bluuebunny/crossref_metadata_2025_split huggingface dataset:
Public danger and mechanisms for preventing damage to land
Authors: Provodina E V , Krasovskaya O Yu , Zhelokov N V , Komissarenko E S , Baranova M A 
Published: April 2021

Abstract
Deterioration of the quality of the environment, including its natural component - land, is becoming stable in modern conditions. Within the framework of this study, the need to form preventive mechanisms for damage to land is substantiated based on the content of its social danger. However, for full-fledged mechanisms that are really capable of realizing soil protection, the assessment of public danger should be carried out based on the actual data of the harm caused, while relying on indicators of environmental pollution of soils, necessarily taking into account the sphere of human activity that they are produced by. Thus, the results of the study showed that the greatest anthropogenic impact on the soil is exerted by industrial facilities, the harmful effect of which has no opposition from the imperative mechanisms of prevention. The elimination of this gap and the development of appropriate mechanisms for protecting the land, its properties and qualities in connection with the functioning of the industry can bring the system of prevention of such acts to a new, higher level.
Genetic classification of lakes of above floodplain terraces of the valley of Oka river in the Nizhniy Novgorod region (Russia), based on its morphometric characteristics
Authors: Astashin A E , Badin M M , Pashkin M N , Cheburkov D F , Samoilov A V 
Published: April 2021

Abstract
The article provides a brief overview of the history of researching of the lakes of the Nizhny Novgorod region. The research area is located in the west of the Nizhny Novgorod region, and characterized by extremely poor knowledge of the main characteristics, origin and development of lakes. The exploration of morphometric and hydrological characteristics of lakes is solved by instrumental measurements in the field. Consideration of the genesis and evolution of lakes is a more complex issue, and its solution without taking into account the landscape structure of the territory and the specifics of the geological structure, geomorphological, botanical and other characteristics of the host landscape cannot be accepted as a complete logical work. In this article, along with the morphometric and hydrological features of the researched lakes, the modern physico-geographical characteristics of the researched territory are presented, based on the results of the analysis of thematic maps, remote sensing data, statistical and literary data and field researches. Bathygraphic schemes of seven largest and most typical lakes, located on the terraces above the floodplain of the Oka River Valley within the Nizhny Novgorod Region, created, based on the results of field research, are presented. The main morphometric and hydrological characteristics of the researched lakes were calculated and analyzed using GIS. On the basis of morphometric characteristics and taking into account the features of the geological structure, topography, hydrographic network of the territory and vegetation features of the superaqual complex, judgments are made about the genesis of the considered lakes.
Extraction-membrane technology for processing oil-based mud
Authors: Blanco-Pedrekhon A M , Shibanov I V , Motuzenko N D , Kagramanov G G 
Published: April 2021

Abstract
The article presents the methods of waste oil-based mud (OBM) treatment by the combined extraction-membrane separation method. The efficiency of various solvents for the hydrocarbon base extraction from drill cuttings is considered and it is found that hexane is the most promising one. The estimation of operating costs for carrying out the OBM treatment using the organic solvent nanofiltration technology are of 0.6-0.84 $/l.
Development of a mathematical model of wind waves in the area of the proposed construction of a hydraulic structure
Authors: Istomin E , Martyn I , Petrov Y , Stepanov S , Sidorenko A 
Published: April 2021

Abstract
The article presents a non-stationary two-dimensional hydrostatic model of wave propagation in the water area of the port of the Bay of Five Hunters, protected by a coastal protection structure in the form of a breakwater. The work uses the methods of mathematical modeling in the Delphi development environment. The results obtained are presented in graphical form, where different wave heights and maximum wave amplitudes are displayed using a color palette. The consistency of the obtained calculations with physical laws is shown, the effectiveness of the construction of a coastal protection structure is analyzed.
Principles of system analysis for sustainable electric power supply to agro-industrial complexes operating in energy isolated territories
Authors: Arkhipova O V 
Published: April 2021

