cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5418655.v1
title: Plant endophytes and arbuscular mycorrhizal fungi alter plant competition.xlsx

description: <b>1. </b>In nature, grasses simultaneously establish multiple
symbiotic associations with endophytic fungi and arbuscular mycorrhizal fungi
(AMF). The effect of these multiple interactions on competitive interactions
between plants remains poorly understood. 

<b>2. </b>In this study, we tested whether endophytes and AMF (<i>Glomus mosseae</i> or <i>Glomus etunicatum</i>) alter plant competition between a subordinate
plant species that associates with both symbionts (<i>Achnatherum sibiricum</i>) and a dominant plant species, <i>Stipa
grandis</i>, that only associates with one symbiont (AMF). And we hypothesized
that endophytes can facilitate the coexistence of the subordinate plant species
(<i>A</i>.<i> sibiricum</i>) and the dominant plant species (<i>S</i>.<i> grandis</i>). 

<b>3. </b>The results demonstrated that endophyte infection
significantly enhanced the competitive ability of the subordinate plant species
compared to the dominant plant species. The effects of AMF on plant competition
were variable and depended on the identity of the AMF species. <i>G</i>.<i>
etunicatum</i> gave <i>A</i>.<i> sibiricum</i> plants a higher competitive
ability, while <i>G</i>.<i> mosseae</i> gave <i>S</i>.<i> grandis</i> a higher competitive ability. Simultaneous
infections of both endophytes and AMF in <i>A</i>.<i> sibiricum</i>
also altered the competitive relationships with <i>S</i>.<i> grandis</i>. 

<b>4. </b>In conclusion, these results suggest that endophytic
fungi can facilitate the coexistence of a subordinate plant species with a
dominant plant species. Moreover, endophytes could not only affect the
competitive ability of the host plant directly but also indirectly by interacting
with different AMF to change the growth of competing plant species.
DOI: 10.6084/m9.figshare.5422678
title: Multiple modulator-induced syntheses, crystal structures, and luminescent properties on hippuric acid and bovine serum albumin of Ln(III) complexes with 2,2′-oxybis(benzoic acid)

description: Six new coordination complexes, Ln<sub>2</sub>(2,2′-oba)<sub>2</sub>(phen)<sub>2</sub>(ox)(H<sub>2</sub>O)<sub>2</sub> (Ln = Eu <b>1</b>, Tb <b>2</b>), Ln<sub>4</sub>(2,2′-oba)<sub>6</sub>(phen)<sub>2</sub> (Ln = Eu <b>3</b>, Tb <b>4</b>), Eu<sub>4</sub>(2,2′-oba)<sub>6</sub>(phen)<sub>2</sub>(H<sub>2</sub>O) (<b>5</b>), and K[Eu(2,2′-oba)<sub>2</sub>(phen)<sub>2</sub>] (<b>6</b>) [2,2′-H<sub>2</sub>oba = 2,2′-oxybis(benzoic acid), phen = 1,10-phenanthroline, H<sub>2</sub>ox = oxalic acid] were synthesized by hydrothermal reactions with the same compound molar ratios but different modulatory reagents (MRs). Complexes <b>1–5</b> have different 1-D chain structures and <b>6</b> shows a mononuclear structure. These complexes form diverse 3-D supramolecular networks through hydrogen bonds. The interaction between these complexes and hippuric acid (HA) or bovine serum albumin (BSA) was investigated by fluorescence spectral analysis. Interestingly, the hippuric acid could quench the luminescence of these complexes while the fluorescence of BSA could be quenched by these complexes. Results suggested that the complexes may be potential luminescent testing reagents for HA or BSA by significant fluorescence quenching of Ln<sup>3+</sup> or BSA, respectively, through a static and dynamic quenching process.
DOI: 10.6084/m9.figshare.5422678.v1
title: Multiple modulator induced syntheses, crystal structures, and luminescent properties on hippuric acid and bovine serum albumin of Ln(III) complexes with 2,2’-oxybis(benzoic acid)

