cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.16928483
title: Additional file 7 of The role of JrLACs in the lignification of walnut endocarp

description: Additional file 7. Primers.
DOI: 10.6084/m9.figshare.19549959.v1
title: Additional file 2 of The Gastrodia menghaiensis (Orchidaceae) genome provides new insights of orchid mycorrhizal interactions

description: Additional file 2.
DOI: 10.6084/m9.figshare.13258526.v1
title: Phase separation of the Cep63•Cep152 complex underlies the formation of dynamic supramolecular self-assemblies at human centrosomes

description: The centrosome is a unique membraneless organelle that plays a pivotal role in the orderly progression of the cell cycle in animal cells. It has been shown that two pericentriolar scaffold proteins, Cep63 and Cep152, generate a heterotetrameric complex to self-assemble into a higher-order cylindrical architecture around a centriole. However, the mechanisms underlying how they reach their threshold concentrations in the vast intracellular space and generate a self-assembled architecture remain mysterious. Here we demonstrate that, like liquid-like assemblies, Cep63 and Cep152 cooperatively generate amorphous aggregates capable of undergoing dynamic turnover and inter-aggregate fusion <i>in vivo</i> and a significant level of internal rearrangemefnt within a condensate <i>in vitro</i>. Consistently, 1,6-hexanediol, a liquid–liquid phase separation disruptor, greatly diminished the ability of endogenous Cep63 and Cep152 to localize to centrosomes. Interestingly, a purified Cep63•Cep152 complex generated either a cylindrical structure or a vesicle-like hollow sphere in a spatially controlled manner. It also formed condensate-like solid spheres in the presence of a macromolecular crowder. At the molecular level, two hydrophobic motifs, one each from Cep63 and Cep152, were required for generating phase-separating condensates and a high molecular–weight assembly. Thus, we propose that the self-assembly of the Cep63•Cep152 complex is triggered by an intrinsic property of the complex undergoing density transition through the hydrophobic-motif-mediated phase separation. <b>Abbreviations:</b> PCM, pericentriolar material; LLPS, liquid–liquid phase separation; MW, molecular-weight; CLEM, correlative light and electron microscopy; WT, wild-type; CMV, cytomegalovirus; FRAP, fluorescence recovery after photobleaching; FITC, fluorescein isothiocyanate; PCR, polymerase chain reaction; 3D-SIM, three-dimensional structured illumination microscopy; DMEM, Dulbecco’s Modified Eagle Medium; PEI Max, Polyethylenimine Max; PBS, phosphate-buffered saline; RT, room temperature; DAPI, 4', 6-diamidino-2-phenylindole; AOTF, acousto-optic tunable filter; LB, Luria broth; OD, optical density; IPTG, isopropyl β-D-1-thiogalactopyranoside; SDS-PAGE, sodium dodecyl sulfate–polyacrylamide gel electrophoresis
DOI: 10.4121/5e55cf64-7912-4b07-8b8e-c2afb067c3e7.v1
title: Data underlying the publication: Capturing Experts’ Knowledge in Heritage Planning Enhanced by AI: A Case Study of Windcatchers in Yazd, Iran

description: These datasets contain the opinions of experts on the cultural significance of windcatchers in Yazd, Iran. The analysis results have been published in the paper titled "Capturing Experts’ Knowledge in Heritage Planning Enhanced by AI: A Case Study of Windcatchers in Yazd, Iran" in the Journal of Cultural Heritage. The data comprises all books and papers related to the case study, along with detailed information about each source. The Excel file contains four sheets:general information: the publications' information namely, title, year of publication, authors, etc.sentences_values: the publications' titles, relevant sentences, and values addressed in the sentencessentences_attributes: the publications' titles, relevant sentences, and attributes addressed in the sentencesname entity recognition (NER): relevant sentences, relevant words, and the class of NER associated with the word<br>
DOI: 10.6084/m9.figshare.16928615.v1
title: Additional file 5 of A simplified synthetic community rescues Astragalus mongholicus from root rot disease by activating plant-induced systemic resistance

description: Additional file 4: Table S3. Root and rhizosphere community KEGG pathways.
DOI: 10.6084/m9.figshare.16928613.v1
title: Additional file 1 of Germline HLA-B evolutionary divergence influences the efficacy of immune checkpoint blockade therapy in gastrointestinal cancer

description: Additional file 1: Table S1. Clinic characteristics of PUCH cohort.
DOI: 10.6084/m9.figshare.16928603
title: Additional file 2 of Zinc antagonizes iron-regulation of tyrosine hydroxylase activity and dopamine production in Drosophila melanogaster

