cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8196989.v1
title: Additional file 2: of Identification and profiling of upland cotton microRNAs at fiber initiation stage under exogenous IAA application

description: Table S2. Names and sequences of the identified known miRNAs in six libraries. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8196995
title: Additional file 3: of Identification and profiling of upland cotton microRNAs at fiber initiation stage under exogenous IAA application

description: Table S3. Names and sequences of the identified novel miRNAs in six libraries. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8196995.v1
title: Additional file 3: of Identification and profiling of upland cotton microRNAs at fiber initiation stage under exogenous IAA application

description: Table S3. Names and sequences of the identified novel miRNAs in six libraries. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8197001
title: Additional file 4: of Identification and profiling of upland cotton microRNAs at fiber initiation stage under exogenous IAA application

description: Structures of all the identified novel miRNAs. (ZIP 1005 kb)
DOI: 10.6084/m9.figshare.8197001.v1
title: Additional file 4: of Identification and profiling of upland cotton microRNAs at fiber initiation stage under exogenous IAA application

description: Structures of all the identified novel miRNAs. (ZIP 1005 kb)
DOI: 10.6084/m9.figshare.20255619
title: FROM-GLC Plus: toward near real-time and multi-resolution land cover mapping

description: Global land cover has undergone extensive and rapid changes as a result of human activities and climate change. These changes have had a significant impact on biodiversity, the surface energy balance, and sustainable development. Global land cover data underpins research on the development of earth system models, resource management, and evaluation of the ecological environment. However, there are limitations in the classification detail, spatial resolution, and rapid change monitoring capability of global land cover change data. Building on the earlier Global Land Cover Mapping (Finer Resolution Observation and Monitoring – Global Land Cover, FROM-GLC), we developed the improved Global Land Cover Change Monitoring Platform (FROM-GLC Plus) using methods such as multi-season sample space-time migration, multi-source data time series reconstruction, and machine learning. The FROM-GLC Plus system provides a capacity for producing global land cover change data set from the 1980s with flexibility in spatio–temporal details. The preliminary results show that FROM-GLC Plus provides a framework for near real-time land cover mapping at multi-temporal (annual to daily) and multi-resolution (30 m to sub-meter) levels.
DOI: 10.6084/m9.figshare.8197007
title: Additional file 5: of Identification and profiling of upland cotton microRNAs at fiber initiation stage under exogenous IAA application

description: Table S4. MiRNAs and the corresponding target genes. (XLSX 30 kb)
DOI: 10.6084/m9.figshare.8197007.v1
title: Additional file 5: of Identification and profiling of upland cotton microRNAs at fiber initiation stage under exogenous IAA application

description: Table S4. MiRNAs and the corresponding target genes. (XLSX 30 kb)
DOI: 10.6084/m9.figshare.20255619.v1
title: FROM-GLC Plus: toward near real-time and multi-resolution land cover mapping

description: Global land cover has undergone extensive and rapid changes as a result of human activities and climate change. These changes have had a significant impact on biodiversity, the surface energy balance, and sustainable development. Global land cover data underpins research on the development of earth system models, resource management, and evaluation of the ecological environment. However, there are limitations in the classification detail, spatial resolution, and rapid change monitoring capability of global land cover change data. Building on the earlier Global Land Cover Mapping (Finer Resolution Observation and Monitoring – Global Land Cover, FROM-GLC), we developed the improved Global Land Cover Change Monitoring Platform (FROM-GLC Plus) using methods such as multi-season sample space-time migration, multi-source data time series reconstruction, and machine learning. The FROM-GLC Plus system provides a capacity for producing global land cover change data set from the 1980s with flexibility in spatio–temporal details. The preliminary results show that FROM-GLC Plus provides a framework for near real-time land cover mapping at multi-temporal (annual to daily) and multi-resolution (30 m to sub-meter) levels.
DOI: 10.6084/m9.figshare.7672787
title: Additional file 1: of PCK1 negatively regulates cell cycle progression and hepatoma cell proliferation via the AMPK/p27Kip1 axis