description: Six new coordination complexes, Ln<sub>2</sub>(2,2′-oba)<sub>2</sub>(phen)<sub>2</sub>(ox)(H<sub>2</sub>O)<sub>2</sub> (Ln = Eu <b>1</b>, Tb <b>2</b>), Ln<sub>4</sub>(2,2′-oba)<sub>6</sub>(phen)<sub>2</sub> (Ln = Eu <b>3</b>, Tb <b>4</b>), Eu<sub>4</sub>(2,2′-oba)<sub>6</sub>(phen)<sub>2</sub>(H<sub>2</sub>O) (<b>5</b>) and K[Eu(2,2′-oba)<sub>2</sub>(phen)<sub>2</sub>] (<b>6</b>) [2,2′-H<sub>2</sub>oba = 2,2’-oxybis(benzoic acid), phen = 1,10-phenanthroline, H<sub>2</sub>ox = oxalic acid] were synthesized by hydrothermal reactions with the same compound molar ratios but different modulatory reagents (MRs). Complexes <b>1</b>-<b>5</b> have different 1D chain structures and <b>6</b> shows a mononuclear structure. These complexes form diverse 3D supramolecular networks through hydrogen bonds. The interaction between these complexes and hippuric acid (HA) or bovine serum albumin (BSA) was investigated by fluorescence spectral analysis. Interestingly, the hippuric acid could quench the luminescence of these complexes while the fluorescence of BSA could be quenched by these complexes. Results suggested that the complexes may be potential luminescent testing reagents for HA or BSA by significant fluorescence quenching of Ln<sup>3+</sup> or BSA, respectively, through a static and dynamic quenching process.
DOI: 10.6084/m9.figshare.5422678.v2
title: Multiple modulator-induced syntheses, crystal structures, and luminescent properties on hippuric acid and bovine serum albumin of Ln(III) complexes with 2,2′-oxybis(benzoic acid)

description: Six new coordination complexes, Ln<sub>2</sub>(2,2′-oba)<sub>2</sub>(phen)<sub>2</sub>(ox)(H<sub>2</sub>O)<sub>2</sub> (Ln = Eu <b>1</b>, Tb <b>2</b>), Ln<sub>4</sub>(2,2′-oba)<sub>6</sub>(phen)<sub>2</sub> (Ln = Eu <b>3</b>, Tb <b>4</b>), Eu<sub>4</sub>(2,2′-oba)<sub>6</sub>(phen)<sub>2</sub>(H<sub>2</sub>O) (<b>5</b>), and K[Eu(2,2′-oba)<sub>2</sub>(phen)<sub>2</sub>] (<b>6</b>) [2,2′-H<sub>2</sub>oba = 2,2′-oxybis(benzoic acid), phen = 1,10-phenanthroline, H<sub>2</sub>ox = oxalic acid] were synthesized by hydrothermal reactions with the same compound molar ratios but different modulatory reagents (MRs). Complexes <b>1–5</b> have different 1-D chain structures and <b>6</b> shows a mononuclear structure. These complexes form diverse 3-D supramolecular networks through hydrogen bonds. The interaction between these complexes and hippuric acid (HA) or bovine serum albumin (BSA) was investigated by fluorescence spectral analysis. Interestingly, the hippuric acid could quench the luminescence of these complexes while the fluorescence of BSA could be quenched by these complexes. Results suggested that the complexes may be potential luminescent testing reagents for HA or BSA by significant fluorescence quenching of Ln<sup>3+</sup> or BSA, respectively, through a static and dynamic quenching process.
DOI: 10.6084/m9.figshare.5422825
title: MyGeoHub Geospatial Gateway

description: MyGeoHub is a science gateway for
researchers working with geospatial data. Based
on the HUBzero cyberinfrastructure framework, it
provides general-purpose software modules
enabling geospatial data management, processing
and visualization. Termed “GABBs” (Geospatial
Data Analysis Building Blocks), these modules can
be leveraged to build geospatial data driven tools
with minimal programming and construct dynamic
workflows chaining both local and remote tools
and data sources. We will present examples of
such end-to-end workflows demonstrating the
underlying software building blocks that have also
found use beyond the MyGeoHub gateway in other
science domains.
DOI: 10.6084/m9.figshare.5422825.v2
title: MyGeoHub Geospatial Gateway

