bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investment-innovation analysis of interactions between technological and economic aspects of industrial development of mineral resources in the Arctic
Authors: Zharov V , Tsukerman V 
Published: August 2019

Abstract
The methodological foundations of investment-innovation analysis for the objective determination of innovation-active enterprises are considered. The particular importance of managing the implementation of new technologies for industrial enterprises operating in the Arctic is noted. The main factors that influence the change in the manufacturability level coefficient value which reflects the proportional dependence of the material intensity of the product from the capital intensity of production are identified. The characteristic of each factor is presented. It was determined that the main influence on the change in the values of the coefficient is made by the rate of renewal of the fixed assets active part of enterprises - machines, equipment and vehicles. The sequence of investment-innovation analysis implementation by the retrospective data of enterprises is presented. A method for determining the completion period of each of the six stages of the technological development life cycle is shown. It is determined that the decrease of the manufacturability level coefficient value or the instability of the stages of the production process life cycle are associated with the low efficiency of the enterprise management process what makes it possible to carry out an economic assessment of the damage from increase of production cost price and decrease of profit as a result of poor management at any level of hierarchy.
Integral Assessment of the Sustainability of Socio-Ecological and Economic Systems and the Quality of Life of the Population in the Regions of the Arctic Zone of the Russian Federation
Authors: Dmitriev V , Kulesh V , Sergeev Yu 
Published: August 2019

Abstract
The article deals with the integral assessment of the state and sustainability of socio-ecological and economic systems (SEES). The integral assessment of SEES, 9 regions of the Arctic Zone of the RF (AZR) and one region of the central Russia (Tver Region) is used as a foundation for the analysis of the state of SEES and the quality of life of the population, as well as the ability of SEESs to maintain their properties and quantitative characteristics in case of an external impact on the system or any intrasystem changes. Eight scenarios of impact on subsystems and systems as a whole at the regional level were developed to assess sustainability. The article presents the results of the evaluation of the quality of environment and the quality of life of the population in the regions in 2003-2015. The main goal of the study was to identify situations in which SEES, upon the impact assigned upon it, will not be able to maintain its properties and parameters and will move to another class, both in separate subsystems and as the whole system.
Relationship between the Russian fishing fleet and domestic ports as the core for performing its state mission
Authors: Vasiliev A M , Komlichenko V V , Lisunova E A 
Published: August 2019

Abstract
The article provides a rationale for the main task of the Russian fishing fleet to implement the Food Security Doctrine of the Russian Federation under the terms of public-private partnership. The paper describes changes in the activities of the fishing fleet in the Northern fishery basin that were caused by the process of operating in the market economy environment, the way these factors impact on the activities of subsidiary and service companies, as well as the development of enterprises and companies involved in the fishery sector. The paper provides the reasons for the low availability and quality of domestic fish products for the population in the Arctic region. In connection with the predominantly export-oriented trends in the fishing industry of the Murmansk region affecting the calls of trawlers at Russian ports it was concluded that there was a need for a national policy regulating these closely related processes. The article justifies measures to improve the relationship between fishing vessels and domestic ports in the Arctic region. To increase the supply of raw fish and fish semi-finished products for coastal fish processing factories, as well as to increase a number of high-level processed fish products, it was suggested to use medium fishing freezer trawlers (MFFT, according to the classification adopted by PINRO) according to the rules of coastal fishing. The paper provides assessment for possible impacts from the delivery of fish products by “non-call” fishing vessels (i.e. fishing vessels that did not perform customs declaring procedures) on the level of economic activities in the fisheries industry. Expert assessments for the costs of repairing “non-call” fishing vessels abroad are provided as well. The paper provides estimates of additional tax investments into the Russian national budget from the Murmansk ship-repair factories in case servicing of “non-call” fishing vessels is provided in the Russian Federation. Refocusing of fish landings will provide a fisheries cluster in the Northern Basin.
Tools for digitalization of economic processes for supporting management decision-making in the region
Authors: Skotarenko O , Babkin A , Senetskaya L , Bespalova S 
Published: August 2019

Abstract
The article proposes a solution to one of the key problems – the use of information technology in the management of territorial processes based on the development of tools for digitalization of economic processes on the basis of the software product to identify the structural elements of the economic potential of the regions of Russia, including the features of such regions as the Arctic. As a tool for the implementation of this approach, the VBA programming language built into the Excel spreadsheet is used, which allows flexible use of a standard software product for solving problems at the macroeconomic level. The aim of the study is to develop tools for digitalization of economic processes on the basis of a computer program to determine the extreme structural elements of the growth of the economic potential of the regions to support management decision-making. The systematic approach, methods of statistical and economic analysis, including horizontal and vertical analysis, allowed the authors to assess the dynamics of extreme values of the level of development of economic sectors in the regions of Russia and to develop recommendations for the development of the Federal districts and regions. The directions of further researches consist in application of multidimensional modeling of data for collecting and automatic processing of statistical information on a condition of subjects of the Arctic region.
Stone objects of Russian Fennoscandia: potential for recreational use
Authors: Grigoryev A A , Gladkiy Yu N , Sevastyanov D V , Shastina G N 
Published: August 2019

