bluuebunny/crossref_metadata_2025 huggingface dataset:
The evolution of Enterprise Architecture in scopes of digital transformation
Authors: Levina A I , Borremans A D , Lepekhin A A , Kalyazina S E , Schröder K M
Published: October 2020

Nowadays the business has to develop in a rapidly changing environment. Globalization, digitalization and emerging information technologies affect not only the business processes of organizations, but they change the enterprise architecture in a complex way. The purpose of this research is to consider standard existing approaches to the Enterprise Architecture description and modeling. Moreover, the aim of this paper is to point out modern modeling frameworks that display such technologies as the Internet of Things, the Industrial Internet of Things and others, for a complete description of the enterprise model within the framework of Industry 4.0 and digital transformation.
Comparative analysis of results of using assessment methods for intellectual capital
Authors: Zaytsev Andrey , Rodionov Dmitriy , Dmitriev Nikolay , Kichigin Oleg
Published: October 2020

The importance of intellectualizing modern society means a more complete study of the role intellectual capital has in the development of industrial relations is required. This is due to the fact that increasing the intellectual component is integral to building an innovation economy. A fair assessment of intellectual capital should be given. This will allow its level in a specific organization to be identified and the amount of intellectual capital to be compared with other business entities. This paper gives a comparative analysis of the use of methods for assessing the intellectual capital of a business, namely: the cost approach method, the market capitalization method, and the intellectual value added method. When examining the intellectual capital, its various components, i.e., its relational, human, and organizational capital, were used. The synergy of these components helps maximize the positive effect. The methods listed above have a practical application and were tested on a business. Using these methods made it possible to determine the quantitative and qualitative value of the intellectual capital. Thus, it was possible to not only judge the availability of intellectual resources at the current time period, but also to study the dynamics of intellectual changes, as well as build a comparative characteristic both at a microlevel with other businesses and comparing it at the meso level with the whole industry. Such practice will make it possible to come up with recommendations on how to use intellectual capital, determine its sufficiency, taking into account the industry average parameters of intellectualization. Despite the growing significance of intellectual capital and the grand scale of this problem, there are big gaps in terms of its evaluation. These are due to the insufficient number of market criteria and the inability to display them in financial statements in full. The guidelines looked at in this paper allow the amount of a company’s intellectual capital to be assessed, thus giving the opportunity to come to objective conclusions about the level of intellectualization while taking into consideration the specifics of the business activities. It also reveals the main factors influencing intellectualization and allows suggestions to be made on how to use the intangible resources available in the most rational way.
Oil Industry in Russia: Retrospective Review, Current State and Development Prospects
Authors: Konnikov Evgenii , Dubolazova Yulia , Zavrichko Olga , Malevskaia-Malevich Ekaterina
Published: October 2020

Relevance of the issue selected for the research is directly correlated with Russia’s specialization in oil product exports. The oil industry competitiveness has become the foundation of the country’s economy and living standards. However, current macroeconomic uncertainty significantly affects this industry and despite the nationwide support, the consequences are seen in lower oil production both in physical and financial terms. This article analyzes changes in Russia’s oil industry during the world economic crisis (2008-2009), as well as during the period of economic sanctions against Russia (2014 till present). The estimated changes in output and return on sales in the period of macroeconomic uncertainty were assessed by means of the factor analysis. The development prospects of the oil industry in Russia were assessed by means of the retrospective analysis.
Transformation of the enterprise cost model in an innovative economy
Authors: Demidenko D S , Vaganov P I
Published: October 2020

Innovative activities currently determine the competitiveness of enterprises in all sectors. A wide range of scientific studies is devoted to the analysis of the innovation economic efficiency, but most Russian and foreign researchers agree that innovation on the one hand causes an increase in production costs, on the other hand, requires additional efforts to commercialize market demand in order to compensate for the increase in costs. The inevitable increase in market prices for innovative products exacerbates the difficulties of an innovative enterprise and adversely affects its competitiveness and market capitalization. Currently, in practice there is no clear concept and methodology for assessing the results of the production enterprises participation in the innovation process. The concept of the “innovative activity economy” is introduced in the article, considered by the authors in comparison with the issues of the quality economy. The cost model of innovation-oriented manufacturing enterprises is also considered, combining the production of “traditional” products with innovation, in comparison with the traditional cost model of an enterprise that does not carry out innovative activities. This combination changes the mechanisms for the formation of enterprise’s economic indicators, complicates the relationship between them, changes the structure of risks and, accordingly, requires special approaches to decision-making, planning and results evaluation.
Implementation of Information Security System in Service and Trade
Authors: Nechai Aleksandra , Pavlova Elena , Batova Tatiana , Petrov Vadim
Published: October 2020