description: Additional file 2. The individual raw data values of figures and Additional files for number of replicates ≤ 6. All the data are cited in the figure legend.
DOI: 10.6084/m9.figshare.16928603.v1
title: Additional file 2 of Zinc antagonizes iron-regulation of tyrosine hydroxylase activity and dopamine production in Drosophila melanogaster

description: Additional file 2. The individual raw data values of figures and Additional files for number of replicates ≤ 6. All the data are cited in the figure legend.
DOI: 10.58073/sruc.25118777
title: Farmer management survey data focusing on survival of triplet lambs

description: Anonymised data derived from a survey of UK, Irish and New Zealand sheep farmers regarding their management practices conducted in 2019. Copy of survey questions available as appendix to Cathrine Erichsens's PhD thesis.
DOI: 10.58073/sruc.25118777.v2
title: Farmer management survey data focusing on survival of triplet lambs

description: Anonymised data derived from a survey of UK, Irish and New Zealand sheep farmers regarding their management practices conducted in 2019. Copy of survey questions available as appendix to Cathrine Erichsens's PhD thesis.
DOI: 10.58073/sruc.25118777.v1
title: Farmer management survey data focusing on survival of triplet lambs

description: Anonymised data derived from a survey of UK, Irish and New Zealand sheep farmers regarding their management practices conducted in 2019. Copy of survey questions available as appendix to Cathrine Erichsens's PhD thesis.
DOI: 10.6084/m9.figshare.7491875.v1
title: Molecular dynamics simulation of the oscillatory behaviour and vibrational analysis of an adamantane molecule encapsulated in a single-walled carbon nanotube

description: In this study, we employed classical molecular dynamics to simulate the encapsulation and examine the dynamical behaviour of an adamantane molecule inside a single-walled carbon nanotube. As a result, we found that the critical and optimal diameters of the tube for molecular encapsulation were about 9.5 and 10.86 Å, respectively, and that the speed of encapsulation mainly depended on tube’s diameter. Furthermore, the encapsulated adamantane molecule exhibited irregular motion and frequent collisional motion along the tube’s longitudinal axis and on the tube’s cross-sectional plane, respectively. In addition, we examined the influence of the tube diameter and temperature on the mean free path and average collisional frequency of the molecule’s motion. Lastly, the influence of the host–guest interaction on the systematic vibrational optic mode was studied using density functional theory calculation.
DOI: 10.6084/m9.figshare.8015969.v3
title: A Sparse Random Projection-Based Test for Overall Qualitative Treatment Effects

description: In contrast to the classical “one-size-fits-all” approach, precision medicine proposes the customization of individualized treatment regimes to account for patients’ heterogeneity in response to treatments. Most of existing works in the literature focused on estimating optimal individualized treatment regimes. However, there has been less attention devoted to hypothesis testing regarding the existence of overall qualitative treatment effects, especially when there are a large number of prognostic covariates. When covariates do not have qualitative treatment effects, the optimal treatment regime will assign the same treatment to all patients regardless of their covariate values. In this article, we consider testing the overall qualitative treatment effects of patients’ prognostic covariates in a high-dimensional setting. We propose a sample splitting method to construct the test statistic, based on a nonparametric estimator of the contrast function. When the dimension of covariates is large, we construct the test based on sparse random projections of covariates into a low-dimensional space. We prove the consistency of our test statistic. In the regular cases, we show the asymptotic power function of our test statistic is asymptotically the same as the “oracle” test statistic which is constructed based on the “optimal” projection matrix. Simulation studies and real data applications validate our theoretical findings. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.12731491
title: Additional file 10 of High-efficiency procedure to characterize, segment, and quantify complex multicellularity in raw micrographs in plants

description: Additional file 10: Dataset S4. The objects stats of cells in a vertical Arabidopsis root section using SR-Tesseler software.
DOI: 10.6084/m9.figshare.8015969.v1
title: A Sparse Random Projection-based Test for Overall Qualitative Treatment Effects

