cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24098373
title: Additional file 5 of Comparative transcriptomes reveal geographic differences in the ability of the liver of plateau zokors (Eospalax baileyi) to respond and adapt to toxic plants

description: Additional file 5: S1 Distribution of skipped exons identified by comparing TZNC and LQNC. S2 Distribution of retained introns identified by comparing TZNC and LQNC. S3 Distribution of mutually exclusive exons identified by comparing TZNC and LQNC. S4 Distribution of alternative 3’ splice sites identified by comparing TZNC and LQNC. S5 Distribution of alternative 5’ splice sites identified by comparing TZNC and LQNC. S6 Distribution of skipped exons identified by comparing TZH and LQH. S7 Distribution of retained introns identified by comparing TZH and LQH. S8 Distribution of mutually exclusive exons identified by comparing TZH and LQH. S9 Distribution of alternative 3’ splice sites identified by comparing TZH and LQH. S10 Distribution of alternative 5’ splice sites identified by comparing TZH and LQH. S11 Distribution of skipped exons identified by comparing TZNC and LQNC. S12 Distribution of retained introns identified by comparing TZNC and LQNC. S13 Distribution of mutually exclusive exons identified by comparing TZNC and LQNC. S14 Distribution of alternative 3’ splice sites identified by comparing TZNC and LQNC. S15 Distribution of alternative 5’ splice sites identified by comparing TZNC and LQNC. S16 Distribution of alternative 3’ splice sites identified by comparing TZH and LQH. S17 Distribution of skipped exons identified by comparing TZH and LQH. S18 Distribution of retained introns identified by comparing TZH and LQH. S19 Distribution of mutually exclusive exons identified by comparing TZH and LQH. S20 Distribution of alternative 5’ splice sites identified by comparing TZH and LQH.
DOI: 10.6084/m9.figshare.24098373.v1
title: Additional file 5 of Comparative transcriptomes reveal geographic differences in the ability of the liver of plateau zokors (Eospalax baileyi) to respond and adapt to toxic plants

description: Additional file 5: S1 Distribution of skipped exons identified by comparing TZNC and LQNC. S2 Distribution of retained introns identified by comparing TZNC and LQNC. S3 Distribution of mutually exclusive exons identified by comparing TZNC and LQNC. S4 Distribution of alternative 3’ splice sites identified by comparing TZNC and LQNC. S5 Distribution of alternative 5’ splice sites identified by comparing TZNC and LQNC. S6 Distribution of skipped exons identified by comparing TZH and LQH. S7 Distribution of retained introns identified by comparing TZH and LQH. S8 Distribution of mutually exclusive exons identified by comparing TZH and LQH. S9 Distribution of alternative 3’ splice sites identified by comparing TZH and LQH. S10 Distribution of alternative 5’ splice sites identified by comparing TZH and LQH. S11 Distribution of skipped exons identified by comparing TZNC and LQNC. S12 Distribution of retained introns identified by comparing TZNC and LQNC. S13 Distribution of mutually exclusive exons identified by comparing TZNC and LQNC. S14 Distribution of alternative 3’ splice sites identified by comparing TZNC and LQNC. S15 Distribution of alternative 5’ splice sites identified by comparing TZNC and LQNC. S16 Distribution of alternative 3’ splice sites identified by comparing TZH and LQH. S17 Distribution of skipped exons identified by comparing TZH and LQH. S18 Distribution of retained introns identified by comparing TZH and LQH. S19 Distribution of mutually exclusive exons identified by comparing TZH and LQH. S20 Distribution of alternative 5’ splice sites identified by comparing TZH and LQH.
DOI: 10.6084/m9.figshare.16912196
title: Essential meiotic structure-specific endonuclease1 (<i>EME1</i>) promotes malignant features in gastric cancer cells via the Akt/GSK3B/CCND1 pathway

