cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19519432
title: Table S2_miRNA-gene interactions.xlsx

description: Table S2_ miRNA-gene interactions
DOI: 10.5517/ccdc.csd.cc26s506
title: CCDC 2049007: Experimental Crystal Structure Determination

description: Related Article: Guangfu Li, Dongjiao Jiang, Guogang Shan, Weilin Song, Jialin Tong, Di Kang, Baoshan Hou, Yingxiao Mu, Kuizhan Shao, Yun Geng, Xinlong Wang, Zhongmin Su|2022|Angew.Chem.,Int.Ed.|61|e202113425|doi:10.1002/anie.202113425
DOI: 10.5517/ccdc.csd.cc26s517
title: CCDC 2049008: Experimental Crystal Structure Determination

description: Related Article: Guangfu Li, Dongjiao Jiang, Guogang Shan, Weilin Song, Jialin Tong, Di Kang, Baoshan Hou, Yingxiao Mu, Kuizhan Shao, Yun Geng, Xinlong Wang, Zhongmin Su|2022|Angew.Chem.,Int.Ed.|61|e202113425|doi:10.1002/anie.202113425
DOI: 10.5517/ccdc.csd.cc26s528
title: CCDC 2049009: Experimental Crystal Structure Determination

description: Related Article: Guangfu Li, Dongjiao Jiang, Guogang Shan, Weilin Song, Jialin Tong, Di Kang, Baoshan Hou, Yingxiao Mu, Kuizhan Shao, Yun Geng, Xinlong Wang, Zhongmin Su|2022|Angew.Chem.,Int.Ed.|61|e202113425|doi:10.1002/anie.202113425
DOI: 10.5517/ccdc.csd.cc288hgj
title: CCDC 2093537: Experimental Crystal Structure Determination

description: Related Article: Guangfu Li, Dongjiao Jiang, Guogang Shan, Weilin Song, Jialin Tong, Di Kang, Baoshan Hou, Yingxiao Mu, Kuizhan Shao, Yun Geng, Xinlong Wang, Zhongmin Su|2022|Angew.Chem.,Int.Ed.|61|e202113425|doi:10.1002/anie.202113425
DOI: 10.5517/ccdc.csd.cc288hhk
title: CCDC 2093538: Experimental Crystal Structure Determination

description: Related Article: Guangfu Li, Dongjiao Jiang, Guogang Shan, Weilin Song, Jialin Tong, Di Kang, Baoshan Hou, Yingxiao Mu, Kuizhan Shao, Yun Geng, Xinlong Wang, Zhongmin Su|2022|Angew.Chem.,Int.Ed.|61|e202113425|doi:10.1002/anie.202113425
DOI: 10.5517/ccdc.csd.cc288hjl
title: CCDC 2093539: Experimental Crystal Structure Determination

description: Related Article: Guangfu Li, Dongjiao Jiang, Guogang Shan, Weilin Song, Jialin Tong, Di Kang, Baoshan Hou, Yingxiao Mu, Kuizhan Shao, Yun Geng, Xinlong Wang, Zhongmin Su|2022|Angew.Chem.,Int.Ed.|61|e202113425|doi:10.1002/anie.202113425
DOI: 10.5517/ccdc.csd.cc272mjh
title: CCDC 2058106: Experimental Crystal Structure Determination

description: Related Article: shimin chen|2021|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc28czk6
title: CCDC 2096888: Experimental Crystal Structure Determination

description: Related Article: Takuya Suga, Yuuki Takahashi, Chinatsu Miki, Yutaka Ukaji|2022|Angew.Chem.,Int.Ed.|61|e202112533|doi:10.1002/anie.202112533
DOI: 10.25345/c56d5pf7w
title: MassIVE MSV000089203 - Molecular Mechanisms in Rasmussen Encephalitis
title: Rasmussen encephalitis is a unilateral encephalitis characterized by treatment-resistant epilepsy and progressive cognitive and motor decline. MRI reveals inflammation and neuropathology reveals reactive astrocytes, microglial activation, microglial nodules, T cell infiltration, and neuronal loss. Despite the abundant evidence of altered signaling pathways in Rasmussen brain tissue and associated genetic variants, the mechanisms remain poorly understood, and it is uncertain which are a part or result of the underlying cause In Rasmussen brain tissue, we identified by RNAseq altered immune signaling pathways, immune cell type annotation enrichment, and by whole exome sequencing HLA variants more common to Rasmussen. These findings demonstrate immune cell infiltration associated with innate and adaptive immune responses, as well as HLA variants that may increase vulnerability to RE.
DOI: 10.18170/dvn/rvqgle
title: BatchUnMix：Isothermal remanent curve fitting tool

