Academic writing for IT students

This textbook is intended for Master and PhD Information Technology students (B1-C1 level of English proficiency). The instructions of how to write a research paper in English and the relevant exercises are given. The peculiarities of each section of a paper are presented. The exercises are based on real science materials taken from peer-reviewed journals. The subject area covers a wide scope of different Information Technology domains

Environmental monitoring of natural waters in Krasnodar and Stavropol Territories

The environmental monitoring of natural waters in Krasnodar (Uspensky and Novokubansky districts) and Stavropol (Kochubeyevsky District) Territories was conducted. In the course of study, various elements and compounds harmful to animals and humans, which exceed maximum permissible concentrations, were identified

Вычислительные аспекты применения метода усеченного сингулярного разложения при решении задачи сейсмической томографии

The method of truncated singular value decomposition is a powerful tool of regularization and solution of inverse problems. Application of this method is limited by the memory requirements for the calculation of singular value decomposition of matrices. The solution is a usage of iterative procedures, that provide the possibility to evaluate only the largest singular values and corresponding vectors. For the practical appli- cation of this methodology one should answer the questions: what part of the spectrum can be determined numerically and whether the number of singular vectors is enough for the solution. These problems are considered in the present paper within the seismic traveltimes inversion frameworkМетод усеченного сингулярного разложения является мощным методом регуляризации и реше- ния обратных задач. Применение данного метода на практике сильно ограниченно объемами ма- шинной памяти, требуемой на вычисление сингулярного разложения матриц большой размер- ности. В этой связи актуально использование итерационных процедур поиска старшей части сингулярного спектра. При этом возникают вопросы, какая часть спектра может быть най- дена достоверно и достаточно ли найденное количество сингулярных векторов для построения решения. Данные вопросы исследуются в настоящей работе численно на примере обратной кине- матической задачи геофизик

Вычислительные аспекты применения метода усеченного сингулярного разложения при решении задачи сейсмической томографии

The method of truncated singular value decomposition is a powerful tool of regularization and solution of inverse problems. Application of this method is limited by the memory requirements for the calculation of singular value decomposition of matrices. The solution is a usage of iterative procedures, that provide the possibility to evaluate only the largest singular values and corresponding vectors. For the practical appli- cation of this methodology one should answer the questions: what part of the spectrum can be determined numerically and whether the number of singular vectors is enough for the solution. These problems are considered in the present paper within the seismic traveltimes inversion frameworkМетод усеченного сингулярного разложения является мощным методом регуляризации и реше- ния обратных задач. Применение данного метода на практике сильно ограниченно объемами ма- шинной памяти, требуемой на вычисление сингулярного разложения матриц большой размер- ности. В этой связи актуально использование итерационных процедур поиска старшей части сингулярного спектра. При этом возникают вопросы, какая часть спектра может быть най- дена достоверно и достаточно ли найденное количество сингулярных векторов для построения решения. Данные вопросы исследуются в настоящей работе численно на примере обратной кине- матической задачи геофизик

Influenza A Virus M1 Protein Non-Specifically Deforms Charged Lipid Membranes and Specifically Interacts with the Raft Boundary

Topological rearrangements of biological membranes, such as fusion and fission, often require a sophisticated interplay between different proteins and cellular membranes. However, in the case of fusion proteins of enveloped viruses, even one molecule can execute membrane restructurings. Growing evidence indicates that matrix proteins of enveloped viruses can solely trigger the membrane bending required for another crucial step in virogenesis, the budding of progeny virions. For the case of the influenza A virus matrix protein M1, different studies report both in favor and against M1 being able to produce virus-like particles without other viral proteins. Here, we investigated the physicochemical mechanisms of M1 membrane activity on giant unilamellar vesicles of different lipid compositions using fluorescent confocal microscopy. We confirmed that M1 predominantly interacts electrostatically with the membrane, and its ability to deform the lipid bilayer is non-specific and typical for membrane-binding proteins and polypeptides. However, in the case of phase-separating membranes, M1 demonstrates a unique ability to induce macro-phase separation, probably due to the high affinity of M1’s amphipathic helices to the raft boundary. Thus, we suggest that M1 is tailored to deform charged membranes with a specific activity in the case of phase-separating membranes

The exposure to gDNA^OX (50 ng/mL) leads to a transient increase in expression cytoplasmic DNA sensor AIM2, while not changing expression levels of TLR9.

<div><p>A - intracellular localization of AIM2 (FITC-conjugated antibodies) and labeled probe gDNA<b>^red-ox</b> (x40). B – the ratio of the levels of AIM1 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077469#B1" target="_blank">1</a>] and TLR9 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077469#B2" target="_blank">2</a>] – encoding RNAs to the levels TBP-encoding reference mRNA in cells exposed to gDNA or gDNA^OX for 2 hrs (grey columns) and 48 hrs (black columns).</p> <p>C and D – Flow cytometry detection of AIM2 (C) and TLR9 (D) expression in MCF-7. Cells were stained with AIM2 (C) or TLR9 (D) antibody (secondary PE-conjugated antibodies). Panels D [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077469#B1" target="_blank">1</a>] and E [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077469#B1" target="_blank">1</a>] – control cells plots: FL2 versus SSC. R: gated area. Panels C [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077469#B2" target="_blank">2</a>] and D [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077469#B2" target="_blank">2</a>]: median signal intensity of FL2 (R) in MCF-7 cells (mean value for three independent experiments). Panels C [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077469#B3" target="_blank">3</a>] and D [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077469#B3" target="_blank">3</a>]: relative proportions of AIM2- or TLR9-positive cells in R gates [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077469#B1" target="_blank">1</a>]. Background fluorescence was quantified using PE-conjugated secondary antibodies. </p> <p>*p < 0.05 against control group of cells, non-parametric U-test.</p></div

Genome instability in MCF-7 cells exposed to gDNA^OX at final concentration 50 ng/mL for 24 hours.

