incidence was highest in FA (5.5%), SAA (1.1%), and other marrow failure syndromes (1.7%); for other NMDs, incidence was <1%. Hematologic (27%), oropharyngeal (25%), and skin cancers (13%) were most common. Leukemia risk was highest in the first 5 years posttransplantation; oropharyngeal, skin, liver, and thyroid tumors primarily occurred after 5 years. Despite a low number of SNs, patients had an 11-fold increased SN risk (SIR, 11; 95% CI, 8.9-13.9) compared with the general population. We report excellent long-term survival and low SN incidence in an international cohort of children undergoing HCT for NMDs. The risk of SN development was highest in patients with FA and marrow failure syndromes, highlighting the need for long-term posttransplantation surveillance in this population.
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| 6. |
- Kalaria, Raj, et al.
(author)
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The 2022 symposium on dementia and brain aging in low- and middle-income countries: Highlights on research, diagnosis, care, and impact.
- 2024
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In: Alzheimer's & dementia : the journal of the Alzheimer's Association. - 1552-5279.
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Journal article (peer-reviewed)abstract
- Two of every three persons living with dementia reside in low- and middle-income countries (LMICs). The projected increase in global dementia rates is expected to affect LMICs disproportionately. However, the majority of global dementia care costs occur in high-income countries (HICs), with dementia research predominantly focusing on HICs. This imbalance necessitates LMIC-focused research to ensure that characterization of dementia accurately reflects the involvement and specificities of diverse populations. Development of effective preventive, diagnostic, and therapeutic approaches for dementia in LMICs requires targeted, personalized, and harmonized efforts. Our article represents timely discussions at the 2022 Symposium on Dementia and Brain Aging in LMICs that identified the foremost opportunities to advance dementia research, differential diagnosis, use of neuropsychometric tools, awareness, and treatment options. We highlight key topics discussed at the meeting and provide future recommendations to foster a more equitable landscape for dementia prevention, diagnosis, care, policy, and management in LMICs. HIGHLIGHTS: Two-thirds of persons with dementia live in LMICs, yet research and costs are skewed toward HICs. LMICs expect dementia prevalence to more than double, accompanied by socioeconomic disparities. The 2022 Symposium on Dementia in LMICs addressed advances in research, diagnosis, prevention, and policy. The Nairobi Declaration urges global action to enhance dementia outcomes in LMICs.
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| 7. |
- Niimi, Jun, et al.
(author)
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Objective measures of grape quality : From Cabernet Sauvignon grape composition to wine sensory characteristics
- 2020
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In: Lebensmittel-Wissenschaft + Technologie. - : Academic Press. - 0023-6438 .- 1096-1127. ; 123
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Journal article (peer-reviewed)abstract
- In an investigation of objective measures that link grape composition to wine quality, this study sought to identify Cabernet Sauvignon grape parameters that predict the sensory properties of the corresponding wines. Eleven chemical measures comprising volatile and non-volatile compounds, enzyme activity plus standard industry harvest measurements were applied to grape samples obtained from different regions throughout South Eastern Australia over three vintages. Grapes underwent controlled vinification and the resulting wines evaluated with sensory descriptive analysis. The entire multi-vintage data sets were combined and modelled using a combination of partial least squares (PLS) and sequential and orthogonalised (SO) -PLS regression techniques. Optimal models were obtained with single sensory attributes rather than global modelling with the entire sensory profile. Five grape chemical measures, which in the main were harvest parameters, were used along with colour, total phenolics and tannin, targeted volatiles, and flavonols, and orthogonalised to model 14 sensory attributes of the Cabernet Sauvignon wines. The seven remaining measures were not used due to their poor ability to model wine sensory attributes, with enzyme activity and tannin by HPLC explaining the least. The study revealed new insights into the relationship between grape chemistry and wine sensory characters, which has implications for developing an objective measurement system for determining grape quality.
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| 8. |
- Petzold, A., et al.
(author)
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Advancing the FAIRness and Openness of Earth system science in Europe
- 2021
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Conference paper (other academic/artistic)abstract
- Focused environmental research projects and continuously operating research infrastructures (RIs) designed for monitoring all subdomains of the Earth system contribute to global observing systems and serve as crucial information sources for environmental scientists in their quest for understanding and interpreting the complex Earth System and contribute to global observing systems. The EU funded ENVRI-FAIR project [1] builds on the Environmental Research Infrastructure (ENVRI) community that includes principal European producers and providers of environmental research data and services.ENVRI-FAIR targets the development and implementation of both technical frameworks and policy solutions that make subdomain boundaries irrelevant for environmental scientists and prepare Earth system science for the new Open Science paradigm. Cross-discipline harmonization and standardization activities, together with the implementation of joint data management and access structures at the RI level, facilitate the strategic coordination of observation systems required for truly interdisciplinary science. ENVRI-FAIR will ultimately create the open access ENVRI-Hub delivering environmental data and services provided by the contributing environmental RIs.The architecture and functionalities of the ENVRI-Hub are driven by the applications, use cases and user needs, and will be based on three main pillars: (1) the ENVRI Knowledge Base as the human interface to the ENVRI ecosystem; (2) the ENVRI Catalogue as the machine-actionable interface to the ENVRI ecosystem; and (3) subdomain and cross-domain use cases as demonstrators for the capabilities of service provision among ENVRIs and across Science Clusters. The architecture is designed in anticipation of interoperation with the European Open Science Cloud (EOSC) and is intended to act as a key platform for users and developers planning to include ENVRI services in their workflows.The ENVRI community objectives of sharing FAIRness experience, technologies and training as well as research products and services will be realized by means of the ENVRI-Hub. The architecture, design features, technology developments and associated policies will highlight this example of how ENVRI-FAIR is promoting FAIRness, openness and multidisciplinarity of an entire scientific area by joint developments and implementation efforts.Acknowledgment: ENVRI-FAIR has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 824068.[1] Petzold, A., Asmi, A., Vermeulen, A., Pappalardo, G., Bailo, D., Schaap, D., Glaves, H. M., Bundke, U., and Zhao, Z.: ENVRI-FAIR - Interoperable environmental FAIR data and services for society, innovation and research, 15th IEEE International Conference on eScience 2019, 1-4, doi: http://doi.org/10.1109/eScience.2019.00038, 2019.
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