Abstract
The article considers application of principles of system analysis while solving the problems of sustainable electric power supply of agro-industrial complexes operating on energy-insulated territories. The involvement of renewable energy sources in electricity generation is substantiated. The term “regionally isolated electrotechnical complex” is introduced. The principles of the theory of system analysis with regard to a regionally isolated electrotechnical complex - were considered: emergence, optimality and equifinality. It is proposed, when solving the problems of sustainable supply of electricity to agro-industrial complexes operating in energy-isolated territories, to proceed from decomposition approaches to assessing the sustainability of development by integral indicator of levelized cost of electricity LCOER.
A Robust Test for Additive Gene-Environment Interaction Under the Trend Effect of Genotype Using an Empirical Bayes-Type Shrinkage Estimator
Authors: Sanyal Nilotpal , Napolioni Valerio , de Rochemonteix Matthieu , Belloy Michaël E , Caporaso Neil E , Landi Maria Teresa , Greicius Michael D , Chatterjee Nilanjan , Han Summer S 
Published: April 2021

AbstractEvaluating gene by environment (G × E) interaction under an additive risk model (i.e., additive interaction) has gained wider attention. Recently, statistical tests have been proposed for detecting additive interaction, utilizing an assumption on gene-environment (G-E) independence to boost power, that do not rely on restrictive genetic models such as dominant or recessive models. However, a major limitation of these methods is a sharp increase in type I error when this assumption is violated. Our goal was to develop a robust test for additive G × E interaction under the trend effect of genotype, applying an empirical Bayes-type shrinkage estimator of the relative excess risk due to interaction. The proposed method uses a set of constraints to impose the trend effect of genotype and builds an estimator that data-adaptively shrinks an estimator of relative excess risk due to interaction obtained under a general model for G-E dependence using a retrospective likelihood framework. Numerical study under varying levels of departures from G-E independence shows that the proposed method is robust against the violation of the independence assumption while providing an adequate balance between bias and efficiency compared with existing methods. We applied the proposed method to the genetic data of Alzheimer disease and lung cancer.
pDriver: a novel method for unravelling personalized coding and miRNA cancer drivers
Authors: Pham Vu V H , Liu Lin , Bracken Cameron P , Nguyen Thin , Goodall Gregory J , Li Jiuyong , Le Thuc D 
Published: April 2021

Abstract

Motivation
Unravelling cancer driver genes is important in cancer research. Although computational methods have been developed to identify cancer drivers, most of them detect cancer drivers at population level. However, two patients who have the same cancer type and receive the same treatment may have different outcomes because each patient has a different genome and their disease might be driven by different driver genes. Therefore new methods are being developed for discovering cancer drivers at individual level, but existing personalized methods only focus on coding drivers while microRNAs (miRNAs) have been shown to drive cancer progression as well. Thus, novel methods are required to discover both coding and miRNA cancer drivers at individual level.

Results
We propose the novel method, pDriver, to discover personalized cancer drivers. pDriver includes two stages: (i) constructing gene networks for each cancer patient and (ii) discovering cancer drivers for each patient based on the constructed gene networks. To demonstrate the effectiveness of pDriver, we have applied it to five TCGA cancer datasets and compared it with the state-of-the-art methods. The result indicates that pDriver is more effective than other methods. Furthermore, pDriver can also detect miRNA cancer drivers and most of them have been confirmed to be associated with cancer by literature. We further analyze the predicted personalized drivers for breast cancer patients and the result shows that they are significantly enriched in many GO processes and KEGG pathways involved in breast cancer.

Availability and implementation
pDriver is available at https://github.com/pvvhoang/pDriver.

Supplementary information
Supplementary data are available at Bioinformatics online.
DeepGraphGO: graph neural network for large-scale, multispecies protein function prediction
Authors: You Ronghui , Yao Shuwei , Mamitsuka Hiroshi , Zhu Shanfeng 
Published: April 2021

Abstract

Motivation
Automated function prediction (AFP) of proteins is a large-scale multi-label classification problem. Two limitations of most network-based methods for AFP are (i) a single model must be trained for each species and (ii) protein sequence information is totally ignored. These limitations cause weaker performance than sequence-based methods. Thus, the challenge is how to develop a powerful network-based method for AFP to overcome these limitations.

