bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact assessment of solid runoff on heavy metals migration during high floods on the Amur river
Authors: Makhinov A N , Makhinova A F , Liu Sh 
Published: November 2021

Abstract
Inhomogeneity of the concentrations of chemical elements in the cross-section of the Amur River is considered as a function of the state of their soluble and suspended forms. Flooding of wetlands and urbanized areas contributes to the removal of pollutants into the river channel. The wide spread of fens on the left bank contributes to the concentration of organic matter along the left bank of the river. Terrigenous material mostly comes from the right bank, where agricultural fields are concentrated. The ratio of their concentrations is maintained by the duration of the flood. The mechanisms of redistribution of elements between their suspended and soluble forms have been studied. The mechanisms of sorption of chemical compounds on mineral and organic colloids are described. It was found that mineral colloids with a negative charge due to electrostatic attraction sorb electrically neutral compounds (hydroxoaqua complexes [Mn(OH)2(OH2]0, ammonia [Cu(NH3)4(OH)2]0. The role of organic material in the redistribution of chemical compounds between soluble and suspended forms is shown. Organic colloids with molecular mass > 5.0 kDa precipitate complex cations – [FeHSO4]+, [FeHSO4]2+, [CuHSO4]+. An organic substance with a molecular mass of <2.0 kDa has a greater complexing ability for Fe(2)3+, Cu2+, Zn2+, Mn2+ ions. They bind metals to organo-mineral complexes by chemical interaction and form mobile organo-mineral complexes and heteropolar salts.
Organic carbon and particle size distribution of aggregates from chernozem under arable land and shelterbelt
Authors: Yu Milanovskiy E , Tyugai Z , Shnyrev N A 
Published: November 2021

Abstract
The particle size distribution (PSD) and the content of organic carbon (Corg) in dry and water-stable aggregates were determined in the upper layer of chernozem under arable land and shelterbelt. In water-stable aggregates, the Corg content is 1.2-1.5 times higher than in dry sieving aggregates. Dry sieving and water-stable aggregates of arable chernozem consist of particles identical in terms of the PSD. And in the chernozem under the shelterbelt the content of physical clay increases with a decrease in the size of the aggregate in water-stable aggregates isolated from the fraction of dry sieving < 1 mm.
Importance and Problems of Landscape Diversity Conservation in the Environmental Policy of Poorly Developed Regions
Authors: Mirzekhanova Z G , Klimina E M 
Published: November 2021

Abstract
The environmental strategy for regional development is implemented through regional environmental programs. Their list of indicators that track the effectiveness of planned tasks shows that the most important regional aspects are not always properly reflected. The specificity of spatial and temporal trends in the development of regions, the peculiarities of territorial changes in geosystems, and the dynamics of the ratio of disturbed and undisturbed territories are of particular importance in highlighting the tasks in the context of the application of particular indicators. In the context of increased economic activity in the Russian Far East, facilitated by the policy of improving priority social and economic development areas, the regions identify their own tasks for sustainable development. From the perspective of the geographical approach, the content of the concept of landscape diversity, contained in the environmental program of Khabarovsk Territory to reflect spatial changes, is briefly presented. Landscapes as integral systems are considered from the point of view of their positions in the system of taxa of the regional hierarchy. The significance of “landscape diversity conservation” criterion for solving the same problem as a priority for this territory has been shown. The necessity of its application in the region has been considered due to the concentration of natural complexes of a high hierarchical rank, their significant share within the region, the uniqueness and at the same time a high degree of landscape vulnerability to anthropogenic impact due to increased economic activity, the imperfection of the PA network etc.
Meaning of protected areas in ecological sustainable city development
Authors: Yu Morozova G , Debelaya I D 
Published: November 2021

