bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic structure of the herd by genes GDF9, GH, CAST in merino sheep of the North Caucasus region of Russia
Authors: Shirokova N V , Kolosov A Yu , Kolosov Yu A , Getmantseva L V , Bakoev N F , Vorontsova E S , Kolosova N N
Published: March 2021

One of the main tasks in sheep breeding is to increase productivity. The use of DNA markers for the selection of animals containing the desired alleles of genes of economically valuable traits is one of the new scientific approaches to solving this problem. The aim of the work was to study the genetic structure of sheep of various breeds by genes GDF9, GH, CAST. The studies were carried out on the basis of the laboratory of molecular diagnostics and biotechnology of farm animals of the Don State Agrarian University and the Center for the collective use of scientific equipment “Bioresources and bioengineering of farm animals” of the All-Russian Scientific Research Institute of Animal Husbandry named after academician L.K. Ernst. To carry out molecular genetic studies, samples of ear pits (tissue from the auricle) with an area of 1 cm2 were taken from sheep. The evaluation was carried out by PCR-RFLP method. As a result of DNA genotyping for genes GDF9, GH, CAST, the genetic structure of sheep of such breeds as: Salskaya, Stavropol, Volgograd and Soviet merino was revealed. A and B allelic variants of the GDF9 gene, alleles A and B of the GH gene, alleles A and B of the CAST gene were identified in all studied groups of sheep. Analysis of the data revealed the breed aspect in the distribution of the allele and genotype frequencies of the GDF9, GH, CAST genes in the populations under consideration.
International joint research: current situation and challenges for the Japan-Russia collaboration in the field of agriculture
Authors: Lyude Anna , Boiarskii Boris , Hasegawa Hideo
Published: March 2021

International communication has sharply increased between educational and research institutions in the various sciences between Japan and Russia amidst globalization’s rapid progress. Niigata University has been deliberately increasing collaboration with counterparts in the Russian Far East in the field of agriculture. However, literature comprehending current trends and issues of the bilateral joint research is insufficient. It implies strategical evaluation of the existing projects’ efficiency and allocation of future collaboration tasks and funding. This study aimed to grasp the actual situation of Japan-Russia international joint research and its implications for agriculture. The authors used the Web of Science database aggregated by Clarivate Analytics to evaluate the general condition of research output and international joint research in both countries, fields of bilateral co-authorship, and Niigata university collaborative projects’ results in terms of publication output in agricultural sciences. Results demonstrated steady efforts to promote international joint research in both countries. However, in terms of the research field, the bilateral relations are strongly manifested in materials science and physics, where the co-authorship rate is high. Agricultural sciences remain insignificant in bilateral cooperation. The number of co-authored publications has slightly increased due to the projects run by the Niigata university from 2015, both in Russian student enrolment and joint research specializing in agriculture. Therefore, the present study concluded that further profound qualitative and quantitative research on factors fostering bilateral collaboration, including international students’ role, is needed.
Estimation and validation of stem volume equations for Pinus sibirica in Russia
Authors: Zavarzin V V , Lebedev A V , Gemonov A V
Published: March 2021

Stem volume models using diameter at breast height (DBH) and height were developed for Pinus sibirica. The data were obtained from Irkutsk Oblast (Eastern Siberia), Tyumen Oblast (Western Siberia) and Sverdlovsk Oblast (Ural). Logarithmic scale models that are widely used in forestry, which are often used to model stem volume and tree biomass, were slightly inferior to models using the response at the original scale. The obtained models can be used for forest inventory, and the proposed methodological approaches can be used for modeling the stem volume of other tree species.
Rice estate areas: a sociocultural and institutional model for lowland rice farming
Authors: Saleh A , Surahman M , Purwono  , Sugiyanta  , Hamzah  , Zamzami A , Desrial  , Wetik J D
Published: March 2021

The rice cultivation business is dominated by small farmers with average land ownership of less than one hectare. Consequently, all efforts that have been made were unable to improve the farmer’s welfare. The small land ownership is a problem in applying mechanization, technology adoption, and management efficiency. The consolidation of the agricultural system in the form of an agricultural, institutional model is essential to be developed to achieve farming efficiency, profit, and, in turn, and farmer’s welfare. An agro-socio-cultural and institutional model was designed to overcome problems faced by farmers. The study was conducted in Banjarnegara and Purbalingga Regencies, Central Java. The study applied FGD and survey methods. The results showed that most farmers’ age was 60 years, and their educational attainment was a primary school, owned less than 0.7 hectares of land size, low technology adoption rates, and yield of fewer than four tons/ha. The condition causes the farmers to get low income, with an amount of fewer than three million rupiahs/month. Sociocultural conditions, land potentials, institutions, access to capital, and product marketing were the basis for developing an institutional model of rice farming. An institutional model concept was offered in the form of management consolidation. Several farmers gathered in a joint venture called the Rice Estate Community (REC), with approximately 300 hectares. Management consolidation supported mechanization application, science and technology transfer, easier access for market access and capital for rice farming. The REC was a model delivering farming efficiency and prosperity to farmers.
Management strategy for household food security in Jambi Province
Authors: Suandi  , Napitupulu D M T , Damayanti Y , Effran E
Published: March 2021

