cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13067049.v1
title: The cytoplasmic SYNCRIP mRNA interactome of mammalian neurons

description: SYNCRIP, a member of the cellular heterogeneous nuclear ribonucleoprotein (hnRNP) family of RNA binding proteins, regulates various aspects of neuronal development and plasticity. Although SYNCRIP has been identified as a component of cytoplasmic RNA granules in dendrites of mammalian neurons, only little is known about the specific SYNCRIP target mRNAs that mediate its effect on neuronal morphogenesis and function. Here, we present a comprehensive characterization of the cytoplasmic SYNCRIP mRNA interactome using iCLIP in primary rat cortical neurons. We identify hundreds of <i>bona fide</i> SYNCRIP target mRNAs, many of which encode for proteins involved in neurogenesis, neuronal migration and neurite outgrowth. From our analysis, the stabilization of mRNAs encoding for components of the microtubule network, such as doublecortin (Dcx), emerges as a novel mechanism of SYNCRIP function in addition to the previously reported control of actin dynamics. Furthermore, we found that SYNCRIP synergizes with pro-neural miRNAs, such as miR-9. Thus, SYNCRIP appears to promote early neuronal differentiation by a two-tier mechanism involving the stabilization of pro-neural mRNAs by direct 3ʹUTR interaction and the repression of anti-neural mRNAs in a complex with neuronal miRISC. Together, our findings provide a rationale for future studies investigating the function of SYNCRIP in mammalian brain development and disease.
DOI: 10.6084/m9.figshare.13181119
title: Xrn1 influence on gene transcription results from the combination of general effects on elongating RNA pol II and gene-specific chromatin configuration

description: mRNA homoeostasis is favoured by crosstalk between transcription and degradation machineries. Both the Ccr4-Not and the Xrn1-decaysome complexes have been described to influence transcription. While Ccr4-Not has been shown to directly stimulate transcription elongation, the information available on how Xrn1 influences transcription is scarce and contradictory. In this study we have addressed this issue by mapping RNA polymerase II (RNA pol II) at high resolution, using CRAC and BioGRO-seq techniques in <i>Saccharomyces cerevisiae</i>. We found significant effects of Xrn1 perturbation on RNA pol II profiles across the genome. RNA pol II profiles at 5ʹ exhibited significant alterations that were compatible with decreased elongation rates in the absence of Xrn1. Nucleosome mapping detected altered chromatin configuration in the gene bodies. We also detected accumulation of RNA pol II shortly upstream of polyadenylation sites by CRAC, although not by BioGRO-seq, suggesting higher frequency of backtracking before pre-mRNA cleavage. This phenomenon was particularly linked to genes with poorly positioned nucleosomes at this position. Accumulation of RNA pol II at 3ʹ was also detected in other mRNA decay mutants. According to these and other pieces of evidence, Xrn1 seems to influence transcription elongation at least in two ways: by directly favouring elongation rates and by a more general mechanism that connects mRNA decay to late elongation.
DOI: 10.6084/m9.figshare.13181119.v1
title: Xrn1 influence on gene transcription results from the combination of general effects on elongating RNA pol II and gene-specific chromatin configuration

description: mRNA homoeostasis is favoured by crosstalk between transcription and degradation machineries. Both the Ccr4-Not and the Xrn1-decaysome complexes have been described to influence transcription. While Ccr4-Not has been shown to directly stimulate transcription elongation, the information available on how Xrn1 influences transcription is scarce and contradictory. In this study we have addressed this issue by mapping RNA polymerase II (RNA pol II) at high resolution, using CRAC and BioGRO-seq techniques in <i>Saccharomyces cerevisiae</i>. We found significant effects of Xrn1 perturbation on RNA pol II profiles across the genome. RNA pol II profiles at 5ʹ exhibited significant alterations that were compatible with decreased elongation rates in the absence of Xrn1. Nucleosome mapping detected altered chromatin configuration in the gene bodies. We also detected accumulation of RNA pol II shortly upstream of polyadenylation sites by CRAC, although not by BioGRO-seq, suggesting higher frequency of backtracking before pre-mRNA cleavage. This phenomenon was particularly linked to genes with poorly positioned nucleosomes at this position. Accumulation of RNA pol II at 3ʹ was also detected in other mRNA decay mutants. According to these and other pieces of evidence, Xrn1 seems to influence transcription elongation at least in two ways: by directly favouring elongation rates and by a more general mechanism that connects mRNA decay to late elongation.
DOI: 10.6084/m9.figshare.12845091
title: Penalized Cox regression with a five-parameter spline model

