cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5220586
title: Paracetamol versus ibuprofen for the treatment of patent ductus arteriosus in preterm neonates: a meta-analysis of randomized controlled trials

description: <b>Background:</b> Paracetamol has been suggested as an effective treatment for patent ductus arteriosus (PDA). However, the comparative efficacy and safety between paracetamol and ibuprofen were not determined. <b>Methods:</b> A meta-analysis of randomized controlled trials (RCTs) was performed. Relevant studies were identified via database searching. A fixed or random effect model was applied depending on the extent of heterogeneity. <b>Results:</b> Five RCTs with 677 neonates were included. The efficacies for the primary (risk ratio [RR]: 1.03, <i>p</i> = .56) and overall PDA closure were comparable between the two medications (RR: 1.02, <i>p</i> = .62). Neonates of the two groups were comparable for the incidence of PDA complications, including necrotizing enterocolitis (RR: 0.86, <i>p</i> = .70), intraventricular hemorrhage (RR: 0.84, <i>p</i> = .55), bronchopulmonary dysplasia (RR: 0.69, <i>p</i> = .16), and retinopathy of prematurity (RR: 0.58, <i>p</i> = .15), and the risks of sepsis (RR = 0.88, <i>p</i> = .48) and death (RR: 1.45, <i>p</i> = .45) within hospitalization. However, treatment with paracetamol was associated with a trend of reduced risk of renal failure (RR: 0.20, <i>p</i> = .07), and a significantly reduced risk of gastrointestinal bleeding (RR: 0.28, <i>p</i> = .009). <b>Conclusions:</b> Paracetamol may confer comparable treatment efficacy for the closure of PDA as ibuprofen, although paracetamol is associated with lower risk of adverse events.
DOI: 10.6084/m9.figshare.5221279
title: Pollen morphology of Polygonatae and its systematic significance

description: The pollen morphology of 54 species and one variety of seven genera in Polygonatae including <i>Clintonia</i>, <i>Disporopsis</i>, <i>Disporum</i>, <i>Maianthemum</i>, <i>Polygonatum</i>, <i>Smilacina</i> and <i>Streptopus</i> was observed and studied in detail; of these, nine species were reported for the first time. Our results showed that the surface ornamentation of pollen grains of the studied materials could be divided into seven types, namely gemmate, granulate-foveolate, perforate, reticulate, rugulate, rugulate-perforate and verrucate. In line with previous studies, we believe that (i) <i>Smilacina ginfushanicum</i> should be classified into the genus <i>Heteropolygonatum</i> rather than the genus <i>Smilacina</i>; (ii) <i>Polygonatum</i> should be divided into section <i>Polygonatum</i> and section <i>Verticillata</i>; (iii) <i>Smilacina</i> and <i>Maianthemum</i> should be combined as one genus, i.e. <i>Maianthemum sensu lato</i>; and (iv) <i>Clintonia</i>, <i>Disporum</i> and <i>Streptopus</i> should be separated from the tribe Polygonatae.
DOI: 10.6084/m9.figshare.5221279.v2
title: Pollen morphology of Polygonatae and its systematic significance

description: The pollen morphology of 54 species and one variety of seven genera in Polygonatae including <i>Clintonia</i>, <i>Disporopsis</i>, <i>Disporum</i>, <i>Maianthemum</i>, <i>Polygonatum</i>, <i>Smilacina</i> and <i>Streptopus</i> was observed and studied in detail; of these, nine species were reported for the first time. Our results showed that the surface ornamentation of pollen grains of the studied materials could be divided into seven types, namely gemmate, granulate-foveolate, perforate, reticulate, rugulate, rugulate-perforate and verrucate. In line with previous studies, we believe that (i) <i>Smilacina ginfushanicum</i> should be classified into the genus <i>Heteropolygonatum</i> rather than the genus <i>Smilacina</i>; (ii) <i>Polygonatum</i> should be divided into section <i>Polygonatum</i> and section <i>Verticillata</i>; (iii) <i>Smilacina</i> and <i>Maianthemum</i> should be combined as one genus, i.e. <i>Maianthemum sensu lato</i>; and (iv) <i>Clintonia</i>, <i>Disporum</i> and <i>Streptopus</i> should be separated from the tribe Polygonatae.
DOI: 10.6084/m9.figshare.5229712
title: Construction and analysis of circular RNA molecular regulatory networks in liver cancer

