Understanding the dynamic of tropical agriculture for remote sensing applications: a case study of Southeastern Brazil.

Abstract: The agricultural activity can greatly benefit from remote sensing technology (RS). Optical passive RS has been vastly explored for agricultural mapping and monitoring, in despite of cloud cover issue. This is observed even in the tropics, where frequency of clouds is very high. However, more studies are needed to better understand the high dynamism of tropical agriculture and its impact on the use of passive RS. In tropical countries, such as in Brazil, the use of current agricultural technologies, associated with favourable climate, allow the planting period to be wide and to have plants of varying phenological cycles. In this context, the main objective of the current study is to better understand the dynamics of a selected area in Southeast of São Paulo state, and its impact on the use of orbital passive RS. For that purpose, data (from field and satellite) from 55 agricultural fields, including annual, semi-perennial and perennial crops and silviculture, were acquired between July 2014 and December 2016. Field campaigns were conducted in a monthly base to gather information about the condition of the crops along their development (data available in a website). Field data corresponding to the 2014-2015 crop year were associated with a time series of Landsat-8/OLI RGB false-colour compositions images and MODIS/Terra NDVI profiles. The type of information that can be extracted (such as specie identification, crop management practices adopted, date of harvest, type o production system used etc) by combining passive remote sensing data with field data is discussed in the paper

The role of mutation rate variation and genetic diversity in the architecture of human disease

Background We have investigated the role that the mutation rate and the structure of genetic variation at a locus play in determining whether a gene is involved in disease. We predict that the mutation rate and its genetic diversity should be higher in genes associated with disease, unless all genes that could cause disease have already been identified. Results Consistent with our predictions we find that genes associated with Mendelian and complex disease are substantially longer than non-disease genes. However, we find that both Mendelian and complex disease genes are found in regions of the genome with relatively low mutation rates, as inferred from intron divergence between humans and chimpanzees, and they are predicted to have similar rates of non-synonymous mutation as other genes. Finally, we find that disease genes are in regions of significantly elevated genetic diversity, even when variation in the rate of mutation is controlled for. The effect is small nevertheless. Conclusions Our results suggest that gene length contributes to whether a gene is associated with disease. However, the mutation rate and the genetic architecture of the locus appear to play only a minor role in determining whether a gene is associated with disease

Lem benchmark database for tropical agricultural remote sensing application.

Abstract: The monitoring of agricultural activities at a regular basis is crucial to assure that the food production meets the world population demands, which is increasing yearly. Such information can be derived from remote sensing data. In spite of topic?s relevance, not enough efforts have been invested to exploit modern pattern recognition and machine learning methods for agricultural land-cover mapping from multi-temporal, multi-sensor earth observation data. Furthermore, only a small proportion of the works published on this topic relates to tropical/subtropical regions, where crop dynamics is more complicated and difficult to model than in temperate regions. A major hindrance has been the lack of accurate public databases for the comparison of different classification methods. In this context, the aim of the present paper is to share a multi-temporal and multi-sensor benchmark database that can be used by the remote sensing community for agricultural land-cover mapping. Information about crops in situ was collected in Luís Eduardo Magalhães (LEM) municipality, which is an important Brazilian agricultural area, to create field reference data including information about first and second crop harvests. Moreover, a series of remote sensing images was acquired and pre-processed, from both active and passive orbital sensors (Sentinel-1, Sentinel-2/MSI, Landsat-8/OLI), correspondent to the LEM area, along the development of the main annual crops. In this paper, we describe the LEM database (crop field boundaries, land use reference data and pre-processed images) and present the results of an experiment conducted using the Sentinel-1 and Sentinel-2 data

Allele-specific miRNA-binding analysis identifies candidate target genes for breast cancer risk

