cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.1032861
title: Nl1137 Gpa-5(Pk376)X | 2009-06-12T11:16:00+01:00

description: This experiment is part of the <em>C.elegans behavioural database</em>. For more information and the complete collection of experiments visit http://movement.openworm.org



<b>preview link</b> : https://www.youtube.com/watch?v=T7sHS6QOV2k
<b>strain</b> : NL1137
<b>timestamp</b> : 2009-06-12T11:16:00+01:00
<b>gene</b> : gpa-5
<b>chromosome</b> : X
<b>allele</b> : pk376
<b>strain_description</b> : gpa-5(pk376)X
<b>sex</b> : hermaphrodite
<b>stage</b> : adult
<b>ventral_side</b> : anticlockwise
<b>media</b> : NGM agar low peptone
<b>arena</b> :   
  <b>style</b> : petri
  <b>size</b> : 35
  <b>orientation</b> : away
  

<b>food</b> : OP50
<b>habituation</b> : 30m wait
<b>who</b> : Laura Grundy
<b>protocol</b> : Method in E. Yemini et al. doi:10.1038/nmeth.2560. Worm transferred to arena 30 minutes before recording starts.
<b>lab</b> :   
  <b>name</b> : William R Schafer
  <b>location</b> : MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK
  

<b>software</b> :   
  <b>name</b> : tierpsy (https://github.com/ver228/tierpsy-tracker)
  <b>version</b> : cbfc23eb4f1ac2f29be75ade7a937eed58a5b219
  <b>featureID</b> : @OMG
  

<b>base_name</b> : gpa-5 (pk376)X on food R_2009_06_12__11_16__4
<b>total time (s)</b> : 299.949
<b>frames per second</b> : 25.641
<b>video micrometers per pixel</b> : 4.95268
<b>number of segmented skeletons</b> : 6370
DOI: 10.5281/zenodo.1032867
title: Nl790 Gpa-4(Pk381)Iv | 2009-06-12T15:38:00+01:00

description: This experiment is part of the <em>C.elegans behavioural database</em>. For more information and the complete collection of experiments visit http://movement.openworm.org



<b>preview link</b> : https://www.youtube.com/watch?v=e-MOQiPcdvs
<b>strain</b> : NL790
<b>timestamp</b> : 2009-06-12T15:38:00+01:00
<b>gene</b> : gpa-4
<b>chromosome</b> : IV
<b>allele</b> : pk381
<b>strain_description</b> : gpa-4(pk381)IV
<b>sex</b> : hermaphrodite
<b>stage</b> : adult
<b>ventral_side</b> : anticlockwise
<b>media</b> : NGM agar low peptone
<b>arena</b> :   
  <b>style</b> : petri
  <b>size</b> : 35
  <b>orientation</b> : away
  

<b>food</b> : OP50
<b>habituation</b> : 30m wait
<b>who</b> : Laura Grundy
<b>protocol</b> : Method in E. Yemini et al. doi:10.1038/nmeth.2560. Worm transferred to arena 30 minutes before recording starts.
<b>lab</b> :   
  <b>name</b> : William R Schafer
  <b>location</b> : MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK
  

<b>software</b> :   
  <b>name</b> : tierpsy (https://github.com/ver228/tierpsy-tracker)
  <b>version</b> : cbfc23eb4f1ac2f29be75ade7a937eed58a5b219
  <b>featureID</b> : @OMG
  

<b>base_name</b> : gpa-1 (PK381)IV on food R_2009_06_12__15_38__22
<b>total time (s)</b> : 299.569
<b>frames per second</b> : 25.974
<b>video micrometers per pixel</b> : 4.95268
<b>number of segmented skeletons</b> : 6345
DOI: 10.5281/zenodo.1032918
title: Nl335 Gpa-3(Pk35)V | 2009-06-12T11:06:00+01:00

description: This experiment is part of the <em>C.elegans behavioural database</em>. For more information and the complete collection of experiments visit http://movement.openworm.org



