cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10697837
title: Benzodiazepines docked into human GABAAR and schistosome TRP channel binding pockets

description: Modeling benzodiazepine binding to TRP and GABAARs

Targets were obtained from public structure repositories. GABAAR coordinates were taken from RSCB, PDB accession 6HUP for a cryo-EM derived structure in its diazepam-bound state. The AlphaFold model AF-A0A5K4FCC0-F1-model provided starting coordinates for the S. mansoni TRP channel Smp_333650. Structure models were prepared for docking using the DockPrep utility of ChimeraX v1.7 (Meng et al. 2023) to fill in missing atoms, add hydrogens, assign partial charges (AMBER ff14SB), and exported in mol2 formats. SMILES for the benzodiazepine chemical series were generated using ChemDraw. Library preparation utilities fixpka (QUACPAC v2.1.2.1), OMEGA2 v4.1.1.1, and molcharge (QUACPAC v2.1.2.1) were used to assign protonation states, build energetically reasonable starting 3D conformers for docking, and assign partial charges (MMFF), respectively (OpenEye Scientific, Cadence Molecular Sciences, Inc.). Single conformations were exported in mol2 format for docking. Docking was performed using the program Gnina v1.0 (McNutt et al. 2021). To localize the search space in docking GABAAR, the binding pocket was specified based on the position of diazepam using the autobox option with a bounding box of 10 Angstroms. No sidechain flexibility was allowed for docking into the GABAAR. For the schistosome TRP channel, the site center was determined using the most probable site in the VSLD domain using the prediction tool p2rank (Krivák and Hoksza 2018). Due to steric restrictions within the putative binding pocket of the TRP channel, sidechain flexibility was enabled for pocket residues H827, H831, Y864, E867, E868, D893, F940, R943, H946, I947, Y1117, R1120. For both targets, extensive sampling was achieved using an exhaustiveness parameter of 64. CNN scoring was used for re-scoring final poses by setting cnn_scoring option to “rescore.” For CNN-based pose scoring, the “crossdock_default2018” model was selected. Docking poses were inspected and images created using PyMOL v2.5.4 (Schrodinger, LLC).

Krivák, Radoslav, and David Hoksza. 2018. “P2Rank: Machine Learning Based Tool for Rapid and Accurate Prediction of Ligand Binding Sites from Protein Structure.” Journal of Cheminformatics 10 (1): 39.

McNutt, Andrew T., Paul Francoeur, Rishal Aggarwal, Tomohide Masuda, Rocco Meli, Matthew Ragoza, Jocelyn Sunseri, and David Ryan Koes. 2021. “GNINA 1.0: Molecular Docking with Deep Learning.” Journal of Cheminformatics 13 (1): 43.

Meng, Elaine C., Thomas D. Goddard, Eric F. Pettersen, Greg S. Couch, Zach J. Pearson, John H. Morris, and Thomas E. Ferrin. 2023. “UCSF ChimeraX: Tools for Structure Building and Analysis.” Protein Science: A Publication of the Protein Society 32 (11): e4792.
DOI: 10.6084/m9.figshare.7762592
title: Additional file 1: of MiR-9 promotes tumorigenesis and angiogenesis and is activated by MYC and OCT4 in human glioma

description: Table S1. Information on the 18 tissues of glioma patients collected for clinical study. Table S2. Information on the oligonucleotide sequences in this study. Table S3. Information on the primer sequences for qRT-PCR analysis in this study. Table S4. Information on the antibodies used in this study. Table S5. Information on the PCR primers for luciferase reporter assay in this study. Table S6. Information on the primer sequences for ChIP assay in this study. (ZIP 450 kb)
DOI: 10.6084/m9.figshare.7762592.v1
title: Additional file 1: of MiR-9 promotes tumorigenesis and angiogenesis and is activated by MYC and OCT4 in human glioma

description: Table S1. Information on the 18 tissues of glioma patients collected for clinical study. Table S2. Information on the oligonucleotide sequences in this study. Table S3. Information on the primer sequences for qRT-PCR analysis in this study. Table S4. Information on the antibodies used in this study. Table S5. Information on the PCR primers for luciferase reporter assay in this study. Table S6. Information on the primer sequences for ChIP assay in this study. (ZIP 450 kb)
DOI: 10.6084/m9.figshare.14578365
title: Metadata record for the manuscript: Nivolumab in combination with cabozantinib for metastatic triple-negative breast cancer: A phase II and biomarker study

description: <b>Summary</b><br>

This
metadata record provides details of the data supporting the claims of the
related manuscript: “Nivolumab in combination with
cabozantinib for metastatic triple-negative breast cancer: A phase II and
biomarker study”.

