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Integrated Single-cell Multiomic Analysis of HIV Latency Reversal Reveals Novel Regulators of Viral Reactivation

Genomics, Proteomics & Bioinformatics 2024年第1期22卷 67-88页

作者： Manickam Ashokkumar Wenwen Mei Jackson J.Peterson Yuriko Harigaya David M.Murdoch David M.Margolis Caleb Kornfein Alex Oesterling Zhicheng Guo Cynthia D.Rudin Yuchao Jiang Edward P.Browne Department of Medicine University of North Carolina at Chapel HillChapel HillNC 27599USA HIV Cure Center University of North Carolina at Chapel HillChapel HillNC 27599USA Department of Biostatistics University of North Carolina at Chapel HillChapel HillNC 27599USA Department of Microbiology and Immunology University of North Carolina at Chapel HillChapel HillNC 27599USA Department of Genetics University of North Carolina at Chapel HillChapel HillNC 27599USA Department of Medicine Duke UniversityDurhamNC 27708USA Department of Computer Science Duke UniversityDurhamNC 27708USA Department of Statistics Texas A&M UniversityCollege StationTX 77843USA Department of Biology Texas A&M UniversityCollege StationTX 77843USA Department of Biomedical Engineering Texas A&M UniversityCollege StationTX 77843USA

Despite the success of antiretroviral therapy,human immunodeficiency virus(HIV)cannot be cured because of a reservoir of latently infected cells that evades *** understand the mechanisms of HIV latency,we employed an integrated single-cell RNA sequencing(scRNA-seq)and single-cell assay for transposase-accessible chromatin with sequencing(scATAC-seq)approach to simultaneously profile the transcriptomic and epigenomic characteristics of~125,000 latently infected primary CD4^(+)T cells after reactivation using three different latency reversing *** expressed genes and differentially accessible motifs were used to examine transcriptional pathways and transcription factor(TF)activities across the cell *** identified cellular transcripts and TFs whose expression/activity was correlated with viral reactivation and demonstrated that a machine learning model trained on these data was 75%-79%accurate at predicting viral ***,we validated the role of two candidate HIV-regulating factors,FOXP1 and GATA3,in viral *** data demonstrate the power of integrated multimodal single-cell analysis to uncover novel relationships between host cell factors and HIV latency.

关键词： HIV latency reversal Primary CD4þT cell Single-cell multiomics HIV-regulating factor Machine learning

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Green hydrogen production from photovoltaic power station as a road map to climate change mitigation

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CLEAN ENERGY 2024年第2期8卷 156-167页

作者： Kamil, Kehinde Ridwan Samuel, Bassey Okon Khan, Umar Edge hill Univ Dept Comp Sci & Engn Ormskirk England ENEL Green Power Rome Italy Steelagon Engn Ltd Mat Res Lab Sabon Gari Kaduna State Nigeria

The increasing recognition of hydrogen as a critical element in the global net-zero transition and its clear role in decarbonizing challenging sectors coincide with the growing urgency to address climate change. Africa's favourable renewable-energy capacity, ranging from 28% to 36% for solar, has been reported by the global solar irradiance index. However, the majority of hydrogen production today relies on fossil fuels (96%), with only a small fraction (4%) being produced through water electrolysis. Even though there have been many studies on climate change mitigation with a focus on Africa, a green hydrogen production from a photovoltaic power station approach has not been reported. Also, literature with a focus on Nigeria is lacking. This study focuses on the African green hydrogen production industry, utilizing Nigeria as a case study to explore the feasibility of generating clean hydrogen vectors from a percentage of photovoltaic power output in various regions of the country through stand-alone solar grid electrification projects. Analyses of the usage and effectiveness of the produced hydrogen fuel in each region are carried out, with the highest region having an annual output of 12 247 278 kg of green hydrogen and 8 573 094 kg of ammonia and the lowest region having an output of 511 245 kg of green hydrogen and 357 871 kg of ammonia, and the expected production from the proposed usage of 50% of the power generation output of the installed 1.6-MWp and 80-kWp solar power minigrids in the regions is calculated. The analyses were repeated for the other considered regions in the country. The results showcased the enormous advantages of the electrolytic production of hydrogen and how the greener economy project can play a major role in mitigating climate change effects and overreliance on fossil fuels as the driver of the economy in many African countries. Nigeria is used as a case study for the African green hydrogen production industry to explore the feasibility

关键词： renewable energy photovoltaic climate change green hydrogen vector fossil fossil fuels decarbonization electrolysis AMMONIA WATER CELL

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Genetic Diversity Analysis of Rice Germplasm in Tripura State of Northeast India Using Drought and Blast Linked Markers