This research was aimed to: (1) analyze household food security and (2) formulate a strategy managing household food security in Jambi Province, Indonesia. The research design was a cross-sectional and conducted in four selected districts in Jambi Province, mainly: Kerinci, Merangin, Muaro Jambi, and Tanjung Jabung Barat Districts. This research was done in six calendar months. The object of this research was farm households with research variables: (1) household food security and (2) strategies for managing household food security based on internal factors (aspects of strengths and weaknesses) and external factors (aspects of opportunities and threats). Data was collected using observation, direct interviews, in-depth interviews, Focus Group Discussion (FGD), and documentation methods. The number of respondents was 100 households at each district, which was chosen taken by cluster stratified simple random sampling in each sample district. The total sample was 400 households. Data were analyzed by using the SWOT approach. The results, of the analysis show that the population in Jambi Province is in the food secured level. Based on the SWOT analysis results Jambi Province household food security could be developed in an aggressive strategy.
Agronomic responses of several rice varieties on ratoon salibu system
Authors: Putera H R , Junaedi A , Wirnas D , Sakagami J
Published: March 2021

Salibu rice cultivation is one of the technological innovations to spur productivity or increase production. Salibu technology (modified ratoon) is a rice cultivation technology that utilizes rootstocks after harvest to produce shoots or tillers for nurturing. These shoots function as seeds in a transplanting system. Cutting treatment on the first generation of salibu crop started when the mother plant harvested at 132 days after sowing at 20 cm above the soil surface, and then re-cut seven days after harvest at 3-5 cm above the soil surface. Cutting treatment on the second generation of salibu crop started when the first generation of salibu crop harvested at 94 days. The results showed that the Batang Piaman variety has the best agronomic responses on the ratoon salibu system because the yield was 60% for the first generation of salibu and 62.5% for the second generation of salibu. Ketan Grendel variety the product was 70.5% for the first generation of salibu and 55% for the second generation of salibu.
Combinations of seaweed extract and NPK on vegetative growth of chili growing under glasshouse condition
Authors: Yusuf R , Syakur A , Awalni F , Kalaba Y
Published: March 2021

Chili (Capsicum frutescens L.) is one of the horticultural crops having many benefits, namely as a cooking spice and a mixture of the food industry. Chili plants need N, P, and K for growth, provided in the form of NPK fertilizer or Seaweed extract as organic fertilizer. This study aimed to determine the effect of various combinations of seaweed extracts and NPK on the vegetative growth of chili. The experiment was arranged based on a randomized complete block design with seven treatments and three replications, so 21 experimental pot was obtained. The treatment of the combination of seaweed extract and NPK fertilizer application was T1 = seaweed extract of Ulfa sp. 100 ml/pot, T2 = seaweed extract of Caulerpa sp. 100 ml/pot, T3 = seaweed extract of Sargassum sp. 100 ml/pot, T4 = 0.5 gNPK fertilizer/pot, T5 = Ulfa sp. 100 ml/pot and 0.5 NPK, T6 = Caulerpa sp 100 ml/pot and 0.5 NPK, T7 = Sargassum sp. 100 ml/pot and 0.5 NPK. The results showed that the T1 treatment produced better results compared to other treatments.
Effects of gibberellin (GA3) on the physical quality of oil palm fresh fruit bunches
Authors: Sudradjat  , Sugianta  , Siregar H A , Purwanto O D
Published: March 2021

Gibberellin (GA3) is known as a plant growth regulator that can stimulate the plant growth and develop the cell and widely used in maintaining the storability of some types of fruit. This research aimed to study the effects of gibberellin concentration, time of gibberellin application and the interaction of both on the physical quality of oil palm fresh fruit bunches. The experiment used a factorial of randomized complete block design with three replications. The first factor was the time of gibberellin application with two levels (pre-harvest and post-harvest), while the second factor was gibberellin concentration with five levels (0, 25, 50, 100 and 200 ppm). Post-harvest treatments of 25 ppm gibberellin reduced the respiration rate, fruit weight loss, number of fruit loss of bunches and mesocarp firmness. Application of gibberellin with concentration 25 ppm after harvesting was the best treatment to maintain the physical quality of fresh fruit bunches (FFB). Time of harvesting is one of the factors affecting the quality of palm oil. After harvesting, FFB should be processed at mill within a maximum of 24 hours because it will increase the content of free fatty acids (FFA) and reduce the content Crude Palm Oil.
Nano silica spray increase Phalaenopsis pulcherrima growth and resistance against Dickeya dadantii infection
Authors: Nisaq G J , Sudarsono S , Sukma D
Published: March 2021

Soft-rot disease because of Dickeya dadantii infection has hampered orchid production in the tropics. Induced resistance using nano-silica may be used to control the soft-rot disease. Nano-Si increases resistance by forming a silica layer on the plant epidermis. Nano-Si has a larger surface area. This study aims to determine the appropriate concentrations of silica to induce resistance to D. dadantii in Phal. pulcherrima. The experiment was set up in a single factor trial and various nano-Si concentrations (0, 7.5, 15, 22.5 and 30 ppm) with an application interval of 3 days for 120 days. The application volume was 4 mL per plant. Each treatment was repeated three times. Statistical analysis was done using ANOVA and mean comparison using LSD. After inoculation with D. dadantii, leaf of Phal. pulcherrima was observed for 48 HPI. The results showed that plant treatment with nano-Si at 30 ppm caused the slowest expansion of the soft-root symptom diameter compared to other concentrations. Si is a promising compound to increase Phal. pulcherrima growth and resistance against D. dadantii infection.
The influence of Mount Merapi eruption on the water balance in Kali Kuning sub-watershed
Authors: Sari J A K , Kusumandari A
Published: March 2021

