cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7678031
title: The temporal stability of recurrence quantification analysis attributes from chronic atrial fibrillation electrograms

description: Abstract Introduction The temporal behavior of atrial electrograms (AEGs) collected during persistent atrial fibrillation (persAF) directly affects ablative treatment outcomes. We investigated different durations of AEGs collected during persAF using recurrence quantification analysis (RQA). Methods 797 bipolar AEGs with different durations (from 0.5 s to 8 s) from 18 patients were investigated. Four RQA-based attributes were evaluated based on AEG durations: determinism (DET); recurrence rate (RR); laminarity (LAM); and diagonal lines’ entropy (ENTR). The Spearman correlation (ρ) between each duration versus 8 s was calculated. AEG classification was performed following the CARTO criteria (Biosense Webster) and receiving operating characteristic (ROC) curves were created for the RQA variables. Results The RQA variables successfully discriminated the AEGs: the area under the ROC curves were as high as 0.70 for AEGs with 3.5 s or greater. Three types of AEGs were found using these variables: normal, fractionated and temporally unstable. The number of unstable AEGs decreased with longer AEG segments. Different AEG durations significantly affected the RQA variables (P&lt;0.0001), with no statistical difference between the durations 6 s, 7 s and 8 s for DET, LAM and ENTR, and no difference between 7 s and 8 s for RR (P&lt;0.0001). AEGs with 3 s or longer have shown ρ ≥ 80% for all variables. Conclusion The RQA variables have been shown effective in the characterization of AEGs collected during persAF with a shorter duration than current recommendations, which motivates their use for the characterization of atrial substrate during persAF ablation.
DOI: 10.6084/m9.figshare.8202419.v2
title: Identification of new transmembrane proteins concentrated at the nuclear envelope using organellar proteomics of mesenchymal cells

description: The double membrane nuclear envelope (NE), which is contiguous with the ER, contains nuclear pore complexes (NPCs) – the channels for nucleocytoplasmic transport, and the nuclear lamina (NL) – a scaffold for NE and chromatin organization. Since numerous human diseases linked to NE proteins occur in mesenchyme-derived cells, we used proteomics to characterize NE and other subcellular fractions isolated from mesenchymal stem cells and from adipocytes and myocytes. Based on spectral abundance, we calculated enrichment scores for proteins in the NE fractions. We demonstrated by quantitative immunofluorescence microscopy that five little-characterized proteins with high enrichment scores are substantially concentrated at the NE, with Itprip exposed at the outer nuclear membrane, Smpd4 enriched at the NPC, and Mfsd10, Tmx4, and Arl6ip6 likely residing in the inner nuclear membrane. These proteins provide new focal points for studying the functions of the NE. Moreover, our datasets provide a resource for evaluating additional potential NE proteins.
DOI: 10.6084/m9.figshare.7678253
title: MODELING OF MULTIPHASE FLOW IN AN AIR-COOLING SYSTEM USING THE CFD-FSCA APPROACH

description: Abstract The deposition of crystallized ammonium salt particles presents serious damage to the hydrogenation reactor effluent air cooler (REAC) in petrochemical engineering. The correlation technology process was analyzed for predicting the particle deposition situation in air coolers. Moreover, the particle crystallization and deposition were revealed, and a mathematical model for flow field simulation was established by computational fluid dynamics (CFD). In addition, the fast search clustering algorithm (FSCA) realized in Matlab software was applied to detect tube anomaly. The relatively greater risk of deposition or blockage in the tube area was detected, and this finding is consistent with the distribution of the surface temperature field in air coolers. Meanwhile, good qualitative agreement was found between the distribution rule of particle deposition rate as simulated by CFD and the situation of opened header box on the spot. Therefore, the combined method of CFD simulation and FSCA detection can be utilized for predicting the condition of particle deposition in the air-cooling systems.
DOI: 10.6084/m9.figshare.16590833
title: Additional file 6 of RPocket: an intuitive database of RNA pocket topology information with RNA-ligand data resources

description: Additional file 6. Folder S2: Interaction info of RNA-ligand complexes.
DOI: 10.6084/m9.figshare.16590836
title: Additional file 7 of RPocket: an intuitive database of RNA pocket topology information with RNA-ligand data resources