description: Primer sequences of target genes. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.7672787.v1
title: Additional file 1: of PCK1 negatively regulates cell cycle progression and hepatoma cell proliferation via the AMPK/p27Kip1 axis

description: Primer sequences of target genes. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.25243318
title: Book_Dementia Data_ABS and AIHW.xlsx

description: Data sets from Australian Bureau of Statistics (ABS) https://www.abs.gov.au/articles/dementia-australia#data-downloads and the Australian Institute of Health and Welfare (AIHW) https://www.aihw.gov.au/reports-data/health-conditions-disability-deaths/dementia/data?&page=1 used in a university assignment. Full data sets and licensing are available at the the ABS and AIHW websites.
DOI: 10.6084/m9.figshare.25243318.v1
title: Book_Dementia Data_ABS and AIHW.xlsx

description: Data sets from Australian Bureau of Statistics (ABS) https://www.abs.gov.au/articles/dementia-australia#data-downloads and the Australian Institute of Health and Welfare (AIHW) https://www.aihw.gov.au/reports-data/health-conditions-disability-deaths/dementia/data?&page=1 used in a university assignment. Full data sets and licensing are available at the the ABS and AIHW websites.
DOI: 10.6084/m9.figshare.22352938
title: Identification and characterization of microRNAs, especially gga-miR-181b-5p, in chicken macrophages associated with avian pathogenic <i>E. coli</i> infection

description: Avian pathogenic <i>E. coli</i> (APEC) is a common pathogen in the poultry industry, which can cause substantial economic losses. Recently, emerging evidence showed that miRNAs were involved in various viral and bacterial infections. To elucidate the role of miRNAs in chicken macrophages in response to APEC infection, we attempted to investigate the miRNAs expression pattern upon APEC infection via miRNA-seq, and to identify the molecular mechanism of the important miRNAs by using RT-qPCR, western blotting, dual-luciferase reporter assay, and CCK-8. The results showed that a total of 80 differentially expressed (DE) miRNAs were identified in comparison of APEC vs. wild-type group, which corresponded to 724 target genes. Moreover, the target genes of the identified DE miRNAs were mainly significantly enriched in the MAPK signalling pathway, autophagy-bird, mTOR signalling pathway, ErbB signalling pathway, Wnt signalling pathway, and TGF-beta signalling pathway. Remarkably, gga-miR-181b-5p is able to participate in host immune and inflammatory responses against APEC infection via targeting of <i>TGFBR1</i> to modulate the activation of TGF-beta signalling pathway. Collectively, this study provides a perspective of miRNA expression patterns in chicken macrophages upon APEC infection. These findings provide insight into miRNAs against APEC infection, and gga-miR-181b-5p might be a potential target for treating APEC infection.
DOI: 10.6084/m9.figshare.22352938.v1
title: Identification and characterization of microRNAs, especially gga-miR-181b-5p, in chicken macrophages associated with avian pathogenic <i>E. coli</i> infection

description: Avian pathogenic <i>E. coli</i> (APEC) is a common pathogen in the poultry industry, which can cause substantial economic losses. Recently, emerging evidence showed that miRNAs were involved in various viral and bacterial infections. To elucidate the role of miRNAs in chicken macrophages in response to APEC infection, we attempted to investigate the miRNAs expression pattern upon APEC infection via miRNA-seq, and to identify the molecular mechanism of the important miRNAs by using RT-qPCR, western blotting, dual-luciferase reporter assay, and CCK-8. The results showed that a total of 80 differentially expressed (DE) miRNAs were identified in comparison of APEC vs. wild-type group, which corresponded to 724 target genes. Moreover, the target genes of the identified DE miRNAs were mainly significantly enriched in the MAPK signalling pathway, autophagy-bird, mTOR signalling pathway, ErbB signalling pathway, Wnt signalling pathway, and TGF-beta signalling pathway. Remarkably, gga-miR-181b-5p is able to participate in host immune and inflammatory responses against APEC infection via targeting of <i>TGFBR1</i> to modulate the activation of TGF-beta signalling pathway. Collectively, this study provides a perspective of miRNA expression patterns in chicken macrophages upon APEC infection. These findings provide insight into miRNAs against APEC infection, and gga-miR-181b-5p might be a potential target for treating APEC infection.
DOI: 10.6084/m9.figshare.12915793
title: Beyond Plug and Pray: Context Sensitivity and <i>in silico</i> Design of Artificial Neomycin Riboswitches