The national park area has a function in conserving the water in the catchment area. This study aimed to compare the changes of the water balance before and after the eruption and to analyse the drought index. This study uses Thornwaite and Mather water balance analysis by calculating the amount of water input and output. The results showed that the water balance in the Kali Kuning sub-watershed was surplus in the wet months, namely January-April and November-December. Meanwhile, the deficit occurs during the dry months, namely May-October. The condition of the water balance in the Kali Kuning sub-watershed before and after the eruption changes but was not significant due to factors of land use, rainfall and temperature before and after the explosion did not change significantly. Before the outbreak (2006-2010), the drought index tended to decrease due to high rainfall every year, while after the explosion (2011-2019) it tended to increase due to changes in land use conditions. Mount Merapi eruption resulted some part of the forest in the Kali Kuning sub-watershed turned into open land.
Characteristic and quality microbiology solid soap citronella oil with the addition of Lactobacillus brevis
Authors: Pratama Y E , Jamsari  , Yuherman  , Melia S , Purwati E
Published: March 2021

Lactic acid bacteria have the potential as probiotic candidates, where probiotics provide many benefits for humans and animals. The use of probiotics in the formulation of fragrant Citronella oil (Citronella oil) soap is expected to kill the pathogen E. coli and S. aureus commonly found on the skin’s surface. This study aimed to determine the addition of lactic acid bacteria in the formulation of fragrant lemongrass soap. Besides, cow’s milk in the formulation aims as a prebiotic for probiotic bacteria during the saponification of solid soap. The method used was a randomized block design with five treatments (A = 0ml, B = 2ml, C = 4ml, D = 6ml and E = 5ml) with each of the four treatments. The addition of Lactobacillus brevis NRC0138 in the formulation of fragrant Citronella oil soap affects the soap’s pH value, moisture content, foam power, and antimicrobial activity. L. brevis can survive in an alkaline atmosphere with an initial pH of 14 and the saponification process for 14 days because strain-dependent to survive and adapt to environmental conditions.
Mining Influence Law’s Application in Coal Bed Gas Extraction Engineering
Authors: Hu Bingnan , Zhang Peng , Guo Wenyan
Published: March 2021

Aimed at further improve the efficiency of coal bed gas extraction, the coal bed gas extraction technology and temporal & spatial law of mining influence are elaborated in this paper. The characteristics of ground movement and deformation, the failure zones in overburden strata, the heights of caving zone and fracture zone in overburden strata, and failure scope in underlying strataare analyzed. According to coal bed gas extraction technology, the requirements of ground movement, deformation, and failure degree are ensured. Based on the laws of coal mining influence and failure in surrounding rock, the principle of coal bed gas extraction engineering design is put forward. It has certain reference value.
An Optimal Allocation Model of Sea Area Utilization Based on Factor Endowment
Authors: Kang Minjie
Published: March 2021

Factor endowment characteristics are important factors to be considered in Marine zoning and Marine spatial planning. How to allocate marine space resources is an important issue in Marine zoning and Marine spatial planning. In this paper, an optimal allocation model of sea area utilization is constructed based on factor endowment. According to the difference of factor endowment of different sea areas and the difference of factor structure of intensive use of different sea areas, the model realizes the division of sea area utilization among different sea areas which giving full play to the advantages of factor endowments of sea areas in various regions and improving the utilization efficiency of sea areas. It can provide theoretical reference for Marine zoning and Marine spatial planning.
Study on Suitable Water Resource Irrigation Rate of Tomato under Solar Greenhouse in Autumn
Authors: Mao Ke , Xiao Huaijuan , Li Juanqi , Du Qingjie , Tian Qiaoling , Wang Jiqing
Published: March 2021

The shortage of water resources is increasing worldwide. For saving water resources, the study of horticultural plant water saving irrigation technology has greatly ecological and social significance. In this experiment, tomato was used as the test material with drip irrigation technology. Under same fertilizer rate, three levels of irrigation water were set: High irrigation Water (HW), Medium Irrigation Water (MW) and Low Irrigation Water (LW). The effects of different Irrigation levels on growth, yield, water use efficiency and soil nutrient content were investigated. The results show that the plant height and the accumulation of soil nutrients declined while the yield and water use efficiency increased with the decrease of irrigation rate. The average plant height of LW tomato was significantly lower than that of HW. Compared with HW, tomato yield and water use efficiency under LW increased by 6.6% and 65.4%, respectively, and the average irrigation rate decreased by 55.21%. The accumulation of N, P and K under LW in the 40∼60cm soil layer was significantly lower than HW by 37.3%, 78.5% and 60.9%, respectively. LW has a positive effect on the increase of tomato yield and the reduction of nutrient leaching and accumulation.
Power Generation Simulation and Comparison of p-PERC and HIT Bifacial Modules
Authors: Jiang Yashuai , Zhuang Hao , Sun Guan , Huang Huoping
Published: March 2021