Most breast cancer (BC) risk-associated single-nucleotide polymorphisms (raSNPs) identified in genome-wide association studies (GWAS) are believed to cis-regulate the expression of genes. We hypothesise that cis-regulatory variants contributing to disease risk may be affecting microRNA (miRNA) genes and/or miRNA binding. To test this, we adapted two miRNA-binding prediction algorithms-TargetScan and miRanda-to perform allele-specific queries, and integrated differential allelic expression (DAE) and expression quantitative trait loci (eQTL) data, to query 150 genome-wide significant ( P≤5×10-8 ) raSNPs, plus proxies. We found that no raSNP mapped to a miRNA gene, suggesting that altered miRNA targeting is an unlikely mechanism involved in BC risk. Also, 11.5% (6 out of 52) raSNPs located in 3'-untranslated regions of putative miRNA target genes were predicted to alter miRNA::mRNA (messenger RNA) pair binding stability in five candidate target genes. Of these, we propose RNF115, at locus 1q21.1, as a strong novel target gene associated with BC risk, and reinforce the role of miRNA-mediated cis-regulation at locus 19p13.11. We believe that integrating allele-specific querying in miRNA-binding prediction, and data supporting cis-regulation of expression, improves the identification of candidate target genes in BC risk, as well as in other common cancers and complex diseases.Funding Agency Portuguese Foundation for Science and Technology CRESC ALGARVE 2020 European Union (EU) 303745 Maratona da Saude Award DL 57/2016/CP1361/CT0042 SFRH/BPD/99502/2014 CBMR-UID/BIM/04773/2013 POCI-01-0145-FEDER-022184info:eu-repo/semantics/publishedVersio

Predicting cell types and genetic variations contributing to disease by combining GWAS and epigenetic data

Genome-wide association studies (GWASs) identify single nucleotide polymorphisms (SNPs) that are enriched in individuals suffering from a given disease. Most disease-associated SNPs fall into non-coding regions, so that it is not straightforward to infer phenotype or function; moreover, many SNPs are in tight genetic linkage, so that a SNP identified as associated with a particular disease may not itself be causal, but rather signify the presence of a linked SNP that is functionally relevant to disease pathogenesis. Here, we present an analysis method that takes advantage of the recent rapid accumulation of epigenomics data to address these problems for some SNPs. Using asthma as a prototypic example; we show that non-coding disease-associated SNPs are enriched in genomic regions that function as regulators of transcription, such as enhancers and promoters. Identifying enhancers based on the presence of the histone modification marks such as H3K4me1 in different cell types, we show that the location of enhancers is highly cell-type specific. We use these findings to predict which SNPs are likely to be directly contributing to disease based on their presence in regulatory regions, and in which cell types their effect is expected to be detectable. Moreover, we can also predict which cell types contribute to a disease based on overlap of the disease-associated SNPs with the locations of enhancers present in a given cell type. Finally, we suggest that it will be possible to re-analyze GWAS studies with much higher power by limiting the SNPs considered to those in coding or regulatory regions of cell types relevant to a given disease

Genetic determinants of co-accessible chromatin regions in activated T cells across humans.

Over 90% of genetic variants associated with complex human traits map to non-coding regions, but little is understood about how they modulate gene regulation in health and disease. One possible mechanism is that genetic variants affect the activity of one or more cis-regulatory elements leading to gene expression variation in specific cell types. To identify such cases, we analyzed ATAC-seq and RNA-seq profiles from stimulated primary CD4+ T cells in up to 105 healthy donors. We found that regions of accessible chromatin (ATAC-peaks) are co-accessible at kilobase and megabase resolution, consistent with the three-dimensional chromatin organization measured by in situ Hi-C in T cells. Fifteen percent of genetic variants located within ATAC-peaks affected the accessibility of the corresponding peak (local-ATAC-QTLs). Local-ATAC-QTLs have the largest effects on co-accessible peaks, are associated with gene expression and are enriched for autoimmune disease variants. Our results provide insights into how natural genetic variants modulate cis-regulatory elements, in isolation or in concert, to influence gene expression

Land-use and land-cover mapping of the Brazilian cerrado based mainly on Landsat-8 satellite images.