Results
We propose DeepGraphGO, an end-to-end, multispecies graph neural network-based method for AFP, which makes the most of both protein sequence and high-order protein network information. Our multispecies strategy allows one single model to be trained for all species, indicating a larger number of training samples than existing methods. Extensive experiments with a large-scale dataset show that DeepGraphGO outperforms a number of competing state-of-the-art methods significantly, including DeepGOPlus and three representative network-based methods: GeneMANIA, deepNF and clusDCA. We further confirm the effectiveness of our multispecies strategy and the advantage of DeepGraphGO over so-called difficult proteins. Finally, we integrate DeepGraphGO into the state-of-the-art ensemble method, NetGO, as a component and achieve a further performance improvement.

Availability and implementation
https://github.com/yourh/DeepGraphGO.

Supplementary information
Supplementary data are available at Bioinformatics online.
Predicting mechanism of action of novel compounds using compound structure and transcriptomic signature coembedding
Authors: Jang Gwanghoon , Park Sungjoon , Lee Sanghoon , Kim Sunkyu , Park Sejeong , Kang Jaewoo 
Published: April 2021

AbstractMotivationIdentifying mechanism of actions (MoA) of novel compounds is crucial in drug discovery. Careful understanding of MoA can avoid potential side effects of drug candidates. Efforts have been made to identify MoA using the transcriptomic signatures induced by compounds. However, these approaches fail to reveal MoAs in the absence of actual compound signatures.ResultsWe present MoAble, which predicts MoAs without requiring compound signatures. We train a deep learning-based coembedding model to map compound signatures and compound structure into the same embedding space. The model generates low-dimensional compound signature representation from the compound structures. To predict MoAs, pathway enrichment analysis is performed based on the connectivity between embedding vectors of compounds and those of genetic perturbation. Results show that MoAble is comparable to the methods that use actual compound signatures. We demonstrate that MoAble can be used to reveal MoAs of novel compounds without measuring compound signatures with the same prediction accuracy as that with measuring them.Availability and implementationMoAble is available at https://github.com/dmis-lab/moableSupplementary informationSupplementary data are available at Bioinformatics online.
MassExplorer: a computational tool for analyzing desorption electrospray ionization mass spectrometry data
Authors: Shankar Vishnu , Tibshirani Robert , Zare Richard N 
Published: April 2021

AbstractSummaryIn the last few years, desorption electrospray ionization mass spectrometry imaging (DESI-MSI) has been increasingly used for simultaneous detection of thousands of metabolites and lipids from human tissues and biofluids. To successfully find the most significant differences between two sets of DESI-MSI data (e.g., healthy vs disease) requires the application of accurate computational and statistical methods that can pre-process the data under various normalization settings and help identify these changes among thousands of detected metabolites. Here, we report MassExplorer, a novel computational tool, to help pre-process DESI-MSI data, visualize raw data, build predictive models using the statistical lasso approach to select for a sparse set of significant molecular changes, and interpret selected metabolites. This tool, which is available for both online and offline use, is flexible for both chemists and biologists and statisticians as it helps in visualizing structure of DESI-MSI data and in analyzing the statistically significant metabolites that are differentially expressed across both sample types. Based on the modules in MassExplorer, we expect it to be immediately useful for various biological and chemical applications in mass spectrometry.Availability and implementationMassExplorer is available as an online R-Shiny application or Mac OS X compatible standalone application. The application, sample performance, source code and corresponding guide can be found at: https://zarelab.com/research/massexplorer-a-tool-to-help-guide-analysis-of-mass-spectrometry-samples/.Supplementary informationSupplementary data are available at Bioinformatics online.
Phylogeography of the stoneflyKamimuria tibialis: multiple glacial refugia and sympatric occurrence of different lineages in the southern islands of Japan
Authors: Otsuki Akiko , Yoshizawa Kazunori , Akimoto Shin-Ichi 
Published: April 2021