Abstract
Protected areas are the key elements of the green infrastructure and environmental city frame that provide variety of ecosystem services to the people as well as serve as the centers of investment attraction. The total area of the protected lands of Khabarovsk is 583.57 ha (1.5% of the city area): 5 protected ones of regional significance, 24 areas of local significance. There are 117 species observed in the dendroflora of all protected areas, which is relatively close to the natural biodiversity indicator. The reserve for expanding the protected areas network in Khabarovsk is mainly represented by the lands of the Russian Ministry of Defense, floodplain lands, the adjacent areas to the water protection zones of small rivers in the city, and ecologically restored technogenic sites. In addition to the forest type areas this will permit to create water and meadow-marsh protected plots, which meets the representativeness criteria of the natural ecosystems of the Amur River Region. The case study of a protected area called Orekhovaya Sopka, allows seeing that keeping record of the ecosystem services increases both the economic and the environmental values of the territories. The results may be applied in: municipal management.
Information and computational GIS for monitoring the natural and technical systems of placer gold deposits
Authors: Usikov V I , Ozaryan Y A 
Published: November 2021

Abstract
It is known that nowadays one of the main problems of mining is the depletion of reserves. The researchers consider mining waste as a source of replenishment of the resource base. Disputes on the prospects for technogenic raw material processing are becoming especially relevant. The object of research chosen by the authors in this article is the technogenic neoplasms resulting from dredging and hydraulic processing of placer gold. The paper presents the results of assessing the prospects and application of the information technologies, in particular, the analysis of data from remote sensing of the Earth in the design and organization of work to involve technogenic placers in operation. It is shown that these technologies are able to increase the efficiency of work and reduce labor costs at the stage of preliminary study of potential development targets. Technogenic complexes of depleted fields are a significant reserve of the mineral resource base of gold and other precious metals. This paper presents the results of the creation of a method for expert assessment of spatial and volumetric indicators of technogenic complexes of alluvial fields and other landscape objects using remote sensing of the territory and analysis of geological information. The Kerbinsky gold-bearing region of the Khabarovsk Region was chosen as the object of research.
Mineralization and salt composition of the waters of the Middle Amur
Authors: Shesterkin V P , Shesterkina N M 
Published: November 2021

Abstract
The spatial and temporal variability of water salinity and salt composition of the Amur River near Khabarovsk in 2017-2021 was considered. An uneven distribution of water salinity over the river width was established, the greatest differences were observed in the winter low-water period, the lowest in the period of spring floods and floods. The maximum value of salinity was noted in winter, in the period of open channel – after very strong floods.
Features of biodiversity of the Uchursky landscape nature reserve (Ayano-Maiskoye district of Khabarovsk Territory)
Authors: Shlotgauer S D 
Published: November 2021

Abstract
It was revealed that the botanical and geographical feature of the vegetation cover of the Uchursky complex nature reserve is its position in the zone of convergence of the continental and monsoon climates, claimed by sharply contrasting phlorogenetic elements of the vegetation cover. The gradient of continentality - oceanicity in the vegetation cover is quite clearly traced between the eastern and western macroslopes of the mountain systems of the Uchur River basin. A complex history of the formation of the territory, the height difference from 1,000 to 2,000 meters, the variety of rocks created the conditions for the existence of floristic complexes of different ecology and origin. In this regard, on the territory of the nature reserve, an overlap of the marginal zones of plants ranges of oceanic and continental origin was found, which defines the richness of the region’s biodiversity, but makes both species and communities unstable. The uniqueness of the flora of the Geran Ridge was revealed, with the main core formed by species of non-Angarid origin, concentrated on the weathering crust of the basic rocks. The participation of alpinogenic, arctic and arctic-alpine species is noted. The pine-larch forests, which are unique in their species composition, are found on the outcrops of carbonate rocks on the right bank of the Uchur River, opposite the mouth of the Lyalmi River and in the Uchur-Ulkan interfluve. In this area, there are 79 species of endemic highland species of North Asia. The Red Book of Khabarovsk Territory includes 37 species of vascular plants, 4 species of lichens and 1 representative of the kingdom of mushrooms.
Dynamic evolution and spatial differentiation of the allocation efficiency of Science and Technology Resources in the countries along the “Belt and Road”
Authors: Zhuang Y , Dong S , Liu Q , Xu S , Zhang H , Li F 
Published: November 2021