description: Hazard models with cubic spline functions have a number of advantages to the existing regression models. For analysis of right-censored data, we introduce a penalized Cox regression method using five M-spline basis functions. The proposed spline model is more flexible than the existing parametric models as it produces the increasing, decreasing, convex, concave, and constant hazard functions. To illustrate the advantage of the proposed model, we analyze a life test dataset on electrical insulations and a gene expression dataset on lung cancer patients. We conduct simulation studies to compare the proposed method with the existing methods.
DOI: 10.6084/m9.figshare.12845091.v1
title: Penalized Cox regression with a five-parameter spline model

description: Hazard models with cubic spline functions have a number of advantages to the existing regression models. For analysis of right-censored data, we introduce a penalized Cox regression method using five M-spline basis functions. The proposed spline model is more flexible than the existing parametric models as it produces the increasing, decreasing, convex, concave, and constant hazard functions. To illustrate the advantage of the proposed model, we analyze a life test dataset on electrical insulations and a gene expression dataset on lung cancer patients. We conduct simulation studies to compare the proposed method with the existing methods.
DOI: 10.5281/zenodo.4419686
title: Insights from Transient Absorption Spectroscopy into Electron Dynamics Along the Ga-Gradient in Cu(In,Ga)Se2 Solar Cells: Data

description: Excel file with data to all figures published in our article found at https://doi.org/10.1002/aenm.202003446 (Advanced Energy Materials), Synopsis user manual, Matlab code to analyse and fit data
DOI: 10.5281/zenodo.4419685
title: Insights from Transient Absorption Spectroscopy into Electron Dynamics Along the Ga-Gradient in Cu(In,Ga)Se2 Solar Cells: Data

description: Excel file with data to all figures published in our article found at https://doi.org/10.1002/aenm.202003446 (Advanced Energy Materials), Synopsis user manual, Matlab code to analyse and fit data
DOI: 10.5281/zenodo.4698954
title: Impact of RbF and NaF Postdeposition Treatments on Charge Carrier Transport and Recombination in Ga-Graded Cu(In,Ga)Se2 Solar Cells

description: Excel file with data to all figures published in our article found at https://doi.org/10.1002/adfm.202103663 (Advanced Functional Materials)
DOI: 10.5281/zenodo.4698953
title: Impact of RbF and NaF Postdeposition Treatments on Charge Carrier Transport and Recombination in Ga-Graded Cu(In,Ga)Se2 Solar Cells

description: Excel file with data to all figures published in our article found at https://doi.org/10.1002/adfm.202103663 (Advanced Functional Materials)
DOI: 10.5517/ccdc.csd.cc25k98b
title: CCDC 2012621: Experimental Crystal Structure Determination

description: Related Article: Ran Li, Lei Yao, Yan-Bo Wang, Jun-Yan Zhu, Lixiong Zhang, Ji-Ya Fu, Chuan-Bao Zhang, Lili Zhao|2021|Org.Lett.|23|5611|doi:10.1021/acs.orglett.1c01510
DOI: 10.5517/ccdc.csd.cc25m0zt
title: CCDC 2014286: Experimental Crystal Structure Determination

description: Related Article: Ya Li, Jun Zeng, Yu-hua Tian, Yanan Hou, Honghong Da, Jianguo Fang, Kun Gao|2021|Phytochemistry|190|112880|doi:10.1016/j.phytochem.2021.112880
DOI: 10.5517/ccdc.csd.cc25m11x
title: CCDC 2014288: Experimental Crystal Structure Determination

description: Related Article: Ya Li, Jun Zeng, Yu-hua Tian, Yanan Hou, Honghong Da, Jianguo Fang, Kun Gao|2021|Phytochemistry|190|112880|doi:10.1016/j.phytochem.2021.112880
DOI: 10.5517/ccdc.csd.cc25m12y
title: CCDC 2014289: Experimental Crystal Structure Determination

