Miracle-dz/UniFAR-FTUs huggingface dataset:
Методы геномного редактирования дрожжей: история и современное состояние

Yeasts are a convenient model eukaryote used for genome studies and genome editing. Saccharomyces cerevisiae is the species most widely employed in biotechnology, since it is easily cultivated in bioreactors and is absolutely safe. The last decade saw a significant development of methods of yeast genetic engineering and the creation of novel instruments adapted from other fields, which allowed one to significantly accelerate the construction of new strains. The most prominent examples are the proteins used for directed DNA editing. For a long time, yeast genome engineering was based on the yeasts’ system of homologous recombination. It was sufficient for several decades before the development of high­throughput methods. Many high­throughput methods were developed in the second decade of the XXI century, including those used in genomics, transcriptomics, proteomics, metabolomics, interactomics, etc. Modern bioinformatic databases now allow one to rapidly process the increasing flow of information and model cellular processes. As a result, the rate of analysis and prediction of targets for genome editing is currently higher than the rate of genome editing, which led to the development of new methods of genetic engineering. This process was particularly pronounced for microorganisms. Modern tasks require tens, hundreds, sometimes even thousands of genome modifications, which made researchers to look for new techniques. As a result, the instruments used for more complex objects, such as animals, plants, and cell lines, were adapted for yeasts. Modern methods for yeast genome editing allow introducing several modifications into the genome in a single step. In this study, we review the methods of directed genome editing and their applications and perspectives for yeasts.
Creative computing with Landlab: an open-source toolkit for building, coupling, and exploring two-dimensional numerical models of Earth-surface dynamics

Abstract. The ability to model surface processes and to couple them to both subsurface and atmospheric regimes has proven invaluable to research in the Earth and planetary sciences. However, creating a new model typically demands a very large investment of time, and modifying an existing model to address a new problem typically means the new work is constrained to its detriment by model adaptations for a different problem. Landlab is an open-source software framework explicitly designed to accelerate the development of new process models by providing (1) a set of tools and existing grid structures – including both regular and irregular grids – to make it faster and easier to develop new process components, or numerical implementations of physical processes; (2) a suite of stable, modular, and interoperable process components that can be combined to create an integrated model; and (3) a set of tools for data input, output, manipulation, and visualization. A set of example models built with these components is also provided. Landlab's structure makes it ideal not only for fully developed modelling applications but also for model prototyping and classroom use. Because of its modular nature, it can also act as a platform for model intercomparison and epistemic uncertainty and sensitivity analyses. Landlab exposes a standardized model interoperability interface, and is able to couple to third-party models and software. Landlab also offers tools to allow the creation of cellular automata, and allows native coupling of such models to more traditional continuous differential equation-based modules. We illustrate the principles of component coupling in Landlab using a model of landform evolution, a cellular ecohydrologic model, and a flood-wave routing model.
Gender Stereotypes in technology use: a content analysis of Mr. Robot

GENDER STEREOTYPES IN TECHNOLOGY USE: A CONTENT ANALYSIS OF Mr. ROBOT ABSTRACT The present research further develops the existing body of knowledge on the representation of gender stereotypes in the usage of technology in media. Gender and technology use are primarily studied in advertising. However, television fictions forms the largest share of audience’s media diets. Therefore, the current study analysed how gender stereotypes with regard to technology are portrayed on television, focusing on the cyber-TV drama Mr. Robot. This program is of interest as its main theme is technology and in particular hacker culture. This study tests the hypotheses gathered from previous research about gender stereotypes in the usage of technology. The quantitative content analysis of Mr. Robot showed that gender stereotypes in relation to the usage of communicational technological devices such as computer, tablets and mobile phones are present. Exploring these results through the lenses of the social role theory (Eagly, 1987) led to the conclusion that, when it comes to using communicational technological devices, men and women are represented quite different. Male characters are portrayed to able to use technology with high skills, for instance hacking, whereas female characters are represented in general as less capable of using advanced CTDs and only a small minority of them are able to carry out difficult tasks with technology. Overall, in this contemporary television drama, men are represented as tech savvy compared to women, suggesting a male-dominated view of the usage of technology.
Perception of Incompletely Neutralized /d/ and /t/ Flaps in American English