The
related study was a single-arm phase II study which investigated the efficacy
and safety of cabozantinib combined with nivolumab in metastatic
triple-negative breast cancer (mTNBC).

 

Type of data:
whole exome sequencing; linked genotype and phenotype data; genomic profiling; open-label,
single-arm, single center phase II study; clinical data

Subject of
data: <i>Homo sapiens</i>

Sample size:
18

Population
characteristics: Eligible patients had histologically or cytologically
confirmed invasive breast cancer with metastatic disease that was measurable
per RECIST 1.1 . Tumors were required to be estrogen receptor (ER)-negative and
progesterone receptor-negative, defined as &lt; 10% expression by
immunohistochemistry, and HER2-negative per the current American Society of
Clinical Oncology/College of American Pathologists guidelines

Trial
registration number: NCT03316586

 

<b>Data
access</b>

The whole
exome and transcriptome data have been deposited in the <i>dbGaP </i>repository under accession https://identifiers.org/dbgap:phs002419.v1.p1. In order to protect patient privacy, these data are controlled access.
Details of how to request access can be found on the <i>dbGaP </i>landing page.

The genomic
profiling data are in Supplementary Tables 2 and 4.

The supplementary
tables of the related article are openly available as part of this <i>figshare </i>data record (as well as via the
supplementary materials of the related article) in the file ‘Supplementary Data 1_5-14-21.xlsx’.

 

<b>Corresponding author(s) for this study</b>

Sara
M. Tolaney, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA
02215. Tel: 617-632-3800. Sara_Tolaney@DFCI.HARVARD.EDU

<br>
<b>Study approval </b>

The
Dana-Farber Cancer Institute institutional review board approved the study and
written informed consent from all trial participants was provided before study
entry. The study was monitored by the Data Safety Monitoring Board of the
Dana-Farber/Harvard Cancer Center.
DOI: 10.6084/m9.figshare.14578365.v1
title: Metadata record for the manuscript: Nivolumab in combination with cabozantinib for metastatic triple-negative breast cancer: A phase II and biomarker study

description: <b>Summary</b><br>

This
metadata record provides details of the data supporting the claims of the
related manuscript: “Nivolumab in combination with
cabozantinib for metastatic triple-negative breast cancer: A phase II and
biomarker study”.

The
related study was a single-arm phase II study which investigated the efficacy
and safety of cabozantinib combined with nivolumab in metastatic
triple-negative breast cancer (mTNBC).

 

Type of data:
whole exome sequencing; linked genotype and phenotype data; genomic profiling; open-label,
single-arm, single center phase II study; clinical data

Subject of
data: <i>Homo sapiens</i>

Sample size:
18

Population
characteristics: Eligible patients had histologically or cytologically
confirmed invasive breast cancer with metastatic disease that was measurable
per RECIST 1.1 . Tumors were required to be estrogen receptor (ER)-negative and
progesterone receptor-negative, defined as &lt; 10% expression by
immunohistochemistry, and HER2-negative per the current American Society of
Clinical Oncology/College of American Pathologists guidelines

Trial
registration number: NCT03316586

 

<b>Data
access</b>

The whole
exome and transcriptome data have been deposited in the <i>dbGaP </i>repository under accession https://identifiers.org/dbgap:phs002419.v1.p1. In order to protect patient privacy, these data are controlled access.
Details of how to request access can be found on the <i>dbGaP </i>landing page.

The genomic
profiling data are in Supplementary Tables 2 and 4.

The supplementary
tables of the related article are openly available as part of this <i>figshare </i>data record (as well as via the
supplementary materials of the related article) in the file ‘Supplementary Data 1_5-14-21.xlsx’.