description: Related Article: Ya Li, Jun Zeng, Yu-hua Tian, Yanan Hou, Honghong Da, Jianguo Fang, Kun Gao|2021|Phytochemistry|190|112880|doi:10.1016/j.phytochem.2021.112880
DOI: 10.5517/ccdc.csd.cc265rgm
title: CCDC 2031320: Experimental Crystal Structure Determination

description: Related Article: Nikola Bedeković, Marta Čavka, Dominik Cinčić, Vladimir Stilinović|2021|J.Mol.Struct.|1246|131130|doi:10.1016/j.molstruc.2021.131130
DOI: 10.5517/ccdc.csd.cc265rhn
title: CCDC 2031321: Experimental Crystal Structure Determination

description: Related Article: Nikola Bedeković, Marta Čavka, Dominik Cinčić, Vladimir Stilinović|2021|J.Mol.Struct.|1246|131130|doi:10.1016/j.molstruc.2021.131130
DOI: 10.5517/ccdc.csd.cc265rjp
title: CCDC 2031322: Experimental Crystal Structure Determination

description: Related Article: Nikola Bedeković, Marta Čavka, Dominik Cinčić, Vladimir Stilinović|2021|J.Mol.Struct.|1246|131130|doi:10.1016/j.molstruc.2021.131130
DOI: 10.5517/ccdc.csd.cc265rkq
title: CCDC 2031323: Experimental Crystal Structure Determination

description: Related Article: Nikola Bedeković, Marta Čavka, Dominik Cinčić, Vladimir Stilinović|2021|J.Mol.Struct.|1246|131130|doi:10.1016/j.molstruc.2021.131130
DOI: 10.5517/ccdc.csd.cc265rlr
title: CCDC 2031324: Experimental Crystal Structure Determination

description: Related Article: Nikola Bedeković, Marta Čavka, Dominik Cinčić, Vladimir Stilinović|2021|J.Mol.Struct.|1246|131130|doi:10.1016/j.molstruc.2021.131130
DOI: 10.5517/ccdc.csd.cc265rms
title: CCDC 2031325: Experimental Crystal Structure Determination

description: Related Article: Nikola Bedeković, Marta Čavka, Dominik Cinčić, Vladimir Stilinović|2021|J.Mol.Struct.|1246|131130|doi:10.1016/j.molstruc.2021.131130
DOI: 10.5517/ccdc.csd.cc265rnt
title: CCDC 2031326: Experimental Crystal Structure Determination

description: Related Article: Nikola Bedeković, Marta Čavka, Dominik Cinčić, Vladimir Stilinović|2021|J.Mol.Struct.|1246|131130|doi:10.1016/j.molstruc.2021.131130
DOI: 10.5517/ccdc.csd.cc265rpv
title: CCDC 2031327: Experimental Crystal Structure Determination

description: Related Article: Nikola Bedeković, Marta Čavka, Dominik Cinčić, Vladimir Stilinović|2021|J.Mol.Struct.|1246|131130|doi:10.1016/j.molstruc.2021.131130
DOI: 10.5517/ccdc.csd.cc265rqw
title: CCDC 2031328: Experimental Crystal Structure Determination

description: Related Article: Nikola Bedeković, Marta Čavka, Dominik Cinčić, Vladimir Stilinović|2021|J.Mol.Struct.|1246|131130|doi:10.1016/j.molstruc.2021.131130
DOI: 10.5517/ccdc.csd.cc265rrx
title: CCDC 2031329: Experimental Crystal Structure Determination

description: Related Article: Nikola Bedeković, Marta Čavka, Dominik Cinčić, Vladimir Stilinović|2021|J.Mol.Struct.|1246|131130|doi:10.1016/j.molstruc.2021.131130
DOI: 10.5517/ccdc.csd.cc265rsy
title: CCDC 2031330: Experimental Crystal Structure Determination

description: Related Article: Nikola Bedeković, Marta Čavka, Dominik Cinčić, Vladimir Stilinović|2021|J.Mol.Struct.|1246|131130|doi:10.1016/j.molstruc.2021.131130
DOI: 10.5517/ccdc.csd.cc265rtz
title: CCDC 2031331: Experimental Crystal Structure Determination

