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CNEReg Interprets Ruminant-specific Conserved Non-coding Elements by Developmental Gene Regulatory Network

Genomics, Proteomics & Bioinformatics 2023年第3期21卷 632-648页

作者： Xiangyu Pan Zhaoxia Ma Xinqi Sun Hui Li Tingting Zhang Chen Zhao Nini Wang Rasmus Heller Wing Hung Wong Wen Wang Yu Jiang Yong Wang Key Laboratory of Animal Genetics Breeding and Reproduction of Shaanxi ProvinceCollege of Animal Science and TechnologyNorthwest A&F UniversityYangling 712100China Department of Medical Research Guangdong Provincial People’s HospitalGuangdong Academy of Medical SciencesGuangzhou 510080China Guangdong Cardiovascular Institute Guangdong Provincial People’s HospitalGuangdong Academy of Medical SciencesGuangzhou 510080China Academy of Mathematics and Systems Science Chinese Academy of SciencesBeijing 100190China School of Mathematics University of Chinese Academy of SciencesBeijing 100049China State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources College of Animal Science and TechnologyGuangxi UniversityNanning 530005China Section for Computational and RNA Biology Department of BiologyUniversity of CopenhagenCopenhagen DK-2100Denmark Department of Statistics Department of Biomedical Data ScienceBio-X ProgramStanford UniversityStanfordCA 94305USA Center for Ecological and Environmental Sciences Northwestern Polytechnical UniversityXi’an 710072China State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of SciencesKunming 650223China Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunming 650223China Key Laboratory of Systems Health Science of Zhejiang Province School of Life ScienceHangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhou 310024China

The genetic information coded in DNA leads to trait innovation via a gene regulatory network(GRN)in ***,we developed a conserved non-coding element interpretation method to integrate multi-omics data into gene regulatory network(CNEReg)to investigate the ruminant multi-chambered stomach *** generated paired expression and chromatin accessibility data during rumen and esophagus development in sheep,and revealed 1601 active ruminantspecific conserved non-coding elements(active-RSCNEs).To interpret the function of these activeRSCNEs,we defined toolkit transcription factors(TTFs)and modeled their regulation on rumenspecific genes via batteries of active-RSCNEs during *** developmental GRN revealed 18 TTFs and 313 active-RSCNEs regulating 7 rumen functional ***,6 TTFs(OTX1,SOX21,HOXC8,SOX2,TP63,and PPARG),as well as 16 active-RSCNEs,functionally distinguished the rumen from the *** study provides a systematic approach to understanding how gene regulation evolves and shapes complex traits by putting evo-devo concepts into practice with developmental multi-omics data.

关键词： Trait innovation Gene regulatory network Conserved non-coding element Toolkit transcription factor Ruminant

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Work capacity of compost applicator on paddy field

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AIP Conference Proceedings 2023年第1期2596卷

作者： Iqbal Muhammad Reza Fikri Azhar Mahmud Achmad Muhammad Tahir Sapsal Andi Azizah Agricultural Engineering Study Program Hasanuddin University Makassar Indonesia Environmental Quality Management Study Program Wrocław University of Science and Technology Wrocław Poland

The addition of compost (organic fertilizer) is essential to maintain agricultural land productivity. Nutrients have a role in plant growth and development, especially in paddy plants. The application of distributing compost (organic fertilizer) on agricultural land requires considerable energy and costs, especially if the land is large. In order to overcome this, an applicator is used to reduce costs and energy and streamline the fertilization process time. This applicator is specially designed to spread compost (organic fertilizer) to agricultural land with a certain dose. This study aimed to calculate the working capacity and efficiency of the compost applicator in paddy fields. The study was conducted by direct testing in the fields with three different speed treatments, namely at 2.71 km/hour, 3.38 km/hour, and 4.62 km/hour. The calculation results show that the optimum speed of the applicator in paddy fields is 2.71 km/hour. The working capacity obtained is 0.35 ha/hour for theoretical field capacity and 0.26 ha/hour for effective field capacity with a field efficiency of 74.74%.