description: Liver cancer is the sixth most prevalent cancer, and the third most frequent cause of cancer-related deaths. Circular RNAs (circRNAs), a kind of special endogenous ncRNAs, have been coming back to the forefront of cancer genomics research. In this study, we used a <i>systems biology approach</i> to construct and analyze the circRNA molecular regulatory networks in the context of liver cancer. We detected a total of 127 differentially expressed circRNAs and 3,235 differentially expressed mRNAs. We selected the top-5 upregulated circRNAs to construct a circRNA-miRNA-mRNA network. We enriched the pathways and gene ontology items and determined their participation in cancer-related pathways such as p53 signaling pathway and pathways involved in angiogenesis and cell cycle. Quantitative real-time PCR was performed to verify the top-five circRNAs. ROC analysis showed circZFR, circFUT8, circIPO11 could significantly distinguish the cancer samples, with an AUC of 0.7069, 0.7575, and 0.7103, respectively. Our results suggest the circRNA-miRNA-mRNA network may help us further understand the molecular mechanisms of tumor progression in liver cancer, and reveal novel biomarkers and therapeutic targets.
DOI: 10.6084/m9.figshare.5229712.v2
title: Construction and analysis of circular RNA molecular regulatory networks in liver cancer

description: Liver cancer is the sixth most prevalent cancer, and the third most frequent cause of cancer-related deaths. Circular RNAs (circRNAs), a kind of special endogenous ncRNAs, have been coming back to the forefront of cancer genomics research. In this study, we used a <i>systems biology approach</i> to construct and analyze the circRNA molecular regulatory networks in the context of liver cancer. We detected a total of 127 differentially expressed circRNAs and 3,235 differentially expressed mRNAs. We selected the top-5 upregulated circRNAs to construct a circRNA-miRNA-mRNA network. We enriched the pathways and gene ontology items and determined their participation in cancer-related pathways such as p53 signaling pathway and pathways involved in angiogenesis and cell cycle. Quantitative real-time PCR was performed to verify the top-five circRNAs. ROC analysis showed circZFR, circFUT8, circIPO11 could significantly distinguish the cancer samples, with an AUC of 0.7069, 0.7575, and 0.7103, respectively. Our results suggest the circRNA-miRNA-mRNA network may help us further understand the molecular mechanisms of tumor progression in liver cancer, and reveal novel biomarkers and therapeutic targets.
DOI: 10.6084/m9.figshare.5229712.v1
title: Construction and analysis of circular RNA molecular regulatory networks In liver cancer

description: Liver cancer is the sixth most prevalent cancer, and the third most frequent cause of cancer-related deaths. Circular RNAs (circRNAs), a kind of special endogenous ncRNAs, have been coming back to the forefront of cancer genomics research. In this study, we employed a <i>systems biology approach</i> to construct and analyze the circRNA molecular regulatory networks in the context of liver cancer. We detected a total of 127 differentially expressed circRNAs and 3,235 differentially expressed mRNAs. We selected the top-5 upregulated circRNAs to construct a circRNA-miRNA-mRNA network. We enriched the pathways and gene ontology items and determined their participation in cancer-related pathways such as, p53 signaling pathway and pathways involved in angiogenesis and cell cycle. Quantitative real-time PCR was performed to verify the top-five circRNAs. ROC analysis showed circZFR, circFUT8, circIPO11 could significantly distinguish the cancer samples, with an AUC of 0.7069, 0.7575, and 0.7103, respectively. Our results suggest the circRNA-miRNA-mRNA network may help us further understand the molecular mechanisms of tumor progression in liver cancer, and reveal novel biomarkers and therapeutic targets.
DOI: 10.6084/m9.figshare.5230387
title: Comparison of the postoperative visual quality after SMILE and LASEK for high myopia: a 1-year outcome