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Rice science 2017年第1期24卷 10-20页

作者： Alpana ANUPAM Jahangir IMAM Syed Mohammad QUATADAH Anantha SIDDAIAH Shankar Prasad DAS Mukund VARIAR Nimai Prasad MANDAL Central Rainfed Upland Rice research station ICAR research Complex for North Eastern hill Region Tripura Centre

We genotyped 74 rice germplasms including Tripura＇s local landraces, improved varieties, cultivars and breeding lines and other rice varieties using molecular markers for genetic diversity, drought QTLs, and blast resistance genes. The number of alleles per locus ranged from 2 to 5 with an average of 2.9. The polymorphic information content value per locus ranged from 0.059（RM537） to 0.755（RM252） with an average of 0.475. Cluster analysis based on 30 simple sequence repeat markers revealed 5 clusters and also indicated the presence of variability within the rice accessions. The drought QTL q DTY2.1 was found in 56.0% of germplasms and q DTY1.1 was detected in only 6.8% of the germplasms. Out of seven rice blast resistance genes screened, only two rice varieties, RCPL-1-82 and Buh Vubuk（Lubuk）, were positive for four blast resistance genes while only Releng possessed two blast resistance genes. Among 74 rice germplasms, only three accessions, Releng, RCPL1-82 and Buh Vubuk（Lubuk）, possessed both drought-related QTLs and blast resistance genes. Overall, the 74 indigenous rice genotypes showed low level of genetic diversity, which is in contrast to high level of genetic diversity among rice varieties in northeast India, where highlights the good farming practice, conservation of germplasms and the limitation of molecular markers employed in this study. The presence of both drought related QTLs and blast resistance genes in some of the germplasms can be useful in future breeding programmes.

关键词： drought blast alleles breeding ranged polymorphic Northeast screened upland germplasm

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A Quantitative Seismic Topographic Effect Prediction Method Based upon BP Neural Network Algorithm and FEM Simulation

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Journal of Earth Science 2024年第4期35卷 1355-1366页

作者： Qifeng Jiang Mianshui Rong Wei Wei Tingting Chen Shandong Seismic Hazard Prevention Center Shandong Earthquake AgencyJinan250014China Shandong Institute of Earthquake Engineering Jinan250021China Key Laboratory of Urban Security and Disaster Engineering of China Ministry of Education Beijing University of TechnologyBeijing100124China Publicity and Education Center Shandong Earthquake AgencyJinan250014China Shandong Earthquake station Shandong Earthquake AgencyJinan250014China

Topography can strongly affect ground motion,and studies of the quantification of hill surfaces’topographic effect are relatively *** this paper,a new quantitative seismic topographic effect prediction method based upon the BP neural network algorithm and three-dimensional finite element method(FEM)was *** FEM simulation results were compared with seismic records and the results show that the PGA and response spectra have a tendency to increase with increasing elevation,but the correlation between PGA amplification factors and slope is not obvious for low *** BP neural network models were established for the prediction of amplification factors of PGA and response *** kinds of input variables’combinations which are convenient to achieve are proposed in this paper for the prediction of amplification factors of PGA and response spectra,*** absolute values of prediction errors can be mostly within 0.1 for PGA amplification factors,and they can be mostly within 0.2 for response spectra’s amplification *** input variables’combination can achieve better prediction performance while the other one has better expandability of the predictive ***,the BP models only employ one hidden layer with about a hundred nodes,which makes it efficient for training.

关键词： seismic topographic effect finite element method BP neural network algorithm earthquake disaster prevention

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Effects of turbulence on carbon emission in shallow lakes

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Journal of Environmental Sciences 2018年第7期30卷 166-172页

作者： Lin Zhu Boqiang Qin Jian Zhou Bryce Van Dam Wenqing Shi Taihu Lake Laboratory Ecosystem station State Key Laboratory of Lake Science and Environment Nanjing Institute of Geography and Limnology Chinese Academy of Sciences Institute of Marine Sciences University of North Carolina at Chapel Hill Center for Eco-Environmental research Nanjing Hydraulics Research Institute

Turbulent mixing is enhanced in shallow lakes. As a result, exchanges across the air–water and sediment–water interfaces are increased, causing these systems to be large sources of greenhouse gases. This study investigated the effects of turbulence on carbon dioxide（CO2）and methane（CH4） emissions in shallow lakes using simulated mesocosm *** demonstrated that turbulence increased CO2 emissions, while simultaneously decreasing CH4 emissions by altering microbial processes. Under turbulent conditions, a greater fraction of organic carbon was recycled as CO2 instead of CH4, potentially reducing the net global warming effect because of the lower global warming potential of CO2 relative to CH4. The CH4/CO2 flux ratio was approximately 0.006 under turbulent conditions, but reached 0.078 in the control. The real-time quantitative PCR analysis indicated that methanogen abundance decreased and methanotroph abundance increased under turbulent conditions, inhibiting CH4 production and favoring the oxidation of CH4 to *** findings suggest that turbulence may play an important role in the global carbon cycle by limiting CH4 emissions, thereby reducing the net global warming effect of shallow lakes.