Abstract
The perspectives for recreational use of attractive stone objects in the natural region of the Russian-owned part of Fennoscandia are considered. Such objects as fjords, canyons, selga, rapids, huge boulders and their clusters, petroglyphs, seitas and labyrinths are very popular among tourists. The article shows new approaches to the interpretation of the primary purpose of the Stone Age objects, based on the priorities of geographical adaptation, rational development of the landscape, space marking and time measurement. The modern problems of preservation of cultural heritage monuments are considered. Special attention is paid to anthropomorphic and zoomorphic rocks and sculptures, the genesis of which is the subject of scientific debate. The use of geographical methods expands the concept of the primary purpose of ancient objects, stone processing technologies, the simplest tools of orientation in space-time and the ancient navigation system. The results of the research allow us to clarify ideas about the evolution of the natural environment in the region, clarify the existing reconstruction of the economic structure and cultural traditions of the indigenous population, optimize the existing and develop new models of rational use of the natural and cultural heritage in the field of tourism and recreation. Prehistoric stone objects are a source of unique information and a valuable resource for the development of recreational activities. The inclusion of these objects in the system of organized tourism contributes to their preservation and economic development of the territory. The article is addressed to researchers and priaktiks involved in the development of projects for the development of the Arctic regions.
An approximate calculation of the S-lay method offshore pipeline
Authors: Kotov A A , Korotaev B A , Vaseha M V , Smolskaia N B 
Published: August 2019

Abstract
The problem of the curvilinear form of the pipeline laid from the pipe-laying vessel to the bottom of the water area and the internal forces associated with this form in the pipeline are considered in the article. The assessment of some existing research methods of the issue under consideration that can lead to the conclusion of its relevance is given. To solve the problem, we propose an original approximate nonlinear differential equation of the second order, compiled for the convenience of its application in relative quantities. A fairly simple algorithm for the numerical solution of this equation in Wolfram Mathematica is developed, a specific numerical example is considered. The results suggest that the proposed method of the stress-strain state analysis of the offshore oil and gas pipeline during its laying can be very useful in practical application.
Legal support of environmental protection in the Arctic region
Authors: Demidov V P , Yu Mokhorova A , Mokhorov D A 
Published: August 2019

Abstract
Abstract The paper discusses the urgent problem of legal regulation of the Arctic territory. Developing the Arctic zone being under Russian jurisdiction has an considerable significance for effective and sustainable management of natural resources. The most important provisions of the Russian legislation, forming the scientifically-based approaches to economic activities in the Arctic region, are considered. The paper focuses on the key aspects of the legal concepts that are aimed at tackling the acute problems arising in the process of developing the Arctic coastal territories. The authors give attention to providing methods of comprehensive use of all Arctic resources and developing effective legal mechanisms to achieve the formulated economic objectives, with simultaneous creation of the legal basis for preserving the unique natural environment. So it is suggested that legal acts be developed to cover the most topical provisions of the economic activity processes in the afore-mentioned region. This objective can be reached relying on the goals of the state policy of the Russian Federation. Intensifying economic activities call for a more detailed legal regulation of the use of the northern territories, so it seems reasonable to adopt federal legal acts which would consider the specifics of the environment of the Arctic.
Context awareness and embedding for biomedical event extraction
Authors: Yan Shankai , Wong Ka-Chun 
Published: August 2019

AbstractMotivationBiomedical event extraction is fundamental for information extraction in molecular biology and biomedical research. The detected events form the central basis for comprehensive biomedical knowledge fusion, facilitating the digestion of massive information influx from the literature. Limited by the event context, the existing event detection models are mostly applicable for a single task. A general and scalable computational model is desiderated for biomedical knowledge management.ResultsWe consider and propose a bottom-up detection framework to identify the events from recognized arguments. To capture the relations between the arguments, we trained a bidirectional long short-term memory network to model their context embedding. Leveraging the compositional attributes, we further derived the candidate samples for training event classifiers. We built our models on the datasets from BioNLP Shared Task for evaluations. Our method achieved the average F-scores of 0.81 and 0.92 on BioNLPST-BGI and BioNLPST-BB datasets, respectively. Comparing with seven state-of-the-art methods, our method nearly doubled the existing F-score performance (0.92 versus 0.56) on the BioNLPST-BB dataset. Case studies were conducted to reveal the underlying reasons.Availability and implementationhttps://github.com/cskyan/evntextrc.Supplementary informationSupplementary data are available at Bioinformatics online.
scHinter: imputing dropout events for single-cell RNA-seq data with limited sample size
Authors: Ye Pengchao , Ye Wenbin , Ye Congting , Li Shuchao , Ye Lishan , Ji Guoli , Wu Xiaohui 
Published: August 2019