description: Figure1; Figure 2; Table 1; Table 2; Table 3 and their original data
DOI: 10.6084/m9.figshare.5230387.v1
title: Comparison of the postoperative visual quality after SMILE and LASEK for high myopia: a 1-year outcome

description: Figure1; Figure 2; Table 1; Table 2; Table 3 and their original data
DOI: 10.6084/m9.figshare.5242138
title: PDD Graph: Bridging Electronic Medical Records and Biomedical Knowledge Graphs via Entity Linking

description: Patient-drug-disease (PDD) Graph dataset, utilising Electronic medical records (EMRS) and biomedical Knowledge graphs. The novel framework to construct the PDD graph is described in the associated publication.<br>PDD is an RDF graph consisting of PDD facts, where a PDD fact is represented by an RDF triple to indicate that a patient takes a drug or a patient is diagnosed with a disease. For instance, (<i>pdd</i>:274671, <i>pdd</i>:diagnosed, sepsis)<br>Data files are in .nt N-Triple format, a line-based syntax for an RDF graph. These can be accessed via openly-available text edit software.<br><b>diagnose_icd_information.nt - </b>contains RDF triples mapping patients to diagnoses. For example:(<i>pdd</i>:18740, <i>pdd</i>:diagnosed, icd99592),where <i>pdd</i>:18740 is a patient entity, and icd99592 is the ICD-9 code of sepsis.<br><b>drug_patients.nt</b><b>- </b>contains RDF triples mapping patients to drugs. For example:(<i>pdd</i>:18740, <i>pdd</i>:prescribed, aspirin),where <i>pdd</i>:18740 is a patient entity, and aspirin is the drug's name.<br><b>Background:</b>Electronic medical records contain multi-format electronic
medical data that consist of an abundance of medical knowledge. Faced with patients' symptoms, experienced caregivers make the right medical decisions
based on their professional knowledge, which accurately grasps relationships
between symptoms, diagnoses and corresponding treatments. In
the associated paper, we aim to capture these relationships by constructing a large
and high-quality heterogenous graph linking patients, diseases, and drugs
(PDD) in EMRs. Specifically, we propose a novel framework to extract
important medical entities from MIMIC-III (Medical Information Mart
for Intensive Care III) and automatically link them with the existing
biomedical knowledge graphs, including ICD-9 ontology and DrugBank.
The PDD graph presented in this paper is accessible on the Web via the
SPARQL endpoint as well as in .nt format in this repository, and provides a pathway for medical discovery and
applications, such as effective treatment recommendations.<br><b>De-identification</b>It is necessary to mention that MIMIC-III contains clinical information of patients. Although the protected health information was de-identifed, researchers who seek to use more clinical data should complete an on-line training course and then apply for the permission to download the complete MIMIC-III dataset: https://mimic.physionet.org/
DOI: 10.6084/m9.figshare.5248489
title: Two-dimensional Superconductivity from Dimerization of Atomically Ordered AuTe2Se4/3 Cubes