AbstractTo elucidate the effect of Pleistocene climatic fluctuations on the historical distribution and geographical genetic structure of temperate Japanese species, we performed phylogeographical and demographic analyses using mitochondrial gene sequences obtained from the stonefly species Kamimuria tibialis, sampled from four main islands of the Japanese Archipelago (i.e. Hokkaido, Honshu, Shikoku and Kyushu) and Tsushima Island. We detected three main clades with distinct geographical distributions, including the Tsushima, Kyushu and Hokkaido–Honshu–Shikoku phylogroups. These groups were estimated to have diverged from one another 0.54–2.02 Mya, suggesting they have undergone several glacial cycles in different refugia. Our results showed that during the glacial epochs and with a fall in sea-level, gene flow was limited among Tsushima and Kyushu, and among Hokkaido and Honshu, probably because the straits between these islands are deep. The population in Kyushu and Shikoku, the southernmost islands, exhibited high genetic diversity, with two distinct haplotype lineages occurring sympatrically. These results suggest that the population division into multiple refugia and the existence of stable southern refugia have contributed to the high genetic diversity of the species in this region.
Dynamic iridescent signals of male copperwing damselflies coupled with wing-clapping displays: the perspective of different receivers
Authors: Cezário Rodrigo Roucourt , Lopez Vinicius Marques , Gorb Stanislav , Guillermo-Ferreira Rhainer 
Published: April 2021

AbstractDynamic signals are a widespread phenomenon in several taxa, usually associated with intraspecific communication. In contrast, dynamic iridescent signals are detectable only at specific angles of illumination; hence, the animal can hide the signal to avoid detection when necessary. This structural coloration is mostly dependent on the illumination, the contrast against the background and the vision of the receiver. Complex behavioural displays can be coupled with structural coloration to create dynamic visual signals that enhance these functions. Here, we address whether iridescence of the males of a damselfly that inhabits dark rainforests, Chalcopteryx scintillans, can be considered a dynamic visual signal. We analyse whether coloration is perceived by conspecifics, while reducing detectability to eavesdroppers against three types of backgrounds. Our results suggest that the visual background affects the detectability of male hindwings by different receivers, mostly predators and prey. We discuss whether these results and the angle dependence of colour could indicate a mechanism to avoid unwanted intraspecific interactions or even to lure both predators and prey. We conclude that the main functions of the dynamic iridescent signal are to communicate with conspecifics while hindering the signal for prey, adding evidence of the multifunctionality of structural coloration coupled with behavioural displays in animals.
Maternal and genetic correlations between morphology and physical performance traits in a small captive primate,Microcebus murinus
Authors: Zablocki-Thomas Pauline , Lailvaux Simon , Aujard Fabienne , Pouydebat Emmanuelle , Herrel Anthony 
Published: April 2021

AbstractPhysical performance traits are key components of fitness and direct targets of selection. Although maternal effects have important influences on integrated phenotypes, their contributions to variation in performance and to phenotypic traits associated with performance remain poorly understood. We used an animal model to quantify the contribution of maternal effects to performance trait variation, in addition to the genetic and maternal correlations between performance and the relevant underlying morphology in Microcebus murinus. We showed that bite force is heritable (h2 ≈ 0.23) and that maternal effects are an important source of variation, resulting in a medium inclusive heritability (IH2 ≈ 0.47). Bite force and head depth showed a significant genetic correlation (0.70), and other genetic correlations were generally high (0.63 for bite force and head width; 0.41 for pull strength and radius length, albeit not significant), as were the maternal correlations for bite force and head dimensions (0.44, 0.73 and 0.29). Finally, we found differences in evolvability for pull strength and bite force that were also consistent with a higher potential for evolutionary change in pull force. This demonstrates clear effects of the maternal environment on performance expression and on the relationships between morphology and performance. This illustrates the importance of accounting for maternal identity when considering the heritabilities of functional traits.
Police Union Political Communications in Canada
Authors: Duncan Jamie , Walby Kevin 
Published: April 2021