Usage of information technologies in service and trade industry is increasing daily which is accompanied by information leakage risks. Information security system can prevent threats from employee’s lack of skills and detect vulnerabilities on early stages. To implement information security system, general steps are to build conceptual model of the subject area, build a semantic network to follow decision making process, adept current situation in company to ISO 27001 requirements and choose information system to atomize business processes. EPC diagram given in this paper shows the steps that service and trade companies can follow to get ISO 27001 certificate. The article describes such security information and event management systems as IBM QRadar security intelligence platform, Splunk Enterprise Security and RSA NetWitness Suite. The results of the research show how implementation of information security policy impact company’s indicators and reputation. Cyber security system’s implementation can lead to low expenses caused by interruption in service or data leakage, increased reliability and security of systems and improved business processes’ optimization.
The Future of Information Technology in the Russian Trade
Authors: Desfonteines L , Korchagina E , Evgrafov A , Khnykina T , Karmanova A , Semenova Y
Published: October 2020

The development of innovative technologies in Russian retail is connected with the change of consumers’ relations models. They acquire a new format, accents and technologies of trade presentation change. Nowadays the omni-channel concept replaces the traditional selling concept. The key goal of the paper is to determine the main directions of digitalization in retail. The sub goals are to study the customers’ preferences in the use of digital sales channels and to identify the prospects of creating an information customer base that available for all sales channels. The study was conducted on the basis of statistical analysis methodology. The study results have showed that the omni-channel concept represents an integrated and systematic approach to sales. The modern customers’ tastes and needs are changing very fast and the priority purchase channels are also changing along with them. The desire of a particular person to make a purchase arises as a result of the impact of diverse and multidirectional information. The purchase decision requires access to a sales channel. It can be offline store, online store, mobile devices, social networks, phone call, etc. A seller that uses all possible sales channels gains a significant competitive advantage. The buyer will be guided by the principles of speed, convenience and minimum costs.
Methodology of Intellectual Property Objects Commercial Potential Evaluation
Authors: Lyamin Boris , Ulanov Vladimir , Cherkasova Tatiana , Milkova Olga
Published: October 2020

The current state of the world economy and crisis phenomena show that the sustainable development of national economies is possible with the development of science and technology embodied in technologies, equipment and personnel qualification systems, production organization. Successful development of the modern economy is impossible without increasing the competitiveness of high-tech innovative products in the total volume of GDP. In order to activate the implementation of innovative developments in the real sector of the economy it is necessary for developing intellectual property objects to have concrete value for enterprises. Conformably, the developed intellectual property must be evaluated for the possibility of commercialization. A methodology is proposed for evaluation the commercial potential of IPO, which takes into account both the actual parameters of the intellectual property rights, its external environment, and the potential of patent holders The approach takes into account the assessments of experts in the field of intellectual property and as a result of the IPO evaluation, we get not the exact value, but the interval that indicates the low, medium or high potential for commercialization of this IPO. The proposed methodology will allow estimating IPO that are still incomplete in order to identify their growth points and determine the prospects for commercialization.
Electrophysical methods for controlling the quality of vegetable oil in a digital economy
Authors: Pilipenko T V , Nilova L P , Malyutenkova S M , Tverskoi V R
Published: October 2020

The article considers the possibility of controlling the quality of vegetable oil by electrophysical methods. In model experiments, refined sunflower oil sold in retail was selected as objects of research. During model studies, samples of vegetable oil were oxidized in air at a temperature of 120°C until the values of peroxide value (PV) were close to the maximum allowable 10 μग kg−1. The dependence, allowing evaluating the effect of the polar products of vegetable oil oxidation on the change in the coordinates of the identification point, was determined by the results of these studies. When developing operational control of the degree of purification of vegetable oil at the stages of refining, samples were studied under industrial conditions. In each sample, the values of acid and peroxide values were determined, as well as the coordinates of the identification point. The technical result of these studies is the development of a single operational digital method to establish the degree of purification of vegetable oils with the requirements of current regulatory documentation at the stages of refining.
Mathematical modeling of an experiment for the growth of chia seeds sprouts (Salvia hispanica L.)
Authors: Nadtochii L.A. , Venkatakrishnan K. , Jing J. , Chechetkina A.Yu. , Muradova M.B.
Published: October 2020

