cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7013156.v1
title: <i>P–T–time</i> (phengite Ar closure) history of spatially close-outcropping HP and UHP oceanic eclogites (southwestern Tianshan): implication for a potential deep juxtaposing process during exhumation?

description: The Chinese southwestern Tianshan HP–UHP/LT metamorphic complex possesses well-preserved mafic layers, tectonic slices/blocks, boudins/lens of different sizes, and lithology embedded within dominant metavolcanoclastics. A recent study on the ultra-high pressure (UHP) eclogite revealed a short timescale of exhumation (≤10 Ma, ~315 ± 5 Ma). However, controversies still exist on some key questions: (1) the reasonable interpretation of spatially close-outcropped high pressure (HP) and UHP slices with respect to regional geodynamics, and (2) if the previous regional scatter Ar–Ar ages proved the existence of internally coherent sub-belts or troubled by dating on samples with notable <sup>40</sup>Ar retention. This study focusses on detailed <i>P</i>–<i>T</i>–time (phengite Ar closure) recovery of samples from a HP eclogite lens and its host rock, the UHP thick-layered eclogite. Based on data from bulk–rock, microprobe analysis, and muscovite Ar–Ar chronological dating, we link phengite growth to potential garnet growth stages via thermodynamic modelling. Facilitated by the <i>P</i>–<i>T</i>–Ar retention% graph, we collect all the regional muscovite Ar–Ar data together with results in this study for evaluating the significance of regional muscovite Ar–Ar ages and set back to geodynamics. According to modelling results, the HP lens eclogite reached peak metamorphism at ~550°C, 2.50 GPa with an Ar–Ar muscovite plateau age of 316.9 ± 1.0 Ma that could date the mass phengite growth event during prograde metamorphism. In contrast, the UHP layered eclogite experienced UHP peak burial at ~510°C, 2.95 GPa, and then to HP peak metamorphism at ~560°C, 2.60 GPa with ~311.6 ± 0.7 Ma plateau age that may constrain the cooling age during early exhumation. Noteworthy, both of them share a quite similar early exhumation path despite bearing contrasting prograde metamorphic experiences. With considering updated regional exhumation pattern, this might imply the existence of a potential deep juxtaposing (capture) process between HP slices and exhumating UHP complex, at about 45–60 km depth along subduction plate interface.
DOI: 10.6084/m9.figshare.7527935.v1
title: Additional file 9: of Genome-wide association study of Mycobacterium avium subspecies Paratuberculosis infection in Chinese Holstein

description: Table S4. Functional enrichment of GO and Pathway analysis of 343 genes. (XLSX 32 kb)
DOI: 10.6084/m9.figshare.7527953
title: Additional file 2 of Evaluation of top-down mass spectral identification with homologous protein sequences

description: Identifications from the EC data set. (XLSX 583 kb)
DOI: 10.6084/m9.figshare.7527959
title: Additional file 3 of Evaluation of top-down mass spectral identification with homologous protein sequences

description: Identifications from the MCF-7 data set. (XLSX 351 kb)
DOI: 10.6084/m9.figshare.12246581
title: Additional file 4 of Development of a novel method for the quantification of tyrosine 39 phosphorylated α- and β-synuclein in human cerebrospinal fluid

description: Additional file 4. Skyline files of the quantification results for pY39 αβ-syn peptide in the CSF of PD patients and control individuals.
DOI: 10.6084/m9.figshare.7528067
title: Additional file 6: of RNA sequencing reveals the expression profiles of circRNA and indicates that circDDX17 acts as a tumor suppressor in colorectal cancer

description: DataÂ 4. Based on the functions of target genes, DIANA-miRPath v.3 platform was used to identify miRNAs associated with the KEGG pathway of COLORECTAL CANER. (XLS 232 kb)
DOI: 10.6084/m9.figshare.7528067.v1
title: Additional file 6: of RNA sequencing reveals the expression profiles of circRNA and indicates that circDDX17 acts as a tumor suppressor in colorectal cancer

description: DataÂ 4. Based on the functions of target genes, DIANA-miRPath v.3 platform was used to identify miRNAs associated with the KEGG pathway of COLORECTAL CANER. (XLS 232 kb)
DOI: 10.6084/m9.figshare.12246575.v1
title: Additional file 3 of Development of a novel method for the quantification of tyrosine 39 phosphorylated α- and β-synuclein in human cerebrospinal fluid

description: Additional file 3: Table S2. Quantification results for Y39 αβ-syn and pY39 αβ-syn peptides in the CSF of PD patients and control individuals.
DOI: 10.6084/m9.figshare.8052380
title: BET report of PEI-CTSms from Preparation of aminated chitosan microspheres by one-pot method and their adsorption properties for dye wastewater