description: Gene regulation in prokaryotes often depends on RNA elements such as riboswitches or RNA thermometers located in the 5′ untranslated region of mRNA. Rearrangements of the RNA structure in response, e.g., to the binding of small molecules or ions control translational initiation or premature termination of transcription and thus mRNA expression. Such structural responses are amenable to computational modelling, making it possible to rationally design synthetic riboswitches for a given aptamer. Starting from an artificial aptamer, we construct the first synthetic transcriptional riboswitches that respond to the antibiotic neomycin. We show that the switching behaviour <i>in vivo</i> critically depends not only on the sequence of the riboswitch itself, but also on its sequence context. We therefore developed <i>in silico</i> methods to predict the impact of the context, making it possible to adapt the design and to rescue non-functional riboswitches. We furthermore analyse the influence of 5′ hairpins with varying stability on neomycin riboswitch activity. Our data highlight the limitations of a simple plug-and-play approach in the design of complex genetic circuits and demonstrate that detailed computational models significantly simplify, improve, and automate the design of transcriptional circuits. Our design software is available under a free licence on GitHub (https://github.com/xileF1337/riboswitch_design).
DOI: 10.6084/m9.figshare.25241449.v1
title: NSS with only the subjects who went through the generalization test

description: A linear mixed model for the number of successful sequences of the tests for only the subjects who went through the generalization test
DOI: 10.6084/m9.figshare.12915793.v2
title: Beyond Plug and Pray: Context Sensitivity and <i>in silico</i> Design of Artificial Neomycin Riboswitches

description: Gene regulation in prokaryotes often depends on RNA elements such as riboswitches or RNA thermometers located in the 5′ untranslated region of mRNA. Rearrangements of the RNA structure in response, e.g., to the binding of small molecules or ions control translational initiation or premature termination of transcription and thus mRNA expression. Such structural responses are amenable to computational modelling, making it possible to rationally design synthetic riboswitches for a given aptamer. Starting from an artificial aptamer, we construct the first synthetic transcriptional riboswitches that respond to the antibiotic neomycin. We show that the switching behaviour <i>in vivo</i> critically depends not only on the sequence of the riboswitch itself, but also on its sequence context. We therefore developed <i>in silico</i> methods to predict the impact of the context, making it possible to adapt the design and to rescue non-functional riboswitches. We furthermore analyse the influence of 5′ hairpins with varying stability on neomycin riboswitch activity. Our data highlight the limitations of a simple plug-and-play approach in the design of complex genetic circuits and demonstrate that detailed computational models significantly simplify, improve, and automate the design of transcriptional circuits. Our design software is available under a free licence on GitHub (https://github.com/xileF1337/riboswitch_design).
DOI: 10.6084/m9.figshare.12915793.v1
title: Beyond Plug and Pray: Context Sensitivity and <i>in silico</i> Design of Artificial Neomycin Riboswitches

description: Gene regulation in prokaryotes often depends on RNA elements such as riboswitches or RNA thermometers located in the 5′ untranslated region of mRNA. Rearrangements of the RNA structure in response, e.g., to the binding of small molecules or ions control translational initiation or premature termination of transcription and thus mRNA expression. Such structural responses are amenable to computational modeling, making it possible to rationally design synthetic riboswitches for a given aptamer. Starting from an artificial aptamer, we construct the first synthetic transcriptional riboswitches that respond to the antibiotic neomycin. We show that the switching behavior <i>in vivo</i> critically depends not only on the sequence of the riboswitch itself, but also on its sequence context. We therefore developed <i>in silico</i> methods to predict the impact of the context, making it possible to adapt the design and to rescue non-functional riboswitches. We furthermore analyze the influence of 5′ hairpins with varying stability on neomycin riboswitch activity. Our data highlight the limitations of a simple plug-and-play approach in the design of complex genetic circuits and demonstrate that detailed computational models significantly simplify, improve, and automate the design of transcriptional circuits. Our design software is available under a free license on GitHub.<sup>7</sup>
DOI: 10.6084/m9.figshare.23926011
title: Larger presence of ectomycorrhizae detected from pygmy pine ecotype in the fire-frequent pine barrens ecosystem