description: DNA damage plays a key role in various biological processes involved in malignant disease, the role of the DNA damage repair gene <i>EME1</i> (essential meiotic structure-specific endonuclease 1) in gastric cancer (GC) development is unknown. This work aimed to investigate expression and role of <i>EME1</i> in tumorigenesis. Quantitative real-time polymerase chain reaction (qRT-PCR), immunoblot, cell viability and dual-luciferase reporter assays, RNAi and gene transfection, and immunofluorescent staining were performed to assess <i>EME1</i> regulation in GC tumorigenesis. Further, mouse xenografts were established for <i>in vivo</i> mechanistic studies. <i>EME1</i> was found to be upregulated in both gastric cancer cells and clinically obtained tumors. Additionally, <i>EME1</i> levels were strongly associated with the differentiation level of GC and lymph node metastasis. <i>In vivo</i> and <i>in vitro</i> knockdown of <i>EME1</i> markedly suppressed the proliferative, migratory, and invasive abilities of GC cells and enhanced apoptotic cell death and cell cycle arrest rates. Mechanistically, <i>EME1</i> modulated Akt/GSK3B/CCND1 signaling. <i>MYB</i> may also have contributed to <i>EME1</i>-dependent gastric carcinogenesis. Elevated <i>EME1</i> expressions may enhance the proliferative and metastatic abilities of GC cells, thereby acting as a tumor-promoting factor via Akt. These findings reveal that <i>EME1</i> is an important biomarker for GC prognosis and treatment in humans. <b>Abbreviations</b>: Essential meiotic structure-specific endonuclease 1 (<i>EME1</i>); MYB proto-oncogene (<i>MYB</i>); Cell counting kit-8 (CCK-8); 4,6-diamimo-2-phenyl indole (DAPI); Quantitative real-time PCR (qRT-PCR); Gastric cancer (GC); Immunofluorescence (IF); Small interfering RNA (siRNA); Small hairpin RNA (shRNA); Alpha serine threonine-protein kinase (Akt); Glycogen synthase kinase 3 beta (GSK3B); Cyclin D1 (CCND1); Glyceraldehyde-3-phosphate dehydrogenase (GAPDH); Disease-free survival (DFS); Overall survival (OS); Negative controls (NC); American Joint Committee on Cancer (AJCC); Coding sequence (CDS); Lymph node metastasis (LNM); Tris-Buffered Saline-Tween-20 (TBST); Horseradish Peroxidase (HRP); Electrochemiluminescence (ECL); Polyvinylidene Fluoride (PVDF); Excision repair cross complementation group 1 (ERCC1).
DOI: 10.6084/m9.figshare.16912199
title: Effect and mechanism of BDNF/TrkB signaling on vestibular compensation

description: Brain-derived neurotrophic factor (BDNF) regulates neuronal plasticity by targeting the tyrosine kinase B receptor (TrkB) receptor, but limited researches concentrate on the role of BDNF/TrkB signaling in vestibular compensation. In this study, rats with unilateral vestibular dysfunction were established by unilateral labyrinthectomy (UL) and infusion with siBDNF or 7, 8-Dihydroxyflavone (7,8-DHF, a TrkB receptor agonist). The behavioral scores of rats with vestibular deficits were determined and the rotarod test was performed after UL. BDNF and TrkB levels after UL were determined by western blot and quantitative reverse transcription PCR (qRT-PCR). 5-bromo-2ʹ-deoxyuridine (BrdU)-positive cells (newly generated cells) and GAD67-positive cells (GABAergic neurons) were identified by immunohistochemistry. Glial fibrillary acidic protein (GFAP) (astrocyte marker)-positive cells were identified and GABA type A receptor (GABA<sub>A</sub>R) expression was detected by immunofluorescence. We found that after UL, BDNF and TrkB levels were up-regulated with a maximum value at 4 h, and then progressively down-regulated during 4 h ~ 7 d. Blocking BDNF/TrkB signaling inhibited the recovery from vestibular deficits, decreased the numbers of newly generated cells and astrocytes in medial vestibular nucleus (MVN), inferior vestibular nerve (IVN), superior vestibular nerve (SVN) and lateral vestibular nucleus (LVN), and disrupted the balances of GABAergic neurons and GABA<sub>A</sub>R expressions in the left (lesioned) side and right (intact) side of MVN, whereas activation of BDNF/TrkB signaling caused opposite results. The current study indicated that BDNF/TrkB signaling avails vestibular compensation, depending on the number of newly generated cells and astrocytes, the rebalance of GABAergic neurons, and GABA<sub>A</sub>R expression in bilateral MVN.
DOI: 10.6084/m9.figshare.13242245.v1
title: Metadata record for the manuscript: Synergistic activation of mutant TERT promoter by Sp1 and GABPA in BRAFV600E-driven human cancers