description: BET report of PEI-CTSms
DOI: 10.6084/m9.figshare.8052383.v1
title: BET report of CTSms from Preparation of aminated chitosan microspheres by one-pot method and their adsorption properties for dye wastewater

description: BET report of CTSms
DOI: 10.6084/m9.figshare.8052386.v1
title: BET report of TETA-CTSms from Preparation of aminated chitosan microspheres by one-pot method and their adsorption properties for dye wastewater

description: BET report of TETA-CTSms
DOI: 10.6084/m9.figshare.12246758
title: Additional file 1 of TS: a powerful truncated test to detect novel disease associated genes using publicly available gWAS summary data

description: Additional file 1 The TS and the other comparison methods are applied to the SCZ data.
DOI: 10.6084/m9.figshare.12246764.v1
title: Additional file 2 of TS: a powerful truncated test to detect novel disease associated genes using publicly available gWAS summary data

description: Additional file 2 The TS and the other comparison methods are applied to the UKB data.
DOI: 10.6084/m9.figshare.12246764
title: Additional file 2 of TS: a powerful truncated test to detect novel disease associated genes using publicly available gWAS summary data

description: Additional file 2 The TS and the other comparison methods are applied to the UKB data.
DOI: 10.6084/m9.figshare.8052380.v1
title: BET report of PEI-CTSms from Preparation of aminated chitosan microspheres by one-pot method and their adsorption properties for dye wastewater

description: BET report of PEI-CTSms
DOI: 10.6084/m9.figshare.8052383
title: BET report of CTSms from Preparation of aminated chitosan microspheres by one-pot method and their adsorption properties for dye wastewater

description: BET report of CTSms
DOI: 10.6084/m9.figshare.8052386
title: BET report of TETA-CTSms from Preparation of aminated chitosan microspheres by one-pot method and their adsorption properties for dye wastewater

description: BET report of TETA-CTSms
DOI: 10.6084/m9.figshare.16965490.v1
title: Table S2 Translation efficiency and protein stability from tRNA copy number and codon usage in the sea cucumber genome provide insights to adaptive translation for saponin biosynthesis

description: Genomic tRNA copy numbers determine cytoplasmic tRNA abundances, which in turn influence translation efficiency, but the underlying mechanism is not well understood. Here, using the sea cucumber <i>Apostichopus japonicus</i> as a model, we combined genomic sequence, transcriptome expression and ecological food resource data to study its codon usage adaptation. The results showed that, unlike intragenic ncRNAs, tRNAs tended to be transcribed independently. This may be attributed to their specific Pol III promoters that lack transcriptional regulation, which may underlie the correlation between genomic copy number and cytoplasmic abundance of tRNAs. Moreover, codon usage optimization was mostly restrained by a gene's amino acid sequence that might be a compromise between functionality and translation efficiency. Genes for stress responses were highly optimized for most echinoderms, while enzymes for saponin biosynthesis (LAS, CYPs and UGTs) were especially optimized in sea cucumbers, which might promote saponin synthesis as a defence strategy. The genomic tRNA content of <i>A. japonicas</i> was positively correlated to amino acid content in its natural food particles, which should promote its efficiency in protein synthesis. We propose that coevolution between genomic tRNA content and codon usage of sea cucumbers facilitate their saponin synthesis and survival on food resource with low nutrient content.
DOI: 10.6084/m9.figshare.16965493.v1
title: Data set S3. Correlation between TAAI, stAI and gene length in different deuterostomes.; Data set S4. Protein sequences of sea cucumber-specific CYPs and UGTs and their closest homologs. from tRNA copy number and codon usage in the sea cucumber genome provide insights to adaptive translation for saponin biosynthesis

description: Genomic tRNA copy numbers determine cytoplasmic tRNA abundances, which in turn influence translation efficiency, but the underlying mechanism is not well understood. Here, using the sea cucumber <i>Apostichopus japonicus</i> as a model, we combined genomic sequence, transcriptome expression and ecological food resource data to study its codon usage adaptation. The results showed that, unlike intragenic ncRNAs, tRNAs tended to be transcribed independently. This may be attributed to their specific Pol III promoters that lack transcriptional regulation, which may underlie the correlation between genomic copy number and cytoplasmic abundance of tRNAs. Moreover, codon usage optimization was mostly restrained by a gene's amino acid sequence that might be a compromise between functionality and translation efficiency. Genes for stress responses were highly optimized for most echinoderms, while enzymes for saponin biosynthesis (LAS, CYPs and UGTs) were especially optimized in sea cucumbers, which might promote saponin synthesis as a defence strategy. The genomic tRNA content of <i>A. japonicas</i> was positively correlated to amino acid content in its natural food particles, which should promote its efficiency in protein synthesis. We propose that coevolution between genomic tRNA content and codon usage of sea cucumbers facilitate their saponin synthesis and survival on food resource with low nutrient content.
DOI: 10.6084/m9.figshare.16965499.v1
title: Dataset S1. tRNA gene structures of A. japonicus. from tRNA copy number and codon usage in the sea cucumber genome provide insights to adaptive translation for saponin biosynthesis