(1) Complete neutralization: two underlyingly different segments become the same in the phonetic output in some context, effectively neutralizing the contrast. a. /X/ → [Z] / (Context A) b. /Y/ → [Z] / (Context A) c. Ex: the ‘traditional’ picture of German final devoicing: /ʁɑt/ ‘advice’ [ʁɑt] /ʁɑd/ ‘wheel’ (2) Incomplete neutralization: two underlyingly different segments become nearly identical in the phonetic output—unlike complete neutralization, some small trace of the underlying distinction remains on the surface: a. /X/ → [ZX] / (Context A) b. /Y/ → [ZY ] / (Context A) c. Ex: the picture of German final devoicing from from acoustic studies (e.g., Port and O’Dell (1985))1: /ʁɑt/ ‘advice’ [ʁɑt]
Multi-Attention Network for Sentiment Analysis

Sentiment analysis is an active research area in natural language processing. However, most existing methods use extra data such as pre-specified syntactic structure or user preference information. In this work, we propose a multiple attention network (MAN) that learns both word- and phrase-level features for sentiment analysis. MAN uses vector representation of the input sequence as target in the first attention layer to locate the words that contribute to the sentence sentiment. However, although an isolated word may indicate subjectivity, there may be insufficient context to determine sentiment orientation. We argue that the sentence sentiment often requires multiple steps of reasoning. Thus, we apply the second attention layer to explore the phrase information around the keyword. We experiment our method on three benchmark datasets and the results show that our model achieves state-of-the-art performance without any extra data. The visualization of the attention layers illustrates the effectiveness of our attention based model.
Influence of biostimulants supplement on maize yield and agronomic traits

Supplements that contain nutrients, amino acids and plant extracts, have been called growth promoters or biostimulants. One of them is the growth promoter VIUSID agro, it acts as a natural bioregulator and it composed of amino acids, vitamins and minerals. VIUSID agro would be taken into consideration as an alternative to increase the production of plants. The present investigation was carried out in the experimental field of Agric. Res. Stat. of Fac. of Agric. , Cairo Univ., Giza, Egypt in 2015 and 2016 seasons. The objectives were to study the effect of VIUSID agro on maize yield and agronomic traits and to study the relationship among grain yield and the different dosages of VIUSID agro. Five maize cultivars were evaluated under four dosages i.e. 0.0, 0.96, 1.44 and 2.0 L/ha of foliar spraying of VIUSID agro. A split-plot design in a randomized complete block arrangement was used with four replications. Grain yield/ha under the dosage of 0.96 L/ha was significantly exceeded the control by 26.0%. Results showed that yield increases for studied cultivars were 81.53 % (SC-30k8), 37.34% (SC-30k9), 28.1% (SC-110), 9.63% (TWC-310) and 7.20% (Cairo-1) by applying the dosage of 0.96 L/ha. The three way cross TWC-310 showed a quadratic relationship with the highest grain yield/ha (8.62 ton/ha) at the dosage of 1.44 L/ha. In contrast, the single cross hybrids SC-30k9, SC-110, SC-30k9 and the open pollinated composite Cairo-1 showed a cubic relationship, with the highest grain yield/ha at the dosage of 0.96 L/ha for SC-30k9 (13.24 ton/ha), Cairo-1 (12.5 ton/ha), SC-110 (8.17 ton/ha) and SC-30k8 ( 7.37 ton/ha). This study concluded that increasing maize grain yield was obvious for most studied cultivars by applying the dosage of 0.96 L/ha of VIUSID agro than other dosages.
Design and development of a new dedicated RF sensor for the MRI of rat brain