description: <b>Summary</b>

This
metadata record provides details of the data supporting the claims of the
related manuscript: “Synergistic activation of mutant TERT
promoter by Sp1 and GABPA in BRAFV600E-driven human cancers”.

The
data consist of 31 Excel .xlsx format spreadsheets and a Word .docx document.

The
related study tested the hypothesis that activated extracellular
signal-regulated kinase (ERK) may be recruited to mutant telomerase reverse
transcriptase (TERT) promoter by pioneer transcription factors.

 

<b>Data
access</b>

The
31 Excel .xlsx spreadsheets underlie the figures in the related manuscript, and
are named according to the figure and subfigure they underlie (e.g., Figure 1B
1.xlsx). These are openly available and are included together with this metadata record, and they contain data concerning qRT-PCR, dual-luciferase reporter assay, ChIP and TRAP assays described in the related manuscript. The sequence homology analsysis (underlying
Supplementary Figure 8) is openly available and is also included together with this
metadata record. Data for the Co-IP assay supporting Figure 3 are in the file WB-CoIPs.tiff and are available upon request to the corresponding author, Prof. Peng Hou: phou@xjtu.edu.cn.
DOI: 10.6084/m9.figshare.21102280.v1
title: Additional file 12 of Landscape of the gut archaeome in association with geography, ethnicity, urbanization, and diet in the Chinese population

description: Additional file 12: Supplementary Table 8. EGGNOG and MetaCyc functions enriched in the gut archaeome of rural versus urban Chinese.
DOI: 10.6084/m9.figshare.21102178.v1
title: Additional file 2 of TRIM proteins in hepatocellular carcinoma

description: Additional file 2: Table S1. Differential gene expression under different mutation status in HCC through TIMER2.0. The logFC with statistical significance (p&lt;0.05) are colored in the table. Table S2. Cox analysis for all TRIM proteins based on TCGA-LIHC patients with OS more than a month. Table S3. Intracellular location of TRIM proteins from uniprot.
DOI: 10.6084/m9.figshare.21102178
title: Additional file 2 of TRIM proteins in hepatocellular carcinoma

description: Additional file 2: Table S1. Differential gene expression under different mutation status in HCC through TIMER2.0. The logFC with statistical significance (p&lt;0.05) are colored in the table. Table S2. Cox analysis for all TRIM proteins based on TCGA-LIHC patients with OS more than a month. Table S3. Intracellular location of TRIM proteins from uniprot.
DOI: 10.6084/m9.figshare.5902345
title: A rapid method to identify <i>Salmonella enterica</i> serovar Gallinarum biovar Pullorum using a specific target gene <i>ipaJ</i>