As p-PERC and HIT being the two representative high-efficiency cell technologies, the matched bifacial module solution has become an important means to reduce LCOE. This article emphasized on the effects of different installation environment on generated power based HIT and p-PERC bifacial modules in Beijing. The power generation of HIT and p-PERC bifacial modules are subject to the same changing trends in different installation environment. The change in power generation with tilt is similar to a parabola, and the optimal installation tilt varies from 25° to 35°. The power increases almost linearly with the height above the ground or the albedo. The HIT bifacial modules show more advantage in energy generation due to lower temperature coefficient and higher bifacility factor.
Calculation of Vacuum Pump Sucking Rate in Fishing Suction Equipment of Trawler
Authors: Shi Xiaomin , Jia Senjun
Published: March 2021

Sucking rate is an important parameter for the design of vacuum pump, in order to obtain the accurate sucking value. Above all, sucking process of vacuum-pump is analyzed in fishing suction equipment, and then by means of Boyle-Malot’s law, a new equation is deduced, and a new method is improved after analyzing calculation formulas about sucking rate of vacuum-pump at the present time, this paper provides basis for selecting and design vacuum-pump in fishing suction equipment. After using the new formula to calculate the sucking rate, the damage rate of fish is greatly reduced in fishing suction.
Improved Method of Local Feeder Automation Considering Small Hydro-power Connection
Authors: Li Kewen , Chen Qianyi , Ou Shifeng , Yan Lijuan , Chen Shaonan
Published: March 2021

With the access of small hydro-power stations (SHS), the distribution system presents a multiple power supply pattern, which has a negative impact on the original local feeder automation (LFA) which is suitable for single side power supply system. In view of this effect, the phase to phase short-circuit fault (PPF) and single-phase grounding fault (SPGF) are treated differently, and an improved LFA method (IMLFA) considering SHS’s access based on low-frequency load shedding (LFLS) and high-frequency generator tripping (HFGT) is proposed. In case of SPGF, the section switch (SSW) and the outgoing circuit breaker of the substation shall be opened in sequence, and the isolated network (IN) generated in the process can be operated stably by cooperating with LFLS or HFGT while the fault is preliminary isolated. The SSW and the breaker are added with the function of no-voltage detection and synchronization detection. In case of instantaneous fault, the power supply in the fault area can be restored after a series of operations, and the IN can be connected to the grid. If it is a permanent fault, the section switches (SSWs) around the fault area will be locked to close in order to isolate the fault effectively, and the IN, not separated by the fault area from the grid, can be connected to the grid. Analysis and simulation show that the method is correct and feasible.
Burst pulses for positive corona discharges in atmospheric air: the collective movement of charged species
Authors: PENG Yongkang , CHEN Xiaoyue , LAN Lei , ZHAN Haoyu , LIU Yongcong , HE Wangling , WEN Xishan
Published: March 2021

Positive corona burst pulses are an unstable pulse mode. They appear in a small range of the onset stage, and their current pulses result from the collective movement of charged species. This paper focused on the connections between these pulses and the collective movement of charged species. The movement of species is divided into four parts with respect to time: the (1) initial growth of species, (2) formation and development of the streamer region and negative ion sheath, (3) dead time (the time interval between the pulses), and (4) rapid re-growth of species. The movement of the species in the four parts and the correspondence with the current pulse were analyzed. The numerical results indicated the following: the rapid rising of the species matched the rising edge of the pulses, the streamer region, and negative ion sheath appeared in the falling edge of the primary pulse, and the rapid re-growth of species matched the re-ignition of the pulses. The results were in qualitative agreement with deductions and experimental observations in the literature.
Generating two-mode squeezing with multimode measurement-induced nonlinearity
Authors: Riabinin M , Sharapova P R , Bartley T J , Meier T
Published: March 2021

Measurement-induced nonclassical effects in a two-mode interferometer are investigated theoretically using numerical simulations and analytical results. We demonstrate that for certain parameters measurements within the interferometer lead to the occurrence of two-mode squeezing. The results strongly depend on the detection probability, the phase inside the interferometer, and the choice of the input states. The appropriate parameters for maximized squeezing are obtained. We analyze the influence of losses and confirm that the predicted effects are within reach of current experimental techniques.
Composite electrolytes based on electrospun PVDF and ionic plastic crystal matrices for Na-metal battery applications
Authors: Makhlooghiazad Faezeh , Nti Frederick , Sun Ju , Mendes Tiago Correia , Malunavar Sneha Subhas , Pringle Jennifer M , Forsyth Maria
Published: March 2021