description: MyGeoHub is a science gateway for
researchers working with geospatial data. Based
on the HUBzero cyberinfrastructure framework, it
provides general-purpose software modules
enabling geospatial data management, processing
and visualization. Termed “GABBs” (Geospatial
Data Analysis Building Blocks), these modules can
be leveraged to build geospatial data driven tools
with minimal programming and construct dynamic
workflows chaining both local and remote tools
and data sources. We will present examples of
such end-to-end workflows demonstrating the
underlying software building blocks that have also
found use beyond the MyGeoHub gateway in other
science domains.
DOI: 10.6084/m9.figshare.5422825.v1
title: MyGeoHub Geospatial Gateway

description: MyGeoHub is a science gateway for
researchers working with geospatial data. Based
on the HUBzero cyberinfrastructure framework, it
provides general-purpose software modules
enabling geospatial data management, processing
and visualization. Termed “GABBs” (Geospatial
Data Analysis Building Blocks), these modules can
be leveraged to build geospatial data driven tools
with minimal programming and construct dynamic
workflows chaining both local and remote tools
and data sources. We will present examples of
such end-to-end workflows demonstrating the
underlying software building blocks that have also
found use beyond the MyGeoHub gateway in other
science domains.
DOI: 10.6084/m9.figshare.5425510
title: Non-digestible oligosaccharides directly regulate host kinome to modulate host inflammatory responses without alterations in the gut microbiota

description: Data
repository for: Wu RY, Määttänen
P, Napper S, Scruten E, Li B, Koike Y, Johnson-Henry KC, Pierro A, Rossi L, Botts
SR, Surette MG, Sherman PM. Non-digestible
oligosaccharides directly regulate host kinome to modulate host inflammatory
responses without alterations in the gut microbiota. Microbiome. 2017;5:135. Available at: https://doi.org/10.1186/s40168-017-0357-4Repository
information: PSWY
FASTQ sequence files - 16S rRNA gene sequence files for P10 mice exposed to
lipopolysaccharide (LPS) and non-digestible oligosaccharides (inulin and scFOS) 16S_metadata.txt
- describes 16S rRNA gene sequence files 16S_preprocessed_sequences.fna
- preprocessed sequence file for 16S rRNA gene data (quality filtering, chimera
checking, etc.) 16S_otu_table_host_singleton_filtered_unrarified.biom
- OTU table for 16S rRNA gene sequence analysis before rarefaction 16S_otu_table_host_singleton_filtered_sd9194.biom
- OTU table for 16S rRNA gene sequence analysis after rarefaction to 9,194 OTU
counts/sample 16S_PICRUSt_analysis_code.txt
- commands for PICRUSt functional metagenome prediction kinome_array_data.txt
- raw kinome array data for Caco-2Bbe1 cells exposed to non-digestible
oligosaccharides (inulin and scFOS) and challenged with enterohemorrhagic <i>Escherichia
coli</i> (EHEC) kinome_array_metadata.txt
- describes raw kinome array data 













































kinome_array_PIIKA_2_parameters.txt
- PIIKA 2 parameters for kinome array analysis
DOI: 10.6084/m9.figshare.5425510.v1
title: Non-digestible oligosaccharides directly regulate host kinome to modulate host inflammatory responses without alterations in the gut microbiota

description: Data
repository for: Wu RY, Määttänen
P, Napper S, Scruten E, Li B, Koike Y, Johnson-Henry KC, Pierro A, Rossi L, Botts
SR, Surette MG, Sherman PM. Non-digestible
oligosaccharides directly regulate host kinome to modulate host inflammatory
responses without alterations in the gut microbiota. Microbiome. 2017;5:135. Available at: https://doi.org/10.1186/s40168-017-0357-4Repository
information: PSWY
FASTQ sequence files - 16S rRNA gene sequence files for P10 mice exposed to
lipopolysaccharide (LPS) and non-digestible oligosaccharides (inulin and scFOS) 16S_metadata.txt
- describes 16S rRNA gene sequence files 16S_preprocessed_sequences.fna
- preprocessed sequence file for 16S rRNA gene data (quality filtering, chimera
checking, etc.) 16S_otu_table_host_singleton_filtered_unrarified.biom
- OTU table for 16S rRNA gene sequence analysis before rarefaction 16S_otu_table_host_singleton_filtered_sd9194.biom
- OTU table for 16S rRNA gene sequence analysis after rarefaction to 9,194 OTU
counts/sample 16S_PICRUSt_analysis_code.txt
- commands for PICRUSt functional metagenome prediction kinome_array_data.txt
- raw kinome array data for Caco-2Bbe1 cells exposed to non-digestible
oligosaccharides (inulin and scFOS) and challenged with enterohemorrhagic <i>Escherichia
coli</i> (EHEC) kinome_array_metadata.txt
- describes raw kinome array data 













