World Health Organization (WHO) has reported that more than 80% of the population in developing countries uses herbal medicine. Modern technologies open up the possibility of controlling the cultivation of medicinal plants for commercial use. The combination of various methods of controlled cultivation is a high-tech and capital-intensive direction for the development of the agricultural industry in Russia. This article considers the selection of optimal conditions for growing of chia seeds sprouts as a multifactor experiment with three incoming factors at two levels. For this study 100 grains of dark varieties of chia seeds (Salvia hispanica L.) purchased from Era Green were used. The 3 major incoming factors include moisture (3, 4 and 5 ml of added water), the temperature (20, 25 and 30 °C), and the light (expose duration for 0, 12 and 24 h) under LED lamps with peaks at 440-450 nm (blue spectrum) and 660 nm (red spectrum). Using different factors, we found that the speed of germination and the seedling vigor were considerably improved. This multifactor model helps to establish more reliable information on the rational ways for obtaining chia seeds sprouts in the conditions of controlled cultivation with high yield.
Development of the planning model of the production and cutting of the paper web ensuring the quality of the finished products
Authors: Remizova Irina , Bondarenkova Irina , Kondrashkova Galina , Chernikova Anna , Demenchenok Tatiana
Published: October 2020

The problem of the planning of pulp and paper production has been investigated, a complex of model and algorithmic programs as well as a software of an automated system of planning and calculating of the cutting methods on a longitudinal slitting machine (LSM) is expected to be a result of this planning. An integrated model for planning paper production and multi-stage cutting of rolled and sheet products has been proposed based on methods, models and algorithms of optimal cutting from the condition of the ensuring the products orders fulfillment with minimal losses. A scientifically based method and algorithm of generating a set of acceptable ways of rolls cutting, criteria of generating a set of acceptable ways of rolls cutting as well as an integer algorithm of the result of the problem solving have been considered. All real restrictions encountered in the manufacturing sector have been taken into account. The results of the planning models usage for real production process have been presented.
VALUE-MOTIVATION MEANINGS OF FINANCIAL-CREDIT ORGANIZATIONS EMPLOYEES UNDER THE CONDITIONS OF DIGITAL ECONOMY
Authors: Velmisova Daria Vladimirovna
Published: October 2020

The paper describes the results of a study (2017-2019) of employees value-motivational meanings applied to financial and credit sector. The purpose of the research was to conduct a sociological analysis of value-motivational meanings and to argue their regulatory role in improving the work efficiency in the context of the economy digitalization. An empirical analysis of the meanings and values of various employee groups was carried out on the basis of the developed author’s diagnosing method. The research results include the following: the essence of value-motivational meanings was determined; an improved methodology for their diagnosis has been developed; a comparative analysis of value-motivational meanings, including statistically significant differences were identified; regularities of the value-motivational dynamics of financial and credit organizations are revealed. The main conclusion that was drawn as a result of the study is that in the structure of value-motivational meanings, which are an attribute of the quality and productivity of the work, there are significant differences depending on whether the employee belongs to a particular status or professional qualification group. Analysis, modeling, monitoring of the value-motivational meanings that characterize certain social and professional roles, the comprehension of this information and the application in the social and labor relations regulation are one of the most important components in the process of managing the labor quality and the organizations effectiveness.
Methodology for evaluating the focus of educational programs in IT sphere
Authors: Budrina Elena V. , Lebedeva Anna S. , Rogavichene Larisa I. , Levina Margarita I. , Kvitko Katerina B.
Published: October 2020

The growing IT market in Russia challenges the education system, requiring it to train highly qualified personnel who are ready to work in the IT industry after graduation. The article contains a research of educational programs in the IT areas of bachelor’s, master’s and specialist degree, purpose of identifying the focus on the development of professional competencies of an IT specialist. A methodology has been developed for evaluating the focus of educational programs in IT sphere to extend the professional skills of an IT specialist. It includes the research of the share of academic hours devoted to the development of professional competencies, which gives an understanding of the level of graduate’s belonging to the IT industry. Results of approbation of method are presented on a basis of educational programs of universities of the Perm region. It’s region where the growth of the IT sector market run ahead of the performance for the Russian Federation. The implementation of the methodology will allow comparing the educational programs of different universities, simplifying the assessment and selection process for job applicants and employers. In addition, the methodology can be used by university methodologists to modernization and maintain the relevance of curricula.
Key Competencies in the Digital Age and Transformation of Education
Authors: Rasskazova Olga , Alexandrov Igor , Burmistrov Andrey , Siniavina Maria , Cornelis Eduard
Published: October 2020

Due to the influence of digitalization and other changes affecting different spheres of people’s lives, it became clear that the modern education system must undergo a serious transformation, because the traditional education system is seriously outdated. It is expected that in the near future a significant part of education will be based on modern digital technologies, and the educational process will be implemented with the use of global educational platforms that provide students with the opportunity for global interaction and advanced knowledge and experience. The aim of the study was to formulate the features of industrial and modern education systems, to compare them, as well as to identify a set of competencies that people need to form in order to effectively cope with their professional tasks in the digital age. The issue of the optimal combination of standard educational approaches with the new technologies used in education, which allow to develop competencies that need to be formed among people in order to be in demand in the labour market, is becoming topical.
STAFF COMPETENCE AND TRAINING FOR DIGITAL INDUSTRY
Authors: Barykin S. , Borovkov A. , Rozhdestvenskiy O. , Tarshin A. , Yadykin V.
Published: October 2020