<b>preview link</b> : https://www.youtube.com/watch?v=dP-zQXSNoHQ
<b>strain</b> : NL335
<b>timestamp</b> : 2009-06-12T11:06:00+01:00
<b>gene</b> : gpa-3
<b>chromosome</b> : V
<b>allele</b> : pk35
<b>strain_description</b> : gpa-3(pk35)V
<b>sex</b> : hermaphrodite
<b>stage</b> : adult
<b>ventral_side</b> : clockwise
<b>media</b> : NGM agar low peptone
<b>arena</b> :   
  <b>style</b> : petri
  <b>size</b> : 35
  <b>orientation</b> : away
  

<b>food</b> : OP50
<b>habituation</b> : 30m wait
<b>who</b> : Laura Grundy
<b>protocol</b> : Method in E. Yemini et al. doi:10.1038/nmeth.2560. Worm transferred to arena 30 minutes before recording starts.
<b>lab</b> :   
  <b>name</b> : William R Schafer
  <b>location</b> : MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK
  

<b>software</b> :   
  <b>name</b> : tierpsy (https://github.com/ver228/tierpsy-tracker)
  <b>version</b> : cbfc23eb4f1ac2f29be75ade7a937eed58a5b219
  <b>featureID</b> : @OMG
  

<b>base_name</b> : gpa-3 (pk35)IV on food L_2009_06_12__11_06__3
<b>total time (s)</b> : 299.544
<b>frames per second</b> : 26.1097
<b>video micrometers per pixel</b> : 4.95268
<b>number of segmented skeletons</b> : 6352
DOI: 10.5281/zenodo.1032919
title: Nl335 Gpa-3(Pk35)V | 2009-06-12T11:06:00+01:00

description: This experiment is part of the <em>C.elegans behavioural database</em>. For more information and the complete collection of experiments visit http://movement.openworm.org



<b>preview link</b> : https://www.youtube.com/watch?v=dP-zQXSNoHQ
<b>strain</b> : NL335
<b>timestamp</b> : 2009-06-12T11:06:00+01:00
<b>gene</b> : gpa-3
<b>chromosome</b> : V
<b>allele</b> : pk35
<b>strain_description</b> : gpa-3(pk35)V
<b>sex</b> : hermaphrodite
<b>stage</b> : adult
<b>ventral_side</b> : clockwise
<b>media</b> : NGM agar low peptone
<b>arena</b> :   
  <b>style</b> : petri
  <b>size</b> : 35
  <b>orientation</b> : away
  

<b>food</b> : OP50
<b>habituation</b> : 30m wait
<b>who</b> : Laura Grundy
<b>protocol</b> : Method in E. Yemini et al. doi:10.1038/nmeth.2560. Worm transferred to arena 30 minutes before recording starts.
<b>lab</b> :   
  <b>name</b> : William R Schafer
  <b>location</b> : MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK
  

<b>software</b> :   
  <b>name</b> : tierpsy (https://github.com/ver228/tierpsy-tracker)
  <b>version</b> : cbfc23eb4f1ac2f29be75ade7a937eed58a5b219
  <b>featureID</b> : @OMG
  

<b>base_name</b> : gpa-3 (pk35)IV on food L_2009_06_12__11_06__3
<b>total time (s)</b> : 299.544
<b>frames per second</b> : 26.1097
<b>video micrometers per pixel</b> : 4.95268
<b>number of segmented skeletons</b> : 6352
DOI: 10.6084/m9.figshare.21202086.v1
title: Additional file 8 of The immune subtypes and landscape of sarcomas

description: Additional file8. Table S5: List of six prognostic genes in the blue module.
DOI: 10.6084/m9.figshare.14379383.v1
title: Additional file 2 of PCIP-seq: simultaneous sequencing of integrated viral genomes and their insertion sites with long reads

description: Additional file 2: Dataset S1. HIV-1 integration sites identified in patients 02006 and 06042.
DOI: 10.6084/m9.figshare.12813634
title: Additional file 3 of Functional analysis of the SlERF01 gene in disease resistance to S. lycopersici

description: Additional file 3: Table S3.
DOI: 10.6084/m9.figshare.14379492.v1
title: Additional file 1 of Genome-scale analyses of transcriptional start sites in Mycobacterium marinum under normoxic and hypoxic conditions