kinome_array_PIIKA_2_parameters.txt
- PIIKA 2 parameters for kinome array analysis
DOI: 10.6084/m9.figshare.5426464
title: ZH PLOS ONE manuscript data

description: This file contains the minimal dataset for Hong et al. submitted to PLoS-One in September, 2017, titled "A Novel Gravity-FREAK Feature Extraction and Gravity-KLT Tracking Registration Algorithm based on iPhone MEMS Mobile Sensor in Mobile Environment".<br>The design of the experiment is fully explained in the manuscript.<br>The mobile phone is also rotated along with the x, y and z axis respectively to evaluate the performance of the algorithm in different rotation patterns. The Three folder images is the deformation of the Object as iPhone rotating along X, Y and Z Axis respectively.
DOI: 10.6084/m9.figshare.5426464.v2
title: ZH PLOS ONE manuscript data

description: This file contains the minimal dataset for Hong et al. submitted to PLoS-One in September, 2017, titled "A Novel Gravity-FREAK Feature Extraction and Gravity-KLT Tracking Registration Algorithm based on iPhone MEMS Mobile Sensor in Mobile Environment".<br>The design of the experiment is fully explained in the manuscript.<br>The mobile phone is also rotated along with the x, y and z axis respectively to evaluate the performance of the algorithm in different rotation patterns. The Three folder images is the deformation of the Object as iPhone rotating along X, Y and Z Axis respectively.
DOI: 10.6084/m9.figshare.5426464.v1
title: ZH PLOS ONE manuscript data

description: This file contains the minimal dataset for Hong et al. submitted to PLoS-One in September, 2017, titled "A Novel Gravity-FREAK Feature Extraction and Gravity-KLT Tracking Registration Algorithm based on iPhone MEMS Mobile Sensor in Mobile Environment".<br>The design of the experiment is fully explained in the manuscript.<br>The mobile phone is also rotated along with the x, y and z axis respectively to evaluate the performance of the algorithm in different rotation patterns. The Three folder images is the deformation of the Object as iPhone rotating along X, Y and Z Axis respectively.
DOI: 10.6084/m9.figshare.5427160
title: Ezetimibe ameliorates steatohepatitis via AMP activated protein kinase-TFEB-mediated activation of autophagy and NLRP3 inflammasome inhibition

description: Impairment in macroautophagy/autophagy flux and inflammasome activation are common characteristics of nonalcoholic steatohepatitis (NASH). Considering the lack of approved agents for treating NASH, drugs that can enhance autophagy and modulate inflammasome pathways may be beneficial. Here, we investigated the novel mechanism of ezetimibe, a widely prescribed drug for hypercholesterolemia, as a therapeutic option for ameliorating NASH. Human liver samples with steatosis and NASH were analyzed. For in vitro studies of autophagy and inflammasomes, primary mouse hepatocytes, human hepatoma cells, mouse embryonic fibroblasts with Ampk or Tsc2 knockout, and human or primary mouse macrophages were treated with ezetimibe and palmitate. Steatohepatitis and fibrosis were induced by feeding Atg7 wild-type, haploinsufficient, and knockout mice a methionine- and choline-deficient diet with ezetimibe (10 mg/kg) for 4 wk. Human livers with steatosis or NASH presented impaired autophagy with decreased nuclear TFEB and increased SQSTM1, MAP1LC3-II, and NLRP3 expression. Ezetimibe increased autophagy flux and concomitantly ameliorated lipid accumulation and apoptosis in palmitate-exposed hepatocytes. Ezetimibe induced AMPK phosphorylation and subsequent TFEB nuclear translocation, related to MAPK/ERK. In macrophages, ezetimibe blocked the NLRP3 inflammasome-IL1B pathway in an autophagy-dependent manner and modulated hepatocyte-macrophage interaction via extracellular vesicles. Ezetimibe attenuated lipid accumulation, inflammation, and fibrosis in liver-specific Atg7 wild-type and haploinsufficient mice, but not in knockout mice. Ezetimibe ameliorates steatohepatitis by autophagy induction through AMPK activation and TFEB nuclear translocation, related to an independent MTOR ameliorative effect and the MAPK/ERK pathway. Ezetimibe dampens NLRP3 inflammasome activation in macrophages by modulating autophagy and a hepatocyte-driven exosome pathway.
DOI: 10.6084/m9.figshare.5427160.v1
title: Ezetimibe ameliorates steatohepatitis via AMP activated protein kinase-TFEB-mediated activation of autophagy and NLRP3 inflammasome inhibition