The design and development of a new dual-frequency RF probe-head are presented. This probe was initially dedicated for the MRI of both proton (1H) and hyperpolarized Xenon-129 (HP 129Xe) in the rat brain at 2.35 Tesla. It consists of a double-tuned (100 MHz- 27.7 MHz) volume coil, which could be used for both transmitting and receiving, and of a receive-only single-tuned (27.7 MHz) coil. The double-tuned coil consists of two concentric birdcage resonators. The inner one is a low-pass design and it is tuned to 27.7 MHz, while the outer one, tuned to 100 MHz, is high-pass. The receive-only coil is a surface coil which is decoupled from the double-tuned volume coil by an active decoupling circuitry based on the use of PIN diodes. A home-built Transmit/Receive (T/R) driver ensures biasing of the PIN diodes in both volume and surface coils. The original concepts of the design are addressed, and practical details of realization are presented. One of the underlying ideas behind this work is to proceed well beyond the application to the MRI of HP 129Xe. Actually, this design could be easily adapted for a large palette of other MRI applications. Indeed, we tried to make the design versatile, simple and easy to replicate by other research groups, with a low-cost, minimum development time and accepted performances. The prototype was validated at 100 MHz and at 26.4 MHz (sodium-23 resonance frequency at 2.35 T). MRI experiments were performed using phantoms. In vivo 1H images and 23Na spectra of the rat brain are also presented.
Controlled transport of single biomolecules through nanopores

Different types of nanopores are nowadays used for the detection of single molecules in solution. This detection is possible due to the changes in the ionic current established between two electrodes when a molecule is partially blocking the entrance of the nanopore. In this work, we have performed translocation experiments of single DNA molecules using glass nanocapillaries as molecular sensors. The obtained results show that using glass nanocapillaries we are able to determine the cross-section of the DNA double helix passing through the nanochannel and distinguish different molecular configurations. Analyzing the kinetics of the translocation process, we are able to describe it as a voltage-induced thermally activated process that follows an Arrhenius behaviour.
Box-Counting Dimension and Beyond

This paper explores different analytical and computational methods of computing the box-counting dimension of a fractal-like set, such as the attractor associated with a chaotic dynamical system. Because attractors cannot be described exactly, but can only be approximated by computational methods, the box-counting dimension is typically measured computationally. Using alternative measures of chaotic behavior, such as the Lyapunov exponents, it is possible to estimate the accuracy of a computational approximation. The box-counting dimension definition is extended to include subsets of regular subspaces of R? These sets include products of Cantor sets and attractors associated with infinite dimensional dynamical systems, such as the Kot-Schaffer model. Computational approaches to computing the box-counting dimension of the Kot-Schaffer attractor are discussed and the results for this attractor are discussed.
A dual-tube model for gas dynamics in fractured nanoporous shale formations

Abstract Gas flow through fractured nanoporous shale formations is complicated by a hierarchy of structural features (ranging from nanopores to microseismic and hydraulic fractures) and by several transport mechanisms that differ from the standard viscous flow used in reservoir modelling. In small pores, self-diffusion becomes more important than advection; also, slippage effects and Knudsen diffusion might become relevant at low densities. We derive a nonlinear effective diffusion coefficient that describes the main transport mechanisms in shale-gas production. In dimensionless form, this coefficient depends only on a geometric factor (or dimensionless permeability) and on the kinetic model that describes the gas. To simplify the description of the complex structure of fractured shales, we observe that the production rate is controlled by the flow from the shale matrix (which has the smallest diffusivity) into the fracture network, which is assumed to produce instantaneously. Therefore, we propose to model the flow in the shale matrix and estimate the production rate with a simple bundle-of-dual-tubes model (BoDTM), in which each tube is characterized by two diameters (one for transport and the other for storage). The solution of a single tube is approximately self-similar at early time, but not at late time, when the gas flux decays exponentially owing to the finite length of the tube. To construct a BoDTM, a reliable estimate of the joint statistics of the matrix-porosity parameters is required. This can be either inferred from core measurements or postulated on the basis of some a priori assumptions when information from laboratory and field measurements is scarce. By comparison with field production data from the Barnett shale-gas field, we demonstrate that BoDTM can be calibrated to estimate structural parameters of the shale formation and to predict the cumulative production of shale gas. Our framework has enough flexibility to construct models of increasing complexity that can be employed in the presence of a complex dataset or when more information is available.
Grasping the Nettle : Neural Entity Recognition for Scientific and Vernacular Plant Names