 

<b>Corresponding author(s) for this study</b>

Sara
M. Tolaney, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA
02215. Tel: 617-632-3800. Sara_Tolaney@DFCI.HARVARD.EDU

<br>
<b>Study approval </b>

The
Dana-Farber Cancer Institute institutional review board approved the study and
written informed consent from all trial participants was provided before study
entry. The study was monitored by the Data Safety Monitoring Board of the
Dana-Farber/Harvard Cancer Center.
DOI: 10.5519/qd.9wipuq8a
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (66 records)
DOI: 10.7284/158359
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise FKt230918 using a Hawaii UHDAS instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/158360
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise FKt230918 using a SeaBird SBE-911+ instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/158381
title: Expendable Probe data collected during research cruise FKt230918 using a Turo Quoll instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/158371
title: Fluorometer data collected during research cruise FKt230918 using a WETLabs ECO-FL instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/158372
title: Fluorometer data collected during research cruise FKt230918 using a WETLabs ECO-FL instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/158363
title: Gyrocompass data collected during research cruise FKt230918 using a Sperry NAVIGAT X MK 1 instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/158364
title: Gyrocompass data collected during research cruise FKt230918 using a Sperry NAVIGAT X MK 1 instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/158365
title: Gyrocompass data collected during research cruise FKt230918 using a Sperry NAVIGAT X MK 1 instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/158361
title: INS (Inertial Navigation System) data collected during research cruise FKt230918 using a Kongsberg Seapath 330+ instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/158362
title: INS (Inertial Navigation System) data collected during research cruise FKt230918 using a Kongsberg DPS122 instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/158382
title: INS (Inertial Navigation System) data collected during research cruise FKt230918 using a Applanix POS/MV-320 V5 instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.15102658
title: Additional file 2 of Systematic assessment of gene co-regulation within chromatin domains determines differentially active domains across human cancers

description: Additional file 2. Table S1. This table provides for each dataset: the number of samples, the FCC AUC ratio, the total number of chromatin domains, the number of differentially active (DA) domains (p&lt;= 0.01), the total number of immune domains and the number of immune domains among the DA domains.
DOI: 10.6084/m9.figshare.15102664.v1
title: Additional file 4 of Systematic assessment of gene co-regulation within chromatin domains determines differentially active domains across human cancers

description: Additional file 4. Table S3. Result of the gene set enrichment analysis for the domains differentially active in multiple comparisons.
DOI: 10.6084/m9.figshare.15102664
title: Additional file 4 of Systematic assessment of gene co-regulation within chromatin domains determines differentially active domains across human cancers

description: Additional file 4. Table S3. Result of the gene set enrichment analysis for the domains differentially active in multiple comparisons.
DOI: 10.7284/158383
title: INS (Inertial Navigation System) data collected during research cruise FKt230918 using a Applanix POS/MV-320 V5 instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/158377
title: Meteorological Station data collected during research cruise FKt230918 using a Paroscientific MET4A instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.15102658.v1
title: Additional file 2 of Systematic assessment of gene co-regulation within chromatin domains determines differentially active domains across human cancers

description: Additional file 2. Table S1. This table provides for each dataset: the number of samples, the FCC AUC ratio, the total number of chromatin domains, the number of differentially active (DA) domains (p&lt;= 0.01), the total number of immune domains and the number of immune domains among the DA domains.
DOI: 10.7284/158378
title: Meteorological Station data collected during research cruise FKt230918 using a Gill MetPak Pro instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/158366
title: Multibeam Echosounder data collected during research cruise FKt230918 using a Kongsberg EM124 instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/158367
title: Multibeam Echosounder data collected during research cruise FKt230918 using a Kongsberg EM712 instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.15102661
title: Additional file 3 of Systematic assessment of gene co-regulation within chromatin domains determines differentially active domains across human cancers

description: Additional file 3. Table S2. Complete set of results obtained by DADo on 58 comparisons.
DOI: 10.7284/158368
title: Multibeam Echosounder data collected during research cruise FKt230918 using a Kongsberg EM712 instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/158369
title: Multibeam Echosounder data collected during research cruise FKt230918 using a Kongsberg EM124 instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.15102661.v1
title: Additional file 3 of Systematic assessment of gene co-regulation within chromatin domains determines differentially active domains across human cancers