Abstract

Motivation
Single-cell RNA-sequencing (scRNA-seq) is fast and becoming a powerful technique for studying dynamic gene regulation at unprecedented resolution. However, scRNA-seq data suffer from problems of extremely high dropout rate and cell-to-cell variability, demanding new methods to recover gene expression loss. Despite the availability of various dropout imputation approaches for scRNA-seq, most studies focus on data with a medium or large number of cells, while few studies have explicitly investigated the differential performance across different sample sizes or the applicability of the approach on small or imbalanced data. It is imperative to develop new imputation approaches with higher generalizability for data with various sample sizes.

Results
We proposed a method called scHinter for imputing dropout events for scRNA-seq with special emphasis on data with limited sample size. scHinter incorporates a voting-based ensemble distance and leverages the synthetic minority oversampling technique for random interpolation. A hierarchical framework is also embedded in scHinter to increase the reliability of the imputation for small samples. We demonstrated the ability of scHinter to recover gene expression measurements across a wide spectrum of scRNA-seq datasets with varied sample sizes. We comprehensively examined the impact of sample size and cluster number on imputation. Comprehensive evaluation of scHinter across diverse scRNA-seq datasets with imbalanced or limited sample size showed that scHinter achieved higher and more robust performance than competing approaches, including MAGIC, scImpute, SAVER and netSmooth.

Availability and implementation
Freely available for download at https://github.com/BMILAB/scHinter.

Supplementary information
Supplementary data are available at Bioinformatics online.
Protein Homeostasis Database: protein quality control in E.coli
Authors: Ramakrishnan Reshmi , Houben Bert , Kreft Łukasz , Botzki Alexander , Schymkowitz Joost , Rousseau Frederic 
Published: August 2019

Abstract

Motivation
In vivo protein folding is governed by molecular chaperones, that escort proteins from their translational birth to their proteolytic degradation. In E.coli the main classes of chaperones that interact with the nascent chain are trigger factor, DnaK/J and GroEL/ES and several authors have performed whole-genome experiments to construct exhaustive client lists for each of these.

Results
We constructed a database collecting all publicly available data of experimental chaperone-interaction and -dependency data for the E.coli proteome, and enriched it with an extensive set of protein-specific as well as cell context-dependent proteostatic parameters. We made this publicly accessible via a web interface that allows to search for proteins or chaperone client lists, but also to profile user-specified datasets against all the collected parameters. We hope this will accelerate research in this field by quickly identifying differentiating features in datasets.

Availability and implementation
The Protein Homeostasis Database is freely available without any registration requirement at http://PHDB.switchlab.org/.
Tersect: a set theoretical utility for exploring sequence variant data
Authors: Kurowski Tomasz J , Mohareb Fady 
Published: August 2019

Abstract

Summary
Comparing genomic features among a large panel of individuals across the same species is considered nowadays a core part of the bioinformatics analyses. This typically involves a series of complex theoretical expressions to compare, intersect, extract symmetric differences between individuals within a large set of genotypes. Several publically available tools are capable of performing such tasks; however, due to the sheer size of variants being queried, such tasks can be computationally expensive with a runtime ranging from few minutes up to several hours depending on the dataset size. This makes existing tools unsuitable for interactive data query or as part of genomic data visualization platforms such as genome browsers. Tersect is a lightweight, high-performance command-line utility which interprets and applies flexible set theoretical expressions to sets of sequence variant data. It can be used both for interactive data exploration and as part of a larger pipeline thanks to its highly optimized storage and indexing algorithms for variant data.

Availability and implementation
Tersect was implemented in C and released under the MIT license. Tersect is freely available at https://github.com/tomkurowski/tersect.