description: Related Article: Nikola Bedeković, Marta Čavka, Dominik Cinčić, Vladimir Stilinović|2021|J.Mol.Struct.|1246|131130|doi:10.1016/j.molstruc.2021.131130
DOI: 10.5517/ccdc.csd.cc26gw0l
title: CCDC 2040079: Experimental Crystal Structure Determination

description: Related Article: Wenxuan Zhang, Jiaying Sun, Linrui Xiang, Wen Si, Ran Song, Daoshan Yang, Jian Lv|2021|Org.Lett.|23|5998|doi:10.1021/acs.orglett.1c02065
DOI: 10.5517/ccdc.csd.cc26gw3p
title: CCDC 2040082: Experimental Crystal Structure Determination

description: Related Article: Wenxuan Zhang, Jiaying Sun, Linrui Xiang, Wen Si, Ran Song, Daoshan Yang, Jian Lv|2021|Org.Lett.|23|5998|doi:10.1021/acs.orglett.1c02065
DOI: 10.5517/ccdc.csd.cc26gwbx
title: CCDC 2040089: Experimental Crystal Structure Determination

description: Related Article: Wenxuan Zhang, Jiaying Sun, Linrui Xiang, Wen Si, Ran Song, Daoshan Yang, Jian Lv|2021|Org.Lett.|23|5998|doi:10.1021/acs.orglett.1c02065
DOI: 10.5517/ccdc.csd.cc26h9wx
title: CCDC 2040509: Experimental Crystal Structure Determination

description: Related Article: Wenxuan Zhang, Jiaying Sun, Linrui Xiang, Wen Si, Ran Song, Daoshan Yang, Jian Lv|2021|Org.Lett.|23|5998|doi:10.1021/acs.orglett.1c02065
DOI: 10.6084/m9.figshare.3761562.v1945
title: Online Labour Index: Measuring the Online Gig Economy for Policy and Research

description: Data repository for the data underlying the Online Labour Index. See http://ilabour.oii.ox.ac.uk online-labour-index/ for details.
DOI: 10.5281/zenodo.4436142
title: Reaching higher: External scapula assistance can improve upper limb function in people with irreversible scapula alata

description: ===========================================================================================<br> Reaching higher: External scapula assistance can improve upper limb function in people with irreversible scapula alata<br> =========================================================================================== Date: July 2021<br> Responsible: Anna-Maria Georgarakis<br> Email: marie.georgarakis@outlook.com Data Files: - demographicData_ScapulaOrthosis2020.csv: Demographic information about participants.<br> - moCapRawData_ScapulaOrthosis2020.csv: Motion Capture Raw data from 10 markers.<br> - moCapData_ScapulaOrthosis2020.csv: Motion Capture processed data, motion angles of the right arm.<br> - forceData_ScapulaOrthosis2020.csv: Processed force data from the scapula orthosis. This data may be re-used for scientific, ethically apporoved purposes under the creative commons CC BY 4.0 license agreement. <br> ===============<br> === SUMMARY ===<br> =============== This data was collected between November 2019 and July 2020 at the Kliniken Schmieder Konstanz.<br> The ethical approval for the study was issued by the ETH Zurich ethics commission (EK 2019-N-11).<br> More details can be found in the scientific publication. All participants participated voluntarily and gave their informed consent. The eight study PARTICIPANTS(P1...P8) were diagnosed with an irreversible scapula alata caused by different muscular dystrophies. Data was anonymized and does not reflect the order of recruitment but the order of baseline ability of arm elevation. Each participant performed two arm elevations each under the following CONDITIONS:<br> &gt;&gt; Functional Task, arm elevations under load<br> FT_NO : without any assistance, basline<br> FT_OS : with orthosis assistance, stabilizing the scapula on the thoracic wall<br> &gt;&gt; Range of motion task, arm elevations without load<br> NO : without any assistance, basline<br> OS1...OS6 : with orthosis assistance, stabilizing the scapula on the thoracic wall, set to 6 different force levels<br> SA : scapula maually assisted and guided by a trained therapist More information can be found in the README file and the scientific publication under the same name and authors.
description: Re-use of this data for ethical scientific purposes only.
DOI: 10.5281/zenodo.4436141
title: Reaching higher: External scapula assistance can improve upper limb function in people with irreversible scapula alata