description: The emergent phenomena such as superconductivity
and topological phase transitions can be observed in strict two-dimensional (2D)
crystalline matters. Artificial interfaces and one atomic thickness layers are typical
2D materials of this kind. Although having 2D characters, most bulky layered
compounds, however, do not possess these striking properties. Here, we report
the 2D superconductivity in bulky AuTe<sub>2</sub>Se<sub>4/3, </sub>where the
reduction in dimensionality is achieved through inducing the elongated covalent
Te-Te bonds. The atomic-resolution images reveal that the Au, Te and Se are
atomically ordered in a cube, among which are Te-Te bonds of 3.18 Å and 3.28 Å.
The superconductivity at 2.85 K is discovered, which is unraveled to be the quasi-2D
nature owing to the Berezinsky–Kosterlitz–Thouless topological transition. The
nesting of nearly parallel Fermi sheets could give rise to strong
electron-phonon coupling. It is proposed to further depleting the thickness
could result in more topologically-related phenomena.
DOI: 10.6084/m9.figshare.5249071
title: Local governance and business performance in Vietnam: the transaction costs’ perspective

description: Local governance and business performance in Vietnam: the transaction costs’ perspective. <i>Regional Studies</i>. This paper adopts a transaction costs’ perspective to explain why the growth of small and medium-sized enterprises (SMEs) may vary across regions of an emerging economy. Furthermore, it is argued that young and small firms gain more from the improvement of local governance than do old and large firms. In addition, depending on the institutional history, SMEs will respond differently to the incentives provided by local governance. Analysing more than 300,000 SMEs in Vietnam during 2006–12, it is shown that higher-quality local governance positively influences local SME revenue growth; this effect is stronger for young and small firms, and matters more where institutional history suggests there is less support for entrepreneurship.
DOI: 10.6084/m9.figshare.5249071.v1
title: Local governance and business performance in Vietnam: the transaction costs’ perspective

description: Local governance and business performance in Vietnam: the transaction costs’ perspective. <i>Regional Studies</i>. This paper adopts a transaction costs’ perspective to explain why the growth of small and medium-sized enterprises (SMEs) may vary across regions of an emerging economy. Furthermore, it is argued that young and small firms gain more from the improvement of local governance than do old and large firms. In addition, depending on the institutional history, SMEs will respond differently to the incentives provided by local governance. Analysing more than 300,000 SMEs in Vietnam during 2006–12, it is shown that higher-quality local governance positively influences local SME revenue growth; this effect is stronger for young and small firms, and matters more where institutional history suggests there is less support for entrepreneurship.
DOI: 10.6084/m9.figshare.5255734
title: GO analysis results based on Suijing18 Denovo assembly version 1

description: GO analysis was carried out based on the above function annotation results were submitted to topGO. The Biological Process (BP), Cellular Component (CC), and Molecular Function (MF) were listed. The secondary binding point was chosen in the analysis. The annotated proteins from Suijing18 were submitted for pathway analysis carried out by KEGG (http://www.genome.jp/kegg/).
DOI: 10.6084/m9.figshare.5255734.v1
title: GO analysis results based on Suijing18 Denovo assembly version 1

description: GO analysis was carried out based on the above function annotation results were submitted to topGO. The Biological Process (BP), Cellular Component (CC), and Molecular Function (MF) were listed. The secondary binding point was chosen in the analysis. The annotated proteins from Suijing18 were submitted for pathway analysis carried out by KEGG (http://www.genome.jp/kegg/).
DOI: 10.6084/m9.figshare.5255737
title: Annotated proteins based on Suijing18 Denovo assembly version 1 and KEGG database

description: The predicted coding genes from Suijing18 were translated into protein sequences and aligned to the proteins from plant species in the KEGG database (http://www.genome.jp/kegg/) by BLASTP. The threshold was set to e-value&lt;1e-8.
DOI: 10.6084/m9.figshare.5255737.v1
title: Annotated proteins based on Suijing18 Denovo assembly version 1 and KEGG database

description: The predicted coding genes from Suijing18 were translated into protein sequences and aligned to the proteins from plant species in the KEGG database (http://www.genome.jp/kegg/) by BLASTP. The threshold was set to e-value&lt;1e-8.
DOI: 10.6084/m9.figshare.5258110
title: Annotated proteins based on Suijing18 Denovo assembly version 1 and Uniprot database