<div><p>A – multiple micronuclei [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077469#B1" target="_blank">1</a>], chromatin bridges [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077469#B2" target="_blank">2</a>], M-phase chromatin decondensation [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077469#B3" target="_blank">3</a>], non-treated control cells [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077469#B4" target="_blank">4</a>] (x100). </p> <p>B – proportions of cells with micronuclei in non-treated control cells, cells exposed to gDNA, cells exposed to gDNA<b>^OX</b>. Grey columns: non-confluent, actively proliferating MCF-7 culture. Black columns: MCF-7 cells at high confluency. *p < 0.05 against control group of cells, non-parametric U-test.</p> <p>С - Exposure to gDNA<b>^OX</b> (50 ng/mL, 2 hours) induces formation of 8-oxodG-containing micronuclei (x100). </p></div

The exposure to gDNA^OX leads to an increase in the production of ROS.

<p>А – Microscopy-based evaluation of MCF-7 cells sequentially treated with DNA (50 ng/mL) and H2DCFH-DA (control, gDNA, gDNA^ox [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077469#B1" target="_blank">1</a>]) and incubated for 30 minutes (x100). Alternatively, MCF-7 cells were incubated with DNA (50 ng/mL) for 1 hour followed by addition of H2DCFH-DA and photography 30 minutes later (gDNA^ox [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077469#B2" target="_blank">2</a>]). B - MCF-7 cells exposed to gDNA^ox (0.5h; 50ng/mL), were sequentially treated with Mito-tracker TMRM (15 min) and H2DCFH-DA (15 min) (x200). C - Co-detection of labeled probe gDNA^red (50 ng/mL) and DCF after 30 minutes of incubation. D - The results of the quantification of fluorescence using plate reader [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077469#B1" target="_blank">1</a>]. The time kinetics of fluorescence outputs in cells sequentially treated with H2DCFH-DA and, three minutes later, a DNA sample at final concentration of 5 or 50 ng/mL [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077469#B2" target="_blank">2</a>]. The same for cells pretreated with DNA (final concentration 5 ng/mL) for one hour, with subsequent addition of H2DCFH-DA. *) p < 0.05 against control group of cells, non-parametric U-test.</p

The analysis of 8-oxodG content in cells exposed to either gDNA or gDNA^OX (50 ng/mL).

<p>A - Cells stained with PE-labeled anti-8-oxodG antibodies and DAPI (x20). B - Three types of anti-8-oxodG stain distribution observed in cells treated with gDNA<b>^OX</b> (x100). Cell were incubated with DNA samples for 1 hour, fixed with 3% formaldehyde, permeated with 0,1 % triton X100 and stained with anti-8-oxodG (PE-conjugated secondary antibodies). C – colocalization of 8-oxodG with mitochondria. Cells were incubated with <b>gDNA^OX</b> for 0.5 hour, обработаны Mito-tracker (30 nM, 15 min), photographed, then fixed with 3% formaldehyde, permeated with 0,1 % triton X100, stained with anti-8-oxodG antibodies (FITC-conjugated secondary antibodies) and photographed again. D - 8-oxodG content in DNA exposed cells pre-treated with NAC (FACS analysis). Cells were incubated with NAC (0.15 mM) for 30 min, then exposed to gDNA^OX for 1 hour and analyzed using anti-8-oxodG antibodies (PE-conjugated secondary antibodies). Background fluorescence was quantified using PE-conjugated secondary antibodies. E - Relative proportions of nuclei stained for 8-oxodG in non-treated control cells, cells exposed to gDNA, cells exposed to gDNA^OX (grey columns). Light grey column reflects cells pre-treated with NAC and exposed to gDNA^OX. *p < 0.05 against control group of cells, non-parametric U-test.</p

Increase in activity of transcriptional factor Nf-kB in MCF-7 cells exposed to gDNA^OX at final concentrations of 50 ng/mL for 2 hours.

<div><p>A Fluorescent microscopy of cells stained with anti-p65 (FITC) antibodies (x40). B Graph of the proportion of cells with nuclear staining for Nf-kB in three studied types of MCF-7 cultures.</p> <p>C, D (FACS) - the average signal intensity of FL1 (p65) in cells stained with anti-p65 (C) and Ser529-phosphorylated р65 (D) antibodies [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077469#B1" target="_blank">1</a>]. - distribution of fluorescence intensities of the cells stained with Ser529-phosphorylated р65 antibodies (FITC) (green color) или FITC-conjugated secondary antibodies (grey color) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077469#B2" target="_blank">2</a>]. - proportion of Ser529-phosphorylated р65 -positive cells in total cell population [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077469#B3" target="_blank">3</a>]. - the average of the median signal intensities of FL1 (Ser529-phosphorylated р65 +). Cells were cultivated either in absence (dark grey columns) or in presence of 0.15 mM NAC (light grey columns). </p></div