description: Impairment in macroautophagy/autophagy flux and inflammasome activation are common characteristics of nonalcoholic steatohepatitis (NASH). Considering the lack of approved agents for treating NASH, drugs that can enhance autophagy and modulate inflammasome pathways may be beneficial. Here, we investigated the novel mechanism of ezetimibe, a widely prescribed drug for hypercholesterolemia, as a therapeutic option for ameliorating NASH. Human liver samples with steatosis and NASH were analyzed. For in vitro studies of autophagy and inflammasomes, primary mouse hepatocytes, human hepatoma cells, mouse embryonic fibroblasts with Ampk or Tsc2 knockout, and human or primary mouse macrophages were treated with ezetimibe and palmitate. Steatohepatitis and fibrosis were induced by feeding Atg7 wild-type, haploinsufficient, and knockout mice a methionine- and choline-deficient diet with ezetimibe (10 mg/kg) for 4 wk. Human livers with steatosis or NASH presented impaired autophagy with decreased nuclear TFEB and increased SQSTM1, MAP1LC3-II, and NLRP3 expression. Ezetimibe increased autophagy flux and concomitantly ameliorated lipid accumulation and apoptosis in palmitate-exposed hepatocytes. Ezetimibe induced AMPK phosphorylation and subsequent TFEB nuclear translocation, related to MAPK/ERK. In macrophages, ezetimibe blocked the NLRP3 inflammasome-IL1B pathway in an autophagy-dependent manner and modulated hepatocyte-macrophage interaction via extracellular vesicles. Ezetimibe attenuated lipid accumulation, inflammation, and fibrosis in liver-specific Atg7 wild-type and haploinsufficient mice, but not in knockout mice. Ezetimibe ameliorates steatohepatitis by autophagy induction through AMPK activation and TFEB nuclear translocation, related to an independent MTOR ameliorative effect and the MAPK/ERK pathway. Ezetimibe dampens NLRP3 inflammasome activation in macrophages by modulating autophagy and a hepatocyte-driven exosome pathway.
DOI: 10.6084/m9.figshare.5427190
title: Phosphoproteome-based kinase activity profiling reveals the critical role of MAP2K2 and PLK1 in neuronal autophagy

description: Recent studies have demonstrated that dysregulation of macroautophagy/autophagy may play a central role in the pathogenesis of neurodegenerative disorders, and the induction of autophagy protects against the toxic insults of aggregate-prone proteins by enhancing their clearance. Thus, autophagy has become a promising therapeutic target against neurodegenerative diseases. In this study, quantitative phosphoproteomic profiling together with a computational analysis was performed to delineate the phosphorylation signaling networks regulated by 2 natural neuroprotective autophagy enhancers, corynoxine (Cory) and corynoxine B (Cory B). To identify key regulators, namely, protein kinases, we developed a novel network-based algorithm of <i>in silico</i> Kinome Activity Profiling (iKAP) to computationally infer potentially important protein kinases from phosphorylation networks. Using this algorithm, we observed that Cory or Cory B potentially regulated several kinases. We predicted and validated that Cory, but not Cory B, downregulated a well-documented autophagy kinase, RPS6KB1/p70S6K (ribosomal protein S6 kinase, polypeptide 1). We also discovered 2 kinases, MAP2K2/MEK2 (mitogen-activated protein kinase kinase 2) and PLK1 (polo-like kinase 1), to be potentially upregulated by Cory, whereas the siRNA-mediated knockdown of <i>Map2k2</i> and <i>Plk1</i> significantly inhibited Cory-induced autophagy. Furthermore, Cory promoted the clearance of Alzheimer disease-associated APP (amyloid β [A4] precursor protein) and Parkinson disease-associated SNCA/α-synuclein (synuclein, α) by enhancing autophagy, and these effects were dramatically diminished by the inhibition of the kinase activities of MAP2K2 and PLK1. As a whole, our study not only developed a powerful method for the identification of important regulators from the phosphoproteomic data but also identified the important role of MAP2K2 and PLK1 in neuronal autophagy.
DOI: 10.6084/m9.figshare.5427190.v2
title: Phosphoproteome-based kinase activity profiling reveals the critical role of MAP2K2 and PLK1 in neuronal autophagy

