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1.
J Pers Med ; 13(6)2023 Jun 13.
Artigo em Inglês | MEDLINE | ID: mdl-37373980

RESUMO

AIMS: This article aims to perform a Systematic Literature Review (SLR) to better understand the structures of different methods, techniques, models, methodologies, and technologies related to provenance data management in health information systems (HISs). The SLR developed here seeks to answer the questions that contribute to describing the results. METHOD: An SLR was performed on six databases using a search string. The backward and forward snowballing technique was also used. Eligible studies were all articles in English that presented on the use of different methods, techniques, models, methodologies, and technologies related to provenance data management in HISs. The quality of the included articles was assessed to obtain a better connection to the topic studied. RESULTS: Of the 239 studies retrieved, 14 met the inclusion criteria described in this SLR. In order to complement the retrieved studies, 3 studies were included using the backward and forward snowballing technique, totaling 17 studies dedicated to the construction of this research. Most of the selected studies were published as conference papers, which is common when involving computer science in HISs. There was a more frequent use of data provenance models from the PROV family in different HISs combined with different technologies, among which blockchain and middleware stand out. Despite the advantages found, the lack of technological structure, data interoperability problems, and the technical unpreparedness of working professionals are still challenges encountered in the management of provenance data in HISs. CONCLUSION: It was possible to conclude the existence of different methods, techniques, models, and combined technologies, which are presented in the proposal of a taxonomy that provides researchers with a new understanding about the management of provenance data in HISs.

2.
Chemosphere ; 330: 138709, 2023 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-37072086

RESUMO

Three sediment cores recovered from the Alvarado Lagoon System (ALS) in the Gulf of Mexico were used to reconstruct the history of metals and metalloids and their environmental importance. The sedimentary profiles were dated with 210Pb and verified with 137Cs. Maximum ages of 77 and 86 years were estimated. Sediment provenance was described by sedimentological and geochemical proxies. The chemical alteration index (CIA) and weathering index (CIW) revealed moderate to high intensity of weathering in the source area that is controlled tropical climatic conditions, runoff, and precipitation in the basin that feeds sediments to this coastal lagoon. The Al2O3/TiO2 ratios indicated that the sediments were derived from intermediate igneous rocks. The enrichment factor values revealed the lithogenic and anthropic contribution of metals and metalloids. Cd is classified under the category extremely severe enrichment; agricultural activities, fertilizers, herbicides, and pesticides containing Cd are expected to supply this metal to the ecosystem. Factor Analysis and Principal Components provided two main factors, terrigenous and biological origins; ANOVA indicated that there are significant differences between the cores for the parameters analyzed and revealed that there are differences in depositional environments between the recovery zones of the cores. The ALS presented natural variations associated with the climatic conditions, terrigenous input, and its relationship with the hydrological variations of the main rivers. The contribution of this work was to identify the magnitude of the natural component versus the human contribution, mainly of risk metals such as Cd, to support better management of the hydrological basin that affects the ALS.


Assuntos
Metais Pesados , Poluentes Químicos da Água , Humanos , Metais Pesados/análise , Chumbo/análise , Ecossistema , Cádmio/análise , México , Sedimentos Geológicos/análise , Poluentes Químicos da Água/análise , Monitoramento Ambiental
3.
Heliyon ; 9(2): e13311, 2023 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-36755614

RESUMO

Open Educational Resources (OER) can be adapted and combined to create new resources that better meet the specific needs of different kinds of users and scenarios. In this sense, OER strongly contributes to generating and sharing educational knowledge. Due to the possibility of creating a new OER through the revision and remix activities, the original OER and the transformation process should be adequately identified. This way, the user of the OER has enough information about the history of the resource and, thus, can use it with confidence and security. In this context, determining data provenance, which describes the history of a data from its origin to its current state, becomes very relevant. For OER, there are examples of metadata standards and digital repositories that help to obtain the data provenance. However, the information collected is insufficient to identify the entire history of the provenance of OER. This article proposes a Provenance Model for OER called the ProvOER Model, which allows the documentation and identification of the provenance of OER. For this purpose, a minimum set of metadata was defined that reflects the OER intrinsic properties and the activities that created a new OER. The experiments showed that the ProvOER Model produced a suitable representation of the provenance of OER. In addition, the ProvOER Model allowed identifying the original OER used in a revise or remix activity and the continuous stretch used to create a new resource.