description: This dataset contains MATLAB code and instructions for using BatchUnMix.
DOI: 10.5281/zenodo.6414757
title: ProB Operation Caching ifm2022 Artefact

description: The artefact accompanies the paper "Operation Caching and State Compression for Model Checking of High-Level Models" to appear in the proceedings of the ifm2022 conference. The artefact enables one to reproduce the results in the paper. The aftefact contains the models and it contains a Makefile which<br> - can download and install ProB<br> - can run the regular benchmarks<br> - can run the TLC benchmarks<br> - can install LTSMin and run the LTSMin benchmarks The source of the models can be found in the README and in the accompanying ifm2022 paper.
description: The source of the models can be found in the README and in the accompanying ifm2022 paper.
DOI: 10.13020/4mc0-vv65
title: An ensonified bubble curtain blocks 4 species of invasive carp in a laboratory flume but also deters other fish, while sound alone is less effective overall and does not target carp
DOI: 10.5281/zenodo.6414854
title: Dataset Methods for stratification and validation cohorts: a scoping review

description: We searched PubMed, EMBASE and the Cochrane Library for reviews that described the tools and methods applied to define cohorts used for patient stratification or validation of patient clustering. We focused on cancer, stroke, and Alzheimer’s disease (AD) and limited the searches to reports in English, French, German, Italian and Spanish, published from 2005 to April 2020. Two authors screened the records, and one extracted the key information from each included review. The result of the screening process was reported through a PRISMA flowchart.
DOI: 10.5281/zenodo.6414853
title: Dataset Methods for stratification and validation cohorts: a scoping review

description: We searched PubMed, EMBASE and the Cochrane Library for reviews that described the tools and methods applied to define cohorts used for patient stratification or validation of patient clustering. We focused on cancer, stroke, and Alzheimer’s disease (AD) and limited the searches to reports in English, French, German, Italian and Spanish, published from 2005 to April 2020. Two authors screened the records, and one extracted the key information from each included review. The result of the screening process was reported through a PRISMA flowchart.
DOI: 10.5281/zenodo.6415021
title: Northern Gulf of Mexico Surface Nutrient Residuals (from Mixing Line)

description: Northern Gulf of Mexico Surface Nutrient Residuals (from Mixing Line) - DIN, DIP
DOI: 10.5285/614752d35dc147a598d5421443fb50e8
title: CANDIFLOS : Surface fluxes from AO2016 measurement campaign on icebreaker Oden, 2014

description: Characterising and Interpreting FLuxes Over Sea Ice (CANDIFLOS) is a data analysis project drawing upon data from multiple field campaigns. It aims to improve the parameterization of surface fluxes over sea ice. This data set consists of the processed surface heat fluxes and sea ice fractions from the Arctic Ocean 2016 (AO2016) project (2016) conducted on the icebreaker Oden. Matching data from the Arctic Clouds Summer Experiment (ACSE) cruise (2014) are provided as a separate data set.
DOI: 10.13020/13xf-nw93
title: Dataset for "Characterization of inexpensive MOx sensor performance for trace methane detection"
DOI: 10.5281/zenodo.6414349
title: DAPSI Open Call2-Subgrantees Dataset

description: This file contains the main data from the awarded applicants in the second open call of the NGI-DAPSI Programme funded under the GA 871498.
DOI: 10.5281/zenodo.6414348
title: DAPSI Open Call2-Subgrantees Dataset

description: This file contains the main data from the awarded applicants in the second open call of the NGI-DAPSI Programme funded under the GA 871498.
DOI: 10.5281/zenodo.5409778
title: DAPSI Open Call1-Subgrantees Dataset