description: <i>Salmonella enterica</i> serovar Gallinarum biovar Pullorum (<i>S.</i> Pullorum) is the pathogen of pullorum disease, which leads to severe economic losses in many developing countries. Traditional methods to identify <i>S. enterica</i> have relied on biochemical reactions and serotyping, which are time-consuming with accurate identification if properly carried out. In this study, we developed a rapid polymerase chain reaction (PCR) method targeting the specific gene <i>ipaJ</i> to detect <i>S.</i> Pullorum. Among the 650 <i>S.</i> Pullorum strains isolated from 1962 to 2016 all over China, 644 strains were identified to harbour <i>ipaJ</i> gene in the plasmid pSPI12, accounting for a detection rate of 99.08%. Six strains were <i>ipaJ</i> negative because pSPI12 was not found in these strains according to whole genome sequencing results. There was no cross-reaction with other <i>Salmonella</i> serotypes, including <i>Salmonella enterica</i> serovar Gallinarum biovar Gallinarum (<i>S</i>. Gallinarum), which show a close genetic relationship with <i>S.</i> Pullorum. This shows that the PCR method could distinguish <i>S.</i> Gallinarum from <i>S.</i> Pullorum in one-step PCR without complicated biochemical identification. The limit of detection of this PCR method was as low as 90 fg/μl or 10<sup>2</sup> CFU, which shows a high sensitivity. Moreover, this method was applied to identify <i>Salmonella</i> isolated from the chicken farm and the results were consistent with what we obtained from biochemical reactions and serotyping. Together, all the results demonstrated that this one-step PCR method is simple and feasible to efficiently identify <i>S.</i> Pullorum.
DOI: 10.5281/zenodo.3952888
title: Evelyn Arabic and French transcripts of description and comments on her recording in Wast al-Balad, Cairo (Egypt), 29-05-2013

description: « Mics in the Ears » binaural experiment in Cairo (Egypt): Vincent Battesti & Nicolas Puig, social anthropologists, asked inhabitants of Cairo megapolis in Egypt to record the surrounding urban sounds during one of their daily journeys (without the researcher), equipped with binaural microphones and GPS device. Participants have recorded in different Cairo neighbourhoods, and are themselves from different generations, social and economic backgrounds, and different genders. These text files (pdf and Word) are the transcripts (original in Arabic and translation in French) of the audio file of the description and comments one of them gave us a posteriori when listening to his/her own route he/she recorded with binaural mics. See https://vbat.org/article831
description: Data linked to the publication: Battesti, Vincent & Nicolas Puig, 2020 — « Towards a sonic ecology of urban life: Ethnography of sound perceptions in Cairo ». The Senses & Society, 15 (2), p. 170-191, doi: 10.1080/17458927.2020.1763606
description: {"references": ["Battesti, Vincent & Nicolas Puig, 2020 \u2014 \u00ab Towards a sonic ecology of urban life: Ethnography of sound perceptions in Cairo \u00bb. The Senses & Society, 15 (2), p. 170-191, doi: 10.1080/17458927.2020.1763606 \u2014 online: https://hal.archives-ouvertes.fr/hal-02890453", "Battesti, Vincent & Nicolas Puig, 2016 \u2014 \u00ab \"The sound of society\": a method for investigating sound perception in Cairo \u00bb. The Senses & Society, 11 (3), p. 298-319, doi: 10.1080/17458927.2016.1195112 \u2014 online: https://hal.archives-ouvertes.fr/hal-01380972"]}
DOI: 10.5281/zenodo.3952887
title: Evelyn Arabic and French transcripts of description and comments on her recording in Wast al-Balad, Cairo (Egypt), 29-05-2013

description: « Mics in the Ears » binaural experiment in Cairo (Egypt): Vincent Battesti & Nicolas Puig, social anthropologists, asked inhabitants of Cairo megapolis in Egypt to record the surrounding urban sounds during one of their daily journeys (without the researcher), equipped with binaural microphones and GPS device. Participants have recorded in different Cairo neighbourhoods, and are themselves from different generations, social and economic backgrounds, and different genders. These text files (pdf and Word) are the transcripts (original in Arabic and translation in French) of the audio file of the description and comments one of them gave us a posteriori when listening to his/her own route he/she recorded with binaural mics. See https://vbat.org/article831
description: Data linked to the publication: Battesti, Vincent & Nicolas Puig, 2020 — « Towards a sonic ecology of urban life: Ethnography of sound perceptions in Cairo ». The Senses & Society, 15 (2), p. 170-191, doi: 10.1080/17458927.2020.1763606
description: {"references": ["Battesti, Vincent & Nicolas Puig, 2020 \u2014 \u00ab Towards a sonic ecology of urban life: Ethnography of sound perceptions in Cairo \u00bb. The Senses & Society, 15 (2), p. 170-191, doi: 10.1080/17458927.2020.1763606 \u2014 online: https://hal.archives-ouvertes.fr/hal-02890453", "Battesti, Vincent & Nicolas Puig, 2016 \u2014 \u00ab \"The sound of society\": a method for investigating sound perception in Cairo \u00bb. The Senses & Society, 11 (3), p. 298-319, doi: 10.1080/17458927.2016.1195112 \u2014 online: https://hal.archives-ouvertes.fr/hal-01380972"]}
DOI: 10.5281/zenodo.3975888
title: List of studies on Covid-19 identified in PubMed and excluded from our systematic review

