bluuebunny/crossref_metadata_2025 huggingface dataset:
Reafirmation of archipelagic state principle through the establishment of archipelagic region law in Indonesia
Authors: Abdulajid S , Tauda G A , Achmad M J
Published: November 2021

Archipelagic regions characterized by vast ocean area and groups of small islands are dominant factor in affirming the identity of the Republic of Indonesia as an archipelagic state. However, it has not been sufficiently accommodated in Indonesian national legislation. The principle of an archipelagic state should be adopted mutatis-mutandis to be formulated in the management of autonomous regions, not only in Law Number 23 of 2014 concerning Regional Government which is lex generalis in nature, but also in the specificity of the administration of regional governance in archipelagic regions which is lex specialis. The “Principle of Archipelagic State” needs to be implemented into “Principle of Archipelagic Region” for regions with archipelagic characteristics. In this context, an Archipelagic Regional Law is very much needed to reinforce the identity of the Republic of Indonesia as an archipelagic country, and to overcome extraordinary development disparities between eastern Indonesia dominated by islands regions and western Indonesia dominated by large islands.
The role of fishery supervisors and community participation to ensure the sustainable fisheries in Indonesia’s Exclusive Economic Zone
Authors: Maskun  , Assidiq H , Bachril S N , Al-Mukarramah N
Published: November 2021

Indonesia has ratified the United Convention Law of the Sea of 1982 with the Law No. 17 of 1985 concerning the Ratification of United Nations Convention on The Law of the Sea 1982. It means that Indonesia has the right to use, conserve, and manage fish resources in the Indonesia’s Exclusive Economic Zone (IEEZ). To guarantee the optimal and sustainable management of Indonesian fish resources, the role of fishery supervisors and community participation in an efficient and effective manner is needed. Law enforcement in the field of fisheries is very important and strategic to support fishery development in accordance with the principle of fishery management, so that the sustainable development of fisheries can be done continuously. Therefore, the existence of legal certainty is absolutely necessary to support fishery management in Indonesia.
Protection of the rights of indigenous people in the archipelagic province in planning on management of coastal areas and small islands post of Law Number 11 of 2020 concerning job creation
Authors: Sinay S B , Nurjaya I N , Koeswahyono I , Safaat M A
Published: November 2021

The inconsistency of the state’s commitment to the protection of the archipelago’s indigenous people in the management of coastal areas and small islands has become more apparent since the passage of Law Number 11 of 2020 concerning Job Creation. This research is normative legal research that analyzes the synchronization of legislation relating to the management of coastal resources and small islands that are responsive to the protection of indigenous people. The results show that (1) Recognition of indigenous people according to the Job Creation Law is placed on government legal politics in accordance with the provisions of the applicable legislation, showing the incompleteness of norms, which has implications for the weak position of indigenous people in managing coastal resources without recognition/determination as legal subjects. (2) Indigenous people who have received recognition/determination from the local government have the privilege of including the management area as part of the RZ WP3K and managing coastal resources and small islands in accordance with customary law, as long as it does not conflict with the applicable laws. As a result, the research’s recommendations are as follows: (1) Policy advocacy, encouraging acceleration of the legislative process for the Draft Law on Indigenous People and the Draft Law on Archipelagic Regions; and (2) Empowerment, support for capacity building of indigenous people to be critical and innovative in sustainable coastal and small island management through community development.
Calculation of design brackish water reverse osmosis and Its financial analysis at Pamekasan coastal area
Authors: Mahabror D , Zulkarnain R , Waryanto
Published: November 2021