description: This file contains the main data from the awarded applicants in the first open call of the NGI-DAPSI Programme funded under the GA 871498.
DOI: 10.5281/zenodo.5158448
title: DAPSI Open Call1-Subgrantees Dataset

description: This file contains the main data from the awarded applicants in the first open call of the NGI-DAPSI Programme funded under the GA 871498.
DOI: 10.5519/qd.4p00idzk
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1 records)
DOI: 10.25919/djmk-pc71
title: Parkes observations for project P456 semester 2021OCTS_10

description: The Parkes Pulsar Timing Array (PPTA) project has three primary goals: (a) detection of gravitational waves from astronomical sources, (b) establishment of a pulsar timescale, and (c) improvement of our understanding of Solar-system dynamics. We are now in an exciting regime where a signal detected in our (and other data sets) has the form expected for a gravitational wave background. We are therefore now attempting to confirm, or deny, this exciting result. With this proposal we aim to maintain our pre-eminent position in the field. Unlike most observing proposals, this is a continuing proposal for which the observations will continue to improve bounds on ultra-low-frequency gravitational waves until they are finally detected. Continued Parkes observations will remain valuable at least until the first stage of the SKA is able to improve on our sensitivity and observing cadence. Even after the gravitational wave background is detected we will want to continue observations in support of the nascent field of gravitational wave astronomy!
DOI: 10.5281/zenodo.5648186
title: Short- and long-term effects of a cardiac rehabilitation program in patients implanted with a left ventricular assist device: dataset

description: public anonymized dataset
DOI: 10.5281/zenodo.5648185
title: Short- and long-term effects of a cardiac rehabilitation program in patients implanted with a left ventricular assist device: dataset

description: public anonymized dataset
DOI: 10.6084/m9.figshare.12123585
title: Simultaneous detection of Mycobacterium tuberculosis complex and resistance to Rifampicin and Isoniazid by MDR/MTB ELITe MGB® Kit for the diagnosis of tuberculosis

description: 100 pulmonary and 160 extra-pulmonary samples (sheet Samples) and 300 samples spiked with 3 MTB isolates phenotypically resistant to Rifampicin and/or Isoniazid, carrying mutations in the rpoB, katG or inhA genes (sheet Spikes) were tested with MDR/MTB ELITe MGB® Kit (ELITe) on ELITe InGenius system and performance (sensitivity and specificity) were elaborated in comparison with culture.<br>The study was conducted at the Unit of Microbiology of the S. Orsola-Malpighi University Hospital in Bologna (Italy).<br>Database reports smear microscopy, mycobacterial culture, MTB drug susceptibility, Xpert MTB/RIF Ultra results, sample type, ELITe results about MTB DNA and resistances detection, Ct and melting temperature of MTB IS6110, rpoB, katG and inhA genes.
DOI: 10.6084/m9.figshare.12123585.v1
title: Simultaneous detection of Mycobacterium tuberculosis complex and resistance to Rifampicin and Isoniazid by MDR/MTB ELITe MGB® Kit for the diagnosis of tuberculosis

description: 100 pulmonary and 160 extra-pulmonary samples (sheet Samples) and 300 samples spiked with 3 MTB isolates phenotypically resistant to Rifampicin and/or Isoniazid, carrying mutations in the rpoB, katG or inhA genes (sheet Spikes) were tested with MDR/MTB ELITe MGB® Kit (ELITe) on ELITe InGenius system and performance (sensitivity and specificity) were elaborated in comparison with culture.<br>The study was conducted at the Unit of Microbiology of the S. Orsola-Malpighi University Hospital in Bologna (Italy).<br>Database reports smear microscopy, mycobacterial culture, MTB drug susceptibility, Xpert MTB/RIF Ultra results, sample type, ELITe results about MTB DNA and resistances detection, Ct and melting temperature of MTB IS6110, rpoB, katG and inhA genes.
DOI: 10.6084/m9.figshare.12482657
title: Quantiferon-TB Gold Plus by CLIA: Do we need a higher cut-off?