description: The predicted coding genes from Suijing18 were translated into protein sequences and aligned to the proteins from plant species in the Uniprot database (http://www.uniprot.org/) by BLASTP. The threshold was set to e-value&lt;1e-8.
DOI: 10.6084/m9.figshare.5258110.v1
title: Annotated proteins based on Suijing18 Denovo assembly version 1 and Uniprot database

description: The predicted coding genes from Suijing18 were translated into protein sequences and aligned to the proteins from plant species in the Uniprot database (http://www.uniprot.org/) by BLASTP. The threshold was set to e-value&lt;1e-8.
DOI: 10.6084/m9.figshare.5258113
title: Annotated Repeats based on Suijing18 Denovo assembly version 1

description: Tandem repeats were recognized by TRF package with the following parameter setting: Match =2, Mismatch =7, Delta=7, PM=80, PI =10, Minscore =50, MaxPeriod =2000, and the other types of repeat sequences were recognized by RepeatModeler (http://www.repeatmasker.org/RepeatModeler/) with default setting. The database adopted for RM analysis was an integrated library composed by Repbase (updated on January 2017), Dfam2, and libraries of the publicly available de novo information of rice. This is the annotated repeat data for Suijing18.
DOI: 10.6084/m9.figshare.5258113.v1
title: Annotated Repeats based on Suijing18 Denovo assembly version 1

description: Tandem repeats were recognized by TRF package with the following parameter setting: Match =2, Mismatch =7, Delta=7, PM=80, PI =10, Minscore =50, MaxPeriod =2000, and the other types of repeat sequences were recognized by RepeatModeler (http://www.repeatmasker.org/RepeatModeler/) with default setting. The database adopted for RM analysis was an integrated library composed by Repbase (updated on January 2017), Dfam2, and libraries of the publicly available de novo information of rice. This is the annotated repeat data for Suijing18.
DOI: 10.6084/m9.figshare.5258116
title: Annotated ncRNAs based on Suijing18 Denovo assembly version 1

description: Annotation for ncRNA was carried out by using cmsearch in Infernal searching Rfam database V12.2 (http://rfam.xfam.org/) with parameter setting of “--cyk -T10” for miRNA, snRNA, and sRNA, and by using tRNAscan-SE with default setting for tRNA. This part of data was the annotated data for ncRNAs for Suijing18.
DOI: 10.6084/m9.figshare.5258116.v1
title: Annotated ncRNAs based on Suijing18 Denovo assembly version 1

description: Annotation for ncRNA was carried out by using cmsearch in Infernal searching Rfam database V12.2 (http://rfam.xfam.org/) with parameter setting of “--cyk -T10” for miRNA, snRNA, and sRNA, and by using tRNAscan-SE with default setting for tRNA. This part of data was the annotated data for ncRNAs for Suijing18.
DOI: 10.6084/m9.figshare.5258125
title: Annotated genes based on Suijing18 Denovo assembly version 1

description: Mask the repeats by RepeatMask with parameter setting as “-nolow -no_is -norna” and then annotate the genome by multiple tools including GENEID with parameters for rice, GeneMark with setting of --ES --cores 24 --min_contig 100, SNAP with default setting, and AUGUSTUS 21 with –species = rice. We compared the CDS and protein sequences from other rice genome by using PASA with default setting and GeneWise with setting of “splice_gtag -sum -gff –quiet”. All the results were integrate and screened by using EVidenceModeler (EVM).
DOI: 10.6084/m9.figshare.5258125.v1
title: Annotated genes based on Suijing18 Denovo assembly version 1

description: Mask the repeats by RepeatMask with parameter setting as “-nolow -no_is -norna” and then annotate the genome by multiple tools including GENEID with parameters for rice, GeneMark with setting of --ES --cores 24 --min_contig 100, SNAP with default setting, and AUGUSTUS 21 with –species = rice. We compared the CDS and protein sequences from other rice genome by using PASA with default setting and GeneWise with setting of “splice_gtag -sum -gff –quiet”. All the results were integrate and screened by using EVidenceModeler (EVM).
DOI: 10.6084/m9.figshare.5258128
title: Repeat masked data based on Suijing18 Denovo assembly version 1