description: In the course of our PubMed searches we identified and screened the title and abstract of a number of studies on Covid-19 that were finally excluded from our systematic review. This file will be updated regularly.
DOI: 10.5281/zenodo.3952884
title: Shady Arabic and French transcripts of description and comments on his recording in Wast al-Balad, Cairo (Egypt), 26-09-2012

description: « Mics in the Ears » binaural experiment in Cairo (Egypt): Vincent Battesti & Nicolas Puig, social anthropologists, asked inhabitants of Cairo megapolis in Egypt to record the surrounding urban sounds during one of their daily journeys (without the researcher), equipped with binaural microphones and GPS device. Participants have recorded in different Cairo neighbourhoods, and are themselves from different generations, social and economic backgrounds, and different genders. These text files (pdf and Word) are the transcripts (original in Arabic and translation in French) of the audio file of the description and comments one of them gave us a posteriori when listening to his/her own route he/she recorded with binaural mics. See https://vbat.org/article831
description: Data linked to the publication: Battesti, Vincent & Nicolas Puig, 2020 — « Towards a sonic ecology of urban life: Ethnography of sound perceptions in Cairo ». The Senses & Society, 15 (2), p. 170-191, doi: 10.1080/17458927.2020.1763606
description: {"references": ["Battesti, Vincent & Nicolas Puig, 2020 \u2014 \u00ab Towards a sonic ecology of urban life: Ethnography of sound perceptions in Cairo \u00bb. The Senses & Society, 15 (2), p. 170-191, doi: 10.1080/17458927.2020.1763606 \u2014 online: https://hal.archives-ouvertes.fr/hal-02890453", "Battesti, Vincent & Nicolas Puig, 2016 \u2014 \u00ab \"The sound of society\": a method for investigating sound perception in Cairo \u00bb. The Senses & Society, 11 (3), p. 298-319, doi: 10.1080/17458927.2016.1195112 \u2014 online: https://hal.archives-ouvertes.fr/hal-01380972"]}
DOI: 10.5281/zenodo.3952883
title: Shady Arabic and French transcripts of description and comments on his recording in Wast al-Balad, Cairo (Egypt), 26-09-2012

description: « Mics in the Ears » binaural experiment in Cairo (Egypt): Vincent Battesti & Nicolas Puig, social anthropologists, asked inhabitants of Cairo megapolis in Egypt to record the surrounding urban sounds during one of their daily journeys (without the researcher), equipped with binaural microphones and GPS device. Participants have recorded in different Cairo neighbourhoods, and are themselves from different generations, social and economic backgrounds, and different genders. These text files (pdf and Word) are the transcripts (original in Arabic and translation in French) of the audio file of the description and comments one of them gave us a posteriori when listening to his/her own route he/she recorded with binaural mics. See https://vbat.org/article831
description: Data linked to the publication: Battesti, Vincent & Nicolas Puig, 2020 — « Towards a sonic ecology of urban life: Ethnography of sound perceptions in Cairo ». The Senses & Society, 15 (2), p. 170-191, doi: 10.1080/17458927.2020.1763606
description: {"references": ["Battesti, Vincent & Nicolas Puig, 2020 \u2014 \u00ab Towards a sonic ecology of urban life: Ethnography of sound perceptions in Cairo \u00bb. The Senses & Society, 15 (2), p. 170-191, doi: 10.1080/17458927.2020.1763606 \u2014 online: https://hal.archives-ouvertes.fr/hal-02890453", "Battesti, Vincent & Nicolas Puig, 2016 \u2014 \u00ab \"The sound of society\": a method for investigating sound perception in Cairo \u00bb. The Senses & Society, 11 (3), p. 298-319, doi: 10.1080/17458927.2016.1195112 \u2014 online: https://hal.archives-ouvertes.fr/hal-01380972"]}
DOI: 10.5281/zenodo.3952879
title: Samir Arabic and French transcripts of description and comments on his recording in Bashtil, Cairo (Egypt), 28-09-2012