description: Head-to-head comparison of qualitative and quantitative QFT-Plus assay results by enzyme-linked immunoassay (ELISA) and chemiluminescence immunoassay (CLIA) was performed on 419 QFT-Plus blood samples.<br>The study was conducted at the Unit of Microbiology of the S. Orsola-Malpighi University Hospital in Bologna (Italy).<br>Database reports Nil, TB1, TB2, Mitogen quantitative values and qualitative results of QFT-Plus both by ELISA and CLIA, assays date and sample storage time.<br><br>
DOI: 10.6084/m9.figshare.12482657.v1
title: Quantiferon-TB Gold Plus by CLIA: Do we need a higher cut-off?

description: Head-to-head comparison of qualitative and quantitative QFT-Plus assay results by enzyme-linked immunoassay (ELISA) and chemiluminescence immunoassay (CLIA) was performed on 419 QFT-Plus blood samples.<br>The study was conducted at the Unit of Microbiology of the S. Orsola-Malpighi University Hospital in Bologna (Italy).<br>Database reports Nil, TB1, TB2, Mitogen quantitative values and qualitative results of QFT-Plus both by ELISA and CLIA, assays date and sample storage time.<br><br>
DOI: 10.6084/m9.figshare.6238433
title: Improvement of Mycobacterium tuberculosis detection by Xpert MTB/RIF Ultra: a head to head comparison on Xpert-negative samples

description: Sixty-eight decontaminated frozen samples (36 respiratory and 32 non-respiratory) collected over a 4-year period which were smear-negative, Xpert-negative but MTB culture-positive, were tested with Xpert MTB/RIF Ultra at the Unit of Microbiology of the S. Orsola-Malpighi University Hospital in Bologna (Italy). Database reports smear microscopy, mycobacterial culture, Xpert and Xpert Ultra results, Rif detection,semi-quantitative load and Ct results of IS1081, IS6110 and rpoB genes, time to positivity, time of storage.<br>
DOI: 10.6084/m9.figshare.6238433.v3
title: Improvement of Mycobacterium tuberculosis detection by Xpert MTB/RIF Ultra: a head to head comparison on Xpert-negative samples

description: Sixty-eight decontaminated frozen samples (36 respiratory and 32 non-respiratory) collected over a 4-year period which were smear-negative, Xpert-negative but MTB culture-positive, were tested with Xpert MTB/RIF Ultra at the Unit of Microbiology of the S. Orsola-Malpighi University Hospital in Bologna (Italy). Database reports smear microscopy, mycobacterial culture, Xpert and Xpert Ultra results, Rif detection,semi-quantitative load and Ct results of IS1081, IS6110 and rpoB genes, time to positivity, time of storage.<br>
DOI: 10.6084/m9.figshare.4763320
title: Diagnosis of smear-negative tuberculosis is greatly improved by Xpert MTB/RIF

description: 5-year (January 2011-December 2015) retrospective analysis of microbiological results for the diagnosis of TB performed at the Unit of Microbiology of the S. Orsola-Malpighi University Hospital in Bologna (Italy). During the study period, 5170 specimens originated from patients with suspected TB have been examined with Xpert MTB/RIF. Database reports smear microscopy, mycobacterial culture, Xpert results (divided by assay version) and Rif detection, sample localization.
DOI: 10.6084/m9.figshare.6238433.v2
title: Improvement of Mycobacterium tuberculosis detection by Xpert MTB/RIF Ultra: a head to head comparison on Xpert-negative samples

description: Sixty-eight decontaminated frozen samples (36 respiratory and 32 non-respiratory) collected over a 4-year period which were smear-negative, Xpert-negative but MTB culture-positive, were tested with Xpert MTB/RIF Ultra at the Unit of Microbiology of the S. Orsola-Malpighi University Hospital in Bologna (Italy). Database reports smear microscopy, mycobacterial culture, Xpert and Xpert Ultra results, Rif detection,semi-quantitative load and Ct results of IS1081, IS6110 and rpoB genes, time to positivity, time of storage.<br>
DOI: 10.5281/zenodo.6413231
title: Annotated genome Pseudomonas species MWU 12.3091

description: Annotated genome Pseudomonas species MWU 12.3091 isolated from cultivated cranberry bogs in southeastern Massachusetts.
DOI: 10.5281/zenodo.6413223
title: Annotated genome Pseudomonas species MWU 12.2319

description: Annotated genome Pseudomonas species MWU 12.2319 isolated from cultivated cranberry bogs in southeastern Massachusetts.
DOI: 10.5281/zenodo.6413230
title: Annotated genome Pseudomonas species MWU 12.3091