4.
Plants (Basel) ; 11(21)2022 Oct 29.
Artigo em Inglês | MEDLINE | ID: mdl-36365371

RESUMO

Natural regeneration of recalcitrant-seeded tree species is strongly limited in Mediterranean-type climate zones due to increasing droughts imposed by climate change. Direct seeding can be a low-cost alternative to seedling establishment, but there is still limited information for some species. This study aimed to assess the effects of the seed source and forest cover on the germination and survival of the endemic Cryptocarya alba Mol. established through direct seeding. Three habitat types differing in forest cover were identified within the natural park Reserva Natural Altos de Cantillana, Metropolitan Region, Chile. The forest cover corresponded to open (canopy density <25%), semi-dense (canopy density around 50%), and dense forest (canopy density >75%). All forest cover had C. alba as one of the dominant species. At each habitat type, 38 families from four seed sources (Cuesta La Dormida (CD), Antumapu (AN), Cantillana (CA, local seed source) and Cayumanque (CY)) were directly seeded. Germination (Germin) and survival (Surv) were evaluated weekly during one growing season. There were significant differences between seed sources in Germin and Surv, with means values varying from 7.8% to 37% for Germin and 0% to 20% for Surv. The local seed source CA had the highest values in both traits. A significant variation was also observed between families within seed sources only for Germin. The dense forest cover had the highest Germin (22%) and Surv (55%) results compared to the other forest cover types, which was partially associated with differences in soil moisture, temperature, and bulk density. Due to the most frequent droughts in these Mediterranean-type climate zones, the use of local seeds on dense forest cover is recommended for the direct seeding of the species in the initial recruitment.

5.
J Plant Res ; 135(4): 579-591, 2022 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-35670888

RESUMO

Desiccation sensitive (DS) seeds are shed at high water contents (WC) and metabolically active, but WC thresholds vary broadly among species even in the same genus. Eugenia is an important ecological genus that has high occurrence in several Brazilian morphoclimatic domains. In this study, we assessed seed desiccation tolerance of five Eugenia species collected in specific meteorological conditions. We reported the species geographical ranges and verified the rainfall and temperature of species sites in the year prior to seed collection. We also assessed initial WC, seed germination and vigor and seedling growth upon desiccation. Eugenia uniflora was the widest spread among the five species, while E. astringens was the most restricted. In this specific study, widespread species showed a higher WC threshold than restricted species. In the same way, the WC of fresh seeds was not correlated to the desiccation tolerance threshold. Seed desiccation tolerance was species dependent and correlated with the environmental status of seed collection sites. Wetter and warmer conditions were correlated to the E. uniflora higher DS threshold. Low rainfall and temperature corresponded to a lower desiccation sensitivity of E. astringens seeds. Seeds of the five species lost half viability between 0.44 and 0.25 g H2O g DW- 1 and after 65-270 h of desiccation. Our results indicate that abiotic factors impact plant populations during the seed production season and can drive seed desiccation tolerance threshold and physiological behavior. These results should be taken into account in ex-situ plant conservation programs and tropical species management.


Assuntos
Eugenia , Myrtaceae , Brasil , Dessecação , Germinação , Sementes/fisiologia , Água
6.
J Plant Res ; 135(2): 221-234, 2022 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-35149910

RESUMO

Prosopis chilensis (Molina) Stuntz (Leguminosae) is a valuable native species in Argentina that has been proposed to be used in reforestation, afforestation and restoration programmes. Natural provenances show important differentiation in height, shape, spine size, fruits and foliar traits throughout their distribution in the semiarid Monte ecoregion. The goal of this work was to characterize the genetic basis of the leaf variation in P. chilensis aiming to contribute to the improvement management program. We analyzed morphological variation and estimate narrow sense heritability for ten quantitative traits from a provenance-progeny trial founded from open pollinated families. We assessed the variance components by a generalized linear mixed model. Differences among provenances were quantified through univariate QST statistics and multivariate discriminant analysis of principal components. Finally, univariate and multivariate neutrality test were conducted to unveil the evolutionary forces that shape the variation. Univariate and multivariate analysis showed low genetic variation in foliar traits among provenances grown in the common garden. Consistently, the QST estimates for each trait were low. Both, the univariate (QST-FST comparison) and the multivariate neutrality test suggest that the leaf variation among provenances may be shaped by genetic drift rather than selective forces. Heritability estimates were significant only for leaflet apex and leaflet apex/leaflet area. Since genetic variation for most foliar traits among provenances estimated under controlled environmental conditions were very low or absent, the variation described in the wild would be explained merely by plastic response to varying environments. These results are discussed in terms of adaptive strategies and the use of different provenances as seed sources within the framework of the improvement program. It is expected that P. chilensis seeds or seedlings from trees selected under economical criteria will be able to develop in different areas thanks to the phenotypic plasticity of leaf traits.