The development of a digital economy based on effective work with big data, intel-ligent digital platforms, artificial intelligence, robotics technology and 3D printing requires the formation and improvement the level of employees’ competence as a set of new high-quality competencies. In recent years, the term “digital competence” has become a key one in discus-sions about what skills and knowledge are needed in a modern knowledge society. The term “Digital competency” has various interpretations in academic literature, in the practice of teaching, training and certification. In this article, we analyze the concept of “digital compe-tence” and related terms as well as possible ways of its formation. Moreover, we consider an example of the “digital competence” formation that has developed at the SPbPU Advanced Manufacturing Technologies Center of NTI. It is important to note that we distinguish the con-cepts of “digital competence” and “digital literacy”. These concepts are not identical, but “digi-tal competency” concept is considered as a key. In this article, we prove that the most suitable approach to training staff for the digital economy is formation of fundamental knowledge as well as developing applied skills. Due to digital platforms, the applied skills realizes funda-mental knowledge through solving practical problems and challenges in the global high-tech market of products and services.
Possible negative legal consequences of unlimited technological expansion in the Arctic basin
Authors: Snetkov V N , Veshkelskiy A S , Askarov Z S
Published: October 2020

The article discusses the problems and features of the legal regulation of environmental management in the constituent entities of the Russian Federation located in the Far North of the Arctic. Due to their geographical location, climatic conditions and underdeveloped infrastructure, these entities were and remain problematic regions in terms of subsoil use. It is indicated that the legal and legislative practice of the Arctic states themselves plays the leading role in the legal status of the Arctic. At the same time, international treaties should be applied taking into account the references to regional agreements contained in them. According to the authors, the regulation of the relations of subsoil use for exploration and production of the main types of minerals should be carried out with the active participation of the constituent entities of the Russian Federation, which may contribute to the rational and integrated use of subsoil. It is proposed to add and amend the relevant legislation of the Russian Federation.
Integrative multifunctional model of bilingual teacher education
Authors: Almazova N. , Eremin Y. , Kats N. , Rubtsova A.
Published: October 2020

Bilingual teacher education is a relatively new area of scientific research. Although different theories and models to language teacher education abound, they are quite fragmented, thus, their implementation in the academic context of pre-service language teachers’ education demands further analysis and research. Therefore, the aim of the present research is to develop an integrative multifunctional model and support it with sequenced steps of its implementation. The multifunctional model, developed by the authors, consists of core components, such as knowledge, context and level of management and demonstrates an integrative approach that enables the balanced combination of diverse teaching techniques at different levels of teacher training. To check the model validity, action research has been adopted as method to organize the course of experiment in collaboration with quantitative and qualitative methods to gather and analyze the data. The research resulted in the following findings: the theoretical and practical knowledge has improved by 28% and 14% respectively whereas the levels of performance achievement and significance have reached 72 %, 72% and 60% accordingly. It can be interpreted as the development of theoretical and practical knowledge, reflective and analytical skills as well as confidence in teaching practice.
Corpus linguistic technology as a digital tool in teaching idioms’ interpretation to EFL students
Authors: Osipova Ekaterina
Published: October 2020

Corpus linguistics technology is considered from the linguodidactic perspective. Discussion of the results of extensive empirical research into efficient ways of teaching EFL (English as a Foreign Language) students to interpret idioms has been presented. The research comprises three steps: ascertaining, educational and control experiments. The aim of the paper is to investigate the efficiency of corpus linguistic technology as a tool in developing corpus-based idioms’ interpretation skill (CBIIS). The methodology has been tested on the EFL students of Bachelor study programs in Civil Engineering, Electrical and Electrical Power Engineering, Machine-building and Information Science and Computer Engineering implemented by Peter the Great St. Petersburg Polytechnic University in the years 2018-2019. The author shares personal experience of how to use corpus linguistics technology in foreign language teaching, presents a set of corpus-based exercises and describes the procedure of the learners’ work with the basic corpus tools while interpreting idioms. The result of the educational experiment shows that the average level of the CBIIS proficiency has increased that confirms the hypothesis of the research on the effectiveness of corpus linguistic technology as a tool in teaching idioms’ interpretation to EFL students.
Implementing a Blended Learning Approach to Foreign Language Teaching at SPbPU
Authors: Ivanova Ekaterina , Polyakova Marina , Abakumova Maria
Published: October 2020