description: Annotated genome Pseudomonas species MWU 12.3091 isolated from cultivated cranberry bogs in southeastern Massachusetts.
DOI: 10.5281/zenodo.6413222
title: Annotated genome Pseudomonas species MWU 12.2319

description: Annotated genome Pseudomonas species MWU 12.2319 isolated from cultivated cranberry bogs in southeastern Massachusetts.
DOI: 10.5281/zenodo.6413119
title: Annotated genome Pseudomonas species MWU 12.3088

description: Annotated genome Pseudomonas species MWU 12.3088 isolated from cultivated cranberry bogs in southeastern Massachusetts.
DOI: 10.5281/zenodo.6413118
title: Annotated genome Pseudomonas species MWU 12.3088

description: Annotated genome Pseudomonas species MWU 12.3088 isolated from cultivated cranberry bogs in southeastern Massachusetts.
DOI: 10.5281/zenodo.6144286
title: Simulations for: Patched 1 regulates Smoothened by controlling sterol binding to its extracellular cysteine-rich domain.

description: <strong>Atomistic simulations of Smoothened:</strong> Atomistic molecular dynamics simulations of glycosylated mouse Smoothened (mSMO) and human Smoothened (hSMO) in distinct liganded states: - mSMO in an apo state (mSMO_apo) - mSMO with TMD cholesterol bound (mSMO_chol_TMD) - mSMO with CRD cholesterol bound (mSMO_chol_CRD) - mSMO with cholesterol bound to the CRD and TMD (mSMO_2chol_TMD_CRD) - mSMO bound to CRD cholesterol and Smoothened agonist (SAG) (mSMO_chol_CRD_SAG) - mSMO bound to CRD and TMD cholesterols, SAG and an intracellular nanobody (mSMO_2chol_SAG_nanobody) - mSMO bound to CRD and TMD cholesterol and with an additional cholesterol bound at a proposed 'mid' position (mSMO_3chol) - hSMO bound to CRD cholesterol and SAG (hSMO_chol_CRD_SAG) All simulations were run for 5x 300 ns. The active mSMO conformation was obtained from the Protein Data Bank (PDB ID: 6O3C). The hSMO structure was determined using X-ray crystallography as outlined within this study. <strong>File description for each system:</strong> - md_fit_firstframe.pdb : Initial frame used for atomistic simulations (replicate 1, each replicate equilibrated independently). - md_fit_<em>X</em>.xtc : Gromacs trajectory file for each replicate (X=replicate number).
DOI: 10.5281/zenodo.6144285
title: Simulations for: Patched 1 regulates Smoothened by controlling sterol binding to its extracellular cysteine-rich domain.

description: <strong>Atomistic simulations of Smoothened:</strong> Atomistic molecular dynamics simulations of glycosylated mouse Smoothened (mSMO) and human Smoothened (hSMO) in distinct liganded states: - mSMO in an apo state (mSMO_apo) - mSMO with TMD cholesterol bound (mSMO_chol_TMD) - mSMO with CRD cholesterol bound (mSMO_chol_CRD) - mSMO with cholesterol bound to the CRD and TMD (mSMO_2chol_TMD_CRD) - mSMO bound to CRD cholesterol and Smoothened agonist (SAG) (mSMO_chol_CRD_SAG) - mSMO bound to CRD and TMD cholesterols, SAG and an intracellular nanobody (mSMO_2chol_SAG_nanobody) - mSMO bound to CRD and TMD cholesterol and with an additional cholesterol bound at a proposed 'mid' position (mSMO_3chol) - hSMO bound to CRD cholesterol and SAG (hSMO_chol_CRD_SAG) All simulations were run for 5x 300 ns. The active mSMO conformation was obtained from the Protein Data Bank (PDB ID: 6O3C). The hSMO structure was determined using X-ray crystallography as outlined within this study. <strong>File description for each system:</strong> - md_fit_firstframe.pdb : Initial frame used for atomistic simulations (replicate 1, each replicate equilibrated independently). - md_fit_<em>X</em>.xtc : Gromacs trajectory file for each replicate (X=replicate number).
DOI: 10.5281/zenodo.6415097
title: Exploratory study of Novel Preprocessing Methods