description: Genomic tRNA copy numbers determine cytoplasmic tRNA abundances, which in turn influence translation efficiency, but the underlying mechanism is not well understood. Here, using the sea cucumber <i>Apostichopus japonicus</i> as a model, we combined genomic sequence, transcriptome expression and ecological food resource data to study its codon usage adaptation. The results showed that, unlike intragenic ncRNAs, tRNAs tended to be transcribed independently. This may be attributed to their specific Pol III promoters that lack transcriptional regulation, which may underlie the correlation between genomic copy number and cytoplasmic abundance of tRNAs. Moreover, codon usage optimization was mostly restrained by a gene's amino acid sequence that might be a compromise between functionality and translation efficiency. Genes for stress responses were highly optimized for most echinoderms, while enzymes for saponin biosynthesis (LAS, CYPs and UGTs) were especially optimized in sea cucumbers, which might promote saponin synthesis as a defence strategy. The genomic tRNA content of <i>A. japonicas</i> was positively correlated to amino acid content in its natural food particles, which should promote its efficiency in protein synthesis. We propose that coevolution between genomic tRNA content and codon usage of sea cucumbers facilitate their saponin synthesis and survival on food resource with low nutrient content.
DOI: 10.6084/m9.figshare.7528163
title: Additional file 1: of Using natural language processing and machine learning to identify breast cancer local recurrence

description: Table S1. Positive sentences. We went through a development corpus of 50 randomly selected positive progress notes and extracted partial sentences that indicated a breast cancer local recurrence event. (XLS 27 kb)
DOI: 10.6084/m9.figshare.7528163.v1
title: Additional file 1: of Using natural language processing and machine learning to identify breast cancer local recurrence

description: Table S1. Positive sentences. We went through a development corpus of 50 randomly selected positive progress notes and extracted partial sentences that indicated a breast cancer local recurrence event. (XLS 27 kb)
DOI: 10.6084/m9.figshare.7528166.v1
title: Additional file 2: of Using natural language processing and machine learning to identify breast cancer local recurrence

description: Table S2. Positive CUIS. A dictionary of CUISs and the corresponding CUI preferred name that were retained after filtering. (XLS 23 kb)
DOI: 10.6084/m9.figshare.7528166
title: Additional file 2: of Using natural language processing and machine learning to identify breast cancer local recurrence

description: Table S2. Positive CUIS. A dictionary of CUISs and the corresponding CUI preferred name that were retained after filtering. (XLS 23 kb)
DOI: 10.6084/m9.figshare.14337595.v1
title: Additional file 12 of Genome-wide identification and expression analysis of the B-box transcription factor gene family in grapevine (Vitis vinifera L.)

description: Additional file 12: Table S5. Primer sequences used in expression analysis of BBX genes in grapevine
DOI: 10.6084/m9.figshare.14337604
title: Additional file 2 of Genome-wide identification and expression analysis of the B-box transcription factor gene family in grapevine (Vitis vinifera L.)

description: Additional file 2: Text S2. The protein sequences of BBX family in six species
DOI: 10.6084/m9.figshare.14337619
title: Additional file 7 of Genome-wide identification and expression analysis of the B-box transcription factor gene family in grapevine (Vitis vinifera L.)

description: Additional file 7: Table S3. Segmental duplications of BBX genes between grapevine and Arabidopsis and Ka/Ks ratios analysis of segmental duplicate gene pairs
DOI: 10.6084/m9.figshare.14337625.v1
title: Additional file 9 of Genome-wide identification and expression analysis of the B-box transcription factor gene family in grapevine (Vitis vinifera L.)

description: Additional file 9: Table S4. The microarray data of the grapevine VviBBX genes in different organs, tissues and developmental stages
DOI: 10.6084/m9.figshare.14337601.v1
title: Additional file 1 of Genome-wide identification and expression analysis of the B-box transcription factor gene family in grapevine (Vitis vinifera L.)