The identification of taxonomic entities plays a decisive role when it comes to natural language understanding and automated knowledge extraction in botanical contexts. In this paper, we present a semi-supervised approach for scientific and vernacular plant name recognition across different text genres for German and English. Our pipeline includes linguistic preprocessing and dictionary-based annotation using gazetteers for multiple scientific and vernacular entity labels. We train a state-of-the-art neural NER system on various datasets exploiting token-level and character-level contextual features of natural language. Finally, an evaluation of the entity tagger showed F1-scores >80% on a manually annotated test set and >90% on the automatic annotations, for both languages. We discuss the insights gained from adopting several dataset and language-specific parameter combinations in single and cross-dataset evaluation settings. Our approach emphasizes the potential of domain-specific entity labels and low-effort data models trained on automatically annotated material to explore and computationally process lower-resourced fields and genres.
Repositioning the Non-incremental Changes and Business Strategic Windows Correlates

Modern firms assume strategic both in thinking and in action to the extent that they manage change to their own advantage. The market evolutionary trends, especially non-incremental ones that relate to new primary demand, new technology, channel changes, market redefinition and new government policies dealt with in this article often question the adaptability of incumbent firms, transform the mode of competition, and usher in new entrants, who may wish to take advantage of the incumbents’ leapfrogs. This article suggests that investment decisions be timed to reflect the moment when the match between a firm’s capabilities and the key market requirements is at optimum or when the strategic window is open. Market withdrawals are often contemplated when the market no longer proves profitable for a firm or when the window is shut behind a firm. Strategic market planners follow the trends of market evolution and proactively assess their firm’s capabilities for the purpose of making timely decisions on either, and when, to throw in the towel or to beef up the organization to adapt to such changes.
Synchronous and Asynchronous Multimedia and Iranian EFL Learners’ Learning of Collocations

The use of effective multimedia instructions such as mobiles, computers, and the internet in language learning has turned out to be useful since the last decades. The impact of multimedia and synchronous approaches of computer-assisted language learning (CALL) on English as a foreign language (EFL) learners' learning of language skills and components has been studied to some extent. However, the impact of computerized mediated instruction through multimedia (text and graphics) on learning collocations requires further investigations. This study aimed at investigating whether synchronous and asynchronous multimedia components: text and text with added graphics had any effects on EFL learners' learning of collocations. In doing so, 150 male EFL learners at pre-intermediate proficiency level were selected through convenience sampling. They were divided into six groups. The results of the study showed that computerized mediated instruction was more effective than non-computerized instruction. Also, synchronous computerized instruction was more effective than asynchronous computerized instruction. The results also showed that presentation through text with added graphics was more effective than presentation through simple text. The results are discussed and some pedagogical implications are presented. Persian Abstract: استفاده ازآموزش های چند رسانه ای مؤثر مانند موبایل، کامپیوتر، و اینترنت در آموزش زبان از چند دهه قبل مرسوم شده است. تأثیر چند رسانه ای و روش های همزمان یادگیری زبان به کمک کامپیوتر (CALL) بر یادگیری مؤلفه ها و مهارتهای زبان انگلیسی به عنوان یک زبان خارجی (EFL) توسط زبان آموزان تا حدی مورد مطالعه قرار گرفته است. بااین حال، تأثیر آموزش با کامپیوتر از طریق چند رسانه ای (متن و گرافیک) در یادگیری هم آیی ها نیاز به تحقیقات بیشتری دارد. هدف از انجام این تحقیق، بررسی تأثیر اجزای چند رسانه ای همزمان و غیرهمزمان: متن و متن بعلاوه گرافیک بر یادگیری هم آیی ها توسط زبان آموزان ایرانی بوده است. برای انجام این تحقیق، 150 زبان آموز مذکر با سطح زبانی پیش از متوسط ​​با روش نمونه گیری در دسترس انتخاب شدند. آنها به شش گروه تقسیم شدند. نتایج حاصل از این مطالعه نشان داد که آموزش با کامپیوتر مؤثرتر از آموزش غیر کامپیوتری بود. همچنین، آموزش کامپیوتری همزمان مؤثرتر از آموزش کامپیوتری ناهمزمان بود. همچنین نتایج نشان داد که ارائه از طریق متن با گرافیک مؤثرتر از ارائه از طریق متن ساده بود. نتایج به دست آمده مورد بحث و برخی از مفاهیم آموزشی ارائه شده است. کلید واژه ها: غیر همزمان، یادگیری زبان به کمک کامپیوتر، هم آیی ها، همزمان، چند رسانه ای، زبان آموزان ایرانی
Iaa Production By Streptomyces Scabies And Its Role In Plant Microbe Interaction