description: Additional file 7. Folder S3: Nine other experimental structures and their modeling structures and pockets.
DOI: 10.6084/m9.figshare.16590839.v1
title: Additional file 8 of RPocket: an intuitive database of RNA pocket topology information with RNA-ligand data resources

description: Additional file 8. Folder S4: RPDescriptor program code for shape classification of RNA pockets.
DOI: 10.6084/m9.figshare.16590836.v1
title: Additional file 7 of RPocket: an intuitive database of RNA pocket topology information with RNA-ligand data resources

description: Additional file 7. Folder S3: Nine other experimental structures and their modeling structures and pockets.
DOI: 10.6084/m9.figshare.21310455.v1
title: Breast cancer-associated SNP rs72755295 is a cis-regulatory variation for human EXO1

description: Abstract Breast cancer is the most common malignant tumor in women. A previous genome-wide association study reports that rs72755295, a SNP locating at intron of EXO1 (exonuclease 1), is associated with breast cancer. Due to the complete linkage disequilibrium between rs72755295 and rs4149909, a nonsynonymous mutation for EXO1, rs4149909 is supposed to be the causal SNP. Since EXO1 is overexpressed in breast carcinoma samples, we hypothesized that the genetic variations in this locus might confer breast cancer risk by regulating EXO1 expression. To substantiate this, a functional genomics study was performed. The dual luciferase assay indicated that G of rs72755295 presents significantly higher relative enhancer activity than A, thus verifying that this SNP can influence gene expression in breast cell. Through chromosome conformation capture it was disclosed that the enhancer containing rs72755295 can interact with the EXO1 promoter. RNA-seq analysis indicated that EXO1 expression is dependent on the rs72755295 genotype. By chromatin immunoprecipitation, the transcription factor PAX6 (paired box 6) was recognized to bind the region spanning rs72755295. In electrophoretic mobility shift assay, G of rs72755295 displays obviously higher binding affinity with nuclear protein than A. Our results indicated that rs72755295 is a cis-regulatory variation for EXO1 and might confer breast cancer risk besides rs4149909.
DOI: 10.6084/m9.figshare.21310455
title: Breast cancer-associated SNP rs72755295 is a cis-regulatory variation for human EXO1

description: Abstract Breast cancer is the most common malignant tumor in women. A previous genome-wide association study reports that rs72755295, a SNP locating at intron of EXO1 (exonuclease 1), is associated with breast cancer. Due to the complete linkage disequilibrium between rs72755295 and rs4149909, a nonsynonymous mutation for EXO1, rs4149909 is supposed to be the causal SNP. Since EXO1 is overexpressed in breast carcinoma samples, we hypothesized that the genetic variations in this locus might confer breast cancer risk by regulating EXO1 expression. To substantiate this, a functional genomics study was performed. The dual luciferase assay indicated that G of rs72755295 presents significantly higher relative enhancer activity than A, thus verifying that this SNP can influence gene expression in breast cell. Through chromosome conformation capture it was disclosed that the enhancer containing rs72755295 can interact with the EXO1 promoter. RNA-seq analysis indicated that EXO1 expression is dependent on the rs72755295 genotype. By chromatin immunoprecipitation, the transcription factor PAX6 (paired box 6) was recognized to bind the region spanning rs72755295. In electrophoretic mobility shift assay, G of rs72755295 displays obviously higher binding affinity with nuclear protein than A. Our results indicated that rs72755295 is a cis-regulatory variation for EXO1 and might confer breast cancer risk besides rs4149909.
DOI: 10.6084/m9.figshare.21834260.v1
title: Compositional Graphical Lasso Resolves the Impact of Parasitic Infection on Gut Microbial Interaction Networks in a Zebrafish Model