description: Additional file 1: Text S1. The CDS sequences of BBX family in grapevine
DOI: 10.6084/m9.figshare.12246653
title: Additional file 1 of Purchase and use of home healthcare devices for the elderly: a pilot study in Shanghai, China

description: Additional file 1. Questionnaire about purchase and use of home healthcare devices for the elderly.
DOI: 10.6084/m9.figshare.12246653.v1
title: Additional file 1 of Purchase and use of home healthcare devices for the elderly: a pilot study in Shanghai, China

description: Additional file 1. Questionnaire about purchase and use of home healthcare devices for the elderly.
DOI: 10.6084/m9.figshare.25211618
title: Influence of Na-feldspar grains within the K-feldspar fraction on IRSL dating

description: The Dataset consists of sample information and the ages results of K-and Na-feldspar from Manuscript entiled "Influence of Na-feldspar grains within the K-feldspar fraction on IRSL dating".
DOI: 10.6084/m9.figshare.25211618.v1
title: Dataset and Figures of Entiled Influence of Na-feldspar grains within the K-feldspar fraction on IRSL dating

description: The data set consists of sample information and the ages results of K-and Na-feldspar from Manuscript entiled "Influence of Na-feldspar grains within the K-feldspar fraction on IRSL dating".
DOI: 10.6084/m9.figshare.25211618.v2
title: Influence of Na-feldspar grains within the K-feldspar fraction on IRSL dating

description: The Dataset consists of sample information and the ages results of K-and Na-feldspar from Manuscript entiled "Influence of Na-feldspar grains within the K-feldspar fraction on IRSL dating".
DOI: 10.6084/m9.figshare.6489431
title: Lentivector information

description: The
lentivector Psico was purchased from Addgene (#11578, Addgene, MA, USA). After
being double digested with HpaI /XhoI, the vector was connected with synthetic
SP1 knockdown or NC sequences. After screened through sequencing, the positive
lentivectors carrying SP1 knock-down sequence or NC were selected for cell
infection. PCI-37B cells cultivated in 6-well plate at a confluence of 70% were
cocultured with lentivirus suspension (SP1 knock-down 1:100; NC 1:200) for 48
hours. Then cells were cultured with complete culture medium with 15ug/ml
puromycin for one week to harvest strains that have stably low levels of SP1
expression.
DOI: 10.6084/m9.figshare.6489464
title: SiRNA, shRNA sequence

description: HNSCC
cell lines PCI-4A/4B and PCI-37A/37B were supplied by the University of
Pittsburgh Cancer Institute (USA). These cell lines were cultured at 37 °C in a
humidified atmosphere of 5% CO<sub>2</sub> in the medium of Dulbecco's modified
Eagle's medium (DMEM; Invitrogen, Carlsbad, CA, USA) supplemented with 10%
fetal bovine serum (FBS; Gibco, Carlsbad, CA, USA), 100U/ml penicillin G and
100U/ml streptomycin. The RNA oligonucleotide miR-92b mimics, inhibitor, SP1
siRNA, and negative control were synthesized by Genepharma (2603, Genepharma, Shanghai,
China). MiR-92b inhibitor and negative control plasmid were purchased from
GeneChem (PMDE249003218, GeneChem, Shanghai, China). Transfection agent
Lipofectamine 2000 (11668500, Invitrogen) was used according to the
manufacturer’s protocol. Cells were harvested 24 hours after transfection for
cell migration, invasion, proliferation and wound healing assay, 48 hours after
for RNA isolation and 72 hours after for western blot analysis.This is the
sequences of siRNA and shRNA used in this study.
DOI: 10.6084/m9.figshare.6489473
title: Transwell data

description: Migration
and invasion assays were performed using Transwell chambers (3422, 24-well
insert; 8-μm pore size; Corning Costar, NY, USA) coated with or without
Matrigel (356234, BD Biosciences, NJ, USA). 4 × 10<sup>5 </sup>HNSCC cells
in DMED medium were placed into the upper chamber, and medium supplementary
with 10 % FBS was added to the lower chamber. Then PCI-37A cells were incubated
for 24 hours for migration and 48 hours for invasion, and PCI-37A cells were
incubated for 8 hours for migration and 24 hours for invasion. Then the migratory
or invasive cells were fixed by 4% paraformaldehyde, stained with 0.1% crystal
violet, and counted in three random fields under 200x magnification. Transwell migration assay and Martrigel invasion assay
showed that an ectopic increased level of miR-92b could raise the migration and
invasion ability of PCI-37A cells, while a reduced level of miR-92b led to a
significant decrease in the number of migrating or invasive cells.After
knocked down with SP1 expression, PCI-37A/B cells showed a significant decrease
in migration and invasion.
DOI: 10.6084/m9.figshare.6489485
title: Wound healing assay data