description: Additional file 1.
DOI: 10.6084/m9.figshare.7570997.v1
title: Foxo3a-dependent miR-633 regulates chemotherapeutic sensitivity in gastric cancer by targeting Fas-associated death domain

description: The development of chemotherapeutic drugs resistance such as doxorubicin (DOX) and cisplatin (DDP) is the major barrier in gastric cancer therapy. Emerging evidences reveal that microRNAs (miRNAs) contribute to chemosensitivity. In this study, we investigated the role of miR-633, an oncogenic miRNA, in gastric cancer chemoresistance. In gastric cancer tissue and cell lines, miR-633 expression was highly increased and correlated with down regulation of Fas-associated protein with death domain (FADD). Inhibition of miR-633 significantly increased FADD protein level and enhanced DOX/DDP induced apoptosis <i>in vitro</i>. MiR-633 antagomir administration remarkably decreased tumor growth in combination with DOX <i>in vivo</i>, suggesting that miR-633 targets FADD to block gastric cancer cell death. We found that the promoter region of miR-633 contained putative binding sites for forkhead box O 3 (Foxo3a), which can directly repress miR-633 transcription. In addition, we observed that DOX-induced nuclear accumulation of Foxo3a leaded to the suppression of miR-633 transcription. Together, our study revealed that miR-633/FADD axis played a significant role in the chemoresistance and Foxo3a regulated this pathway in gastric cancer. Thus, miR-633 antagomir resensitized gastric cancer cells to chemotherapy drug and had potentially therapeutic implication.
DOI: 10.6084/m9.figshare.14379498
title: Additional file 3 of Genome-scale analyses of transcriptional start sites in Mycobacterium marinum under normoxic and hypoxic conditions

description: Additional file 3.
DOI: 10.6084/m9.figshare.14379485
title: Additional file 1 of Gene co-expression network analysis reveals key pathways and hub genes in Chinese cabbage (Brassica rapa L.) during vernalization

description: Additional file 1: Table S1. Log2FPKM values of the 5748 variable genes in ‘JWW’ (J for ‘JWW’). Table S2. Log2 FPKM values of the 5527 variable genes in ‘XBJ’ (X for ‘XBJ’). Table S3. Significant GO terms for each gene set of ‘JWW’. Table S4. Significant GO terms for each gene set of ‘XBJ’. Table S5. Annotation information of the hub genes of each module in ‘JWW’. Table S6. Annotation information of the hub genes of each module in ‘XBJ’. Table S7. qRT-PCR specific primers for hub gene related to flower development.
DOI: 10.6084/m9.figshare.14379495
title: Additional file 2 of Genome-scale analyses of transcriptional start sites in Mycobacterium marinum under normoxic and hypoxic conditions

description: Additional file 2.
DOI: 10.6084/m9.figshare.14903802
title: Additional file 1 of Prediction of early vascular cement leakage following percutaneous vertebroplasty in spine metastases: the Peking University First Hospital Score (PUFHS)

description: Additional file 1.
DOI: 10.6084/m9.figshare.14903802.v1
title: Additional file 1 of Prediction of early vascular cement leakage following percutaneous vertebroplasty in spine metastases: the Peking University First Hospital Score (PUFHS)

description: Additional file 1.
DOI: 10.6084/m9.figshare.14379612
title: Additional file 4 of Single cell RNA sequencing identifies IGFBP5 and QKI as ciliated epithelial cell genes associated with severe COPD

description: Additional file 4: Table S4. Biological process gene ontology enrichment in genes downregulated in each cluster in COPD.
DOI: 10.6084/m9.figshare.21202692.v1
title: Additional file 1 of Unilateral buphthalmos, corneal staphyloma and corneal fistula caused by pathogenic variant in the PITX3 gene: a case report

description: Additional file 1.
DOI: 10.6084/m9.figshare.14379621
title: Additional file 7 of Single cell RNA sequencing identifies IGFBP5 and QKI as ciliated epithelial cell genes associated with severe COPD

