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International Journal of Biological, Life and Agricultural Sciences

ISSN: 2415-6612

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Efficient Pre-Processing of Single-Cell Assay for Transposase Accessible Chromatin with High-Throughput Sequencing Data

Year: 2021 Volume: 15 Issue: 10 126 - 131 Pages

Abstract: The primary tool currently used to pre-process 10X chromium single-cell ATAC-seq data is Cell Ranger, which can take very long to run on standard datasets. To facilitate rapid pre-processing that enables reproducible workflows, we present a suite of tools called scATAK for pre-processing single-cell ATAC-seq data that is 15 to 18 times faster than Cell Ranger on mouse and human samples. Our tool can also calculate chromatin interaction potential matrices and generate open chromatin signal and interaction traces for cell groups. We use scATAK tool to explore the chromatin regulatory landscape of a healthy adult human brain and unveil cell-type specific features, and show that it provides a convenient and computational efficient approach for pre-processing single-cell ATAC-seq data.

Farming Production in Brazil: Innovation and Land-Sparing Effect

Year: 2021 Volume: 15 Issue: 10 118 - 125 Pages

Abstract: Innovation and technology can be determinant factors to ensure agricultural and sustainable growth, as well as productivity gains. Technical change has contributed considerably to supply agricultural expansion in Brazil. This agricultural growth could be achieved by incorporating more land or capital. If capital is the main source of agricultural growth, it is possible to increase production per unit of land. The objective of this paper is to estimate: 1) total factor productivity (TFP), which is measured in terms of the rate of output per unit of input; and 2) the land-saving effect (LSE) that is the amount of land required in the case that yield rate is constant over time. According to this study, from 1990 to 2019, it appears that 87% of Brazilian agriculture product growth comes from the gains of productivity; the remaining 13% comes from input growth. In the same period, the total LSE was roughly 400 Mha, which corresponds to 47% of the national territory. These effects reflect the greater efficiency of using productive factors, whose technical change has allowed an increase in the agricultural production based on productivity gains.