description: In
wound-healing system a scratch was generated in subconfluent layers of cells and the repopulation of
the denuded areas was measured. High miR-92b expression accelerated wound
closure by 63.97% at 24h and by 66.96% at 48h after transfection in comparison
with negative control group in PCI-37A cells. Additionally, an apparent reduced
repopulation area was observed at 24h and 48h after transfection in miR-92b
knockdown group. Similar results were also obtained from the experiments
performed with PCI-37B cells.Wound
healing assay in PCI-37A cells revealed that the healing percentage of SP1
siRNA group was decreased by 15.47% at 24h and by 26.51% at 48h in comparison
with negative control group, respectively.
DOI: 10.6084/m9.figshare.6489506
title: In vivo tumor growth data

description: For
subcutaneous injection, 1x10<sup>7</sup> blank control, SP1 control and SP1
knock-down PCI-37B cells in 200uL DMEM were subcutaneous injected into axillary
of BALB/c nude mice with 5 mice each group. Since 10 days after injection, the
length and width of tumor were measured. At 25 days after injection, the mice
were sacrificed and the tumor was excised and weighed. In comparison with blank and control group, SP1 knock-down group had
a significantly reduced tumor growth and low miR-92b expression levels, thus
suggesting the SP1/miR-92b positive feedback loop was generally knocked down.
We also found down-regulated CCR7 protein expression levels in SP1 knock-down
group samples.
DOI: 10.6084/m9.figshare.1289842
title: Receptor tyrosine kinase ERBB4 mediates acquired resistance to ERBB2 inhibitors in breast cancer cells

description: Approximately 25% of breast cancers overexpress and depend on the receptor tyrosine kinase ERBB2, one of 4 ERBB family members. Targeted therapies directed against ERBB2 have been developed and used clinically, but many patients continue to develop resistance to such therapies. Although much effort has been focused on elucidating the mechanisms of acquired resistance to ERBB2-targeted therapies, the involvement of ERBB4 remains elusive and controversial. We demonstrate that genetic ablation of ERBB4, but not ERBB1-3, led to apoptosis in lapatinib-resistant cells, suggesting that the efficacy of pan-ERBB inhibitors was, at least in part, mediated by the inhibition of ERBB4. Moreover, ERBB4 was upregulated at the protein level in ERBB2+ breast cancer cell lines selected for acquired lapatinib resistance <i>in vitro</i> and in <i>MMTV-Neu</i> mice following prolonged lapatinib treatment. Knockdown of ERBB4 caused a decrease in AKT phosphorylation in resistant cells but not in sensitive cells, suggesting that ERBB4 activated the PI3K/AKT pathway in lapatinib-resistant cells. Importantly, ERBB4 knockdown triggered apoptosis not only in lapatinib-resistant cells but also in trastuzumab-resistant cells. Our results suggest that although ERBB4 is dispensable for naïve ERBB2+ breast cancer cells, it may play a key role in the survival of ERBB2+ cancer cells after they develop resistance to ERBB2 inhibitors, lapatinib and trastuzumab.
DOI: 10.6084/m9.figshare.12781004
title: Nomogram-Based Preoperative Score for Predicting Clinical Outcome in Unilateral Primary Aldosteronism

description: <b>Nomogram-Based
Preoperative Score for Predicting Clinical Outcome in Unilateral Primary
Aldosteronism </b>
DOI: 10.6084/m9.figshare.8062478
title: Additional file 2: of Comparative transcriptomic analysis of hypothalamus-pituitary-liver axis in bighead carp (Hypophthalmichthys nobilis) with differential growth rate

description: Table S2. List of 50 top highly expressed genes in liver tissue. (XLSX 12 kb)
DOI: 10.21227/2efr-2d41
title: Indoor Localization Data Based on SNR and RSSI within Multistory Round Building Scenario over LoRa Network

description: In situations when the precise position of a machine is unknown, localization becomes crucial. It is crucial to identify and ascertain the machine's position. This research focuses on improving the position prediction accuracy over long-range networks using a unique machine learning-based technique. In order to increase the prediction accuracy of the reference point position on the data collected using the fingerprinting approach using LoRa technology, this study suggested an ML-based algorithm. Signal strength data from the sensors at different positions was first gathered via an experiment through the LoRa network in a multi-story round layout building. The noise factor is also taken into account, and the signal-to-noise ratio (SNR) value is recorded for every RSSI measurement. This concludes the examination of reference point accuracy with the Modified KNN method (MKNN). MKNN was created to more precisely anticipate the position of the reference point. The findings showed that MKNN outperformed other algorithms in terms of accuracy and complexity.