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Contamination of microplastics in Brantas River, East Java, Indonesia and its distribution in gills and digestive tracts of fish Gambusia affinis

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Emerging Contaminants 2021年第1期7卷 172-178页

作者： Nanik Retno Buwono Yenny Risjani Agoes Soegianto Doctoral Study Program of Mathematics and Natural Sciences Faculty of Science and TechnologyUniversitas AirlanggaSurabayaIndonesia Departement of Aquatic Resources Management Faculty of Fisheries and Marine SciencesBrawijaya UniversityJl.Veteran Malang65145Indonesia AquaRES Research Group Faculty of Fisheries and Marine Sciences Brawijaya UniversityJl.Veteran Malang65145Indonesia Department of Biology Faculty of Science and TechnologyUniversitas AirlanggaJl.Mulyorejo Surabaya60115Indonesia Research Group of Environmental Technology and Innovation Faculty of Science and TechnologyUniversitas AirlanggaJl.Mulyorejo Surabaya60115Indonesia

The Brantas River is currently vulnerable to microplastics *** not only pollute the aquatic environment but also enter the body of fish and other aquatic *** research is aimed at deciding if microplastics were present in the waters and the gills and digestive tract of the Gambusia affinis fish of the *** also looked at differences in the abundance of several types of microplastics found in the various organ samples and *** research was conducted from January 2020 to March *** microplastics were identified by type,size,color,and the abundance of each type was *** types of microplastics identified were fragments,fibres,films,and *** of 0.1 mm size are predominant and formed about 76%-100%of the microplastics that were *** microplastics were more common in water samples(24%),gills(43%),and digestive tract(46%).The greatest abundance of microplastic fragments was found in water samples of 4066.67 particles/m^(3),1352.78 particles/gram in gill samples,and 2138.89 particles/gram in the digestive *** tests for variants of microplastic types found in the organs at different sampling locations gave a p-value<*** results indicate a difference in the abundance values of microplastic species in different organ samples and sites.

关键词： Gill Digestive tract Fragments Fish Freshwater Water pollution

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Population structure and regeneration of Himalayan endemic Larix species in three high-altitude valleys in Nepal Himalaya

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Journal of Ecology and Environment 2020年第3期44卷 1页

作者： Dhamala, Man Kumar Aryal, Prakash Chandra Suwal, Madan Krishna Bhatta, Sijar Bhuju, Dinesh Raj Central Department of Environmental Science Tribhuvan University Kathmandu Kirtipur Nepal Environmental Science Program GoldenGate International College Battisputali Kathmandu Nepal Environment Protection and Study Center (ENPROSC) Baneshwor Kathmandu Nepal Department of Geography University of Bergen Bergen Norway Nepal Academy of Science and Technology Khumaltar Lalitpur Nepal

Background: The Himalayan forests are of great importance to sustain the nature and community resource demands. These forests are facing pressures both from anthropogenic activities and ongoing global climatic changes. Poor natural regeneration has been considered a major problem in mountainous forests. To understand the population structure and regeneration status of Larix (Larix griffithiana and Larix himalaica), we conducted systematic vegetation surveys in three high-altitude valleys namely Ghunsa (Kanchenjunga Conservation Area, KCA), Langtang (Langtang National Park, LNP), and Tsum (Manaslu Conservation Area, MCA) in Nepal Himalaya. The average values of diameter at breast height (DBH), height, and sapling height were compared for three sites and two species using Kruskal-Wallis test. Population structure was assessed in terms of proportion of seedlings, saplings, and trees. Regeneration was analyzed using graphical representation of frequencies of seedlings, saplings, and trees in histograms. Results: The results showed that the population structure of Larix in terms of the proportion of seedling, sapling, and tree varied greatly in the three study areas. KCA had the highest record of seedling, sapling, and tree compared to other two sites. Seedlings were the least among three forms and many plots were without seedlings. We found no seedling in MCA study plots. The plot level average DBH variation among sites was significant (Kruskal-Wallis χ² = 7.813, df = 2, p = 0.02) as was between species (Kruskal-Wallis χ² = 5.9829, df = 1, p = 0.014). Similarly, the variation in average tree height was significant (Kruskal-Wallis χ² = 134.23, df = 2, p < 0.001) among sites as well as between species (Kruskal-Wallis χ² = 128.01, df = 1, p < 0.001). All the sites showed reverse J-shaped curve but more pronounced for KCA and MCA. In comparing the two species, Larix griffithiana has clear reverse J-shaped diameter distribution but

关键词： Anthropogenic disturbance Climate change Endemic Forest management Subalpine

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Classification Of Aedes Mosquito Larva Using Convolutional Neural Networks And Extreme Learning Machine

Classification Of Aedes Mosquito Larva Using Convolutional N...