description: Additional file 3. Table S2. Complete set of results obtained by DADo on 58 comparisons.
DOI: 10.7284/158370
title: Multibeam Echosounder data collected during research cruise FKt230918 using a Kongsberg EM2040 instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/158379
title: SSV (Sound Speed Velocimeter) data collected during research cruise FKt230918 using a Valeport MiniSVS instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/158380
title: SSV (Sound Speed Velocimeter) data collected during research cruise FKt230918 using a Valeport MiniSVS instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/158374
title: Transmissometer data collected during research cruise FKt230918 using a SeaBird C-Star instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/158375
title: TSG (Thermosalinograph) data collected during research cruise FKt230918 using a SeaBird SBE-45 instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/158376
title: TSG (Thermosalinograph) data collected during research cruise FKt230918 using a SeaBird SBE-45 instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7238372
title: Additional file 3: of Genotype effects contribute to variation in longitudinal methylome patterns in older people

description: Table S2. Probes with a significant random slope in two groups of different individuals. Probe id, chi-square and P value were provided. (XLS 258Â kb)
DOI: 10.6084/m9.figshare.7238372.v1
title: Additional file 3: of Genotype effects contribute to variation in longitudinal methylome patterns in older people

description: Table S2. Probes with a significant random slope in two groups of different individuals. Probe id, chi-square and P value were provided. (XLS 258Â kb)
DOI: 10.6073/pasta/075fbfe89bd4ab194c92a6d1c9f7e162
title: Minnowtrap Data from Rookery Branch and the North, Watson, and Roberts Rivers National Park (FCE) from November 2004 to April 2008

description: This study examines temporal and spatial dynamics in the fish community of the oligohaline to mesohaline reaches of ecotonal creeks along the southwest region of Everglades National Park. Sampling is conducted at 15 mangrove creeks in two drainages: Rookery Branch and the North, Roberts, and Watson rivers. The sampling in Rookery Branch expands over a 12-km stretch of ecotonal mangrove creeks upstream of Tarpon Bay. Minnow traps are used to target small-bodied forage fish. Sampling started in the wet season of 2004, and has been conducted three times per year at these approximate times: November (wet season); February (transition); and April (dry season). In the Rookery Branch region, fish abundance varies markedly yearly and seasonally. Catches peak in the drier months, reflecting a pulse of movement by freshwater taxa into creeks as marshes upstream dry. The timing of this pulse is closely tied to the pattern of water recession in upstream marshes, and has important ramifications for wading bird prey availability.
DOI: 10.6084/m9.figshare.15102691
title: Additional file 1 of Identification and integrative analysis of ACLY and related gene panels associated with immune microenvironment reveal prognostic significance in hepatocellular carcinoma

description: Additional file 1: Supplementary Data 1A Huashan HCC Cohort clinical data and brief summary. Supplementary Data 1B TCGA HCC Cohort Clinical Data. Supplementary Data 2 gene list rank-ordered with enrichment score by signal2Noise in GSEA analysis. Supplementary Data 3A Whole transcriptomic expression estimation of different TIICs in GSE77509 cohort. Supplementary Data 3B Whole transcriptomic expression estimation of different TIICs in TCGA HCC cohort. Supplementary Data 4A Detailed results of multivariable Cox proportional hazard model of 20 genes in fatty acid biosynthesis process in 40 kinds of tumors in TCGA database. Supplementary Data 4B Detailed results of multivariable Cox proportional hazard model of 20 genes in cholesterol biosynthesis process in 40 kinds of tumors in TCGA database.
DOI: 10.25549/impa-c123-104903
title: Arne, Else and Olav Heggheim, Bankim, Adamaoua, Cameroon, 1955-1962

description: "Hagen, Bankim". ("The garden, Bankim".) Olav, Else and Arne picking flowers?
DOI: 10.25549/impa-c123-104904
title: Arne and chimpanzee, Magba, West Region, Cameroon, 1955-1968