One of the most significant trends in higher education today is combining conventional classroom instruction with online learning, or blended learning. Implementing blended learning for foreign language teaching has proven effective due to a variety of factors. Universities in Russia also switch to this new teaching model and design online courses to accompany and support traditional full-time teaching. In accordance with the SPbPU Provision on online-learning, a blended course of General English was launched in the Institute of Industrial Management, Economics and Trade (IIMET). The paper describes the aspects of course development and its structure. With the aim of evaluating the pilot blended project, we have conducted a survey to define the complexity level and elicit the most difficult aspects of the course, give account of students’ motivation level and ability to work self-consistently and responsibly, and measure the satisfaction level with the course. Test results show that much bigger number of students in pilot groups got excellent and good grades which increased by 40% compared to the results of control groups. Although some aspects of the experimental course were rather challenging and caused some complications, the majority of students opted for blended learning model, as it gives more flexibility, convenience and allows students to achieve good learning outcomes.
The Higher School Community Resilience as a Predictor of Efficient System of Education
Authors: Valieva F
Published: October 2020

Over the last two decades, terms connected with efficient functioning emerged within the education paradigm. The scientific research is aimed at investigating the education community’s resilience as a predictor of efficient educational system. Resilience may be defined as the power or ability to recover readily from adversity, stresses or the like to the original form or elasticity. The study included short theoretical analysis of different schools of thought, self-assessment of students and teachers abilities to discern and identify the constructs of resilience phenomenon. The survey sample included about 150 participants. The set of questionnaires the respondents were asked to complete consisted of three sections, including assessment, discerning the resilient behaviour and respondents’ personal information. The empirical study findings included the description of the sample in terms of resilience level; correlation analysis identifying the relationships between factors stated and resilience subscales as well as among all variables; factor analysis reducing the number of variables and extracting principal factors associated with resilience, personal data. Comparison of the results of the three groups identified differences not only on the level of resilience, but also on the characteristics the research project participants endued with teachers and students.
The Disadvantages of Using Scientometric Indicators in the Digital Age
Authors: Grinäv Andrei V.
Published: October 2020

Scientometric data is now widely used in solving personnel issues, grants, and financing universities, as well as monitoring their activities. However, in the course of the study using a variety of theoretical and practical methods, it was found that the main scientometric indicators, such as the total number of publications, citation index, and Hirsch Index, even in the aggregate, can rarely give a relatively objective picture of the real scholarly contribution of a particular researcher or team. Therefore, the problem of expanding the list of basic scientometric indicators and the use of new scientometric instruments (as an example, the quartile index developed by the author) becomes more urgent than ever. It is necessary to abandon the indexing of “Collider publications,” self-citations, and negative links and go from the calculation of single citations to the full accounting of all references to the author’s work. In the era of digital technology it will not be difficult to implement at least some of such recommendations. After all, the more diverse the scientometric indicators are, the more fully and more accurately they will reflect the publication activity of an individual author, team, or university as a whole.
Tracking Primary Dendritic Arm Evolution through Single Crystal CMSX-10® Ni-Base Superalloy
Authors: Strickland J , Nenchev B , Perry S , Tassenberg K , Dong HB
Published: October 2020

A novel packing pattern and local primary dendrite arm spacing (PDAS) algorithm, Shape-Limited Primary Spacing (SLPS), is applied to single crystal CMSX-10® Ni-base superalloy. The characterisation technique is rapid, repeatable and comparable, enabling the standardisation of single crystal microstructure analysis. It is deduced, that the increase in local PDAS range observed within the last to solidify sections of the CMSX-10® sample used this study, is due to lateral macrosegregation. SLPS enables quantification of the influence of the processing parameters on resultant packing patterns and local PDAS distribution. Through refinement of local PDAS, deleterious non-hexagonal pattern formation can be reduced. SLPS permits the optimisation of single crystal microstructure and the development of superior quality components.
Experimental analysis on tribological properties and lubricating mechanisms of oil-based Al2O3 nanofluids applied on steel-brass frictional pairs
Authors: Yang Jinlin , Wang Bingxu , Barber Gary C. , Hu Ming , Na Tyrer , Yang Fan
Published: October 2020

The present research studied the tribological properties of Al2O3 nanofluids applied on steel-brass contacts. It was found that the coefficient of friction could be stabilized and reduced by approximately 40.7% after adding Al2O3 nanoparticles. The wear width and wear depth could be reduced by up to 39.6% and 69.3% while using 1 wt% Al2O3 nanofluid. By examining the worn surfaces, Al2O3 nanoparticles were embedded into brass by external load to form a hard case, which could protect the brass surfaces from wear loss. In addition, some black spots with low shear resistance containing high carbon content were formed which were the result of the presence of oleic acid. In summary, the excellent lubricating performance of Al2O3 nanofluids was mainly associated with the physical embedment of Al2O3 nanoparticles and tribo-films of oleic acid. The results obtained in this research can be used to enhance the performance and extend the service life of some engineering components such as journal bearings with inner brass bushings.
Enhanced mechanical properties are possible with urethane dimethacrylate-based experimental restorative dental composite
Authors: Khan Aftab Ahmed , AlKhureif Abdulaziz Abdullah , Mohamed Badreldin A , Bautista Leonel S J
Published: October 2020