description: Recent studies have demonstrated that dysregulation of macroautophagy/autophagy may play a central role in the pathogenesis of neurodegenerative disorders, and the induction of autophagy protects against the toxic insults of aggregate-prone proteins by enhancing their clearance. Thus, autophagy has become a promising therapeutic target against neurodegenerative diseases. In this study, quantitative phosphoproteomic profiling together with a computational analysis was performed to delineate the phosphorylation signaling networks regulated by 2 natural neuroprotective autophagy enhancers, corynoxine (Cory) and corynoxine B (Cory B). To identify key regulators, namely, protein kinases, we developed a novel network-based algorithm of <i>in silico</i> Kinome Activity Profiling (iKAP) to computationally infer potentially important protein kinases from phosphorylation networks. Using this algorithm, we observed that Cory or Cory B potentially regulated several kinases. We predicted and validated that Cory, but not Cory B, downregulated a well-documented autophagy kinase, RPS6KB1/p70S6K (ribosomal protein S6 kinase, polypeptide 1). We also discovered 2 kinases, MAP2K2/MEK2 (mitogen-activated protein kinase kinase 2) and PLK1 (polo-like kinase 1), to be potentially upregulated by Cory, whereas the siRNA-mediated knockdown of <i>Map2k2</i> and <i>Plk1</i> significantly inhibited Cory-induced autophagy. Furthermore, Cory promoted the clearance of Alzheimer disease-associated APP (amyloid β [A4] precursor protein) and Parkinson disease-associated SNCA/α-synuclein (synuclein, α) by enhancing autophagy, and these effects were dramatically diminished by the inhibition of the kinase activities of MAP2K2 and PLK1. As a whole, our study not only developed a powerful method for the identification of important regulators from the phosphoproteomic data but also identified the important role of MAP2K2 and PLK1 in neuronal autophagy.
DOI: 10.6084/m9.figshare.5431984.v1
title: Function and regulation mechanism of <i>Chk1</i> during meiotic maturation in porcine oocytes

description: Checkpoint 1 (Chk1), as an important member of DNA replication checkpoint and DNA damage response, has an important role during the G2/M stage of mitosis. In this study, we used porcine oocyte as a model to investigate the function of <i>Chk1</i> during porcine oocyte maturation. <i>Chk1</i> was expressed from germinal vesicle (GV) to metaphase II (MII) stages, mainly localized in the cytoplasm at GV stage and moved to the spindle after germinal vesicle breakdown (GVBD). <i>Chk1</i> depletion not only induced oocytes to be arrested at MI stage with abnormal chromosomes arrangement, but also inhibited the degradation of Cyclin B1 and decreased the expression of Mitotic Arrest Deficient 2-Like 1 (Mad2L1), one of spindle assembly checkpoint (SAC) proteins, and cadherin 1 (Cdh1), one of coactivation for anaphase-promoting complex/cyclosome (APC/C). Moreover, <i>Chk1</i> overexpression delayed GVBD. These results demonstrated that <i>Chk1</i> facilitated the timely degradation of Cyclin B1 at anaphase I (AI) and maintained the expression of Mad2L1 and Cdh1, which ensured that all chromosomes were accurately located in a line, and then oocytes passed metaphase I (MI) and AI and exited from the first meiotic division successfully. In addition, we proved that Chk1 had not function on GVBD of porcine oocytes, which suggested that maturation of porcine oocytes did not need the DNA damage checkpoint, which was different from the mouse oocyte maturation.