description: https://www.cincibrainlab.com/post/deep-dive-on-artifact-material/
DOI: 10.6084/m9.figshare.19519483
title: Screening for depressive symptoms in Mexican people living with HIV during the first and second waves of the COVID-19 Pandemic

description: Dataset
DOI: 10.6084/m9.figshare.19519483.v2
title: Screening for depressive symptoms in Mexican people living with HIV during the first and second waves of the COVID-19 Pandemic

description: Dataset
DOI: 10.6084/m9.figshare.19519483.v1
title: Screening for depressive symptoms in Mexican people living with HIV during the first and second waves of the COVID-19 Pandemic

description: Dataset
DOI: 10.6084/m9.figshare.14717061.v2
title: 500 dereplicated_genomes

description: <b>500 metagenome-assembled microbial genomes from 30 subtropical estuaries in South China</b>
DOI: 10.25919/3bf9-rg22
title: Parkes observations for project P960 semester 2021OCTS_05

description: We aim to carry out receiver pointing and characterisation tests of Parkes receivers. Typically, these tests are carried out after the receiver package is installed, but time does not always allow for proper characterisation. Receivers for consideration include UWL, MARS and 13MM packages. In addition to cross-referencing C007 for flux calibration via pointing, we aim to conduct gain-elevation and system temperature experiments using the Moon, to ensure users of the Parkes Observatory have the most accurate information available for calibration purposes. We also wish to fully characterise the spectro-polarimetry response of the UWL and cryoPAF, by determining the Mueller Matrix for the receivers.
DOI: 10.25919/ptxk-ew23
title: Parkes observations for project P971 semester 2021OCTS_07

description: We propose further timing observations of the relativistic pulsar - white-dwarf binary, PSR J1141$-$6545. This unique system offers access to a wide range of physics, from relativistic phenomena through pulsar emission cone studies, to the structure and distribution of interstellar plasma along our line-of-sight. The analysis of existing data has already revealed the first detection of Lense-Thirring precession in a binary star system, and hinted at complex emission beam structure probed via geodetic precession. Further timing of this system for the next few years is needed for studies of these effects at higher precision. From this semester, we are converting this project into a large project proposal. We request the TAC to award us pre-graded status for the next semester.
DOI: 10.5281/zenodo.6415136
title: PGxMine

description: This describes the output files for the PGxMine project. The code for this viewer is available in the PGxMine Github repo if you want to run it independently. Each file is a tab-delimited file with a header, no comments and no quoting. You likely want <strong>pgxmine_collated.tsv</strong> if you just want the list of chemical/variant assocations. If you want the supporting sentences, look at <strong>pgxmine_sentences.tsv</strong>. You can use the <em>matching_id</em> column to connect the two files. If you want to dig further and are okay with a higher false positive rate, look at <strong>pgxmine_unfiltered.tsv</strong>. <strong>pgxmine_collated.tsv:</strong> This contains the chemical/variant associations with citation counts supporting them. It contains the normalized chemical, variant and where appropriate gene names with identifiers for PharmGKB, dbSNP and Entrez. <strong>pgxmine_sentences.tsv:</strong> This contains the supporting sentences for the chemical/variant associations in the collated file. Each row is a single supporting sentence for one association. This file contains information on the source publication (e.g. journal, publication date, etc), the actual sentence and the chemical/variant association extracted. <strong>pgxmine_unfiltered.tsv:</strong> This is the combined raw output of the createKB.py script across all of PubMed, Pubmed Central Open Access and PubMed Central Author Manuscript Collection. It contains every predicted relation with a prediction score above 0.5. So this may contain many false positives. Each row contain information on the publication (e.g. journal, publication date, etc) along with the sentence and the specific chemical/variant association.
DOI: 10.6084/m9.figshare.19519753
title: KEGG numbers of Glidobacterium mauchi and S. xhesshqipensis

description: KEGG-numbers of<i> Glidobacterium mauchi </i>(kegg_list by Emanuel Mauch) <i>and </i>S. xhesshqipensis<i> </i>(KEGG_XA by Xhesida Ajvazi)<i> </i>for metabolic investigation.