This laboratory study aimed to replace the traditional bisphenol A-glycidyl methacrylate (bisGMA) resin system with a urethane dimethacrylate (UDMA)-based resin system to enhance the physicomechanical properties of dental restorative composite (DRC). We evaluated surface roughness, porosity %, nanohardness, elastic modulus, and compressive strength (CS) in the control group (the bisGMA-resin system) and two experimental groups (UDMA-based resin systems with 20 wt.% SiO2 or Al2O3, each 30 μm in size spherical fillers). Cylindrically shaped samples 4 mm in diameter and 6 mm in height were fabricated using light curing (n = 10). One-way analysis of variance method was used to statistically analyze the results (p ≤ 0.05). The data suggest that both UDMA-based resin systems showed increased surface roughness (Ra) and porosity % in the sample fabrication compared with the control. However, the nanohardness in both SiO2-based UDMA composite (0.20 ± 0.09 GPa) and Al2O3-based UDMA composite (0.22 ± 0.07 GPa) was not significantly higher compared with the control (0.19 ± 0.05 GPa). Likewise, while improved CS values were observed in both SiO2-based UDMA composite (15.5 ± 1.9 MPa) and Al2O3-based UDMA composite (16.2 ± 0.7 MPa) compared to the control (14.5 ± 4.5 MPa), this increase was not statistically significant. The newly developed UDMA-based resin formulation with Al2O3 micro-filler showed promising physicomechanical properties and may be appropriate for use as DRC.
Effect of weak Mn doping on optical properties of ZnGeP2 single crystal grown by vertical gradient freezing method
Authors: Yang Deng-Hui , Cao Xin-Ling
Published: October 2020

ZnGeP2 single crystals weakly doped by manganese (Mn) were grown by vertical gradient freezing method from polycrystalline batch which was synthesized by the modified two temperature vapor phase transport method. Energy Disperse Spectroscopy (EDS), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS) and Fourier Transform Infrared Spectrometry (FTIR) were employed to characterize the doping single crystals. The un-doped and Mn doped single crystals show the same color. XRD results manifest that the obtained Mn doped ZnGeP2 has tetragonal structure with slight lattice distortion and has no segregation. The EDS results indicate a good stoichiometry of ZnGeP2 weakly doped with Mn. From the XPS results, the doped single crystal with no impurity phases were successfully obtained by the vertical gradient freezing method. FTIR spectra show a slight decrease in infrared transmittance of Mn doped single crystals.
Deciphering the mechanism of hafnium oxide nanoparticles perturbation in the bio-physiological microenvironment of catalase
Authors: Ahmad Farooq , Muhmood Tahir , Mahmood Asif
Published: October 2020

Nanoparticles (NPs) are extensively being used in state-of-the-art nano-based therapies, modern electronics, and consumer products, so can be released into the environment with enhancement interaction with humans. Hence, the exposures to these multifunctional NPs lead to changes in protein structure and functionality, raising serious health issues. This study thoroughly investigated the interaction and adsorption of catalase (CAT) with HfO2-NPs by circular dichroism (CD), Fourier transform infrared (FTIR), absorption, and fluorescence spectroscopic techniques. The results indicate that HfO2 NPs cause fluorescence quenching in CAT by a static quenching mechanism. The negative values of Vant Hoff thermodynamic expressions (ΔH

o
, ΔS

o
, and ΔG

o
) corroborate the spontaneity and exothermic nature of static quenching driven by van der Waals forces and hydrogen bonding. Also, FTIR, UV-CD, and UV–visible spectroscopy techniques confirmed that HfO2 NPs binding could induce microenvironment perturbations leading to secondary and tertiary conformation changes in CAT. Furthermore, synchronous fluorescence spectroscopy confirmed the significant changes in the microenvironment around tryptophan (Trp) residue caused by HfO2 NPs. The time depending denaturing of CAT biochemistry through HfO2-NPs was investigated by assaying catalase activity elucidates the potential toxic action of HfO2-NPs at the macromolecular level. Briefly, this provides an empathetic knowledge of the nanotoxicity and likely health effects of HfO2 NPs exposure.
Association of Mammography Screening With a Reduction in Breast Cancer Mortality: A Modeling Study Using Population-Based Data From 2 French Departments
Authors: Seigneurin Arnaud , Exbrayat Catherine , Molinié Florence , Croisier Lucie , Poncet Florence , Berquet Karine , Delafosse Patricia , Colonna Marc
Published: October 2020