Assuntos
Fabaceae , Prosopis , Adaptação Fisiológica , Fabaceae/genética , Variação Genética , Fenótipo , Prosopis/genética
7.
Sci Total Environ ; 807(Pt 2): 151231, 2022 Feb 10.
Artigo em Inglês | MEDLINE | ID: mdl-34715230

RESUMO

The Abrolhos bank is home of the richest coral reef system of the Southwestern Atlantic, where endemic coral species are found. It has been reported that Abrolhos' corals are under intense stress due to increasing of Marine Heat Waves during the last decades. Additionally, anthropic interventions along the adjacent coastal regions are a factor of concern since they contribute to the increase in the sediment load and to organic debris input in the reef domain. In November 2015, the collapse of the Fundão mining tailings dam resulted in the release of approximately 50 million m3 of iron oxide and quartz-rich slurry into the Doce River. Aiming at using a fingerprint of the tailings and to assess the presence of traces of the Fundão dam material from this event on the Abrolhos bank, this work presents new 87Sr/86Sr and 143Nd/144Nd isotope ratios of marine suspended sediment samples collected between 2016 and 2020 from a network of sediment traps throughout the reef and complementary suspended material at sea. In parallel, we monitored meteo-oceanographic parameters and modeled surface marine currents as an attempt to identify the sediment transport between the Doce River mouth and Abrolhos bank. The r isotopes were used as provenance proxies based on the fact that minerals and rocks tend to have specific isotopic signatures reflecting their own geological derivation. In this context, the isotopic ratios of various potential regional sources for the sedimentation in Abrolhos bank were evaluated. Our monitoring and isotopic measurements indicate that Doce River signatures are detected at Abrolhos bank, following the seasonal Doce River discharge at sea. Isotopic signature of Doce River at Abrolhos bank was also observed during the austral winter (July-August) when cold fronts migrate at the Brazilian coast with higher frequency and energy.


Assuntos
Antozoários , Colapso Estrutural , Animais , Brasil , Recifes de Corais , Sedimentos Geológicos , Isótopos
8.
Forensic Sci Int ; 330: 111109, 2022 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-34839156

RESUMO

In this study, we present a correlation between δ18OC values of carbonate in tooth enamel samples from the modern Brazilian population and the available δ18ODW data for the meteoric water from the Global Network of Isotopes in Precipitation (GNIP). Tooth enamel from 119 Brazilian individuals from five different regions of the country were analyzed. The δ18OC isoscape obtained is in good agreement with the isoscape based on regional meteoric and drinking water. The regression matrix obtained for the δ18O values of the carbonate tooth enamel and meteoric water was used to build an isoscape using the regression-kriging approach. Our data show that Brazil can be divided in two main regions with respect to the δ18O values of the carbonate tooth enamel: (1) the most easterly part of the northeast region, which is characterized by a warm and dry climate and (2) the remainder of the country, stretching from the Amazon rain forest to the more southernly regions. The data herein reported can be used for forensic purposes related to human identification.


Assuntos
Carbonatos , Esmalte Dentário , Água Potável , Brasil , Esmalte Dentário/química , Odontologia Legal , Humanos , Isótopos de Oxigênio/análise
9.
J Forensic Sci ; 66(3): 1048-1055, 2021 May.
Artigo em Inglês | MEDLINE | ID: mdl-33583031