description: « Mics in the Ears » binaural experiment in Cairo (Egypt): Vincent Battesti & Nicolas Puig, social anthropologists, asked inhabitants of Cairo megapolis in Egypt to record the surrounding urban sounds during one of their daily journeys (without the researcher), equipped with binaural microphones and GPS device. Participants have recorded in different Cairo neighbourhoods, and are themselves from different generations, social and economic backgrounds, and different genders. These text files (pdf and Word) are the transcripts (original in Arabic and translation in French) of the audio file of the description and comments one of them gave us a posteriori when listening to his/her own route he/she recorded with binaural mics. See https://vbat.org/article831
description: Data linked to the publication: Battesti, Vincent & Nicolas Puig, 2020 — « Towards a sonic ecology of urban life: Ethnography of sound perceptions in Cairo ». The Senses & Society, 15 (2), p. 170-191, doi: 10.1080/17458927.2020.1763606
description: {"references": ["Battesti, Vincent & Nicolas Puig, 2020 \u2014 \u00ab Towards a sonic ecology of urban life: Ethnography of sound perceptions in Cairo \u00bb. The Senses & Society, 15 (2), p. 170-191, doi: 10.1080/17458927.2020.1763606 \u2014 online: https://hal.archives-ouvertes.fr/hal-02890453", "Battesti, Vincent & Nicolas Puig, 2016 \u2014 \u00ab \"The sound of society\": a method for investigating sound perception in Cairo \u00bb. The Senses & Society, 11 (3), p. 298-319, doi: 10.1080/17458927.2016.1195112 \u2014 online: https://hal.archives-ouvertes.fr/hal-01380972"]}
DOI: 10.5281/zenodo.3952878
title: Samir Arabic and French transcripts of description and comments on his recording in Bashtil, Cairo (Egypt), 28-09-2012

description: « Mics in the Ears » binaural experiment in Cairo (Egypt): Vincent Battesti & Nicolas Puig, social anthropologists, asked inhabitants of Cairo megapolis in Egypt to record the surrounding urban sounds during one of their daily journeys (without the researcher), equipped with binaural microphones and GPS device. Participants have recorded in different Cairo neighbourhoods, and are themselves from different generations, social and economic backgrounds, and different genders. These text files (pdf and Word) are the transcripts (original in Arabic and translation in French) of the audio file of the description and comments one of them gave us a posteriori when listening to his/her own route he/she recorded with binaural mics. See https://vbat.org/article831
description: Data linked to the publication: Battesti, Vincent & Nicolas Puig, 2020 — « Towards a sonic ecology of urban life: Ethnography of sound perceptions in Cairo ». The Senses & Society, 15 (2), p. 170-191, doi: 10.1080/17458927.2020.1763606
description: {"references": ["Battesti, Vincent & Nicolas Puig, 2020 \u2014 \u00ab Towards a sonic ecology of urban life: Ethnography of sound perceptions in Cairo \u00bb. The Senses & Society, 15 (2), p. 170-191, doi: 10.1080/17458927.2020.1763606 \u2014 online: https://hal.archives-ouvertes.fr/hal-02890453", "Battesti, Vincent & Nicolas Puig, 2016 \u2014 \u00ab \"The sound of society\": a method for investigating sound perception in Cairo \u00bb. The Senses & Society, 11 (3), p. 298-319, doi: 10.1080/17458927.2016.1195112 \u2014 online: https://hal.archives-ouvertes.fr/hal-01380972"]}