description: Additional file 7: Table S7. Genes from the sever COPD signature (LTRC) differentially expressed by cell type.
DOI: 10.6084/m9.figshare.22786730
title: <strong>AIMD-Chig: exploring the conformational space of 166-atom protein </strong><em><strong>Chignolin</strong></em><strong> with </strong><em><strong>ab initio</strong></em> <strong>molecular dynamics</strong>

description: AIMD-Chig is an MD dataset including 2 million conformations of 166-atom protein Chignolin sampled at the density functional theory (DFT) level with 7,763,146 CPU hours. 10,000 conformations were initialized covering the whole conformational space of Chignolin, including folded, unfolded, and metastable states. <i>Ab initio</i> simulations were driven by M062X/6-31G* with a Berendsen thermostat at 340K. We reported coordinates, energies, and forces for each conformation.
DOI: 10.6084/m9.figshare.11776713
title: New fossil material of <i>Equicalastrobus</i> (Equisetales) and associated leaves from the Late Triassic of Baojishan basin, Gansu Province, China

description: A new species of <i>Equicalastrobus pusillus</i> L. Zhang et D.F. Yan sp. nov. and associated leaves <i>Schizoneura koningensis</i> were reported from the Late Triassic of Baojishan basin, Gansu Province, China. Cones found here were spicate, with peltate discs surrounding the axis, and the leaf-like umbo projections were identifiably smaller in size compared to the type species. Sporangiophores showed a loose arrangement implying the cones had been expanded before they were buried. Associated leaves were attributed to <i>Schizoneura koningensis</i>, due to their characteristic features. In order to discuss the relationship of fertile genus <i>Equicalastrobus</i> with other Equisetales cones, a clustering analysis on characters of reproductive organs covering 46 equisetalean cones (14 extant and 32 extinct) was performed. The character matrix was based on 36 discrete characters and 6 continuous characters. According to the clustering result, it was suggested that the new species, as well as the genus <i>Equicalastrobus</i> had a closer relationship with <i>Equisetum</i>-type cones, rather than <i>Calamites</i>-type cones. The co-occurrence of the two genera, <i>Equicalastrobus</i> and <i>Schizoneura</i>, demonstrated a wide distribution of equisetaleans with a rich and diverse morphology around the Triassic World.
DOI: 10.6084/m9.figshare.11776713.v1
title: New fossil material of <i>Equicalastrobus</i> (Equisetales) and associated leaves from the Late Triassic of Baojishan basin, Gansu Province, China

description: A new species of <i>Equicalastrobus pusillus</i> L. Zhang et D.F. Yan sp. nov. and associated leaves <i>Schizoneura koningensis</i> were reported from the Late Triassic of Baojishan basin, Gansu Province, China. Cones found here were spicate, with peltate discs surrounding the axis, and the leaf-like umbo projections were identifiably smaller in size compared to the type species. Sporangiophores showed a loose arrangement implying the cones had been expanded before they were buried. Associated leaves were attributed to <i>Schizoneura koningensis</i>, due to their characteristic features. In order to discuss the relationship of fertile genus <i>Equicalastrobus</i> with other Equisetales cones, a clustering analysis on characters of reproductive organs covering 46 equisetalean cones (14 extant and 32 extinct) was performed. The character matrix was based on 36 discrete characters and 6 continuous characters. According to the clustering result, it was suggested that the new species, as well as the genus <i>Equicalastrobus</i> had a closer relationship with <i>Equisetum</i>-type cones, rather than <i>Calamites</i>-type cones. The co-occurrence of the two genera, <i>Equicalastrobus</i> and <i>Schizoneura</i>, demonstrated a wide distribution of equisetaleans with a rich and diverse morphology around the Triassic World.
DOI: 10.6084/m9.figshare.20677966
title: Additional file 1 of Opening the black box: interpretable machine learning for predictor finding of metabolic syndrome

description: Additional file 1:Supplementary file S1.The original dataset for this study.
DOI: 10.6084/m9.figshare.20677966.v1
title: Additional file 1 of Opening the black box: interpretable machine learning for predictor finding of metabolic syndrome