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International Conference on Electrical, Telecommunication and Computer Engineering (ELTICOM)

作者： Pauzi Ibrahim Nainggolan Syahril Efendi Mohammad Andri Budiman Maya Silvi Lydia Ivan Joshua Dhani Syahputra Bukit Romi Fadillah Rahmat Ledy Afrida Sinaga Edi Subroto Department of Computer Science Universitas Sumatera Utara Medan Indonesia Department of Information Technology Universitas Sumatera Utara Medan Indonesia Department of Public Health Universitas Sumatera Utara Medan Indonesia Environmental health and diseases control Ministry of Health Medan Indonesia Department of midwifery study program STIKes Mitra Husada Medan Sumatera Utara Indonesia

The spread of diseases transmitted by Aedes mosquitoes, such as Dengue fever, Chikungunya (CHIKV), and Zika, poses a severe health problem in many countries. Aedes mosquitoes can be found in tropical and subtropical areas. One method to control the diseases is by controlling the population of Aedes mosquitoes, and one way to control the population of Aedes mosquito is by exterminating Aedes mosquito larvae. Identifying mosquito larvae, however, demands a considerable amount of effort, time, and specialized knowledge about the morphology and anatomy of mosquito larvae to accurately classify the various types. Therefore, a system is needed to classify Aedes and non-Aedes mosquito larvae. In this study, classification was carried out using larvae images taken using a digital microscope. The methods used to classify mosquito larvae images are Convolutional Neural Networks (CNN) to extract features from the larvae image and Extreme Learning Machine (ELM) to classify the larvae image. The result obtained from evaluating the CNN-ELM model is an accuracy of 98%, f1-score of 99% for Aedes larvae, and fl-score of 96% for non-Aedes larvae.

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Effort of utilizing foundry sand waste and paper sludge as raw materials replacement for red brand without burning process 1

Effort of utilizing foundry sand waste and paper sludge as r...

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1st International Conference on science and technology for environmental Protection, ICSTEP 2018

作者： Wati, S.E.D.F.S. Putranto, T.W.C. Citrasari, N. Environmental Science and Technology Study Program Biology Department Faculty of Science and Technology Universitas Airlangga Surabaya Indonesia

This research's goal is to know the content of SiO2 and Al2O3 in the foundry sand, to know the selected variation as material for red brick without burning process based on SNI 15-2094-2000 on concrete red brick for walls and SNI 15-2094-1991 on the quality and the test method for concrete red brick and to know the content of heavy metal Zn from leaching process of the selected variations. The content of SiO2 and Al2O3 were tested by using X-Ray Fluorescence method, while the content of Zn at leached was tested by using Atomic Abrsoption Spectophotometry. The non-burning brick quality test was conducted in 5 stages, which are external display test, size and tolerance test, compressive strength test, harmful salt test, pseudo-density test and water absorption test. Variations of materials used are foundry sand: paper sludge: compactor ingredient in percentage is Variation A 75%:15%:10%;B 65%:25%:10%;C 55%:35%:10%;D 45%:45%:10%;E 0%:90%:10%;F 90%:0%:10%;and the Control Variation is G 90% sand:10%. The content of SiO2 and Al2O3 in the foundry sand are respectively 66.90% and 12.78%. The content of Zn in paper sludge is 54 mg/kg. The results of red brick testing shows that the selected variations are variations A, B, F which classified to Brick classs 50. Content of Zn in red brick leaching process of the selected variations are variations A, B, and F are respectively 0.61;0.89;0.21 mg/L. © 2019 IOP Publishing Ltd.

关键词： Silica

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Performance of sequencing batch reactor (SBR) of treated tofu wastewater: Variation of contact time and activated sludge sources 1

Performance of sequencing batch reactor (SBR) of treated tof...

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1st International Conference on science and technology for environmental Protection, ICSTEP 2018

作者： Sakinah, N.E. Rahmatullah, L.T. Kuncoro, E.P. Oktavitri, N.I. Study Program of Environmental Science and Technology Department of Biology Faculty of Science and Technology Airlangga University Surabaya Indonesia

One of the wastewater treatment system that is able to reduce levels of contamination are industrial wastewater using Sequencing Batch Reactor (SBR). Important in the early stages of SBR is filling phase (filling) consisting of seeding and acclimatization period. In the seeding and acclimatization period, the reactor will be filled with activated sludge and wastewater aeration process during the next study period. This research was conducted to find out sources and the best contact time of the activated sludge in lowering the concentration of COD and TSS from wastewater of tofu industry. Activated sludge which will be used is sourced from slaughter house, gutters of tofu industry, and polluted rivers. The variation of contact time which will be used is day 0;1;3;5;9 and 13. The results showed that the activated sludge are sourced from a polluted river sludge with the best percent COD reduction of 81% and TSS by 94% at day 13. © 2019 IOP Publishing Ltd.

关键词： Batch reactors

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Phytoremediation of lead-contaminated soil by ornament plant Codiaeum variegatum 6

Phytoremediation of lead-contaminated soil by ornament plant...