Sodium ion batteries are widely considered to be a feasible, cost-effective, and sustainable energy storage alternative to Lithium, especially for large-scale energy storage applications. Next generation, safer electrolytes based on ionic liquid (IL) and organic ionic plastic crystals (OIPCs) have been demonstrated as electrochemically stable systems which show superior performance in both Li and Na applications. In particular, phosphonium‐based systems outperform most studied nitrogen‐based ILs and OIPCs. In this study triisobutyl(methyl)phosphonium bis(fluorosulfonyl)imide ([P1i444][FSI]) OIPC mixed with 20 mol% of NaFSI or NaTFSI were combined with an electrospun polyvinylidene fluoride (PVDF) support to create self-standing electrolyte membranes, and their thermal phase behaviour and ionic conductivity were investigated and compared with the bulk electrolytes. The ability of the solid-state composite electrolytes to support the cycling of sodium metal with good efficiency and without breakdown were examined in sodium metal symmetrical coin cells. The sodium transference number was determined to be 0.21. The electrochemical performance of Na/Na3V2(PO4)3 cells incorporating the composite electrolytes, including good cycling stability and rate capability, is also reported. Interestingly, the mixed anion systems appear to outperform the composite electrolyte containing only FSI anions, which may relate to electrolyte interactions with the PVDF fibres.
Optimizing geometry of low-Q all-metal Fabry-Pérot microcavity for fluorescence spectroscopy
Authors: Dutta Arpan , Tiainen Ville , Toppari J Jussi
Published: March 2021

Fluorescence spectroscopy is commonly employed to study the excited-state photophysics of organic molecules. Planar Fabry-Pérot microcavities play an essential role in such studies and a strategic cavity design is necessary to attain an enhanced light-matter interaction. In this work, we computationally study different geometries for a planar metallic Fabry-Pérot microcavity tuned for the absorption of Sulforhodamine 101, a typical dye for fluorescence spectroscopy. The cavity consists of a polymer layer enclosed between two silver mirrors, where the thicknesses of all the three layers are varied to optimize the cavity. Our transfer-matrix and finite-difference time-domain simulations suggest that a cavity with 30 nm thin top mirror and 200 nm fully reflective thick bottom mirror, thus having only reflection and absorption and no transmission, is an optimal design for maximizing the Purcell factor and spectral overlap between the cavity and molecule, while still sustaining an efficient measurability of the fluorescence.
Deep drug-target binding affinity prediction with multiple attention blocks
Authors: Zeng Yuni , Chen Xiangru , Luo Yujie , Li Xuedong , Peng Dezhong
Published: March 2021

Drug-target interaction (DTI) prediction has drawn increasing interest due to its substantial position in the drug discovery process. Many studies have introduced computational models to treat DTI prediction as a regression task, which directly predict the binding affinity of drug-target pairs. However, existing studies (i) ignore the essential correlations between atoms when encoding drug compounds and (ii) model the interaction of drug-target pairs simply by concatenation. Based on those observations, in this study, we propose an end-to-end model with multiple attention blocks to predict the binding affinity scores of drug-target pairs. Our proposed model offers the abilities to (i) encode the correlations between atoms by a relation-aware self-attention block and (ii) model the interaction of drug representations and target representations by the multi-head attention block. Experimental results of DTI prediction on two benchmark datasets show our approach outperforms existing methods, which are benefit from the correlation information encoded by the relation-aware self-attention block and the interaction information extracted by the multi-head attention block. Moreover, we conduct the experiments on the effects of max relative position length and find out the best max relative position length value $k \in \{3, 5\}$. Furthermore, we apply our model to predict the binding affinity of Corona Virus Disease 2019 (COVID-19)-related genome sequences and $3137$ FDA-approved drugs.
Integrating multi-scale neighbouring topologies and cross-modal similarities for drug–protein interaction prediction
Authors: Xuan Ping , Zhang Yu , Cui Hui , Zhang Tiangang , Guo Maozu , Nakaguchi Toshiya
Published: March 2021

Motivation

Identifying the proteins that interact with drugs can reduce the cost and time of drug development. Existing computerized methods focus on integrating drug-related and protein-related data from multiple sources to predict candidate drug–target interactions (DTIs). However, multi-scale neighboring node sequences and various kinds of drug and protein similarities are neither fully explored nor considered in decision making.

Results

We propose a drug-target interaction prediction method, DTIP, to encode and integrate multi-scale neighbouring topologies, multiple kinds of similarities, associations, interactions related to drugs and proteins. We firstly construct a three-layer heterogeneous network to represent interactions and associations across drug, protein, and disease nodes. Then a learning framework based on fully-connected autoencoder is proposed to learn the nodes’ low-dimensional feature representations within the heterogeneous network. Secondly, multi-scale neighbouring sequences of drug and protein nodes are formulated by random walks. A module based on bidirectional gated recurrent unit is designed to learn the neighbouring sequential information and integrate the low-dimensional features of nodes. Finally, we propose attention mechanisms at feature level, neighbouring topological level and similarity level to learn more informative features, topologies and similarities. The prediction results are obtained by integrating neighbouring topologies, similarities and feature attributes using a multiple layer CNN. Comprehensive experimental results over public dataset demonstrated the effectiveness of our innovative features and modules. Comparison with other state-of-the-art methods and case studies of five drugs further validated DTIP’s ability in discovering the potential candidate drug-related proteins.
Bioinformatics and machine learning approach identifies potential drug targets and pathways in COVID-19
Authors: Auwul Md Rabiul , Rahman Md Rezanur , Gov Esra , Shahjaman Md , Moni Mohammad Ali
Published: March 2021