RESUMO

Material characterization is essential to the provenance of graphic arts. Non-destructive analytical techniques are increasingly required in the authentication process of cultural heritage. This work presents a suite of portable, non-destructive, and complementary analytical techniques, energy dispersive x-ray fluorescence (EDXRF), Fourier transform infrared (FTIR) spectroscopies, and brightfield microscopy, applied to the analysis of historical photographs depicting São Paulo city architecture, whose registration date and process of fabrication are unknown. The EDXRF analysis emphasizes the use of typical POP (printing-out paper) photograph with baryta (BaSO4 ) coated paper substrate while the FTIR and microscopy analyses confirm the presence of collodion and a gelatin-based baryta layer. This photographic process was widely employed by professional photographers from 1889 to 1930, when it was gradually abandoned in commercial use. This time interval (1889-1930) is consistent with the information surveyed on the photographic collection. In conclusion, employing complementary techniques (elemental and molecular spectroscopies and image magnification) is essential in identifying the manufacturing materials of cultural heritage material, which is the basis of contemporary authentication procedures. These data provide to curators and historians fundamental information for cataloging, adding subsidies for the correct storage and preservation ("heritage appreciation"). Still, for professional photographers, they present information on the manufacturing processes of historical photographs. The data from the present study also emphasize its perspective of use in graphic arts to aid connoisseurship in identifying forgeries during provenance and authentication studies.

10.
Environ Monit Assess ; 193(2): 100, 2021 Jan 29.
Artigo em Inglês | MEDLINE | ID: mdl-33515075

RESUMO

This work sheds light on the recent evolution (≈1915-2015 AD) of Sepetiba Bay (SB; SE Brazil), a subtropical coastal lagoon on the southwestern Brazilian coast, based on a multiproxy approach. Variations in geochemical proxies as well as textural, mineralogical and geochronological data allow us to reconstruct temporally constrained changes in the depositional environments along the SP3 sediment core collected from the central area of SB. At the beginning of the twentieth century, the substrate of the study site was composed of coarse-grained sediments, largely sourced from felsic rocks of proximal areas and deposited under moderate to strong shallow marine hydrodynamics. Since the 1930s, the study area has undergone silting and received high contributions of materials from mafic rocks sourced by river basins. The SP3 core reveals a shallowing-upward sequence due to human-induced silting with significant eutrophication since the middle of 1970, which was caused by significant enrichment of organic matter that was provided by not only marine productivity but also continental and human waste. In addition, the sediments deposited after 1980 exhibit significant enrichment and are moderately to strongly polluted by Cd and Zn. Metals were dispersed by hydrodynamics from the source areas, but diagenetic processes promoted their retention in the sediments. The potential ecological risk index (PERI) indicates that the level of high (considerable) ecological risk is in sediments deposited in ≈1995 (30-32 cm; subsurface). The applied methodology allowed us to understand the thickness of the bottom sediment affected by eutrophication processes and contaminants. Identical methodologies can be applied in other coastal zones, and can provide useful information to decision makers and stakeholders that manage those areas.


Assuntos
Metais Pesados , Poluentes Químicos da Água , Baías , Brasil , Monitoramento Ambiental , Eutrofização , Sedimentos Geológicos , Humanos , Metais Pesados/análise , Poluentes Químicos da Água/análise
11.
Mol Ecol Resour ; 21(1): 14-17, 2021 01.
Artigo em Inglês | MEDLINE | ID: mdl-32748518

RESUMO

As most ecosystems around the world are threatened by anthropogenic degradation and climate change, there is an increasing urgency to implement restoration strategies aiming at ensuring ecosystem self-sustainability and resilience. An initial step towards that goal relies on selecting the most suitable seed sources for a successful revegetation, which can be extremely challenging in highly degraded landscapes. The most common seed sourcing strategy is to select local seeds because it is assumed that plants experience strong adaptations to their natal sites. An alternative strategy is the selection of climate-adapted genotypes to future conditions. While considering future climatic projections is important to account for spatial shifts in climate to inform assisted gene flow and translocations, to restore highly degraded landscapes we need a comprehensive approach that first accounts for species adaptations to current at-site environmental conditions. In this issue of Molecular Ecology Resources, Carvalho et al. present a novel landscape genomics framework to identify the most appropriate seed sourcing strategy for moderately and highly degraded sites by integrating genotype, phenotype and environmental data in a spatially explicit context for two native plant species with potential to help restore iron-rich Amazonian savannas. This framework is amenable to be applicable and adapted to a broad range of restoration initiatives, as the dichotomy between focusing on the current or future climatic conditions should depend on the goals and environmental circumstances of each restoration site.