Meta-analyses of randomized controlled trials that started from 1963 to 1991 reported a decrease of breast cancer mortality, associated with mammography screening. However, the effectiveness of population-based screening programs conducted currently might have changed due to the higher effectiveness of treatments for late-stage cancers and the better diagnostic performance of mammography. The main objective of this study was to predict the reduction of breast cancer mortality associated with mammography screening in the current French setting. We compared breast cancer mortality in 2 simulated cohorts of women, which differed from each other solely in a 70% biennial participation in screening from 50 to 74 years old. The microsimulation model used for predictions was calibrated with incidence rates of breast cancer according to stage that were observed in Isère and Loire-Atlantique departments, France, in 2007–2013. The model predicted a decrease of breast cancer mortality associated with mammography screening of 18% (95% CI: 5, 31) and 17% (95% CI: 3, 29) for models calibrated with data from Isère and Loire-Atlantique departments, respectively. Our results highlight the interest in biennial mammography screening from ages 50 to 74 years old to decrease breast cancer mortality in the current setting, despite improvements in treatment effectiveness.
Hypercrisy and standing to self-blame
Authors: Tierney Hannah
Published: October 2020

In a 2020 article in Analysis, Lippert-Rasmussen argues that the moral equality account of the hypocrite’s lack of standing to blame fails. To object to this account, Lippert-Rasmussen considers the contrary of hypocrisy: hypercrisy. In this article, I show that if hypercrisy is a problem for the moral equality account, it is also a problem for Lippert-Rasmussen’s own account of why hypocrites lack standing to blame. I then reflect on the hypocrite’s and hypercrite’s standing to self-blame, which reveals that the challenge hypercrisy poses for accounts of standing is different from the challenge Lippert-Rasmussen articulates.
AlgPred 2.0: an improved method for predicting allergenic proteins and mapping of IgE epitopes
Authors: Sharma Neelam , Patiyal Sumeet , Dhall Anjali , Pande Akshara , Arora Chakit , Raghava Gajendra P S
Published: October 2020

AlgPred 2.0 is a web server developed for predicting allergenic proteins and allergenic regions in a protein. It is an updated version of AlgPred developed in 2006. The dataset used for training, testing and validation consists of 10 075 allergens and 10 075 non-allergens. In addition, 10 451 experimentally validated immunoglobulin E (IgE) epitopes were used to identify antigenic regions in a protein. All models were trained on 80% of data called training dataset, and the performance of models was evaluated using 5-fold cross-validation technique. The performance of the final model trained on the training dataset was evaluated on 20% of data called validation dataset; no two proteins in any two sets have more than 40% similarity. First, a Basic Local Alignment Search Tool (BLAST) search has been performed against the dataset, and allergens were predicted based on the level of similarity with known allergens. Second, IgE epitopes obtained from the IEDB database were searched in the dataset to predict allergens based on their presence in a protein. Third, motif-based approaches like multiple EM for motif elicitation/motif alignment and search tool have been used to predict allergens. Fourth, allergen prediction models have been developed using a wide range of machine learning techniques. Finally, the ensemble approach has been used for predicting allergenic protein by combining prediction scores of different approaches. Our best model achieved maximum performance in terms of area under receiver operating characteristic curve 0.98 with Matthew’s correlation coefficient 0.85 on the validation dataset. A web server AlgPred 2.0 has been developed that allows the prediction of allergens, mapping of IgE epitope, motif search and BLAST search (https://webs.iiitd.edu.in/raghava/algpred2/).
Text mining approaches for dealing with the rapidly expanding literature on COVID-19
Authors: Wang Lucy Lu , Lo Kyle
Published: October 2020

More than 50 000 papers have been published about COVID-19 since the beginning of 2020 and several hundred new papers continue to be published every day. This incredible rate of scientific productivity leads to information overload, making it difficult for researchers, clinicians and public health officials to keep up with the latest findings. Automated text mining techniques for searching, reading and summarizing papers are helpful for addressing information overload. In this review, we describe the many resources that have been introduced to support text mining applications over the COVID-19 literature; specifically, we discuss the corpora, modeling resources, systems and shared tasks that have been introduced for COVID-19. We compile a list of 39 systems that provide functionality such as search, discovery, visualization and summarization over the COVID-19 literature. For each system, we provide a qualitative description and assessment of the system’s performance, unique data or user interface features and modeling decisions. Many systems focus on search and discovery, though several systems provide novel features, such as the ability to summarize findings over multiple documents or linking between scientific articles and clinical trials. We also describe the public corpora, models and shared tasks that have been introduced to help reduce repeated effort among community members; some of these resources (especially shared tasks) can provide a basis for comparing the performance of different systems. Finally, we summarize promising results and open challenges for text mining the COVID-19 literature.
Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities
Authors: Chiara Matteo , D’Erchia Anna Maria , Gissi Carmela , Manzari Caterina , Parisi Antonio , Resta Nicoletta , Zambelli Federico , Picardi Ernesto , Pavesi Giulio , Horner David S , Pesole Graziano
Published: October 2020