The minimal availability of fresh water during the dry season seems to be a classic problem that occurs in Pamekasan Regency. Based on data from the Regional Disaster Management Agency (BPBD) of the Pamekasan Regency Government, it shows that the drought that occurred in Pamekasan in 2019 was 325 hamlets in 82 well-known villages in 11 sub-districts. This data shows that most of the coastal areas in Pamekasan Regency are still experiencing a fresh water crisis. Therefore, alternative water treatment is needed to help provide fresh water in this area. Desalination is an important technology for coastal areas far from fresh water sources. The main objective of this study is to create a mini design for reverse osmosis desalination (RO) production in coastal areas to supply fresh water at the hamlet scale. The RO design for fresh water production of 5 m3/day is compact with brackish water well as raw material which has a TDS ranging from 5,000-10,000 ppm. In addition, this study also analyzes the economics of small-scale desalination based on the Revenue Cost Ratio (RC Ratio) with an RC Ratio value of 5.03, a Payback Period value of 0.17 years (2 months), and a production Break Event Point (BEP). Amounting to 149,007 liters (7843 gallons) and a BEP price of IDR 79.47/liter, the small-scale desalination business is declared profitable and feasible to be realized.
Toxic element distribution analysis in tailing technozems of the lead-zinc deposits in Eastern Transbaikalia
Authors: Abramov B N , Tsyrenov T G
Published: November 2021

An analysis of chemical element distribution in technozems of tailing dumps of the lead-zinc deposits of Eastern Transbaikalia is carried out. The potential toxicity of tailing mine technozems was calculated. A comparative analysis of the toxic element concentrations in the technozems of the lead-zinc deposit tailing dumps has revealed significant differences in the concentrations of toxic elements. It was found that the highest concentrations of toxic elements of the first class of hazard (As, Pb, Zn, and Cd) are characterized by the technozems of the Blagodatsky Deposit, while the lowest concentrations by those of the Khapcheranginsky Deposit. It has been established that the greatest ecological hazard is posed by the tailing dump of the Blagodatsky lead-zinc deposit, whereas a significantly smaller one by tailing dumps of the Khapcheranginsky and Novo-Shirokinsky deposits.
Formation of indicators of sustainable development for the resource region: the Amur ecoregion
Authors: Antonova N E , Lomakina N V
Published: November 2021

The article discusses the formation and practical use of indicators for assessing the sustainability of development at the regional level. Using the example of the Amur ecoregion, we study the dynamics of some economic, social and environmental indicators in 2013-2019, their compliance with the objectives of the state policy for the accelerated development of the Far Eastern Federal District. It is shown that the result of the action of preferential regimes was the growth of resource industries in the structure of the economy of the Amur ecoregion. A certain decrease in the parameters of sustainability according to social indicators was revealed with positive dynamics of economic and relative stability of environmental indicators in the Amur ecoregion. The relevance and scientific significance of the development of methodological and methodological support for assessing socio-ecological-economic sustainability and the formation of its indicators for the regional level was confirmed.
Land use analysis of Lake Khanka basin using remote sensing data
Authors: Yu Bazarov K , Egidarev E G , Mishina N V
Published: November 2021

The paper presents results of the analysis of the land use map compiled for transboundary Lake Khanka Basin using remote sensing data and geoinformation systems. The map reflects the distribution of 12 land categories in Lake Khanka basin in 2017 (arable land, abandoned arable land, paddy field, abandoned paddy field, shrubs and sparse growth, forest land, open pit, settlements, meadows and pastures, wet meadows and marshes, water bodies, forest cuttings and fire sites). The data of land use structure in the whole Lake’s watershed, in its Russian and Chinese parts are given. Data on the distribution of different land categories in the administrative territories of the rank of districts (Russia) and counties (China) are also presented. The analysis of land use structure showed that about 50 % of the Chinese part of the basin is covered by anthropogenically transformed natural complexes. The share of such lands in the territory of Russia amounts to 28 %. Agriculture is the most important factor in the change of natural complexes in Lake Khanka basin. Before early 1990s, the area of farmland had increased in the basin on both sides of the border, after that there was a significant reduction in cultivated lands, which had lasted for 10 years in the territory of China and for 20 years in Russia. Over the past decade, the area of cultivated areas in the basin and adjacent territories has extended again, which indicates an increase of anthropogenic impact and requires serious attention to monitoring of the ecological state of lands in the basin.
Biodiversity of a small water body during the initial filling phase (the Amazar River of the Amur River Basin, Russia)
Authors: Bazarova B B , Kuklin A P , Mikheev I E , Yu Afonina E , Tashlykova N A , Mataphonov P V , Ts Tsybekmitova G
Published: November 2021