Current coronavirus disease-2019 (COVID-19) pandemic has caused massive loss of lives. Clinical trials of vaccines and drugs are currently being conducted around the world; however, till now no effective drug is available for COVID-19. Identification of key genes and perturbed pathways in COVID-19 may uncover potential drug targets and biomarkers. We aimed to identify key gene modules and hub targets involved in COVID-19. We have analyzed SARS-CoV-2 infected peripheral blood mononuclear cell (PBMC) transcriptomic data through gene coexpression analysis. We identified 1520 and 1733 differentially expressed genes (DEGs) from the GSE152418 and CRA002390 PBMC datasets, respectively (FDR < 0.05). We found four key gene modules and hub gene signature based on module membership (MMhub) statistics and protein–protein interaction (PPI) networks (PPIhub). Functional annotation by enrichment analysis of the genes of these modules demonstrated immune and inflammatory response biological processes enriched by the DEGs. The pathway analysis revealed the hub genes were enriched with the IL-17 signaling pathway, cytokine–cytokine receptor interaction pathways. Then, we demonstrated the classification performance of hub genes (PLK1, AURKB, AURKA, CDK1, CDC20, KIF11, CCNB1, KIF2C, DTL and CDC6) with accuracy >0.90 suggesting the biomarker potential of the hub genes. The regulatory network analysis showed transcription factors and microRNAs that target these hub genes. Finally, drug–gene interactions analysis suggests amsacrine, BRD-K68548958, naproxol, palbociclib and teniposide as the top-scored repurposed drugs. The identified biomarkers and pathways might be therapeutic targets to the COVID-19.
iSMNN: batch effect correction for single-cell RNA-seq data via iterative supervised mutual nearest neighbor refinement
Authors: Yang Yuchen , Li Gang , Xie Yifang , Wang Li , Lagler Taylor M , Yang Yingxi , Liu Jiandong , Qian Li , Li Yun
Published: March 2021

Batch effect correction is an essential step in the integrative analysis of multiple single-cell RNA-sequencing (scRNA-seq) data. One state-of-the-art strategy for batch effect correction is via unsupervised or supervised detection of mutual nearest neighbors (MNNs). However, both types of methods only detect MNNs across batches of uncorrected data, where the large batch effects may affect the MNN search. To address this issue, we presented a batch effect correction approach via iterative supervised MNN (iSMNN) refinement across data after correction. Our benchmarking on both simulation and real datasets showed the advantages of the iterative refinement of MNNs on the performance of correction. Compared to popular alternative methods, our iSMNN is able to better mix the cells of the same cell type across batches. In addition, iSMNN can also facilitate the identification of differentially expressed genes (DEGs) that are relevant to the biological function of certain cell types. These results indicated that iSMNN will be a valuable method for integrating multiple scRNA-seq datasets that can facilitate biological and medical studies at single-cell level.
Reactive microglia enhance the transmission of exosomal α-synuclein via toll-like receptor 2
Authors: Xia Yun , Zhang Guoxin , Kou Liang , Yin Sijia , Han Chao , Hu Junjie , Wan Fang , Sun Yadi , Wu Jiawei , Li Yunna , Huang Jinsha , Xiong Nian , Zhang Zhentao , Wang Tao
Published: March 2021

Increasing evidence suggests that microglial activation is strongly linked to the initiation and progression of Parkinson’s disease. Cell-to-cell propagation of α-synuclein pathology is a highlighted feature of Parkinson’s disease, and the focus of such research has been primarily on neurons. However, recent studies as well as the data contained herein suggest that microglia, the primary phagocytes in the brain, play a direct role in the spread of α-synuclein pathology. Recent data revealed that plasma exosomes derived from Parkinson’s disease patients (PD-EXO) carry pathological α-synuclein and target microglia preferentially. Hence, PD-EXO are likely a key tool for investigating the role of microglia in α-synuclein transmission. We showed that intrastriatal injection of PD-EXO resulted in the propagation of exosomal α-synuclein from microglia to neurons following microglia activation. Toll-like receptor 2 (TLR2) in microglia was activated by exosomal α-synuclein and acted as a crucial mediator of PD-EXO-induced microglial activation. Additionally, partial microglia depletion resulted in a significant decrease of exogenous α-synuclein in the substantia nigra. Furthermore, exosomal α-synuclein internalization was initiated by binding to TLR2 of microglia. Excessive α-synuclein phagocytosis may induce the inflammatory responses of microglia and provide the seed for microglia-to-neuron transmission. Consistently, TLR2 silencing in microglia mitigated α-synuclein pathology in vivo. Overall, the present data support the idea that the interaction of exosomal α-synuclein and microglial TLR2 contribute to excessive α-synuclein phagocytosis and microglial activation, which lead to the further propagation and spread of α-synuclein pathology, thereby highlighting the pivotal roles of reactive microglia in α-synuclein transmission.
Organ-on-a-chip technology: a novel approach to investigate cardiovascular diseases
Authors: Paloschi Valentina , Sabater-Lleal Maria , Middelkamp Heleen , Vivas Aisen , Johansson Sofia , van der Meer Andries , Tenje Maria , Maegdefessel Lars
Published: March 2021