description: In contrast to the classical “one size fits all” approach, precision medicine proposes the customization of individualized treatment regimes to account for patients’ heterogeneity in response to treatments. Most of existing works in the literature focused on estimating optimal individualized treatment regimes. However, there has been less attention devoted to hypothesis testing regarding the existence of overall qualitative treatment effects, especially when there is a large number of prognostic covariates. When covariates don’t have qualitative treatment effects, the optimal treatment regime will assign the same treatment to all patients regardless of their covariate values. In this paper, we consider testing the overall qualitative treatment effects of patients’ prognostic covariates in a high dimensional setting. We propose a sample splitting method to construct the test statistic, based on a nonparametric estimator of the contrast function. When the dimension of covariates is large, we construct the test based on sparse random projections of covariates into a low-dimensional space. We prove the consistency of our test statistic. In the regular cases, we show the asymptotic power function of our test statistic is asymptotically the same as the “oracle” test statistic which is constructed based on the “optimal” projection matrix. Simulation studies and real data applications validate our theoretical findings.
DOI: 10.6084/m9.figshare.8015969.v2
title: A Sparse Random Projection-Based Test for Overall Qualitative Treatment Effects

description: In contrast to the classical “one-size-fits-all” approach, precision medicine proposes the customization of individualized treatment regimes to account for patients’ heterogeneity in response to treatments. Most of existing works in the literature focused on estimating optimal individualized treatment regimes. However, there has been less attention devoted to hypothesis testing regarding the existence of overall qualitative treatment effects, especially when there are a large number of prognostic covariates. When covariates do not have qualitative treatment effects, the optimal treatment regime will assign the same treatment to all patients regardless of their covariate values. In this article, we consider testing the overall qualitative treatment effects of patients’ prognostic covariates in a high-dimensional setting. We propose a sample splitting method to construct the test statistic, based on a nonparametric estimator of the contrast function. When the dimension of covariates is large, we construct the test based on sparse random projections of covariates into a low-dimensional space. We prove the consistency of our test statistic. In the regular cases, we show the asymptotic power function of our test statistic is asymptotically the same as the “oracle” test statistic which is constructed based on the “optimal” projection matrix. Simulation studies and real data applications validate our theoretical findings. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.7491875
title: Molecular dynamics simulation of the oscillatory behaviour and vibrational analysis of an adamantane molecule encapsulated in a single-walled carbon nanotube

description: In this study, we employed classical molecular dynamics to simulate the encapsulation and examine the dynamical behaviour of an adamantane molecule inside a single-walled carbon nanotube. As a result, we found that the critical and optimal diameters of the tube for molecular encapsulation were about 9.5 and 10.86 Å, respectively, and that the speed of encapsulation mainly depended on tube’s diameter. Furthermore, the encapsulated adamantane molecule exhibited irregular motion and frequent collisional motion along the tube’s longitudinal axis and on the tube’s cross-sectional plane, respectively. In addition, we examined the influence of the tube diameter and temperature on the mean free path and average collisional frequency of the molecule’s motion. Lastly, the influence of the host–guest interaction on the systematic vibrational optic mode was studied using density functional theory calculation.
DOI: 10.6084/m9.figshare.12731533.v1
title: Additional file 7 of High-efficiency procedure to characterize, segment, and quantify complex multicellularity in raw micrographs in plants

description: Additional file 7: Dataset S1. Parameter identification of Populus trichocarpa embryo cells by ImageJ and Imaris software.
DOI: 10.6084/m9.figshare.12731494
title: Additional file 11 of High-efficiency procedure to characterize, segment, and quantify complex multicellularity in raw micrographs in plants

description: Additional file 11: Dataset S5. Parameter identification of cells in an Arabidopsis seed section by ImageJ software.
DOI: 10.6084/m9.figshare.12731500
title: Additional file 13 of High-efficiency procedure to characterize, segment, and quantify complex multicellularity in raw micrographs in plants

description: Additional file 13: Dataset S7. The objects stats of cells in an Arabidopsis seed section using SR-Tesseler software.
DOI: 10.6084/m9.figshare.6967652.v1
title: NF-kB mediated CX3CL1 activation in the dorsal root ganglion contributes to the maintenance of neuropathic pain induced in adult male Sprague Dawley rats

description: Abstract Purpose: To evaluate the role of CX3CL1 and NF-κB in the lumbar disc herniation induced neuropathic pain. Methods: After LDH induced by implantation of autologous nucleus pulposus (NP) on the left L5 nerve root was established, mechanical thresholds and thermal hyperalgesia were tested at relevant time points during an observation period of 28 days. Expression of CX3CL1 and NF-κBin the dorsal root ganglion (DRG) were performed by using Western blotting and RT-PCR. Results: Implantation of autologous nucleus pulposus (NP) induced neuropathic pain, associated with increased mRNA and protein expression of CX3CL1 in the DRG. Moreover, intrathecal injection of neutralizing antibody against CX3CL1 could attenuates LDH-induced persistent pain hypersensitivity. Interestingly, NF-κB activation in the DRGs were found in LDH-induced neuropathic pain. Furthermore, NF-κB downregulation by p65 inhibitor PDTC markedly alleviated LDH-induced mechanical allodynia and thermal hyperalgesia in rat. Importantly, CX3CL1 neutralizing antibody (10 μg/10 μl, i.t.) reduces p-p65 protein level in DRG Conclusions: CX3XL1 could regulate LDH-induced neuropathic pain through NF-κB pathway. Targeting CX3CL1 and NF-κB may represent a potential treatment for neuropathic pain caused by LDH.
DOI: 10.6084/m9.figshare.12731506
title: Additional file 15 of High-efficiency procedure to characterize, segment, and quantify complex multicellularity in raw micrographs in plants