In 2017, for the purposes of the Pulp and Saw Mill (PSM) “Polyarnaya”, the spillover dam was constructed on the Amazar River, a left tributary of the Amur River. Upon completion of the dam construction, the waters of the river formed a small river reservoir PSM “Polyarnaya”. This work covers findings on components and quantities of the newly formed reservoir at its initial stage and the data on biodiversity of its feeding flows. At this stage, the species composition of the flora and fauna in the reservoir falls in between the lacustrine and the riverine ones. The riverine conditions are observed in the upstream area of the reservoir; the middle area bears an intermediate status; while the limnetic zone near the dam features transformation of the river system into a lake-like running-water ecosystem. Seasonally, in the period from spring to autumn, phytoplankton showed a decreasing trend of the quantitative values; whereas the total abundance and biomass of zooplankton were increasing; zoobenthos featured lack of trends; macrophytes contents were different from season to season being abundant in the Amazar River near the urban settlement in spring and in the Amazar River downstream from the dam in autumn. Consequently, the initial stage of the formation of the reservoir is rather similar to original watercourses in the physical and chemical parameters and in the composition of flora and fauna as well.
Impact of fires on eutrophication in rivers (the Simmy River, the Bolon Nature Reserve)
Authors: Kharitonova G V , Ostrouhov A V , Tyugai Z , Krutikova V O
Published: November 2021

Compared to research on eutrophication in lakes, our understanding of eutrophication in rivers remains extremely limited. This is especially true of the impact of fires, which have become much more frequent in recent decades. Since the risks of eutrophication in rivers as a result of fires increase, it is important to timely assess the impact of fires on the state of rivers draining fire-prone territories. The aim of the study is to select and evaluate the reliability of criteria for impact of fires on eutrophication in stream on the example of the Simmi River (Bolon Nature Reserve, Far East, Russia). The tasks of the work are to assess the fire-prone of the territory from remote sensing data and and to identify markers of the impact of fires on the Simmi River. The fire-prone of the river watershed was estimated by the fire repeatability. The in situ study dealt with river bottom sediments. The sampling was carried out in in three month and the third year after the fire. To assess the impact of fires on eutrophication in the Simmi River, we used the P content in bottom sediments as a marker of the nutrient loading. The obtained results indicate high fire-prone and repeatability of fires the river watershed. In the first months after the fire, the response of the river system is the sequestration of P soluble compounds as a result of the binding of phosphate ions to vivianite. Vivianite is formed on the surface of clay microaggregates, which are removed by the stream over time. In three years after fire, vivianite-clay microaggregates were not detected. Flushing in flow system tends to reduce the scale of the fire impact.
Pollution and biodiversity: a case study of the Argun River Basin
Authors: Kuklin A P , Ts Tsybekmitova G
Published: November 2021

We analyzed the studies on the hydrochemical composition in the Argun basin and evaluated the level of pollution. We found that the water of the Argun River was contaminated by organic substances and toxic elements. We distinguished 9 major types of the ecosystems based on the prior findings. The prevalent species of Cladophora fracta was chosen as an indicator for the monitoring of the Argun drainage basin pollution by toxic elements. The concentrations of toxic elements in algae remained unchanged for a long term and they appeared to be more informative for the assessment of pollution than the rapidly changing water quality. It is necessary to determine indicator hydrobionts for each type of the ecosystems within such a vast territory as the Argun basin. Our findings showed that current mining production produces a negative ecological impact on the quality of the water ecosystems which should be considered during further developments. It is necessary to conduct a research on the regional background concentrations for toxic elements in water and hydrobionts, and to enlarge the list of indicator hydrobionts for water quality assessment.
Interaction of fresh and submarine saline groundwater in the coastal zone of the Sea of Okhotsk and the Sea of Japan
Authors: Kulakov V V
Published: November 2021