关键词： Turbulence Carbon dioxide Methane Methanogen Methanotroph

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First Record of Male Combat in a Wild Malayan Pit Viper(Calloselasma rhodostoma)

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Asian Herpetological research 2015年第3期6卷 237-239页

作者： Colin T.STRINE Curt BARNES Inês SILVA Bartosz NADOLSKI Taksin ARTCHAWAKOM Jacques G.hill Pongthep SUWANWAREE Suranaree University of Technology Sakaerat Environmental research station Department of Biological Science University of Arkansas

The first record of ritualized combat behavior between two male Calloselasma rhodostoma（Malayan Pit Viper） was observed in Sakaerat Biosphere Reserve, Nakhon Ratchasima, Thailand. Although most of the behavior of C. rhodostoma was similar to that recorded for other viperids, an instance of submissive behavior, which to our knowledge, has not been recorded in any snake species. Additional field observations are required to better understand the structure and function of combat behavior in C. rhodostoma.

关键词： Calloselasma rhodostoma Ritualized combat Sakaerat Southeast Asia

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New Estimates of 24-Hour Probable Maximum Precipitation (PMP) for the British Isles

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Journal of Geoscience and Environment Protection 2021年第7期9卷 209-228页

作者： Colin Clark James Dent Charldon hill research station The Batch Shute Lane Bruton Somerset UK Laxfield House Cundy’s Lane Brent Eleigh Suffolk UK

Estimates of PMP are needed in order to estimate the spillway design flood for dams which must be capable of safely passing the probable maximum flood (PMF). For over forty years the standard estimates of the Flood Studies Report (FSR) have almost always been used. However, since then several studies have shown that these values are too low, and new estimates for South West England and then Britain were published. This paper extends these studies to include the whole of the British Isles. The study uses 6570 station years’ data in a new method of frequency analysis that identifies part of the data which represents the long term situation. Further analyses to support the results of this approach have been produced from the in situ maximisation of 12 historic storms using World Meteorological Organisation methods. The results are broadly consistent with those obtained from frequency analysis. Values of 24 hour PMP in Britain range from 600 mm in upland areas of the Lake District, to 400 mm in parts of East Anglia. This range of values is present in Wales and parts of South West England. For Ireland the highest values are over the upland areas, such as in the Wicklow Mountains (550 mm) and SW Ireland (600 mm), while in the lowlands values around 350 mm can be expected. The question of uncertainty in estimating PMP is considered, most of which is due to the temporal and spatial shortcomings of the data. The implications for the probable maximum flood (PMF) and spillway design flood mean that widespread reassessment of dam safety should be carried out at once.

关键词： Probable Maximum Precipitation Moisture Maximisation Modified Gumbel Reduced Variate

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Morphology and formation mechanism of sand shadow dunes on the Qinghai-Tibet Plateau

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Journal of Arid Land 2015年第1期7卷 10-26页

作者： JianHua XIAO JianJun QU ZhengYi YAO YingJun PANG KeCun ZHANG Key Laboratory of Desert and Desertification Cold and Arid Regions Environmental and Engineering Research InstituteChinese Academy of Sciences Dunhuang Gobi and Desert Ecology and Environment research station Cold and Arid Regions Environmental and Engineering Research Institute Chinese Academy of Sciences Gansu Center for Sand Hazard Reduction Engineering and Technology

The formation and development of dunes depend on wind-blown sand movement which is affected by the characteristics of sand material, topography, wind regimes and other factors. In this paper, we investigated two sand shadow dune groups in Shigatse and Za＇gya Zangbo of Tibet and an individual dune in Da Qaidam of Qinghai, and analyzed their topographies and morphologies, and the physical characteristics of the sand, wind regime and sand transport. Formed under harsh conditions behind hills, these mature sand shadow dunes are hundreds of meters long, have significant ridges and crescent dunes downwind, and have a hill pass on one or both sides. Wind tunnel experiments revealed that the hill gap and wind velocity are important factors in the formation of these dunes Sand shadow dunes formed only when the gap spacing is two-thirds of the hill height. When wind velocities are 20 m/s, the sand body is divided into two parts. The hill pass allows the transport of sand by wind, creating a ＂nar- row-pipe effect＂, which causes the transported material to gradually accumulate in the center of the shadow zone. We observed that the following are needed for sand shadow dunes to form：（1） strong winds, sufficient sand, suitable obstacles and a dry climate; （2） one or both sides of the obstacle forming the shadow zone must have a hill pass; and （3） the windward side of the obstacle must have a wide, flat area, providing adequate spacing for wind flow and transport of material and the leeward side must have a sufficiently broad, flat area to allow the release of the transported material. research results on these newly discovered dunes on the Qinghai-Tibet Plateau could contribute to the understanding of dune geomorphology.