Abstract
Science and technology resources are the strategic resources for the development of today’s society and the basic conditions for improving the ability of independent innovation. For scientific and technological innovation, the optimal allocation of science and technology resources is crucial. For countries along the “Belt and Road”, the efficiency of the allocation of science and technology resources has become the key to the development of innovative international construction. Therefore, this study takes the countries along the “Belt and Road” as the research area, and takes the period of rapid development of science and technology resources from 2005 to 2018 as the research period, comprehensively using the DEA-SBM model and ArcGIS spatial analysis methods to deeply analyze the allocation of science and technology resources in the countries along the “Belt and Road”. The long-term dynamic evolution law and spatial differentiation pattern of efficiency. The research methods and conclusions can provide useful reference for the efficient allocation of the international science and technology resources along the “Belt and Road” and realization of the “the innovative Belt and Road”.
Surface modification of recycled coir fibers with hybrid coating and its effect on the properties of ABS composites
Authors: Cai Jiafeng , Li Qiuying , Wu Chifei 
Published: November 2021

Abstract
In this work, a hybrid coating (TSMA) was produced using tetraethyl orthosilicate (TEOS)/KH550/Styrene maleic anhydride copolymer (SMA) as raw materials. The coating was afterwards applied to modify recycled coir (r-coir) fibers via dip-coating. R-coir fibers reinforced ABS composites were then prepared and the reinforcing effect of fibers on the composite structure was investigated, as well. The r-coir fibers coated with TSMA were hydrolyzed in air for 3 days. The SiO2 particles produced by sol-gel reaction of TEOS were used to connect KH550 and SMA to the surface of the fibers and form an organic-inorganic ‘armor’ structure. The successful surface modification of the r-coir fibers was proved via FTIR spectroscopic study and the improvement of their decomposition temperature was evidenced by TGA. Furthermore, the homogeneous dispersion of TSMA on the surface of r-coir fibers was observed via SEM. In addition, the tensile strength of single fibers was found to increase by 36.1%. According to the results, TSMA can be successfully homogenized on the fiber surface, enabling one to repair the damaged areas and improve the tensile strength of single fibers. Besides, good compatibility between r-coir fibers and ABS was revealed by contact angle measurements. Furthermore, the bending strength and elastic modulus of TSMA-modified r-coir fibers/ABS composites were improved by 6% and 27%, respectively. Therefore, the method of plant fiber modification proposed in present work provides a reliable way for effective reuse of r-coir fibers.
Preparation of electrospun nanofiber membrane for air filtration and process optimization based on BP neural network
Authors: Kang Le , Liu Yuankun , Wang Liping , Gao Xiaoping 
Published: November 2021

Abstract
The filtration layer in a medical protective mask can effectively prevent aerosol particles that might carry viruses from air. A nanofiber/microfiber composite membrane (NMCM) was successfully fabricated by electrospinning polyvinylidene fluoride (PVDF) nanofibers collected on the electrified and melt-blown polypropylene (PP) nonwovens, aiming to improve the filtration efficiency and reduce the resistance of respiration of mask. A four-factor and three-level orthogonal experiment was designed to study the effect of electrospinning parameters such as spinning solution concentration, voltage, tip-collect distance (TCD), and flow rate of solution on the filtration efficiency, resistance of respiration as well as quality factor of NMC developed to predict the resistance of respiration. Experimental results demonstrated that the filtration efficiency of NMCM ≥ 95% in comparison to that of electrified and melt-blown PP nonwovens 79.38%, which increases by 19.68%. Additionally, the average resistance of respiration is 94.78 Pa, which meets the protection requirements. Multivariate analysis of variance indicated that the resistance of respiration of the NMCM has significantly dependent on the concentration, voltage, TCD, and flow rate of the spinning solution and the quality factor of the NMCM has dependent on the resistance of respiration. The air permeability ranges from 166.23 to 314.35 mm s−1, which is inversely proportional to the filtration resistance. As far as the filtration resistance is concerned, the optimal spinning parameters were obtained as follows. The concentration of spinning solution is 15%, the voltage is 27 kV, the TCD is 22 cm, and the flow rate is 2.5 ml h−1. The relative error of the BP neural network varies from 0.49505% to 1.49217%, i.e. the error value varies from 0.17 to1.33 Pa. The predicted resistance of respiration corresponding to the optimal process is 68.1374 Pa.
Evidence for morph-specific substrate choice in a green-brown polymorphic grasshopper
Authors: Heinze Pauline , Dieker Petra , Rowland Hannah M , Schielzeth Holger 
Published: November 2021