The multidirectional interaction of fresh groundwater of land with a mineralization of 0.1 - 0.2 g/dm3 and submarine saline groundwater in the coastal zone of the western coast of the Sea of Okhotsk and the Sea of Japan has been characterized. The main hydrochemical background in the coastal zone of the seas is created by ultra-fresh and fresh hydrocarbonate groundwater of land in the free gravity runoff zone. The main types of submarine groundwater are silt sediment waters, pore-stratal and fissure-stratal waters of sedimentary rocks, fissure and fissure-vein waters of effusive, metamorphic and intrusive rocks. With the salinity of the modern sea waters within the range of 30-34.4 g/dm3, a decrease is traced from 27-30 g/dm3 in the sediments of the Upper Miocene-Holocene aquifer complex to 14-20 g/dm3 in the sediments of the Oligocene-Lower Miocene complex. Fresh groundwater of volcanogenic hydrogeological basins, the deposits of which have been explored in basalts, are distinguished by special advantages. These waters do not have environmental restrictions for drinking, they belong to the highest class and their resources may well be involved for a worthy use within the region and beyond.
Forecasting of hazardous marine hydrometeorological phenomena for the regions of oil and gas deposit development on the Sea of Okhotsk Shelf
Authors: Lyubitskiy Yu V , Vrazhkin A N , Kharlamov P O
Published: November 2021

A brief description of the marine hazard forecast methods and technology for the Sea of Okhotsk developed in the Federal State Budgetary Institution “ Far Eastern Regional Hydrometeorological Research Institute (FERHRI)” is presented. These methods and technology provide numerical prognostic products for the following parameters: wave height, period and direction; sea ice concentration, thickness, drift and compression; sea level and storm surges. The successful cases of practical applications of these forecasts demonstrate the effectiveness of the developed forecast methods and technology.
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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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.
Modeling dependency structures in 450k DNA methylation data
Authors: Nustad Haakon E , Steinsland Ingelin , Ollikainen Miina , Cazaly Emma , Kaprio Jaakko , Benjamini Yuval , Gervin Kristina , Lyle Robert
Published: November 2021

Motivation

DNA methylation has been shown to be spatially dependent across chromosomes. Previous studies have focused on the influence of genomic context on the dependency structure, while not considering differences in dependency structure between individuals.

Results

We modeled spatial dependency with a flexible framework to quantify the dependency structure, focusing on inter-individual differences by exploring the association between dependency parameters and technical and biological variables. The model was applied to a subset of the Finnish Twin Cohort study (N = 1611 individuals). The estimates of the dependency parameters varied considerably across individuals, but were generally consistent across chromosomes within individuals. The variation in dependency parameters was associated with bisulfite conversion plate, zygosity, sex and age. The age differences presumably reflect accumulated environmental exposures and/or accumulated small methylation differences caused by stochastic mitotic events, establishing recognizable, individual patterns more strongly seen in older individuals.

Availability and implementation

The twin dataset used in the current study are located in the Biobank of the National Institute for Health and Welfare, Finland. All the biobanked data are publicly available for use by qualified researchers following a standardized application procedure (https://thl.fi/en/web/thl-biobank/for-researchers). A R-script for fitting the dependency structure to publicly available DNA methylation data with the software used in this article is provided in supplementary data.

Supplementary information

Supplementary data are available at Bioinformatics online.
Co-administration of platelet-rich plasma and small intestinal submucosa is more beneficial than their individual use in promoting acute skin wound healing
Authors: Lei Xiaoxuan , Cheng Liuhanghang , Yang Yu , Pang Mengru , Dong Yunqing , Zhu Xuanru , Chen Caihong , Yao Zexin , Wu Gang , Cheng Biao , Forouzanfar Tymour
Published: November 2021

Background

Acute skin wounds may compromise the skin barrier, posing a risk of infection. Small intestinal submucosa (SIS) is widely used to treat acute and chronic wounds. However, the efficacy of SIS to accelerate wound healing still needs to be improved to meet clinical demands. To tackle this problem, platelet-rich plasma (PRP) is used due to its potency to promote proliferation, migration and adhesion of target cells. In this study, we applied PRP and SIS to skin wounds to explore their effects on wound healing by evaluating re-epithelialization, collagen production, angiogenesis and the inflammatory response.