AbstractThe political communications of police unions in the digital age deserve more attention from criminologists. This article examines the communications of two Canadian police associations in Toronto and Winnipeg. Using multimodal discourse analysis, we describe how police unions tactically engage with multiple forms of media to disseminate strategic narratives that reflect police identity and ideology. We conceptualize the mobilization of ‘thin blue line’ narratives and maintenance of a ‘blue wall of silence’ as forms of boundary work, which serve to favourably delineate the role of police in their communities while sidestepping critical views. The proliferation of digital media amplifies the unions’ capacities to influence local politics by undermining elected authorities and community activists while advancing a police-centric view of society.
Gynostemium structure and development in subtribe Spiranthinae (Cranichideae, Orchidaceae)
Authors: Figueroa Coyolxauhqui , Terrazas Teresa , Dávila Patricia , Salazar Gerardo A 
Published: April 2021

AbstractWe analysed gynostemium development and morphology of 13 species of Spiranthinae to understand the structure and homology of this organ. Flowers and flower buds in different developmental stages were examined with scanning electron and light microscopy. Gynostemium ontogeny is similar in the early stages among the analysed species, and most of the differences arose at later developmental stages. Gynostemium development starts with the appearance of the anther primordium, followed by the median carpel and finally by the lateral carpel apices. The last emerges as two congenitally united, crescent-shaped prominences located between the median carpel apex and the labellum, eventually forming a rim of tissue on the proximal margin of the stigma. The rim can be receptive or not. The base of the median carpel apex contributes mostly to the receptive stigmatic zone and its apical region develops into the viscidium. The entrance of the stylar canal is located between the two partially non-receptive lateral carpel apices and the receptive base of the median carpel apex, refuting the idea that in Sarcoglottis it is located above the stigmatic area. There are no staminodal primordia, and the membranaceous appendages at each side of the column apex represent extensions of the clinandrium margins.
Human Immunodeficiency Virus Infection in Adolescents and Mode of Transmission in Southern Africa: A Multinational Analysis of Population-Based Survey Data
Authors: Low Andrea , Teasdale Chloe , Brown Kristin , Barradas Danielle T , Mugurungi Owen , Sachathep Karam , Nuwagaba-Biribonwoha Harriet , Birhanu Sehin , Banda Andrew , Frederix Koen , Payne Danielle , Radin Elizabeth , Wiesner Lubbe , Ginindza Choice , Philip Neena , Musuka Godfrey , Sithole Sakhile , Patel Hetal , Maile Limpho , Abrams Elaine J , Arpadi Stephen 
Published: April 2021

Abstract

Background
Adolescents aged 10–19 years living with human immunodeficiency virus (HIV) (ALHIV), both perinatally infected adolescents (APHIV) and behaviorally infected adolescents (ABHIV), are a growing population with distinct care needs. We characterized the epidemiology of HIV in adolescents included in Population-based HIV Impact Assessments (2015–2017) in Zimbabwe, Malawi, Zambia, Eswatini, and Lesotho.

Methods
Adolescents were tested for HIV using national rapid testing algorithms. Viral load (VL) suppression (VLS) was defined as VL &lt;1000 copies/mL, and undetectable VL (UVL) as VL &lt;50 copies/mL. Recent infection (within 6 months) was measured using a limiting antigen avidity assay, excluding adolescents with VLS or with detectable antiretrovirals (ARVs) in blood. To determine the most likely mode of infection, we used a risk algorithm incorporating recency, maternal HIV and vital status, history of sexual activity, and age at diagnosis.

Results
HIV prevalence ranged from 1.6% in Zambia to 4.8% in Eswatini. Of 707 ALHIV, 60.9% (95% confidence interval, 55.3%–66.6%) had HIV previously diagnosed, and 47.1% (41.9%–52.3%) had VLS. Our algorithm estimated that 72.6% of ALHIV (485 of 707) were APHIV, with HIV diagnosed previously in 69.5% of APHIV and 39.4% of ABHIV, and with 65.3% of APHIV and 33.5% of ABHIV receiving ARV treatment. Only 67.2% of APHIV and 60.5% of ABHIV receiving ARVs had UVL.

Conclusions
These findings suggest that two-thirds of ALHIV were perinatally infected, with many unaware of their status. The low prevalence of VLS and UVL in those receiving treatment raises concerns around treatment effectiveness. Expansion of opportunities for HIV diagnoses and the optimization of treatment are imperative.