description: Pine barrens ecosystem has acidic, sandy, and nutrient-poor soil and is prone to drought and fire. In the New Jersey Pine Barrens, the predominant pitch pine (<i>Pinus rigida</i>) consists of two ecotypes: the regular pitch pines with heights of 4.6–12 m, and the pygmy pines of low stature (1.2–1.8 m) in the New Jersey Pine Plains. Previous ecological studies suggested that the dwarf pines in the Pine Plains that are embedded within the Pine Barrens were an evolutionary adaptation to frequent fire. Pines are obligate ectomycorrhizal (EcM) mutualists, and their root mycobiota may contribute to stress protection and plant health. However, information on the mycobiota associated with plants in the pine barrens ecosystem is lacking. To have a holistic understanding of the evolution and adaptation in this stressed environment, we used both culture-independent metabarcoding and culture-based method to characterize the mycobiota from soil and root of the two ecotypes and to identify core mycobiota. We found that Agaricomycetes, Leotiomycetes, and Mucoromycotina are predominant fungi in the New Jersey Pine Barrens ecosystem, which is rich in root mutualistic fungi. We observed that the pygmy pine roots had significantly higher density of EcM tips than the regular pine roots. This was corroborated by our metabarcoding analysis, which showed that the pygmy pine trees had higher ratio of ectomycorrhiza-forming fungi than the regular-statured pines. We hypothesize that symbiotrophic EcM fungi associated with pygmy pines are capable of mitigating high fire stress in the Pine Plains.
DOI: 10.6084/m9.figshare.23926011.v1
title: Larger presence of ectomycorrhizae detected from pygmy pine ecotype in the fire-frequent pine barrens ecosystem

description: Pine barrens ecosystem has acidic, sandy, and nutrient-poor soil and is prone to drought and fire. In the New Jersey Pine Barrens, the predominant pitch pine (<i>Pinus rigida</i>) consists of two ecotypes: the regular pitch pines with heights of 4.6–12 m, and the pygmy pines of low stature (1.2–1.8 m) in the New Jersey Pine Plains. Previous ecological studies suggested that the dwarf pines in the Pine Plains that are embedded within the Pine Barrens were an evolutionary adaptation to frequent fire. Pines are obligate ectomycorrhizal (EcM) mutualists, and their root mycobiota may contribute to stress protection and plant health. However, information on the mycobiota associated with plants in the pine barrens ecosystem is lacking. To have a holistic understanding of the evolution and adaptation in this stressed environment, we used both culture-independent metabarcoding and culture-based method to characterize the mycobiota from soil and root of the two ecotypes and to identify core mycobiota. We found that Agaricomycetes, Leotiomycetes, and Mucoromycotina are predominant fungi in the New Jersey Pine Barrens ecosystem, which is rich in root mutualistic fungi. We observed that the pygmy pine roots had significantly higher density of EcM tips than the regular pine roots. This was corroborated by our metabarcoding analysis, which showed that the pygmy pine trees had higher ratio of ectomycorrhiza-forming fungi than the regular-statured pines. We hypothesize that symbiotrophic EcM fungi associated with pygmy pines are capable of mitigating high fire stress in the Pine Plains.
DOI: 10.6084/m9.figshare.23926013
title: PCABM: Pairwise Covariates-Adjusted Block Model for Community Detection*