Assuntos
Mudança Climática , Ecossistema , Adaptação Fisiológica , Ecologia , Genômica
12.
Front Neuroinform ; 15: 768615, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-35069167

RESUMO

Computational tools can transform the manner by which neuroscientists perform their experiments. More than helping researchers to manage the complexity of experimental data, these tools can increase the value of experiments by enabling reproducibility and supporting the sharing and reuse of data. Despite the remarkable advances made in the Neuroinformatics field in recent years, there is still a lack of open-source computational tools to cope with the heterogeneity and volume of neuroscientific data and the related metadata that needs to be collected during an experiment and stored for posterior analysis. In this work, we present the Neuroscience Experiments System (NES), a free software to assist researchers in data collecting routines of clinical, electrophysiological, and behavioral experiments. NES enables researchers to efficiently perform the management of their experimental data in a secure and user-friendly environment, providing a unified repository for the experimental data of an entire research group. Furthermore, its modular software architecture is aligned with several initiatives of the neuroscience community and promotes standardized data formats for experiments and analysis reporting.

13.
Methods Protoc ; 3(1)2020 Jan 13.
Artigo em Inglês | MEDLINE | ID: mdl-31941007

RESUMO

Finding the source or provenance of quartz grains occurring in a specific location allows us to constrain their transport pathway, which is crucial information to solve diverse problems in geosciences and related fields. The optically stimulated luminescence (OSL) sensitivity (light intensity per unit mass per unit radiation dose) has a high capacity for discrimination of quartz sediment grains and represents a promising technique for provenance analysis. In this study, we tested the use of quartz OSL sensitivity (ultraviolet emission) measured under different preheating temperatures and with blue light stimulation at room temperature (~20 °C) for sediment provenance analysis. Quartz OSL sensitivity measured at 20 °C is positively correlated with the sensitivity of an OSL signal measured using procedures (preheat at 190 °C for 10 s, blue stimulation at 125 °C and initial 1 s of light emission) to increase the contribution of the fast OSL component, which has been successfully applied for sediment provenance analysis. The higher OSL signal intensity measured without preheating and with light stimulation at room temperature allows the use of lower given doses, thus reducing measurement time. Additionally, the OSL sensitivity measured at 20 °C in polymineral silt samples of a marine sediment core is also suitable for provenance analysis, as demonstrated by comparison with other independent proxies. OSL signals obtained through light stimulation at room temperature have thus the potential to considerably expand measurement possibilities, including in situ measurements using portable OSL readers.

14.
Evol Bioinform Online ; 15: 1176934319889974, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31839702

RESUMO

Scientific workflows can be understood as arrangements of managed activities executed by different processing entities. It is a regular Bioinformatics approach applying workflows to solve problems in Molecular Biology, notably those related to sequence analyses. Due to the nature of the raw data and the in silico environment of Molecular Biology experiments, apart from the research subject, 2 practical and closely related problems have been studied: reproducibility and computational environment. When aiming to enhance the reproducibility of Bioinformatics experiments, various aspects should be considered. The reproducibility requirements comprise the data provenance, which enables the acquisition of knowledge about the trajectory of data over a defined workflow, the settings of the programs, and the entire computational environment. Cloud computing is a booming alternative that can provide this computational environment, hiding technical details, and delivering a more affordable, accessible, and configurable on-demand environment for researchers. Considering this specific scenario, we proposed a solution to improve the reproducibility of Bioinformatics workflows in a cloud computing environment using both Infrastructure as a Service (IaaS) and Not only SQL (NoSQL) database systems. To meet the goal, we have built 3 typical Bioinformatics workflows and ran them on 1 private and 2 public clouds, using different types of NoSQL database systems to persist the provenance data according to the Provenance Data Model (PROV-DM). We present here the results and a guide for the deployment of a cloud environment for Bioinformatics exploring the characteristics of various NoSQL database systems to persist provenance data.