The Brazilian Cerrado is one of the world´s biodiversity hotspot and hosts some of the most intensive agricultural activities for food production in the world. The objective of this study was to produce a land-use and land-cover (LULC) map of the Cerrado based on Landsat-8 Operational Land Imager (OLI) images. A set of 121 scenes from 2013 was processed using the image segmentation technique. The segments were exported in the shapefile format and interpreted visually in a geographical information system software using RGB/564 color composites. The following LULC classes were considered: annual croplands, perennial croplands, cultivated pasturelands, reforestation, mosaic of occupation, urban areas, mining areas, bare soil, forestlands, non-forestlands, water bodies, and non-identified (clouds and burned areas). The overall accuracy was estimated by an independent scientist with large experience in Cerrado´s image interpretation. The results showed that 43.4% of the study area (88.5 million hectares) were already converted into agricultural, urban and mining areas, 54.6% (111 million hectares) were still natural areas, and 1.9% (3.9 million hectares) was classified as non-identified. Cultivated pasturelands were the most representative land-use type (29.5%), followed by annual croplands (8.5%) and perennial croplands (3.1%). The overall accuracy of the final map was 80.2%.Título em português: Mapeamento de uso e cobertura de terras do cerrado com base principalmente em imagens do satélite Landsat-8

Land-use and land-cover mapping of the Brazilian cerrado based mainly on Landsat-8 satellite images.

The Brazilian Cerrado is one of the world´s biodiversity hotspot and hosts some of the most intensive agricultural activities for food production in the world. The objective of this study was to produce a land-use and land-cover (LULC) map of the Cerrado based on Landsat-8 Operational Land Imager (OLI) images. A set of 121 scenes from 2013 was processed using the image segmentation technique. The segments were exported in the shapefile format and interpreted visually in a geographical information system software using RGB/564 color composites. The following LULC classes were considered: annual croplands, perennial croplands, cultivated pasturelands, reforestation, mosaic of occupation, urban areas, mining areas, bare soil, forestlands, non-forestlands, water bodies, and non-identified (clouds and burned areas). The overall accuracy was estimated by an independent scientist with large experience in Cerrado´s image interpretation. The results showed that 43.4% of the study area (88.5 million hectares) were already converted into agricultural, urban and mining areas, 54.6% (111 million hectares) were still natural areas, and 1.9% (3.9 million hectares) was classified as non-identified. Cultivated pasturelands were the most representative land-use type (29.5%), followed by annual croplands (8.5%) and perennial croplands (3.1%). The overall accuracy of the final map was 80.2%.Título em português: Mapeamento de uso e cobertura de terras do cerrado com base principalmente em imagens do satélite Landsat-8

LEM BENCHMARK DATABASE FOR TROPICAL AGRICULTURAL REMOTE SENSING APPLICATION

The monitoring of agricultural activities at a regular basis is crucial to assure that the food production meets the world population demands, which is increasing yearly. Such information can be derived from remote sensing data. In spite of topic’s relevance, not enough efforts have been invested to exploit modern pattern recognition and machine learning methods for agricultural land-cover mapping from multi-temporal, multi-sensor earth observation data. Furthermore, only a small proportion of the works published on this topic relates to tropical/subtropical regions, where crop dynamics is more complicated and difficult to model than in temperate regions. A major hindrance has been the lack of accurate public databases for the comparison of different classification methods. In this context, the aim of the present paper is to share a multi-temporal and multi-sensor benchmark database that can be used by the remote sensing community for agricultural land-cover mapping. Information about crops in situ was collected in Luís Eduardo Magalhães (LEM) municipality, which is an important Brazilian agricultural area, to create field reference data including information about first and second crop harvests. Moreover, a series of remote sensing images was acquired and pre-processed, from both active and passive orbital sensors (Sentinel-1, Sentinel-2/MSI, Landsat-8/OLI), correspondent to the LEM area, along the development of the main annual crops. In this paper, we describe the LEM database (crop field boundaries, land use reference data and pre-processed images) and present the results of an experiment conducted using the Sentinel-1 and Sentinel-2 data