description: Understanding how microbes interact with each other is key to revealing the underlying role that microorganisms play in the host or environment and to identifying microorganisms as an agent that can potentially alter the host or environment. For example, understanding how the microbial interactions associate with parasitic infection can help resolve potential drug or diagnostic test for parasitic infection. To unravel the microbial interactions, existing tools often rely on graphical models to infer the conditional dependence of microbial abundances to represent their interactions. However, current methods do not simultaneously account for the discreteness, compositionality, and heterogeneity inherent to microbiome data. Thus, we build a new approach called “compositional graphical lasso” upon existing tools by incorporating the above characteristics into the graphical model explicitly. We illustrate the advantage of compositional graphical lasso over current methods under a variety of simulation scenarios and on a benchmark study, the Tara Oceans Project. Moreover, we present our results from the analysis of a dataset from the Zebrafish Parasite Infection Study, which aims to gain insight into how the gut microbiome and parasite burden covary during infection, thus uncovering novel putative methods of disrupting parasite success. Our approach identifies changes in interaction degree between infected and uninfected individuals for three taxa, Photobacterium, Gemmobacter, and Paucibacter, which are inversely predicted by other methods. Further investigation of these method-specific taxa interaction changes reveals their biological plausibility. In particular, we speculate on the potential pathobiotic roles of Photobacterium and Gemmobacter in the zebrafish gut, and the potential probiotic role of Paucibacter. Collectively, our analyses demonstrate that compositional graphical lasso provides a powerful means of accurately resolving interactions between microbiota and can thus drive novel biological discovery.
DOI: 10.6084/m9.figshare.7153832
title: <i>Picea purpurea</i> has a physiological advantage over its progenitors in alpine ecosystems due to transgressive segregation

description: <i>Picea purpurea</i> originated from the homoploid hybrid speciation, which occupy novel alpine habitats in the north-east region of the Qinghai-Tibet Plateau (QTP) where its progenitors, <i>P. wilsonii</i> and <i>P. likiangensis</i> are excluded. Alpine habitats are usually characterized by low atmospheric CO<sub>2</sub> concentrations and strong solar radiation with a large fraction of shortwave radiation (i.e. blue light). To test whether <i>P. purpurea</i> has the transgressive segregation in photosynthetic capacity and stomatal characteristics contributed to occupying such extreme habitats, we investigated the leaf gas exchange properties at two level of CO<sub>2</sub> concentration (<i>C</i><sub>a</sub>: 200 and 400 μmol mol<sup>−1</sup>), light responsive curves of photosynthesis under three light qualities (red, blue and a mixture of both red and blue light at the ratio of 94:6), stomatal and other relative physiological traits for all three species. Our results show evidence of transgressive segregation in hybrid species; for instance, under blue and red light <i>P. purpurea</i> was demonstrated has the higher quantum yield of CO<sub>2</sub> assimilation (<i>φ</i>) and maximum CO<sub>2</sub> assimilation rate (<i>A</i><sub>max</sub>) than its progenitors. Particularly <i>φ</i> and <i>A</i><sub>max</sub> in <i>P. purpurea</i> were 2-fold higher than these in <i>P. likiangensis. P. purpurea</i> also exhibited higher stomatal conductance at low CO<sub>2</sub> concentrations and instantaneous water use efficiency under all light qualities, have greater leaf pigments content, longer guard cell length and lower linear stomatal density relative to its progenitors. These traits may have enhanced the physiological fitness of <i>P. purpurea</i> and facilitated its colonization to alpine habitats.
DOI: 10.6084/m9.figshare.16590827
title: Additional file 4 of RPocket: an intuitive database of RNA pocket topology information with RNA-ligand data resources

description: Additional file 4. Table S3: Binding sites of RNA-ligand complexes and functional groups of ligands involved in interaction with RNA.
DOI: 10.6084/m9.figshare.7678553
title: Stillbirth risk on <i>fat-1</i> transgenic foetus of sheep caused by deregulated DNA methylation of imprinted genes

description: Imprinted genes play important roles on embryonic development. Aiming at the stillbirths in <i>fat-1</i> transgenic foetuses of sheep, we detected the DNA methylation levels of candidate CpG regions in five imprinted genes (<i>h19</i>, <i>igf2</i>, <i>igf2r</i>, <i>dlk1</i> and <i>gtl2</i>) of diverse tissues in the sheep foetuses, including both male and female <i>fat-1</i> transgenic stillbirths of sheep and the wild live-births of sheep. Imprinted gene <i>igf2</i>, <i>igf2r</i> and <i>dlk1</i> exhibited gender-neutral methylation except <i>h19</i>, which implies that the deregulated DNA methylation influenced by exogenous gene <i>fat-1</i> in imprinted gene <i>h19</i> more likely differs with gender. Besides, we found that exogenous gene <i>fat-1</i> could tend to influence DNA methylation of imprinted gene <i>igf2r</i> in kidney of sheep male-foetus by comparing number of differentially methylated CpG sites. Since the bio-function of <i>fat-1</i> on growth is consistent with <i>h19</i> and <i>igf2r</i>, but opposite with <i>igf2</i> and <i>dlk1</i>, we suggest that the stillbirth risk factors on sheep foetus with exogenous gene <i>fat-1</i> should be focused on abnormal development (of organs or cells) that probably caused by deregulated methylation status of imprinted genes, and the deregulated methylation may be driven by conflicting and overlapped bio-function between exogenous gene and imprinted genes, rather than extrinsic source of gene. <b>Abbreviations:</b> CSF: control sheep female-foetuses; CSM: control sheep male-foetuses; HTLA: Humane Treatment of Laboratory Animals; n-3 PUFA(s): omega-3 polyunsaturated fatty acid(s); TSF: <i>fat-1</i> transgenic sheep-stillbirths of female; TSM: <i>fat-1</i> transgenic sheep-stillbirths of male
DOI: 10.6084/m9.figshare.16590830.v1
title: Additional file 5 of RPocket: an intuitive database of RNA pocket topology information with RNA-ligand data resources