15.
Sci Justice ; 59(3): 322-331, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-31054821

RESUMO

Human provenance studies employing isotopic analysis have become an essential tool in forensic and archaeological sciences, with multi-isotope approaches providing more specific location estimates compared to single isotope studies. This study reports on the human provenancing capability of neodymium isotopes (143Nd/144Nd), a relatively conservative tracer in the environment. Neodymium isotope ratios have only recently been determined on human remains due to low concentrations in human dental enamel (ppb range), requiring thermal ionisation mass spectrometry (TIMS) using 1013â€¯Ω resistors. Dental elements (third molars) from 20 individuals born and raised in the Netherlands were analysed for Nd concentration (n = 12) and Nd isotope ratios (n = 15). The geological control on Nd isotope composition was examined using coupled Nd-Sr isotope analysis of the same third molar. Teeth from different geological environments were also analysed (Caribbean, Columbian, and Icelandic, n = 5). Neodymium elemental concentrations in dental elements ranged between 0.1 and 7.9 ppb (median 0.5 ppb). The Dutch 143Nd/144Nd ratios of the provinces of Limburg and Friesland were between 0.5118 and 0.5121, with Dutch 87Sr/86Sr ratios in agreement with the previously established local range (0.708-0.710). The current findings were compared to previously published results on Nd concentration and composition from Dutch individuals. The concentration of Nd and 143Nd/144Nd ratios were weakly correlated (R2 = 0.47, n = 17) in Dutch human dental enamel. The majority (n = 25, 83.3%) of individuals had Nd and Sr isotope values isotopically indistinguishable from the geological environment in which their third molars formed and mineralised. However, the Nd isotope ratios of the Icelandic individual and several Dutch individuals (n = 4) suggested that Nd in enamel is not solely influenced by geological environment. In order for neodymium isotopes to be quantitatively applied in forensic and archaeological settings further analyses of individuals from various geographical regions with well-defined dietary Nd isotope data are required.


Assuntos
Esmalte Dentário/química , Isótopos/análise , Espectrometria de Massas , Dente Serotino/química , Neodímio/análise , Radioisótopos/análise , Adolescente , Região do Caribe , Criança , Colômbia , Dieta , Impedância Elétrica , Odontologia Legal/métodos , Humanos , Islândia , Países Baixos , Dinâmica Populacional , Isótopos de Estrôncio/análise
16.
Food Chem ; 283: 549-558, 2019 Jun 15.
Artigo em Inglês | MEDLINE | ID: mdl-30722911

RESUMO

The aim of this work was to verify the usefulness of multielemental and isotopic fingerprint to differentiate the origin of milk samples from different areas, linking milk fingerprint with those corresponding to soil, water, and forage. Samples from four production areas in Argentina were analysed: 26 elements, δ2H, δ13C, δ15N and δ18O. Milk provenance was assessed using 16 variables (Na, Mg, Al, V, Co, Ni, As, Se, Rb, Sr, Mo, Hg, δ2H, δ18O, δ13C and K/Rb). Generalized Procrustes Analysis (GPA) demonstrated the consensus between soil, water, forage and milk, in addition to differences between studied areas. Canonical Correlation Analysis (CCA) demonstrated significant correlations between the milk-drinking water, milk-forage, and milk-soil. So far, we report a feasible method to establish the milk provenance, assessing the follow up from environmental matrixes (soil + water) to dairy products through the food web (forage) by a combined chemical-isotopic fingerprint.


Assuntos
Análise de Alimentos/métodos , Isótopos/análise , Metais/análise , Leite/química , Solo/química , Animais , Argentina , Água Potável/análise , Análise de Alimentos/estatística & dados numéricos
17.
PeerJ ; 6: e5551, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-30186700

RESUMO

Advances in sequencing techniques have led to exponential growth in biological data, demanding the development of large-scale bioinformatics experiments. Because these experiments are computation- and data-intensive, they require high-performance computing techniques and can benefit from specialized technologies such as Scientific Workflow Management Systems and databases. In this work, we present BioWorkbench, a framework for managing and analyzing bioinformatics experiments. This framework automatically collects provenance data, including both performance data from workflow execution and data from the scientific domain of the workflow application. Provenance data can be analyzed through a web application that abstracts a set of queries to the provenance database, simplifying access to provenance information. We evaluate BioWorkbench using three case studies: SwiftPhylo, a phylogenetic tree assembly workflow; SwiftGECKO, a comparative genomics workflow; and RASflow, a RASopathy analysis workflow. We analyze each workflow from both computational and scientific domain perspectives, by using queries to a provenance and annotation database. Some of these queries are available as a pre-built feature of the BioWorkbench web application. Through the provenance data, we show that the framework is scalable and achieves high-performance, reducing up to 98% of the case studies execution time. We also show how the application of machine learning techniques can enrich the analysis process.