Abstract
Orthopteran insects are characterized by high variability in body coloration, in particular featuring a widespread green-brown color polymorphism. The mechanisms that contribute to the maintenance of this apparently balanced polymorphism are not yet understood. To investigate whether morph-dependent microhabitat choice might contribute to the continued coexistence of multiple morphs, we studied substrate choice in the meadow grasshopper Pseudochorthippus parallelus. The meadow grasshopper occurs in multiple discrete, genetically determined color morphs that range from uniform brown to uniform green. We tested whether three common morphs preferentially choose differently colored backgrounds in an experimental arena. We found that a preference for green backgrounds was most pronounced in uniform green morphs. If differential choices improve morph-specific performance in natural habitats via crypsis and/or thermoregulatory benefits, they could help to equalize fitness differences among color morphs and potentially produce frequency-dependent microhabitat competition, though difference appear too small to serve as the only explanation. We also measured the reflectance of the grasshoppers and backgrounds and used visual modeling to quantify the detectability of the different morphs to a range of potential predators. Multiple potential predators, including birds and spiders, are predicted to distinguish between morphs chromatically, while other species, possibly including grasshoppers themselves, will perceive only differences in brightness. Our study provides the first evidence that morph-specific microhabitat choice might be relevant to the maintenance of the green-brown polymorphisms in grasshoppers and shows that visual distinctness of color morphs varies between perceivers.
PheneBank: a literature-based database of phenotypes
Authors: Pilehvar Mohammad Taher , Bernard Adam , Smedley Damian , Collier Nigel 
Published: November 2021

Abstract

Motivation
Significant effort has been spent by curators to create coding systems for phenotypes such as the Human Phenotype Ontology, as well as disease–phenotype annotations. We aim to support the discovery of literature-based phenotypes and integrate them into the knowledge discovery process.

Results
PheneBank is a Web-portal for retrieving human phenotype–disease associations that have been text-mined from the whole of Medline. Our approach exploits state-of-the-art machine learning for concept identification by utilizing an expert annotated rare disease corpus from the PMC Text Mining subset. Evaluation of the system for entities is conducted on a gold-standard corpus of rare disease sentences and for associations against the Monarch initiative data.

Availability and implementation
The PheneBank Web-portal freely available at http://www.phenebank.org. Annotated Medline data is available from Zenodo at DOI: 10.5281/zenodo.1408800. Semantic annotation software is freely available for non-commercial use at GitHub: https://github.com/pilehvar/phenebank.