description: Additional file 15: Dataset S9. Modification of centroid coordinates of cells in a transverse section of a Populus trichocarpa stem for analysis with SR-Tesseler software.
DOI: 10.6084/m9.figshare.12731500.v1
title: Additional file 13 of High-efficiency procedure to characterize, segment, and quantify complex multicellularity in raw micrographs in plants

description: Additional file 13: Dataset S7. The objects stats of cells in an Arabidopsis seed section using SR-Tesseler software.
DOI: 10.6084/m9.figshare.12210497
title: Enhanced anti-tumor efficacy of 5-aminolevulinic acid-gold nanoparticles-mediated photodynamic therapy in cutaneous squamous cell carcinoma cells

description: The objective of this study was to investigate whether the conjugation of gold nanoparticles (GNPs) to 5-aminolevulinic acid (5-ALA) could enhance the anti-tumor efficiency of photodynamic therapy (PDT) in epidermoid carcinoma cells. The mRNA and protein expression levels were determined by quantitative real-time PCR and western blot, respectively. Cell viability, apoptosis, invasion, and migration were determined by MTT assay, flow cytometry, transwell invasion assay, and migration assay, respectively. Singlet oxygen generation was detected by the singlet oxygen sensor green reagent assay. Our results showed that PDT with 5-ALA and GNPs-conjugated 5-ALA (5-ALA-GNPs) significantly suppressed cell viability, increased cell apoptosis and singlet oxygen generation in both HaCat and A431 cells, and PDT with 5-ALA and 5-ALA-GNPs had more profound effects in A431 cells than that in HaCat cells. More importantly, 5-ALA-GNPs treatment potentiated the effects of PDT on cell viability, cell apoptosis, and singlet oxygen generation in A431 cells compared to 5-ALA treatment. Further in vitro assays showed that PDT with 5-ALA-GNPs significantly decreased expression of STAT3 and Bcl-2 and increased expression of Bax in A431 cells compared with PDT with 5-ALA. In addition, 5-ALA-GNPs treatment enhanced the inhibitory effects of PDT on cell invasion and migration and Wnt/β-catenin signaling activities in A431 cells compared to 5-ALA treatment. In conclusion, our results suggested that GNPs conjugated to 5-ALA significantly enhanced the anti-tumor efficacy of PDT in A431 cells, which may represent a better strategy to improve the outcomes of patients with cutaneous squamous cell carcinoma.
DOI: 10.6084/m9.figshare.12210497.v1
title: Enhanced anti-tumor efficacy of 5-aminolevulinic acid-gold nanoparticles-mediated photodynamic therapy in cutaneous squamous cell carcinoma cells

description: The objective of this study was to investigate whether the conjugation of gold nanoparticles (GNPs) to 5-aminolevulinic acid (5-ALA) could enhance the anti-tumor efficiency of photodynamic therapy (PDT) in epidermoid carcinoma cells. The mRNA and protein expression levels were determined by quantitative real-time PCR and western blot, respectively. Cell viability, apoptosis, invasion, and migration were determined by MTT assay, flow cytometry, transwell invasion assay, and migration assay, respectively. Singlet oxygen generation was detected by the singlet oxygen sensor green reagent assay. Our results showed that PDT with 5-ALA and GNPs-conjugated 5-ALA (5-ALA-GNPs) significantly suppressed cell viability, increased cell apoptosis and singlet oxygen generation in both HaCat and A431 cells, and PDT with 5-ALA and 5-ALA-GNPs had more profound effects in A431 cells than that in HaCat cells. More importantly, 5-ALA-GNPs treatment potentiated the effects of PDT on cell viability, cell apoptosis, and singlet oxygen generation in A431 cells compared to 5-ALA treatment. Further in vitro assays showed that PDT with 5-ALA-GNPs significantly decreased expression of STAT3 and Bcl-2 and increased expression of Bax in A431 cells compared with PDT with 5-ALA. In addition, 5-ALA-GNPs treatment enhanced the inhibitory effects of PDT on cell invasion and migration and Wnt/β-catenin signaling activities in A431 cells compared to 5-ALA treatment. In conclusion, our results suggested that GNPs conjugated to 5-ALA significantly enhanced the anti-tumor efficacy of PDT in A431 cells, which may represent a better strategy to improve the outcomes of patients with cutaneous squamous cell carcinoma.
DOI: 10.6084/m9.figshare.16928775
title: Additional file 1 of Genome-wide investigation of the GRAS transcription factor family in foxtail millet (Setaria italica L.)