description: "Sjimpanse, sagbruket, Magba". ("Chimpanzee, the sawmill, Magba".) A chimpanzee baby and Arne Heggheim.
DOI: 10.25549/impa-c123-104905
title: Arne Heggheim and Olav, Meiganga, Adamaoua, Cameroon, 1960-1968

description: "Arne og Olav, Meiganga". ("Arne and Olav, Meiganga".) Olav Heggheim and Arne Heggheim with the yard and a building in the background.
DOI: 10.25549/impa-c123-104906
title: Arne and Olav Heggheim, Bankim, Adamaoua, Cameroon, 1955-1962

description: "Stasjonen, Bankim". ("The mission, Bankim".) Olav Heggheim and Arne Heggheim in the garden, a building in the background.
DOI: 10.25549/impa-c123-104907
title: Arne and Olav Heggheim, Ngaoundéré, Adamaoua, Cameroon, 1955-1968

description: "Arne og Olav, Ngaoundéré". ("Arne and Olav, Ngaoundéré".) Olav Heggheim and Arne Heggheim with a yard and flowerbeds in the background.
DOI: 10.25549/impa-c123-104908
title: Arne and Olav Heggheim, Meiganga, Adamaoua, Cameroon, 1960-1968

description: "Arne og Olav [i Meiganga]". ("Arne and Olav [in Meiganga].") The boys with yard and building in the background.
DOI: 10.25549/impa-c123-104909
title: Streetscene, Meiganga, Adamaoua, Cameroon, 1953-1968

description: "Mbororo, Meiganga". Mbororo woman[?] out of focus with trees, buildings and crowds in the background.
DOI: 10.25549/impa-c123-104910
title: Woman pounding maize, Ngaoundéré, Adamaoua, Cameroon, 1953-1968

description: "Maisen støtes, Ngaoundéré". ("The maize being mashed, Ngaoundéré".) Working woman. Yard with table, calabashes and a child in the background.
DOI: 10.25549/impa-c123-104911
title: Mbororo woman, Cameroon, 1953-1968

description: "Mbororokvinne". ("Mbororo woman".) Young woman.
DOI: 10.25549/impa-c123-104912
title: Men, Bankim, Adamaoua, Cameroon, 1953-1968

description: "Bankim". Åsmund Johan Heggheim and others, a dog, a boy and part of a car. Smoky or foggy background.
DOI: 10.25549/impa-c123-104913
title: Arne and Olav Heggheim smiling, Bankim, Adamaoua, Cameroon, 1955-1962

description: "Arne og Olav, Bankim". ("Arne and Olav, Bankim".) Two laughing boys in the dining room.
DOI: 10.25549/impa-c123-104914
title: Arne and Olav Heggheim with a goat, Cameroon, 1955-1968

description: "Arne og Olav med geita". ("Arne and Olav with the goat".) Two happy boys with a kid.
DOI: 10.25549/impa-c123-104915
title: Arne and Olav Heggheim in the driveway, Bankim, Adamaoua, Cameroon, 1955-1962

description: "Arne og Olav, Bankim". ("Arne and Olav, Bankim".) Olav and Arne by the driveway. The homes entrance and the pick up.
DOI: 10.25549/impa-c123-104916
title: Tikar, Cameroon, 1953-1968

description: "Tikar". Landscape with plain and trees.
DOI: 10.25549/impa-c123-104917
title: The Tikar plain, Centre Region, Cameroon, 1953-1968

description: "Tikar-sletta fra Bankim-falaisen". ("The Tikar plain from the Bankim falaise".)
DOI: 10.25549/impa-c123-104918
title: The road to Foumban, Cameroon, 1953-1968

description: "Nyveien gjennom regnskogen mot Foumban". ("The new road through the rain forest towards Foumban".) Long road with palms and other vegetation along both sides.
DOI: 10.25549/impa-c123-104919
title: Termite mound, Cameroon, 1953-1968

description: "Termittue". ("Termite mound".)
DOI: 10.25549/impa-c123-104920
title: Blue sky and palms in silhouette, Bankim, Adamaoua, Cameroon, 1953-1968

description: "Regnskogssilhuett, Bankim". ("Rainforest silhouette, Bankim".) Palms and trees in dark contrast against the sky.