关键词： sand shadow dune morphology aeolian landform wind tunnel Qinghai-Tibet Plateau

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Overview of Stachybotrys(Memnoniella)and current species status

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Fungal Diversity 2015年第2期71卷 17-83页

作者： Yong Wang Kevin D.Hyde Eric H.C.McKenzie Yu-Lan Jiang De-Wei Li De-Gang Zhao Guizhou Key Laboratory Agro-Bioengineering Guizhou UniversityGuiyangGuizhou 550025People’s Republic of China Department of Plant Pathology College of AgricultureGuizhou UniversityGuiyangGuizhou 550025China Institute of Excellence in Fungal research School of ScienceMae Fah Luang UniversityChiang RaiThailand Landcare research Private Bag 92170AucklandNew Zealand Valley Laboratory The Connecticut Agricultural Experiment Station153 Cook Hill RoadWindsorCT 06095USA

Stachybotrys(asexual Hypocreales)has a worldwide *** genus inhabits substrates rich in cellulose and is closely related to *** of species has previously been based on morphology,with conidial characters being considered as *** study reevaluates Stachybotrys and Memnoniella,which is shown to include at least seven species-groups;while Memnoniella is a synonym of *** sexual genera Ornatispora and Melanopsamma are also synonyms of *** the exception of Stachybotrys subsimplex,species formed a wellsupported monophyletic group in LSU data analysis belonging to ***-four accepted Stachybotrys species are discussed,while eight species are considered to belong to other genera or are doubtful in this paper and a key to these species *** new combinations and 1 nomina nova is *** status of Stachybotrys species on health,as human or animal pathogens,in indoor environments,and use as biocontrol agents and compound discovery are also discussed.

关键词： Current species Nomen excludendum Phylogeny Synonyms Taxonomic history

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New Agri-Silvo-Pastoral Model Utilizing Terrace RiserEnhancing Crop and Livestock Production Developed inNepal

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Journal of Agricultural Science and Technology(A) 2019年第6期9卷 371-389页

作者： Barakoti Tanka Prasad Sah Raj Kumar Agricultural research station Nepal Agricultural Research CouncilDhankuta 56800PakhribasNepal

Twelve fodder species with maize (Zea mays) and millet (Eleusine coracana) were evaluated under agri-silvo-pastoral system along the Terrace risers (T-risers) of cropping land in the Agricultural research station Pakhribas, Nepal. Major aim of innovative agroforestry experiment designed and tested first time in Nepal was to utilize one-third land in risers of cropping terraces due to limited lands of smallholders to produce green fodders needed for livestock. Trees were planted at 1.5 m on the terrace edges and ground fodders at 30-50 cm on the risers. Trees were not allowed to grow tall to avoid shade effect on crops grown in terraces. They were felled at breast height in second year growing coppices for fodder. The results showed higher survival (76% to 100%), growth (1-3 m high) and yield of improved forages and fodder trees indicating potential for cultivation on T-risers. Dry matter (DM) of tree fodders varied 31%-49%, and ground fodders 19%-32%. DM yields ranged 3.0 t/ha (Stylosanthes guanensis) to 26.5 t/ha (Pennisetum purpureum). Combined effects of fodder species on major hill crops, maize and finger millet growth, yield and other attributes were monitored in the terraces. Most mean data were significant and at par between the treatments. Better combinations of tree and ground fodders for higher grain and stover yields (3.1 t/ha and 3.4 t/ha, respectively) of maize were Grewia optiva/Thysalonaema maxima, Desmodium intortum, Ficus auriculata/Setaria anceps, D. intortum (2.7 t/ha and 3.3 t/ha, respectively). Promising combinations for finger millet growth and yields (2-3 t/ha) were G. optiva/T. maxima, Bauhinia purpurea/S. anceps, F. semicordata/P. cetaceum. Soil analysis result showed positive impact of fodders on the risers where organic matter was highly increased after three years. Farmers and stakeholders also evaluated this technology that has been successful and recommended for similar ecological regions.

关键词： Terrace riser fodder trees forage species maize and millet agri-silvo-pastoral system new model.

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