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6th International Conference on Mathematics, science, and Education, ICMSE 2019

作者： Herlina, L. Purnaweni, H. Sudarno, S. Widianarko, B. Sunoko, H.R. Doctoral Program of Environmental Science School of Postgraduate Studies Diponegoro University Semarang Indonesia Program Study of Environmental Science School of Postgraduate Studies Diponegoro University Semarang Indonesia Faculty of Agricultural Technology Soegijapranata Catholic University Semarang Indonesia Faculty of Medicine Diponegoro University Semarang Indonesia Department of Biology Faculty Mathematics and Natural Science Universitas Negeri Semarang Indonesia

Phytoremediation is an emerging technology that employs the use of higher plants for the clean upt he contaminated environment, a cost-effective, environment-friendly. In this study, the role of puring(Codiaeumvarigatum) plants as a potential phytoremediator to soils contaminated with lead (Pb) was investigated. A pot experiment was conducted for four and eight weeks to compare the biomass andlead content in root, stem and leaf by puring. The plant grew well exposed Plants that grow well are exposed to Pb with as much as 250 ***-1 and 375 ***-1 soil. The result presented here showed that root, stem and leaf biomassdecrease with increasing concentration and exposure time. Pb accumulation increases with increasing concentration and time of exposure. Pb accumulation in roots> stems> leaves. Bioaccumulation of factors is less than 1 while factor translocation is more than one. Metal tolerance index values range 95.545%to103.406%. This suggests that Codiaeumvarigatum was a candidate for phytoremediation of lead. © Published under licence by IOP Publishing Ltd.

关键词： Soils

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Textural Features for Blb Disease Damage Assessment in Paddy Fields Using Drone Data and Machine Learning: Enhancing Disease Detection Accuracy

SSRN

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SSRN 2024年

作者： Wijayanto, Arif Kurnia Prasetyo, Lilik Budi Hudjimartsu, Sahid Agustian Sigit, Gunardi Hongo, Chiharu Department of Forest Resource Conservation and Ecotourism Faculty of Forestry and Environment IPB University Bogor16680 Indonesia Ronpaku Fellow Tokyo102-0083 Japan Environmental Research Center IPB University Bogor16680 Indonesia Study Program of Information Technology Faculty of Science and Engineering Ibn Khaldun University Bogor16129 Indonesia Regional Office of Food Crops Service West Java Province Cianjur43283 Indonesia Chiba University Chiba263-8522 Japan

Detecting Bacterial Leaf Blight (BLB) in paddy fields is one of the essential issues in Indonesia to prevent losses in rice production. This study reports the effectiveness of textural analysis using drone-acquired data over paddy fields in West Java, evaluating the potential of integrating textural and thermal characteristics. We used drone data combined with machine learning techniques to distinguish different levels of BLB impact. The normalized difference texture index derived from Haralick textural features was used as a predictor. The findings revealed that incorporating textural features enhanced the disease detection accuracy significantly compared with the traditional approach based on spectral indices. The random forest algorithm, which merges texture and vegetation indices, achieved a classification accuracy of 0.984. The proposed method offers a robust, noninvasive solution for BLB disease detection, contributing substantially to safeguarding crop yields and mitigating global food security issues. © 2024, The Authors. All rights reserved.

关键词： Drones

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Evaluation of communal wastewater treatment plant based on technical, institutional, and community participation aspects in South Surabaya 1

Evaluation of communal wastewater treatment plant based on t...

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1st International Conference on science and technology for environmental Protection, ICSTEP 2018

作者： Purnawanti, E. Oktavitri, N.I. Isnadina, D.R.M. Fitriani, N. Environmental Engineering Study Program Department of Biology Faculty of Science and Technology Universitas Airlangga Indonesia

This study aims to discover the obstacles and provide recommendations on the technical and institutional aspects of the chosen communal WWTP. The methods used in this study were field survey and questionnaire. the data were analyzed using quantitative, qualitative, and SWOT analysis. There are 11 out of 13 communal WWTPs that do not work optimally. The technical obstacle encountered in the operation of the chosen communal WWTPs is the huge building capacity that does not meet the criteria of HRT design. The recommendations for the technical problem include lowering the water level and reducing the number of baffles in communal WWTP. The obstacle faced in the operation of chosen communal WWTPs in terms of institutional and community participation aspects is that the maintenance is only known by few people. The recommendation for the aspects of institutional and community participation is for KPP to arrange a socialization on the maintenance of communal WWTP based on its maintenance module. © 2019 IOP Publishing Ltd.

关键词： Maintenance

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