Methods

A 1 × 1-cm full-thickness skin defect was established in mice. Sixty mice were divided into four treatment groups: PRP + SIS, PRP, SIS and control. On days 3, 5, 7, 10 and 14 post-surgery, tissue specimens were harvested. Haematoxylin and eosin, Masson’s trichrome, immunohistochemical and immunofluorescence double staining were used to visualize epidermal thickness, collagen and vascular regeneration and inflammation.

Results

Wound contraction in the PRP and PRP + SIS groups was significantly greater, compared with the other groups, on days 3 and 5 post-surgery. A histological analysis showed higher collagen expression in the PRP and PRP + SIS groups on day 7, which was associated with a thicker epidermal layer on day 14. In addition, immunohistochemical staining showed that CD31-positive blood vessels and vascular endothelial growth factor expression in the PRP + SIS and PRP groups were significantly higher, compared with the control group. Furthermore, immunofluorescence double staining showed that the number of M1 and M2 macrophages in the PRP + SIS and PRP groups was higher, compared with the control and SIS groups alone, on day 3. However, on day 7, the number of M1 macrophages dramatically decreased in the PRP + SIS and PRP groups. The ratio of M2 to M1 macrophages in the PRP + SIS and PRP groups was 3.97 and 2.93 times that of the control group and 4.56 and 3.37 times that of the SIS group, respectively.

Conclusion

Co-administration of SIS and PRP has a better effect on promoting angiogenesis, re-epithelialization and collagen regeneration in managing acute wound healing than either agent alone.
The developmental changes in intrinsic and synaptic properties of prefrontal neurons enhance local network activity from the second to the third postnatal weeks in mice
Authors: Kalemaki Katerina , Velli Angeliki , Christodoulou Ourania , Denaxa Myrto , Karagogeos Domna , Sidiropoulou Kyriaki
Published: November 2021

The prefrontal cortex (PFC) is characterized by protracted maturation. The cellular mechanisms controlling the early development of prefrontal circuits are still largely unknown. Our study delineates the developmental cellular processes in the mouse medial PFC (mPFC) during the second and the third postnatal weeks and characterizes their contribution to the changes in network activity. We show that spontaneous inhibitory postsynaptic currents (sIPSC) are increased, whereas spontaneous excitatory postsynaptic currents (sEPSC) are reduced from the second to the third postnatal week. Drug application suggested that the increased sEPSC frequency in mPFC at postnatal day 10 (P10) is due to depolarizing γ-aminobutyric acid (GABA) type A receptor function. To further validate this, perforated patch-clamp recordings were obtained and the expression levels of K–Cl cotransporter 2 (KCC2) protein were examined. The reversal potential of IPSCs in response to current stimulation was significantly more depolarized at P10 than P20 while KCC2 expression is decreased. Moreover, the number of parvalbumin-expressing GABAergic interneurons increases and their intrinsic electrophysiological properties significantly mature in the mPFC from P10 to P20. Using computational modeling, we show that the developmental changes in synaptic and intrinsic properties of mPFC neurons contribute to the enhanced network activity in the juvenile compared with neonatal mPFC.
Spatial probability maps of the segments of the postcentral sulcus in the human brain
Authors: Zlatkina Veronika , Sprung-Much Trisanna , Petrides Michael
Published: November 2021

The postcentral sulcus is the posterior boundary of the postcentral gyrus where the somatosensory cortex is represented. In the human brain, the postcentral sulcus is composed of five distinct segments that are related to the somatosensory representation of different parts of the body. Segment 1 of the postcentral sulcus, located near the dorsomedial boundary of each hemisphere, is associated with toe/leg representations, segment 2 with arm/hand representations, segment 3 with blinking, and segments 4 and 5, which are near the lateral fissure and the parietal operculum, with the mouth and tongue representations. The variability in location and spatial extent of these five segments were quantified in 40 magnetic resonance imaging (MRI) anatomical brain scans registered to the stereotaxic space of the Montreal Neurological Institute (MNI space), in the form of volumetric (using MINC Toolkit) and surface (using FreeSurfer) spatial probability maps. These probability maps can be used by researchers and clinicians to improve the localization of the segments of the postcentral sulcus in MRI images of interest and also to improve the interpretation of the location of activation peaks generated in functional neuroimaging studies investigating somatosensory cortex.