description: One of the most fundamental problems in network study is community detection. The stochastic block model (SBM) is a widely used model, and various estimation methods have been developed with their community detection consistency results unveiled. However, the SBM is restricted by the strong assumption that all nodes in the same community are stochastically equivalent, which may not be suitable for practical applications. We introduce a pairwise covariates-adjusted stochastic block model (PCABM), a generalization of SBM that incorporates pairwise covariate information. We study the maximum likelihood estimates of the coefficients for the covariates as well as the community assignments. It is shown that both the coefficient estimates of the covariates and the community assignments are consistent under suitable sparsity conditions. Spectral clustering with adjustment (SCWA) is introduced to efficiently solve PCABM. Under certain conditions, we derive the error bound of community detection under SCWA and show that it is community detection consistent. In addition, we investigate model selection in terms of the number of communities and feature selection for the pairwise covariates, and propose two corresponding algorithms. PCABM compares favorably with the SBM or degree-corrected stochastic block model (DCBM) under a wide range of simulated and real networks when covariate information is accessible.
DOI: 10.6084/m9.figshare.23926013.v1
title: PCABM: Pairwise Covariates-Adjusted Block Model for Community Detection*

description: One of the most fundamental problems in network study is community detection. The stochastic block model (SBM) is a widely used model, and various estimation methods have been developed with their community detection consistency results unveiled. However, the SBM is restricted by the strong assumption that all nodes in the same community are stochastically equivalent, which may not be suitable for practical applications. We introduce a pairwise covariates-adjusted stochastic block model (PCABM), a generalization of SBM that incorporates pairwise covariate information. We study the maximum likelihood estimates of the coefficients for the covariates as well as the community assignments. It is shown that both the coefficient estimates of the covariates and the community assignments are consistent under suitable sparsity conditions. Spectral clustering with adjustment (SCWA) is introduced to efficiently solve PCABM. Under certain conditions, we derive the error bound of community detection under SCWA and show that it is community detection consistent. In addition, we investigate model selection in terms of the number of communities and feature selection for the pairwise covariates, and propose two corresponding algorithms. PCABM compares favorably with the SBM or degree-corrected stochastic block model (DCBM) under a wide range of simulated and real networks when covariate information is accessible.
DOI: 10.6084/m9.figshare.19731717
title: Changes in testing and incidence of <i>Chlamydia trachomatis</i> and <i>Neisseria gonorrhoeae</i> – the possible impact of the COVID-19 pandemic in the three Scandinavian countries

description: This study aimed to investigate what impact the COVID-19 pandemic and its associated restrictions had on <i>Chlamydia trachomatis</i> and <i>Neisseria gonorrhoeae</i> infections in Sweden, Denmark and Norway, countries with very different governmental strategies for handling this pandemic. Retrospective analysis of data collected <i>via</i> requests to Swedish regions and to health authorities in Denmark and Norway. The data were collected for the years 2018–2020 and the data from Sweden were more detailed. When the pandemic restrictions were installed in 2020, the number of reported chlamydia cases decreased. The decline was most pronounced in Norway 10.8% (2019: <i>n</i> = 28,446; 2020: <i>n</i> = 25,444) while it was only 3.1% in Denmark (2019: <i>n</i> = 35,688; 2020: <i>n</i> = 34,689) and 4.3% in Sweden (2019: <i>n</i> = 34,726; 2020: <i>n</i> = 33,339). Nucleic acid amplifications tests for chlamydia decreased in Sweden (10%) and Norway (18%) in 2020 compared to 2019, while in Denmark a 21% decrease was noted in April 2020 but thereafter increased to a higher level than 2019. The number of reported gonorrhoea cases decreased in Sweden (17%) and in Norway (39%) in 2020 compared to 2019, while a 21% increase was noted in Denmark. Pandemic restrictions had an impact on the number of reported chlamydia infections in all three countries, but only temporarily and did not seem to be correlated to the restriction levels. The number of reported gonorrhoea infections in Sweden and Norway significantly decreased but not in Denmark. Pandemic restrictions appear to have had a limited effect on the spread of chlamydia and gonorrhoea.