description: ===========================================================================================<br> Reaching higher: External scapula assistance can improve upper limb function in people with irreversible scapula alata<br> =========================================================================================== Date: July 2021<br> Responsible: Anna-Maria Georgarakis<br> Email: marie.georgarakis@outlook.com Data Files: - demographicData_ScapulaOrthosis2020.csv: Demographic information about participants.<br> - moCapRawData_ScapulaOrthosis2020.csv: Motion Capture Raw data from 10 markers.<br> - moCapData_ScapulaOrthosis2020.csv: Motion Capture processed data, motion angles of the right arm.<br> - forceData_ScapulaOrthosis2020.csv: Processed force data from the scapula orthosis. This data may be re-used for scientific, ethically apporoved purposes under the creative commons CC BY 4.0 license agreement. <br> ===============<br> === SUMMARY ===<br> =============== This data was collected between November 2019 and July 2020 at the Kliniken Schmieder Konstanz.<br> The ethical approval for the study was issued by the ETH Zurich ethics commission (EK 2019-N-11).<br> More details can be found in the scientific publication. All participants participated voluntarily and gave their informed consent. The eight study PARTICIPANTS(P1...P8) were diagnosed with an irreversible scapula alata caused by different muscular dystrophies. Data was anonymized and does not reflect the order of recruitment but the order of baseline ability of arm elevation. Each participant performed two arm elevations each under the following CONDITIONS:<br> &gt;&gt; Functional Task, arm elevations under load<br> FT_NO : without any assistance, basline<br> FT_OS : with orthosis assistance, stabilizing the scapula on the thoracic wall<br> &gt;&gt; Range of motion task, arm elevations without load<br> NO : without any assistance, basline<br> OS1...OS6 : with orthosis assistance, stabilizing the scapula on the thoracic wall, set to 6 different force levels<br> SA : scapula maually assisted and guided by a trained therapist More information can be found in the README file and the scientific publication under the same name and authors.
description: Re-use of this data for ethical scientific purposes only.
DOI: 10.5517/ccdc.csd.cc26nw6z
title: CCDC 2045851: Experimental Crystal Structure Determination

description: Related Article: Shuai Li, Liyuan Fu, Xiaoxiao Xiao, Hua Geng, Qing Liao, Yi Liao, Hongbing Fu|2021|Angew.Chem.,Int.Ed.|60|18059|doi:10.1002/anie.202103192
DOI: 10.5517/ccdc.csd.cc26t6bl
title: CCDC 2050009: Experimental Crystal Structure Determination

description: Related Article: Qingying Yang, Xinyu Sun, Jianwei Han, Limin Wang|2021|Dyes Pigm.|194|109655|doi:10.1016/j.dyepig.2021.109655
DOI: 10.5517/ccdc.csd.cc275lst
title: CCDC 2060966: Experimental Crystal Structure Determination

description: Related Article: Ran Li, Lei Yao, Yan-Bo Wang, Jun-Yan Zhu, Lixiong Zhang, Ji-Ya Fu, Chuan-Bao Zhang, Lili Zhao|2021|Org.Lett.|23|5611|doi:10.1021/acs.orglett.1c01510
DOI: 10.5517/ccdc.csd.cc277rqz
title: CCDC 2063041: Experimental Crystal Structure Determination

description: Related Article: Ran Li, Lei Yao, Yan-Bo Wang, Jun-Yan Zhu, Lixiong Zhang, Ji-Ya Fu, Chuan-Bao Zhang, Lili Zhao|2021|Org.Lett.|23|5611|doi:10.1021/acs.orglett.1c01510
DOI: 10.5517/ccdc.csd.cc27flw5
title: CCDC 2068657: Experimental Crystal Structure Determination

description: Related Article: Yong-Xian Huang, Hua-Juan Hu, Rong-Jia Wei, Guo-Hong Ning, Dan Li|2021|Cryst.Growth Des.|21|4587|doi:10.1021/acs.cgd.1c00457
DOI: 10.5517/ccdc.csd.cc27flx6
title: CCDC 2068658: Experimental Crystal Structure Determination

description: Related Article: Yong-Xian Huang, Hua-Juan Hu, Rong-Jia Wei, Guo-Hong Ning, Dan Li|2021|Cryst.Growth Des.|21|4587|doi:10.1021/acs.cgd.1c00457
DOI: 10.5517/ccdc.csd.cc27fly7
title: CCDC 2068659: Experimental Crystal Structure Determination

