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.
Abstract: A total of 115 yeast strains isolated from local cassava
processing wastes were measured for crude protein content. Among
these strains, the strain MSY-2 possessed the highest protein
concentration (>3.5 mg protein/mL). By using molecular
identification tools, it was identified to be a strain of Pichia
kudriavzevii based on similarity of D1/D2 domain of 26S rDNA
region. In this study, to optimize the protein production by MSY-2
strain, Response Surface Methodology (RSM) was applied. The
tested parameters were the carbon content, nitrogen content, and
incubation time. Here, the value of regression coefficient (R2) =
0.7194 could be explained by the model which is high to support the
significance of the model. Under the optimal condition, the protein
content was produced up to 3.77 g per L of the culture and MSY-2
strain contains 66.8 g protein per 100 g of cell dry weight. These
results revealed the plausibility of applying the novel strain of yeast
in single-cell protein production.
Abstract: In this paper, the problem of estimating the optimal
radio capacity of a single-cell spread spectrum (SS) multiple-inputmultiple-
output (MIMO) system operating in a Rayleigh fading environment
is examined. The optimisation between the radio capacity
and the theoretically achievable average channel capacity (in the
sense of information theory) per user of a MIMO single-cell SS system
operating in a Rayleigh fading environment is presented. Then,
the spectral efficiency is estimated in terms of the achievable average
channel capacity per user, during the operation over a broadcast
time-varying link, and leads to a simple novel-closed form expression
for the optimal radio capacity value based on the maximization
of the achieved spectral efficiency. Numerical results are presented to
illustrate the proposed analysis.