Supplementary information
Supplementary data are available at Bioinformatics online.
Virtual Empathy
Authors: Andrejevic Mark , Volcic Zala 
Published: August 2019

Abstract
This article offers a theoretical response to the recent interest in virtual reality (VR) as a technology for enhancing empathy. It argues that the version of empathy envisioned by the champions of the technology—one in which care for the other is a function of being able to collapse the other’s experience into one’s own—runs counter to the very concept of empathy, as originally construed, which preserves otherness in its alterity. The point is not simply to invoke a historical concept of empathy to contrast with the VR version, but to emphasize its enduring salience in response to recent technological developments. There is little doubt regarding the need for empathy, in the sense explored in this article, as we confront the pathologies of political fragmentation and social polarization facilitated by the current iteration of social media. However, this article argues that the VR version is more likely to exacerbate than redress these concerns.
Neoliberalism, deliberation and dissent: critical reflections on the ‘community activation’ turn in Ireland’s community development programme
Authors: Gaynor Niamh 
Published: August 2019

AbstractIn this article, I aim to add to the literature on the impact of neoliberalism on community development by focusing on two recent seemingly unrelated developments in Ireland. The first is the reframing of ‘community development’ as ‘community activation’ in Ireland’s latest community development programme. I suggest that this ‘community activation’ turn marks a new departure in the social and political embedding of neoliberalism in community development and in Irish society more broadly in that its reframing of both the identity of ‘the poor’ and of the nature of supports that they require individualizes responsibility and action. This, I argue, not only fragments and atomizes communities, it also risks foreclosing any substantive discussion and deliberation of structural issues, thereby posing a threat to democracy. The second development is the concomitant emergence of a new, more critically engaged form of community activism in the form of the so-called ‘water movement’. The actions and aspirations of the women we interviewed within this movement highlight their role in revitalizing and re-energizing communities, animating public debate and redirecting power back into communities. Activation clearly comes in many forms and, under the shadow of neoliberal reforms, results in many different outcomes. How or if the formal community sector chooses to respond to this diversity and what impacts this will have will prove critical to local communities as well as providing important avenues for future research.
Artificial Cultivation of the Chinese Cordyceps From Injected Ghost Moth Larvae
Authors: Liu Guiqing , Han Richou , Cao Li 
Published: August 2019

AbstractThe Chinese cordyceps, regarded as the ‘Himalayan Viagra’, is highly valued for its medicinal benefits. The decline of its yield due to over-exploitation and increased market demand have stimulated efforts to artificially cultivate Chinese cordyceps for over half a century. However, successful cultivation of Chinese cordyceps through caterpillar infection by the fungus Ophiocordyceps sinensis (Berk.) and the induction of the fruiting body from each mummified cadaver remains difficult for its complex life cycle. Herein, we report the developmental dynamics of hyphal bodies in hemolymph of injected Thitarodes xiaojinensis (Tu, Ma & Zhang) larvae and the success in artificial cultivation of sexual fruiting bodies from the mummified cadavers in the low-altitude area. We find that not only the numbers of hyphal bodies but also the conversion of hyphal bodies into hyphae played important roles in the mummification of the injected larvae. This cultivation will be beneficial for sustainable utilization of natural resources and provides the possibility for further research on the mechanism of the interaction between pathogenic fungus and host insect.
Acetaminophen use during pregnancy and DNA methylation in the placenta of the extremely low gestational age newborn (ELGAN) cohort
Authors: Addo Kezia A , Bulka Catherine , Dhingra Radhika , Santos Hudson P , Smeester Lisa , O’Shea T Michael , Fry Rebecca C 
Published: August 2019

AbstractAcetaminophen is considered the safest antipyretic and analgesic medication for pregnant women. However, studies have reported that acetaminophen has endocrine disrupting properties and prenatal exposure has been associated with early life epigenetic changes and later life health outcomes. As the placenta is the central mediator of maternal and fetal interactions, exposure to acetaminophen during pregnancy could manifest as perturbations in the placenta epigenome. Here, we evaluated epigenome-wide cytosine-guanine dinucleotide (CpG) methylation in placental tissue in relation to maternal acetaminophen use during pregnancy in a cohort of 286 newborns born prior to 28 weeks gestation. According to maternal self-report, more than half (166 of 286) of the newborns were exposed to acetaminophen in utero. After adjustment for potential confounders, a total of 42 CpGs were identified to be differentially methylated at a false discovery rate < 0.05, with most displaying increased methylation as it relates to acetaminophen exposure. A notable gene that was significantly associated with acetaminophen is the prostaglandin receptor (PTGDR) which plays an essential role in mediating placental blood flow and fetal growth. Moreover, for 6 of the 42 CpGs, associations of acetaminophen use with methylation were significantly different between male and female placentas; 3 CpG sites were associated with acetaminophen use in the male placenta and 3 different sites were associated with acetaminophen use in the female placenta (Pinteraction < 0.2). These findings highlight a relationship between maternal acetaminophen use during pregnancy and the placental epigenome and suggest that the responses for some CpG sites are sex dependent.