description: Additional file 1:Supplementary file S1.The original dataset for this study.
DOI: 10.6084/m9.figshare.20677969
title: Additional file 2 of Opening the black box: interpretable machine learning for predictor finding of metabolic syndrome

description: Additional file 2: Supplementary file S2. The dataset processed by MICE method for this study.
DOI: 10.6084/m9.figshare.14398325
title: materials list in part2

description: materials id are given
DOI: 10.6084/m9.figshare.14398325.v1
title: materials list in part2

description: materials id are given
DOI: 10.6084/m9.figshare.14398328
title: materials list in part1

description: materials id are given
DOI: 10.6084/m9.figshare.14398328.v1
title: materials list in part1

description: materials id are given
DOI: 10.6084/m9.figshare.14398331
title: materials list in part3

description: mateials id are given
DOI: 10.6084/m9.figshare.14398331.v1
title: materials list in part3

description: mateials id are given
DOI: 10.6084/m9.figshare.1291176
title: MiR-194, commonly repressed in colorectal cancer, suppresses tumor growth by regulating the MAP4K4/c-Jun/MDM2 signaling pathway

description: Tumor growth cascade is a complicated and multistep process with numerous obstacles. Until recently, evidences have shown the involvement of microRNAs (miRNAs) in tumorigenesis and tumor progression of various cancers, including colorectal cancer (CRC). In this study, we explored the role of miR-194 and its downstream pathway in CRC. We acquired data through miRNA microarray profiles, showing that the expression of miR-194 was significantly suppressed in CRC tissues compared with corresponding noncancerous tissues. Decreased miR-194 expression was obviously associated with tumor size and tumor differentiation, as well as TNM stage. Both Kaplan–Meier and multivariate survival analysis showed that downregulated miR-194 was associated with overall survival. Moreover, functional assays indicated that overexpression of miR-194 in CRC cell lines inhibited cell proliferation both <i>in vitro</i> and <i>in vivo</i>. In addition, using dual-luciferase reporter gene assay, we found MAP4K4 was the direct target of miR-194. Silencing of MAP4K4 resulted in similar biological behavior changes to that of overexpression of miR-194. We also observed through Human Gene Expression Array that MDM2 was one of the downstream targets of MAP4K4. Knockdown of MAP4K4 downregulated MDM2 expression through transcription factor c-Jun binding to the −1063 to -1057 bp of the promoter. These results suggest that miR-194, regulating the MAP4K4/c-Jun/MDM2 signaling pathway, might act as a tumor suppressor and serve as a novel target for CRC prevention and therapy.
DOI: 10.6084/m9.figshare.6534077
title: Influence of ethanol on the metabolism of alprazolam.

description: <b>Background</b>: Alprazolam is a commonly used benzodiazepine in clinical practice, and when coingested with ethanol, alprazolam can increase behavioral irritability and aggression. However, the mechanism of its interaction with ethanol remains unknown. <b>Research design and methods</b>: The pharmacokinetics of alprazolam was studied <i>in vivo</i> in rat experiments involving the simultaneous administration of alprazolam and ethanol, and the interactions between ethanol and alprazolam were investigated <i>in vitro</i> in human liver microsomes. <i>In silico</i> molecular docking was applied to analyze the change in the CYP3A4–alprazolam-binding conformation when ethanol was coadministered with alprazolam. <b>Results</b>: Compared with alprazolam administered alone (2 mg/kg), the <i>C</i><sub>max</sub> of alprazolam increased when ethanol was simultaneously administered at 3 g/kg. The concentrations of alprazolam significantly increased by 39%, 17%, 105%, and 642% at 5, 10, 30, and 120 min intervals in the brain when coadministered with ethanol, respectively. Molecular docking results suggested that the conformation of CYP3A4 with alprazolam changed when ethanol was bound to the SER119 residue, which seems critical in the process of CYP3A4–alprazolam binding. <b>Conclusions</b>: Ethanol might increase the toxicity of alprazolam by inhibiting the activity of CYP3A4, although other pharmacokinetic processes may be affected. Ethanol could change the conformation of CYP3A4 and affect alprazolam binding.
DOI: 10.6084/m9.figshare.6534077.v1
title: Influence of ethanol on the metabolism of alprazolam.