description: Additional file 1 : Table S1. List of the 57 S. italica GRAS genes identified in this study.
DOI: 10.6084/m9.figshare.16928781.v1
title: Additional file 3 of Genome-wide investigation of the GRAS transcription factor family in foxtail millet (Setaria italica L.)

description: Additional file 3 : Table S3. Analysis and distribution of the conserved motifs of GRAS proteins.
DOI: 10.6084/m9.figshare.16928781
title: Additional file 3 of Genome-wide investigation of the GRAS transcription factor family in foxtail millet (Setaria italica L.)

description: Additional file 3 : Table S3. Analysis and distribution of the conserved motifs of GRAS proteins.
DOI: 10.6084/m9.figshare.16928805.v1
title: Additional file 9 of Genome-wide investigation of the GRAS transcription factor family in foxtail millet (Setaria italica L.)

description: Additional file 9 : Table S9. Primer sequences for qRT-PCR.
DOI: 10.6084/m9.figshare.16928621
title: Additional file 7 of A simplified synthetic community rescues Astragalus mongholicus from root rot disease by activating plant-induced systemic resistance

description: Additional file 6: Table S5. Abundance of bacterial genera decreased in diseased roots.
DOI: 10.21233/wrw4-q139
title: Lake Erie water chemistry dataset

description: Raw data for the Lake Erie water chemistry dataset obtained from the Neotoma Paleoecology Database.
DOI: 10.21233/kssv-rb27
title: LDDsite2932 ostracode surface sample dataset

description: Raw data for the LDDsite2932 ostracode surface sample dataset obtained from the Neotoma Paleoecology Database.
DOI: 10.21233/2paq-3n57
title: LDDsite4295 water chemistry dataset

description: Raw data for the LDDsite4295 water chemistry dataset obtained from the Neotoma Paleoecology Database.
DOI: 10.21233/z5py-d803
title: LDDsite4167 ostracode surface sample dataset

description: Raw data for the LDDsite4167 ostracode surface sample dataset obtained from the Neotoma Paleoecology Database.
DOI: 10.21233/8abe-te22
title: Limekiln Hollow [23SH109] vertebrate fauna dataset

description: Raw data for the Limekiln Hollow [23SH109] vertebrate fauna dataset obtained from the Neotoma Paleoecology Database.
DOI: 10.21233/e11g-5638
title: Point Edward vertebrate fauna dataset

description: Raw data for the Point Edward vertebrate fauna dataset obtained from the Neotoma Paleoecology Database.
DOI: 10.21233/e2c9-hz36
title: LDDsite3254 ostracode surface sample dataset

description: Raw data for the LDDsite3254 ostracode surface sample dataset obtained from the Neotoma Paleoecology Database.
DOI: 10.21233/f7gy-xj18
title: LDDsite2972 ostracode surface sample dataset

description: Raw data for the LDDsite2972 ostracode surface sample dataset obtained from the Neotoma Paleoecology Database.
DOI: 10.21233/ba1h-1z05
title: Old Crow Basin Locality CRH-29 [NbVl-2] vertebrate fauna dataset

description: Raw data for the Old Crow Basin Locality CRH-29 [NbVl-2] vertebrate fauna dataset obtained from the Neotoma Paleoecology Database.
DOI: 10.21233/jg6c-st88
title: Newo Asiniak [FbNp-16] vertebrate fauna dataset

description: Raw data for the Newo Asiniak [FbNp-16] vertebrate fauna dataset obtained from the Neotoma Paleoecology Database.
DOI: 10.21233/st5j-vf26
title: LDDsite6594 ostracode surface sample dataset

description: Raw data for the LDDsite6594 ostracode surface sample dataset obtained from the Neotoma Paleoecology Database.
DOI: 10.21233/7a2n-k177
title: Bay of Quinte/Hungary Bay ostracode surface sample dataset

description: Raw data for the Bay of Quinte/Hungary Bay ostracode surface sample dataset obtained from the Neotoma Paleoecology Database.