The development of organs-on-chip (OoC) has revolutionized in vitro cell-culture experiments by allowing a better mimicry of human physiology and pathophysiology that has consequently led researchers to gain more meaningful insights into disease mechanisms. Several models of hearts-on-chips and vessels-on-chips have been demonstrated to recapitulate fundamental aspects of the human cardiovascular system in the recent past. These 2D and 3D systems include synchronized beating cardiomyocytes in hearts-on-chips and vessels-on-chips with layer-based structures and the inclusion of physiological and pathological shear stress conditions. The opportunities to discover novel targets and to perform drug testing with chip-based platforms have substantially enhanced, thanks to the utilization of patient-derived cells and precise control of their microenvironment. These organ models will provide an important asset for future approaches to personalized cardiovascular medicine and improved patient care. However, certain technical and biological challenges remain, making the global utilization of OoCs to tackle unanswered questions in cardiovascular science still rather challenging. This review article aims to introduce and summarize published work on hearts- and vessels-on chips but also to provide an outlook and perspective on how these advanced in vitro systems can be used to tailor disease models with patient-specific characteristics.
Is the local wheat market a ‘market for lemons’? Certifying the supply of individual wheat farmers in Ethiopia
Authors: Anissa Banawe Plambou , Abate Gashaw , Bernard Tanguy , Bulte Erwin
Published: March 2021

Bulking and mixing of smallholder supply dilutes incentives to supply high quality. We introduce wheat ‘grading and certification shops’ in Ethiopia and use an auction design to gauge willingness-to-pay (WTP) for certification. Bids correlate positively with wheat quality, and ex ante notification of the opportunity of certification improves wheat quality. These findings suggest that local wheat markets resemble a ‘market for lemons’, crippled by asymmetric information. However, aggregate WTP for grading and certification services does not re-coup the sum of fixed, flow and variable costs associated with running a single certification shop.
The varied role, scope of practice, and education of cardiovascular nurses in ESC-affiliated countries: an ACNAP survey
Authors: Fitzsimons Donna , Carson Matthew A , Hansen Tina B , Neubeck Lis , Tanash Mu’ath I , Hill Loreena
Published: March 2021

Aims

Cardiovascular disease burden is increasing globally, pressuring nursing staff to deliver high-quality care across a diverse range of treatment areas. As such, an evaluation of the educational preparation of nurses is needed. To determine the current role, scope of practice, education level, and needs of cardiovascular nurses working across the European Society of Cardiology (ESC)-affiliated countries.

Methods and results

A short survey was distributed in paper (EuroHeartCare 2018) or electronic format to nurses delivering cardiovascular care. A total of 876 cardiovascular nurses from 26 ESC-affiliated countries completed the survey. Most respondents (79%), were educated to at least bachelor level, with 46% having a masters or doctorate, and were highly motivated to continue their educational development. Despite this, a large number (44.3%) of respondents believed they were not fully prepared for their job. The main areas where further education was requested included acute care in cardiovascular disease (CVD) and CVD risk factor management. Face-to-face courses/training were the most requested delivery mode, followed by E-learning—which appears to be underutilized in this population. Awareness of the existing curricula for cardiovascular nurse education was minimal, and therefore these resources require further promotion and implementation.

Conclusions

This international sample of cardiovascular nurses was generally educated to degree level and motivated to improve their cardiovascular knowledge. Many believed they were underprepared for their role, highlighting the need for increased investment in education. This should be focused on specific needs and delivered using a face-to-face, E-learning, or blended-learning format. Furthermore, increased signposting of existing resources is required.
MetaPrism: A versatile toolkit for joint taxa/gene analysis of metagenomic sequencing data
Authors: Kim Jiwoong , Jiang Shuang , Wang Yiqing , Xiao Guanghua , Xie Yang , Liu Dajiang J , Li Qiwei , Koh Andrew , Zhan Xiaowei
Published: March 2021

In microbiome research, metagenomic sequencing generates enormous amounts of data. These data are typically classified into taxa for taxonomy analysis, or into genes for functional analysis. However, a joint analysis where the reads are classified into taxa-specific genes is often overlooked. To enable the analysis of this biologically meaningful feature, we developed a novel bioinformatic toolkit, MetaPrism, which can analyze sequence reads for a set of joint taxa/gene analyses to: 1) classify sequence reads and estimate the abundances for taxa-specific genes; 2) tabularize and visualize taxa-specific gene abundances; 3) compare the abundances between groups; and 4) build prediction models for clinical outcome. We illustrated these functions using a published microbiome metagenomics dataset from patients treated with immune checkpoint inhibitor therapy and showed the joint features can serve as potential biomarkers to predict therapeutic responses. MetaPrism is a toolkit for joint taxa and gene analysis. It offers biological insights on the taxa-specific genes on top of the taxa-alone or gene-alone analysis.