Supplementary information
Supplementary data are available at Bioinformatics online.
A comparison of rule-based and centroid single-sample multiclass predictors for transcriptomic classification
Authors: Eriksson Pontus , Marzouka Nour-al-dain , Sjödahl Gottfrid , Bernardo Carina , Liedberg Fredrik , Höglund Mattias 
Published: November 2021

Abstract

Motivation
Gene expression-based multiclass prediction, such as tumor subtyping, is a non-trivial bioinformatic problem. Most classifier methods operate by comparing expression levels relative to other samples. Methods that base predictions on the expression pattern within a sample have been proposed as an alternative. As these methods are invariant to the cohort composition and can be applied to a sample in isolation, they can collectively be termed single sample predictors (SSP). Such predictors could potentially be used for preprocessing-free classification of new samples and be built to function across different expression platforms where proper batch and dataset normalization is challenging. Here, we evaluate the behavior of several multiclass SSPs based on binary gene-pair rules (k-Top Scoring Pairs, Absolute Intrinsic Molecular Subtyping and a new Random Forest approach) and compare them to centroids built with centered or raw expression values, with the criteria that an optimal predictor should have high accuracy, overcome differences in tumor purity, be robust across expression platforms and provide an informative prediction output score.

Results
We found that gene-pair-based SSPs showed excellent performance on many expression-based classification tasks. The three methods differed in prediction score output, handling of tied scores and behavior in low purity samples. The k-Top Scoring Pairs and Random Forest approach both achieved high classification accuracy while providing an informative prediction score. Although gene-pair-based SSPs have been touted as being cross-platform compatible (through training on mixed platform data), out-of-the-box compatibility with a new dataset remains a potential issue that warrants cohort-to-cohort verification.

Availability and implementation
Our R package ‘multiclassPairs’ (https://cran.r-project.org/package=multiclassPairs) (https://doi.org/10.1093/bioinformatics/btab088) is freely available and enables easy training, prediction, and visualization using the gene-pair rule-based Random Forest SSP method and provides additional multiclass functionalities to the switchBox k-Top-Scoring Pairs package.

Supplementary information
Supplementary data are available at Bioinformatics online.
Vernal: a tool for mining fuzzy network motifs in RNA
Authors: Oliver Carlos , Mallet Vincent , Philippopoulos Pericles , Hamilton William L , Waldispühl Jérôme 
Published: November 2021

Abstract

Motivation
RNA 3D motifs are recurrent substructures, modeled as networks of base pair interactions, which are crucial for understanding structure–function relationships. The task of automatically identifying such motifs is computationally hard, and remains a key challenge in the field of RNA structural biology and network analysis. State-of-the-art methods solve special cases of the motif problem by constraining the structural variability in occurrences of a motif, and narrowing the substructure search space.

Results
Here, we relax these constraints by posing the motif finding problem as a graph representation learning and clustering task. This framing takes advantage of the continuous nature of graph representations to model the flexibility and variability of RNA motifs in an efficient manner. We propose a set of node similarity functions, clustering methods and motif construction algorithms to recover flexible RNA motifs. Our tool, Vernal can be easily customized by users to desired levels of motif flexibility, abundance and size. We show that Vernal is able to retrieve and expand known classes of motifs, as well as to propose novel motifs.

Availability and implementation
The source code, data and a webserver are available at vernal.cs.mcgill.ca. We also provide a flexible interface and a user-friendly webserver to browse and download our results.

Supplementary information
Supplementary data are available at Bioinformatics online.
DD-GUI: a graphical user interface for deep learning-accelerated virtual screening of large chemical libraries (Deep Docking)
Authors: Yaacoub Jean Charle , Gleave James , Gentile Francesco , Stern Abraham , Cherkasov Artem 
Published: November 2021

Abstract

Summary
Deep learning (DL) can significantly accelerate virtual screening of ultra-large chemical libraries, enabling the evaluation of billions of compounds at a fraction of the computational cost and time required by conventional docking. Here, we introduce DD-GUI, the graphical user interface for such DL approach we have previously developed, termed Deep Docking (DD). The DD-GUI allows for quick setups of large-scale virtual screens in an intuitive way, and provides convenient tools to track the progress and analyze the outcomes of a drug discovery project.

Availability and implementation
DD-GUI is freely available with an MIT license on GitHub at https://github.com/jamesgleave/DeepDockingGUI.

Supplementary information
Supplementary data are available at Bioinformatics online.