description: Related Article: Yong-Xian Huang, Hua-Juan Hu, Rong-Jia Wei, Guo-Hong Ning, Dan Li|2021|Cryst.Growth Des.|21|4587|doi:10.1021/acs.cgd.1c00457
DOI: 10.5517/ccdc.csd.cc27flz8
title: CCDC 2068660: Experimental Crystal Structure Determination

description: Related Article: Yong-Xian Huang, Hua-Juan Hu, Rong-Jia Wei, Guo-Hong Ning, Dan Li|2021|Cryst.Growth Des.|21|4587|doi:10.1021/acs.cgd.1c00457
DOI: 10.5517/ccdc.csd.cc27fm1c
title: CCDC 2068662: Experimental Crystal Structure Determination

description: Related Article: Yong-Xian Huang, Hua-Juan Hu, Rong-Jia Wei, Guo-Hong Ning, Dan Li|2021|Cryst.Growth Des.|21|4587|doi:10.1021/acs.cgd.1c00457
DOI: 10.5517/ccdc.csd.cc27fm2d
title: CCDC 2068663: Experimental Crystal Structure Determination

description: Related Article: Yong-Xian Huang, Hua-Juan Hu, Rong-Jia Wei, Guo-Hong Ning, Dan Li|2021|Cryst.Growth Des.|21|4587|doi:10.1021/acs.cgd.1c00457
DOI: 10.25375/uct.14635503.v1
title: Data used in the manuscript 'Mycobacterium tuberculosis-specific T cell functional, memory and activation profiles in QuantiFERON-reverters are consistent with controlled infection.'

description: Reversion of immune sensitization tests for <i>Mycobacterium tuberculosis</i> (<i>M.tb</i>) infection, such as interferon-gamma release assays or tuberculin skin test, has been reported in multiple studies. We hypothesised that QuantiFERON-TB Gold (QFT) reversion is associated with a decline of <i>M.tb</i>-specific functional T cell responses, and a distinct pattern of T cell and innate responses compared to persistent QFT+ and QFT- individuals. This dataset consists of meta data from the Adolescent Cohort Study (ACS) and innate and adaptive cellular responses that were measured in stimulated Peripheral blood mononuclear cells (PBMCs). <br>PBMCs were collected at enrolment and at 6-monthly intervals during the 2-years of follow-up (termed months 0, 6, 12 and 18) when the QFT tests were performed to determine <i>M.tb</i> infection. Three groups of participants were defined based on their longitudinal QFT results: persistent QFT positives (QFT positive results &gt; 0.35 IU/mL at four consecutive visits), QFT reverters (two QFT positive results, at least one &gt; 0.7 IU/mL, followed by two QFT negative results, at least one &lt; 0.2 IU/mL), and non-converters (QFT negative results &lt; 0.2 at four consecutive visits). Overall, all three groups were matched by age, sex, ethnicity, school and known TB exposure. <br>Five stimulations were used to induce <i>M.tb</i>-specific T cell responses of the adaptive arm, including <i>M.tb</i>-specific peptide pools spanning ESAT-6/CFP-10 or EspC, EspF and Rv2348c (collectively termed Esp), and<i> M.tb</i>-lysate; Staphylococcus Enterotoxin B (SEB), as a positive control; or the cells were left unstimulated as a negative control. The variables include a combination of 5 effector functions (IL2, TNF, IFNg, CD107, CD154) produced by CD4+ and CD8+ T cells upon stimulation. Combinations of the phenotypic markers CD45RA, CCR7, CD27, KLRG1, HLA-DR and CXCR3 were further measured on IFNg, IL2 or TNF producing T cells (total Th1).<br>In the innate cells, effector responses were measured in unstimulated PBMC or after stimulation with <i>M.tb</i>-lysate or <i>E. Coli </i>(positive control). The variables in this dataset included a combination of 6 functional markers (Granzyme B, IL6, IL10, IL12, IFNg, TNF) produced by NK cells, B cells, monocytes, and DURT cells.<br>This dataset was used in the manuscript <i>Mycobacterium tuberculosis-specific T cell functional, memory and activation profiles in QuantiFERON-reverters are consistent with controlled infection. </i>See the full manuscript for more details.