MetaPrism is open-source software and freely available at https://github.com/jiwoongbio/MetaPrism. The example script to reproduce the manuscript is also provided in the above code repository.
Do efficiency gains really translate into more budget for health? An assessment framework and country applications
Authors: Barroy Hélène , Cylus Jonathan , Patcharanarumol Walaiporn , Novignon Jacob , Evetovits Tamás , Gupta Sanjeev
Published: March 2021

Efficiency has historically been considered a key mechanism to increase the amount of available revenues to the health sector, enabling countries to expand services and benefits to progress towards universal health coverage (UHC). Country experience indicates, however, that efficiency gains do not automatically translate into greater budget for health, to additional revenues for the sector. This article proposes a framework to assess whether and how efficiency interventions are likely to increase budgetary space in health systems Based on a review of the literature and country experiences, we suggest three enabling conditions that must be met in order to transform efficiency gains into budgetary gains for health. First there must be well-defined efficiency interventions that target health system inputs, implemented over a medium-term time frame. Second, efficiency interventions must generate financial gains that are quantifiable either pre- or post-intervention. Third, public financial management systems must allow those gains to be kept within the health sector and repurposed towards priority health needs. When these conditions are not met, efficiency gains do not lead to more budgetary space for health. Rather, the gains may instead result in budget cuts that can be detrimental to health systems’ outputs and ultimately disincentivize further attempts to improve efficiency in the sector. The framework, when applied, offers an opportunity for policymakers to reconcile efficiency and budget expansion goals in health.
How does health literacy affect the utilization of basic public health services in Chinese migrants?
Authors: Yu Yan , He Anqi , Zheng Si , Jiang Junfeng , Liang Jing , Shrestha Bhawana , Wang Peigang
Published: March 2021

Previous studies have focused on the determinants of basic public health services utilization, such as socioeconomic status and mobility characteristics, rather than on health literacy. Thus, this study aimed to estimate the effect of health literacy on the utilization of basic public health services among Chinese migrants. Based on the 2016 China Migrants Dynamic Survey data (N = 2335), this study used propensity score matching approach to estimate the effect of health literacy on the utilization of basic public health services, including the establishment of health records and receipt of health education, and to explore heterogeneity in this effect based on educational attainment and urban–rural status. The findings show that high levels of health literacy increased the probability of establishing health records and receiving more health education. Also, high levels of health literacy had a positive effect on the utilization of basic public health services among Chinese migrants, especially those with less education or living in urban areas. Policy makers should more carefully consider the actual situation and needs of migrants who are living in urban areas or have less education, constructing more targeted service programs.
Long-term risk of epilepsy, cerebral palsy and attention-deficit/hyperactivity disorder in children affected by a threatened abortion in utero
Authors: Dudukina Elena , Horváth-Puhó Erzsébet , Sørensen Henrik Toft , Ehrenstein Vera
Published: March 2021

Background

The birth of a child affected by a threatened abortion (TAB) in utero is associated with autism spectrum disorder; association with other neurological disorders is unknown.

Methods

This nationwide registry-based cohort study included singletons live-born in Denmark (1979–2010), followed through 2016. The outcomes were epilepsy, cerebral palsy (CP) and attention-deficit/hyperactivity disorder (ADHD). We used Cox regression to compute hazard ratios (HRs), adjusted for birth year, birth order, parental age, morbidity, medication use and maternal socio-economic factors. To remove time-invariant family-shared confounding, we applied sibling analyses.

Results

The study population included 1 864 221 singletons live-born in 1979–2010. Among the TAB-affected children (N = 59 134) vs TAB-unaffected children, at the end of follow-up, the cumulative incidence was 2.2% vs 1.6% for epilepsy, 0.4% vs 0.2% for CP and 5.5% vs 4.2% for ADHD (for children born in 1995–2010). The adjusted HRs were 1.25 [95% confidence interval (CI) 1.16–1.34] for epilepsy, 1.42 (95% CI 1.20–1.68) for CP and 1.21 (95% CI 1.14–1.29) for ADHD. In the sibling design, the adjusted HRs were unity for epilepsy (full siblings: 0.96, 95% CI 0.82–1.12; maternal: 1.04, 95% CI 0.90–1.20; paternal: 1.08, 95% CI 0.93–1.25) and ADHD (full: 1.08, 95% CI 0.92–1.27; maternal: 1.04, 95% CI 0.90–1.20; paternal: 1.08, 95% CI 0.93–1.25). For CP, HRs shifted away from unity among sibling pairs (full: 2.92, 95% CI 1.33–6.39; maternal: 2.03, 95% CI 1.15–3.57; paternal: 3.28, 95% CI 1.36–7.91).

Conclusions

The birth of a child affected by TAB in utero was associated with a greater risk of CP, but not epilepsy or ADHD.
The Law of ‘Never Again’: Transitional Justice and the Transformation of the Norm of Non-Recurrence
Authors: Davidovic Maja
Published: March 2021

This article analyses the transformation of guarantees of non-recurrence (GNRs), the least developed pillar of transitional justice (TJ), and sets a legal and conceptual foundation of the norm for TJ theory and practice. It draws out key characteristics of GNRs including the norm’s various contents and contexts, stressing its exceptional future-oriented nature in international law. The article investigates conceptual origins of preventing non-recurrence in the early developments of TJ and the recent normative expansions undertaken by the UN Special Rapporteur. The main contributions of the article are establishing GNRs as normatively distinct in TJ and identifying transfers of local-level advocacy from Latin America to general norm creation. Finally, the article proposes a tension between decontextualizing the norm content to make it universally applicable and recent attempts to normatively expand the norm and improve its context-specificity, and discusses its potential consequences for TJ practice.