18.
Artigo em Inglês | MEDLINE | ID: mdl-29051698

RESUMO

Data citation is an interesting computational challenge, whose solution draws on several well-studied problems in database theory: query answering using views, and provenance. We describe the problem, suggest an approach to its solution, and highlight several open research problems, both practical and theoretical.

19.
PeerJ ; 5: e3509, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28695067

RESUMO

There are many steps in analyzing transcriptome data, from the acquisition of raw data to the selection of a subset of representative genes that explain a scientific hypothesis. The data produced can be represented as networks of interactions among genes and these may additionally be integrated with other biological databases, such as Protein-Protein Interactions, transcription factors and gene annotation. However, the results of these analyses remain fragmented, imposing difficulties, either for posterior inspection of results, or for meta-analysis by the incorporation of new related data. Integrating databases and tools into scientific workflows, orchestrating their execution, and managing the resulting data and its respective metadata are challenging tasks. Additionally, a great amount of effort is equally required to run in-silico experiments to structure and compose the information as needed for analysis. Different programs may need to be applied and different files are produced during the experiment cycle. In this context, the availability of a platform supporting experiment execution is paramount. We present GeNNet, an integrated transcriptome analysis platform that unifies scientific workflows with graph databases for selecting relevant genes according to the evaluated biological systems. It includes GeNNet-Wf, a scientific workflow that pre-loads biological data, pre-processes raw microarray data and conducts a series of analyses including normalization, differential expression inference, clusterization and gene set enrichment analysis. A user-friendly web interface, GeNNet-Web, allows for setting parameters, executing, and visualizing the results of GeNNet-Wf executions. To demonstrate the features of GeNNet, we performed case studies with data retrieved from GEO, particularly using a single-factor experiment in different analysis scenarios. As a result, we obtained differentially expressed genes for which biological functions were analyzed. The results are integrated into GeNNet-DB, a database about genes, clusters, experiments and their properties and relationships. The resulting graph database is explored with queries that demonstrate the expressiveness of this data model for reasoning about gene interaction networks. GeNNet is the first platform to integrate the analytical process of transcriptome data with graph databases. It provides a comprehensive set of tools that would otherwise be challenging for non-expert users to install and use. Developers can add new functionality to components of GeNNet. The derived data allows for testing previous hypotheses about an experiment and exploring new ones through the interactive graph database environment. It enables the analysis of different data on humans, rhesus, mice and rat coming from Affymetrix platforms. GeNNet is available as an open source platform at https://github.com/raquele/GeNNet and can be retrieved as a software container with the command docker pull quelopes/gennet.

20.
Glob Chang Biol ; 23(7): 2565-2576, 2017 07.
Artigo em Inglês | MEDLINE | ID: mdl-28045226

RESUMO

Addressing population declines of migratory insects requires linking populations across different portions of the annual cycle and understanding the effects of variation in weather and climate on productivity, recruitment, and patterns of long-distance movement. We used stable H and C isotopes and geospatial modeling to estimate the natal origin of monarch butterflies (Danaus plexippus) in eastern North America using over 1000 monarchs collected over almost four decades at Mexican overwintering colonies. Multinomial regression was used to ascertain which climate-related factors best-predicted temporal variation in natal origin across six breeding regions. The region producing the largest proportion of overwintering monarchs was the US Midwest (mean annual proportion = 0.38; 95% CI: 0.36-0.41) followed by the north-central (0.17; 0.14-0.18), northeast (0.15; 0.11-0.16), northwest (0.12; 0.12-0.16), southwest (0.11; 0.08-0.12), and southeast (0.08; 0.07-0.11) regions. There was no evidence of directional shifts in the relative contributions of different natal regions over time, which suggests these regions are comprising the same relative proportion of the overwintering population in recent years as in the mid-1970s. Instead, interannual variation in the proportion of monarchs from each region covaried with climate, as measured by the Southern Oscillation Index and regional-specific daily maximum temperature and precipitation, which together likely dictate larval development rates and food plant condition. Our results provide the first robust long-term analysis of predictors of the natal origins of monarchs overwintering in Mexico. Conservation efforts on the breeding grounds focused on the Midwest region will likely have the greatest benefit to eastern North American migratory monarchs, but the population will likely remain sensitive to regional and stochastic weather patterns.


Assuntos
Migração Animal , Borboletas , Clima , Animais , México , Reprodução
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