description: Additional file 5. Folder S1: The structure of all RNA pockets.
DOI: 10.6084/m9.figshare.7678553.v1
title: Stillbirth risk on <i>fat-1</i> transgenic foetus of sheep caused by deregulated DNA methylation of imprinted genes

description: Imprinted genes play important roles on embryonic development. Aiming at the stillbirths in <i>fat-1</i> transgenic foetuses of sheep, we detected the DNA methylation levels of candidate CpG regions in five imprinted genes (<i>h19</i>, <i>igf2</i>, <i>igf2r</i>, <i>dlk1</i> and <i>gtl2</i>) of diverse tissues in the sheep foetuses, including both male and female <i>fat-1</i> transgenic stillbirths of sheep and the wild live-births of sheep. Imprinted gene <i>igf2</i>, <i>igf2r</i> and <i>dlk1</i> exhibited gender-neutral methylation except <i>h19</i>, which implies that the deregulated DNA methylation influenced by exogenous gene <i>fat-1</i> in imprinted gene <i>h19</i> more likely differs with gender. Besides, we found that exogenous gene <i>fat-1</i> could tend to influence DNA methylation of imprinted gene <i>igf2r</i> in kidney of sheep male-foetus by comparing number of differentially methylated CpG sites. Since the bio-function of <i>fat-1</i> on growth is consistent with <i>h19</i> and <i>igf2r</i>, but opposite with <i>igf2</i> and <i>dlk1</i>, we suggest that the stillbirth risk factors on sheep foetus with exogenous gene <i>fat-1</i> should be focused on abnormal development (of organs or cells) that probably caused by deregulated methylation status of imprinted genes, and the deregulated methylation may be driven by conflicting and overlapped bio-function between exogenous gene and imprinted genes, rather than extrinsic source of gene. <b>Abbreviations:</b> CSF: control sheep female-foetuses; CSM: control sheep male-foetuses; HTLA: Humane Treatment of Laboratory Animals; n-3 PUFA(s): omega-3 polyunsaturated fatty acid(s); TSF: <i>fat-1</i> transgenic sheep-stillbirths of female; TSM: <i>fat-1</i> transgenic sheep-stillbirths of male
DOI: 10.6084/m9.figshare.21835120
title: Optimization of a cationic liposomal gene delivery system and study of its endocytic pathway

description: Abstract A cationic liposomal gene delivery system comprising DOTAP, DOPE, and cholesterol was prepared and optimized. The results showed that the liposome/DNA (LP/DNA) system had spherical morphology, with a particle size of around 150 nm and zeta potential of approximately 30 mV. Cytotoxicity experiments showed that cells treated with all of the liposome carriers- with the exception of LP1-had more than 80% viability even at a weight ratio of 30. The in vitro transfection efficiency was measured using a Promega™ Luciferase Assay System. Of the tested lipoplexes, LP2/DNA showed the highest cell transfection efficiency (at a weight ratio of 10)-which was similar to or slightly lower than that of Lipofectamine® 2000 in HeLa, A549, and SPC-A1 cell lines. After freeze-drying, the cell transfection efficiency decreased slightly (P&gt;0.05). The cell uptake mechanism study showed that LP/DNA lipoplexes mainly entered cells via clathrin-mediated and caveolin-mediated endocytic pathways. The results confirmed that LP2 has potential for use as an effective gene carrier, and provides experimental evidence to support its further development as a safe and effective gene delivery system.
DOI: 10.6084/m9.figshare.6105968
title: Using the device-oriented subjective outcome (DOSO) scale to measure outcomes of different hearing aids