Various next generation sequencing (NGS) based strategies have been successfully used in the recent past for tracing origins and understanding the evolution of infectious agents, investigating the spread and transmission chains of outbreaks, as well as facilitating the development of effective and rapid molecular diagnostic tests and contributing to the hunt for treatments and vaccines. The ongoing COVID-19 pandemic poses one of the greatest global threats in modern history and has already caused severe social and economic costs. The development of efficient and rapid sequencing methods to reconstruct the genomic sequence of SARS-CoV-2, the etiological agent of COVID-19, has been fundamental for the design of diagnostic molecular tests and to devise effective measures and strategies to mitigate the diffusion of the pandemic.

Diverse approaches and sequencing methods can, as testified by the number of available sequences, be applied to SARS-CoV-2 genomes. However, each technology and sequencing approach has its own advantages and limitations. In the current review, we will provide a brief, but hopefully comprehensive, account of currently available platforms and methodological approaches for the sequencing of SARS-CoV-2 genomes. We also present an outline of current repositories and databases that provide access to SARS-CoV-2 genomic data and associated metadata. Finally, we offer general advice and guidelines for the appropriate sharing and deposition of SARS-CoV-2 data and metadata, and suggest that more efficient and standardized integration of current and future SARS-CoV-2-related data would greatly facilitate the struggle against this new pathogen. We hope that our ‘vademecum’ for the production and handling of SARS-CoV-2-related sequencing data, will contribute to this objective.
Self-supervised feature extraction from image time series in plant phenotyping using triplet networks
Authors: Marin Zapata Paula A , Roth Sina , Schmutzler Dirk , Wolf Thomas , Manesso Erica , Clevert Djork-Arné
Published: October 2020

Motivation

Image-based profiling combines high-throughput screening with multiparametric feature analysis to capture the effect of perturbations on biological systems. This technology has attracted increasing interest in the field of plant phenotyping, promising to accelerate the discovery of novel herbicides. However, the extraction of meaningful features from unlabeled plant images remains a big challenge.

Results

We describe a novel data-driven approach to find feature representations from plant time-series images in a self-supervised manner by using time as a proxy for image similarity. In the spirit of transfer learning, we first apply an ImageNet-pretrained architecture as a base feature extractor. Then, we extend this architecture with a triplet network to refine and reduce the dimensionality of extracted features by ranking relative similarities between consecutive and non-consecutive time points. Without using any labels, we produce compact, organized representations of plant phenotypes and demonstrate their superior applicability to clustering, image retrieval and classification tasks. Besides time, our approach could be applied using other surrogate measures of phenotype similarity, thus providing a versatile method of general interest to the phenotypic profiling community.

Availability and implementation

Source code is provided in https://github.com/bayer-science-for-a-better-life/plant-triplet-net.

Supplementary information

Supplementary data are available at Bioinformatics online.
Leveraging heterogeneous network embedding for metabolic pathway prediction
Authors: M A Basher Abdur Rahman , Hallam Steven J
Published: October 2020

Motivation

Metabolic pathway reconstruction from genomic sequence information is a key step in predicting regulatory and functional potential of cells at the individual, population and community levels of organization. Although the most common methods for metabolic pathway reconstruction are gene-centric e.g. mapping annotated proteins onto known pathways using a reference database, pathway-centric methods based on heuristics or machine learning to infer pathway presence provide a powerful engine for hypothesis generation in biological systems. Such methods rely on rule sets or rich feature information that may not be known or readily accessible.

Results

Here, we present pathway2vec, a software package consisting of six representational learning modules used to automatically generate features for pathway inference. Specifically, we build a three-layered network composed of compounds, enzymes and pathways, where nodes within a layer manifest inter-interactions and nodes between layers manifest betweenness interactions. This layered architecture captures relevant relationships used to learn a neural embedding-based low-dimensional space of metabolic features. We benchmark pathway2vec performance based on node-clustering, embedding visualization and pathway prediction using MetaCyc as a trusted source. In the pathway prediction task, results indicate that it is possible to leverage embeddings to improve prediction outcomes.

Availability and implementation

The software package and installation instructions are published on http://github.com/pathway2vec.

Supplementary information

Supplementary data are available at Bioinformatics online.