Streptomyces scabies is the cause of the economically important disease potato scab, and a pathogen of tap and fibrous roots. A previous study indicated that Streptomyces can synthesize indole-3-acetic acid (IAA) through the Indole-3acetamide (IAM) pathway (Manulis et al., 1994). Two enzymes, tryptophan monoxygenase (IaaM) and indole-3-acetamide hydrolase (IaaH), participate in IAA synthesis via the IAM pathway. Based on homology to other IAM and IAH amino acid sequences we identified candidate iaaM (SCAB75511) and iaaH (SCAB75501) genes in the completely sequenced genome of S. scabies 87-22. The function of the candidate genes in the IAA biosynthetic pathway was evaluated by creating the deletion mutants iaaH, iaaM5 and iaaM8. IAA production by all three mutant strains was lower than production by the wild type strain (87-22). When inoculated onto radish seedlings, all three mutant strains were reduced in virulence relative to the wild type strain, as measured by root necrosis. Genetic complementation of iaaM5 and iaaM8 deletion strains partially restored both IAA production and virulence on radish seedlings. These results suggest that the iaaM (SCAB75511) and iaaH (SCAB75501) genes are IAA biosynthetic genes and that they contribute to virulence of S. scabies through the synthesis of IAA as a virulence factor.
Shell-model interactions from chiral effective field theory

We construct valence-space Hamiltonians for use in shell-model calculations, where the residual two-body interaction is based on symmetry principles and the low-momentum expansion from chiral effective field theory. In addition to the usual free-space contact interactions, we also include novel center-of-mass--dependent operators that arise due to the Galilean invariance breaking by in-medium effects. We fitted the low-energy constants to 441 ground- and excited-state energies in the sd shell and obtained a root-mean-square derivation of 1.8 MeV at leading order and of 0.5 MeV at next-to-leading order, with natural low-energy constants in all cases. The developed chiral shell-model interactions enable order-by-order uncertainty estimates and show promising predictions for neutron-rich isotopes beyond the fitted data set.
2PAC: Two Point Attractors for Center of Mass Trajectories in Multi Contact Scenarios 2PAC: Two Point Attractors for Center of Mass Trajectories in Multi Contact Scenarios

Synthesizing motions for legged characters in arbitrary environments is a long-standing problem that has recently received a lot of attention from the computer graphics community. We tackle this problem with a procedural approach that is generic, fully automatic and independent from motion capture data. The main contribution of this paper is a point-mass-model- based method to synthesize Center Of Mass trajectories. These trajectories are then used to generate the whole-body motion of the character. The use of a point mass model results in physically inconsistent motions and joint limit violations when mapped back to a full- body motion. We mitigate these issues through the use of a novel formulation of the kinematic constraints which allows us to generate a quasi-static Center Of Mass trajectory, in a way that is both user-friendly and computationally efficient. We also show that the quasi-static constraint can be relaxed to generate motions usable for computer animation, at the cost of a moderate violation of the dynamic constraints. Our method was integrated in our open-source contact planner and tested with different scenarios - some never addressed before- featuring legged characters performing non-gaited motions in cluttered environments. The computational efficiency of our trajectory generation algorithm (under one ms to compute one second of trajectory) enables us to synthesize motions in a few seconds, one order of magnitude faster than state-of-the-art methods. Although our method is empirically able to synthesize collision-free motions, the formal handling of environmental constraints is not part of the proposed method, and left for future work.