description: <i>Objective</i>: The device-oriented subjective outcome (DOSO) is a device-oriented questionnaire, intended to minimise the influence of personality on self-reported measures. The aim of this study was to provide normative data with 2015-era hearing aid technologies. <i>Design</i>: This retrospective study evaluated data from records of three clinical trials. The DOSO was administered for the participants’ own devices as a part of the intake and after using research devices in the field. <i>Study sample</i>: The DOSO data were collected from 132 experienced bilateral hearing aid wearers who participated in the clinical trials. <i>Results</i>: The DOSO data collected with the participants’ own devices were compared to the interim normative data collected between 2004 and 2005. The DOSO subscale scores from the participants’ own devices were significantly higher than those from the interim norms, except Listening Effort subscale. To demonstrate the utility of the new norms, a separate set of DOSO data collected from the same participants after using research hearing aids were contrasted to the new normative data. After accounting for possible placebo effects, the DOSO data with research devices revealed additional self-reported benefit of technological advancements. <i>Conclusions</i>: Norms for the DOSO are recommended for evaluating hearing aids with more recent technologies.
DOI: 10.6084/m9.figshare.16590990
title: Additional file 1 of ALKBH5-HOXA10 loop-mediated JAK2 m6A demethylation and cisplatin resistance in epithelial ovarian cancer

description: Additional file 1. Gene Ontology (GO) analysis of differentially expressed genes of RNA-seq.
DOI: 10.6084/m9.figshare.21835201.v1
title: Variations of soil bacterial microbial community and functional structure under different land-uses

description: ABSTRACT To reveal the differences between land-use patterns and the changes in soil properties, the changes in soil bacterial microbial communities and functions driven by land-use patterns were studied by 16SrRNA Gene Fragments and its high-throughput sequencing, relying on the wetland, farmland and forestland soils in the Hongxing National Nature Reserve of Heilongjiang Province. The study area was slightly acidic soil, and the water content, soil organic carbon content, total soil nitrogen and phosphorus contents of wetland soil were higher than farmland and forestland. The suitable C/N of wetland and farmland soil could promote the decomposition of organic matter by microorganisms. The OTUs sequence, Shannon diversity index, ACE index and Chao1 index were significantly higher in wetland than in farmland and forestland. Proteobacteria, Acidobacteria, Bacteroidetes and Actinobacteria were the dominant bacteria in the tested soil samples. The abundance of Proteobacteria in wetland soil samples was significantly higher than in farmland and forestland. The abundance of Acidobacteria in farmland soil samples was significantly higher than in wetland and forestland. According to FAPROTAX algorithm and BugBase phenotype analysis, land-uses can change the abundance of soil functional microorganisms. The dominant functional genes are mainly Chemoheterotrophy and Aerobic chemoheterotrophy bacteria. Nitrification and Aerobic ammonia oxidation bacteria involved in nitrogen cycle in farmland soil are significantly different from wetland and forestland. Land-use mode leads to significant differences between Mobile elements and Gram negative bacteria. It is mainly related to the changes in soil physical and chemical properties such as soil pH, bulk density, soil organic carbon and total nitrogen contents.
DOI: 10.6084/m9.figshare.7678253.v1
title: MODELING OF MULTIPHASE FLOW IN AN AIR-COOLING SYSTEM USING THE CFD-FSCA APPROACH

description: Abstract The deposition of crystallized ammonium salt particles presents serious damage to the hydrogenation reactor effluent air cooler (REAC) in petrochemical engineering. The correlation technology process was analyzed for predicting the particle deposition situation in air coolers. Moreover, the particle crystallization and deposition were revealed, and a mathematical model for flow field simulation was established by computational fluid dynamics (CFD). In addition, the fast search clustering algorithm (FSCA) realized in Matlab software was applied to detect tube anomaly. The relatively greater risk of deposition or blockage in the tube area was detected, and this finding is consistent with the distribution of the surface temperature field in air coolers. Meanwhile, good qualitative agreement was found between the distribution rule of particle deposition rate as simulated by CFD and the situation of opened header box on the spot. Therefore, the combined method of CFD simulation and FSCA detection can be utilized for predicting the condition of particle deposition in the air-cooling systems.