description: <b>Background</b>: Alprazolam is a commonly used benzodiazepine in clinical practice, and when coingested with ethanol, alprazolam can increase behavioral irritability and aggression. However, the mechanism of its interaction with ethanol remains unknown. <b>Research design and methods</b>: The pharmacokinetics of alprazolam was studied <i>in vivo</i> in rat experiments involving the simultaneous administration of alprazolam and ethanol, and the interactions between ethanol and alprazolam were investigated <i>in vitro</i> in human liver microsomes. <i>In silico</i> molecular docking was applied to analyze the change in the CYP3A4–alprazolam-binding conformation when ethanol was coadministered with alprazolam. <b>Results</b>: Compared with alprazolam administered alone (2 mg/kg), the <i>C</i><sub>max</sub> of alprazolam increased when ethanol was simultaneously administered at 3 g/kg. The concentrations of alprazolam significantly increased by 39%, 17%, 105%, and 642% at 5, 10, 30, and 120 min intervals in the brain when coadministered with ethanol, respectively. Molecular docking results suggested that the conformation of CYP3A4 with alprazolam changed when ethanol was bound to the SER119 residue, which seems critical in the process of CYP3A4–alprazolam binding. <b>Conclusions</b>: Ethanol might increase the toxicity of alprazolam by inhibiting the activity of CYP3A4, although other pharmacokinetic processes may be affected. Ethanol could change the conformation of CYP3A4 and affect alprazolam binding.
DOI: 10.6084/m9.figshare.20154221
title: Additional file 3 of Characteristics and interplay of esophageal microbiota in esophageal squamous cell carcinoma

description: Additional file 3: Table S1. The relative abundance of 955 features in ESCC tumor and tumor-adjacent tissues.
DOI: 10.6084/m9.figshare.20154389
title: 840–820 Ma Dahongshan bimodal volcanic rocks: new constraints on the Neoproterozoic arc–back-arc basin system along the northern margin of the Yangtze Block

description: The newly identified earliest part of the Sanligang bimodal volcanic succession in the Dahongshan area of the northern Yangtze Block provides insight into the role of this block in the evolution of the Rodinia supercontinent. Field contact relationships and dating indicate that these rocks are contemporaneous and formed at 840–820 Ma. The Sanligang mafic rocks have low SiO<sub>2</sub> (40.33–48.17 wt.%) and K<sub>2</sub>O (0.07–1.65 wt.%), high TiO<sub>2</sub> (2.64–3.52 wt.%) contents, and low U/Th (0.33–0.38), Th/Zr (0.001–0.002), and Nb/Y (0.059–0.064) ratios with positive ε<sub>Nd</sub>(t) (+5.08 to +7.59). This suggests that they are formed from magmas derived from an asthenospheric mantle source that had not been modified by slab-derived materials, with a low degree of crustal contamination during their eruption. Contemporaneous felsic rocks in the study area have high SiO<sub>2</sub> (73.1–80.0 wt.%), variable K<sub>2</sub>O (0.63–4.39 wt.%) and Na<sub>2</sub>O (1.73–6.54 wt.%), and low MgO (0.1–0.58 wt.%) contents and are light rare earth element enriched, with (La/Yb)<sub>N</sub> values of 1.37–2.65 and significantly negative Eu anomalies. They have A<sub>2</sub>-type granite affinities, as evidenced by their high 10,000 Ga/Al values (3.51–4.55) and Zr contents (285–620 ppm), and positive whole-rock ε<sub>Nd</sub>(t) (+6.16–+6.52), zircon ε<sub>Hf</sub>(t) (+9.69–+12.29) and δ<sup>18</sup>O (+4.82–+6.11) values, suggesting they formed by partial melting of juvenile crustal material caused by heating associated with contemporaneous mantle-derived mafic magmatism. Combining the data for these bimodal volcanic successions with other rock assemblages in the Dahongshan area indicates that this magmatism occurred in a back-arc extensional setting. This magmatism was caused by slab detachment and separation along a vertical tear during the Neoproterozoic evolution of the arc to arc–back-arc system of the northern margin of the Yangtze Block.