description: This part of data was derived from the Suijing18 Denovo assembly version 1 masked the repeats.
DOI: 10.6084/m9.figshare.5258128.v1
title: Repeat masked data based on Suijing18 Denovo assembly version 1

description: This part of data was derived from the Suijing18 Denovo assembly version 1 masked the repeats.
DOI: 10.6084/m9.figshare.5258518
title: Suijing18 Denovo assembly version 1

description: De novo assembly was carried out using the LRS data by CANU pipeline with default parameters except for errorRate = 0.045 genomeSize = 350m, and the SRS data were then aligned to the preliminary assembly by BWA. Also, the pilon package was adopted for the amendment process. The amended assembly was the present submitted version 1 of Suijing18 sequence.
DOI: 10.6084/m9.figshare.5258518.v1
title: Suijing18 Denovo assembly version 1

description: De novo assembly was carried out using the LRS data by CANU pipeline with default parameters except for errorRate = 0.045 genomeSize = 350m, and the SRS data were then aligned to the preliminary assembly by BWA. Also, the pilon package was adopted for the amendment process. The amended assembly was the present submitted version 1 of Suijing18 sequence.
DOI: 10.6084/m9.figshare.5259892
title: 2859710.mpeg

description: The results of the multiviews results
DOI: 10.6084/m9.figshare.5259892.v1
title: 2859710.mpeg

description: The results of the multiviews results
DOI: 10.6084/m9.figshare.5260411
title: Petrogenesis and tectonic implications of early Palaeozoic igneous rocks of the western South Qilian Belt, central China

description: Early Palaeozoic granitoids in the South Qilian Belt, central China, record details of the tectonic evolution and crustal growth of the Qilian orogenic belt. Five representative granitoids from the western South Qilian Belt were sampled for zircon LA-ICPMS U–Pb dating, Lu–Hf isotopes, and whole-rock geochemical analyses. Zircon U–Pb dating of two porphyritic granodiorites and a porphyritic monzogranite yielded ages of 442.7 ± 3.5, 441.8 ± 4.3, and 435.4 ± 3.5 Ma, respectively. These granitoids exhibit a geochemical affinity to I-type granite, are metaluminous with a low aluminium saturation index (A/CNK = 0.75–1.15), have moderate Al<sub>2</sub>O<sub>3</sub> and low MgO contents, high La/Yb and low Sr/Y ratios, and are depleted in Nb, Ta, P, and Ti, which suggests a subduction zone magmatic arc affinity, with mixing between a primary mantle-derived magma with lesser continental crustal material. The syenogranite and monzogranite from the South Qilian Belt, which yield U–Pb zircon ages of 440.4 ± 9.0 and 442.3 ± 1.2 Ma, respectively, have pronounced S-type geochemical affinities, are peraluminous with A/CNK values of 1.07–1.16, have relatively high SiO<sub>2</sub>, Al<sub>2</sub>O<sub>3</sub>, K<sub>2</sub>O, and Rb contents, low Y and Yb, low Sr/Y and La/Yb ratios, positive Th, U, and light Rare Earth Element (REE) anomalies, and depletions in Nb, Ta, Sr, and Ti. Their geochemical signature suggests derivation from partial melting of continental crust in a syn-collisional setting. The Hf isotopic data of zircons from the granitoids show a significant input of Paleoproterozoic crust in the crustal formation of the western South Qilian Belt in Palaeozoic. Compare the <i>ε</i><sub>Hf</sub>(<i>t</i>) value of S-type granite with that of I-type granite, the former may have a comparatively homogeneous source. Together with regional evidence, it is proposed that a collisional event occurred between the South Qilian Belt and the Central Qilian Belt at ca. 442–435 Ma.