cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5705449
title: Supplementary Material for: Sesamin Protects Against Cardiac Remodeling Via Sirt3/ROS Pathway

description: <b><i>Background/Aims:</i></b> Cardiac remodeling is associated with oxidative stress. Sesamin, a well-known antioxidant from sesamin seeds, have been used extensively as traditional health foods. However, there is little known about the effect of sesamin on cardiac remodeling. Therefore, the present study aimed to determine whether sesamin could protect against cardiac remodeling and to clarify potential molecular mechanisms. <b><i>Methods:</i></b> The mice were subjected to either transverse aortic constriction (TAC) or sham surgery (control group). Beginning one week after surgery, the mice were oral gavage treated with sesamin (100mg·kg<sup>-1</sup>·day<sup>-1</sup>) or vehicle for 3 weeks. Cardiac hypertrophy was assessed by echocardiographic parameters, histological analyses and hypertrophic markers. <b><i>Results:</i></b> Sesamin alleviated cardiac hypertrophy, inhibited fibrosis and attenuated the inflammatory response. The increased production of reactive oxygen species, the activation of ERK1/2-dependent nuclear factor-κB and the increased level of Smad2 phosphorylation were observed in cardiac remolding model that were treated with sesamin. Furthermore, TAC induced alteration of Sirt3 and SOD2 was normalized by sesamin treatment. Finally, a selective Sirt3 inhibitor 3-TYP blocks all the protective role of sesamin, suggesting that a Sirt3-dependent effect of sesamin on cardiac remodeling. <b><i>Conclusion:</i></b> Sesamin improves cardiac function and prevents the development of cardiac hypertrophy via Sirt3/ROS pathway. Our results suggest the protective effect of sesamin on cardiac remolding.
DOI: 10.6084/m9.figshare.5705449.v1
title: Supplementary Material for: Sesamin Protects Against Cardiac Remodeling Via Sirt3/ROS Pathway

description: <b><i>Background/Aims:</i></b> Cardiac remodeling is associated with oxidative stress. Sesamin, a well-known antioxidant from sesamin seeds, have been used extensively as traditional health foods. However, there is little known about the effect of sesamin on cardiac remodeling. Therefore, the present study aimed to determine whether sesamin could protect against cardiac remodeling and to clarify potential molecular mechanisms. <b><i>Methods:</i></b> The mice were subjected to either transverse aortic constriction (TAC) or sham surgery (control group). Beginning one week after surgery, the mice were oral gavage treated with sesamin (100mg·kg<sup>-1</sup>·day<sup>-1</sup>) or vehicle for 3 weeks. Cardiac hypertrophy was assessed by echocardiographic parameters, histological analyses and hypertrophic markers. <b><i>Results:</i></b> Sesamin alleviated cardiac hypertrophy, inhibited fibrosis and attenuated the inflammatory response. The increased production of reactive oxygen species, the activation of ERK1/2-dependent nuclear factor-κB and the increased level of Smad2 phosphorylation were observed in cardiac remolding model that were treated with sesamin. Furthermore, TAC induced alteration of Sirt3 and SOD2 was normalized by sesamin treatment. Finally, a selective Sirt3 inhibitor 3-TYP blocks all the protective role of sesamin, suggesting that a Sirt3-dependent effect of sesamin on cardiac remodeling. <b><i>Conclusion:</i></b> Sesamin improves cardiac function and prevents the development of cardiac hypertrophy via Sirt3/ROS pathway. Our results suggest the protective effect of sesamin on cardiac remolding.
DOI: 10.6084/m9.figshare.5705437
title: Supplementary Material for: Proteomic Mapping of Dental Enamel Matrix from Inbred Mouse Strains: Unraveling Potential New Players in Enamel

description: Enamel formation is a complex 2-step process by which proteins are secreted to form an extracellular matrix, followed by massive protein degradation and subsequent mineralization. Excessive systemic exposure to fluoride can disrupt this process and lead to a condition known as dental fluorosis. The genetic background influences the responses of mineralized tissues to fluoride, such as dental fluorosis, observed in A/J and 129P3/J mice. The aim of the present study was to map the protein profile of enamel matrix from A/J and 129P3/J strains. Enamel matrix samples were obtained from A/J and 129P3/J mice and analyzed by 2-dimensional electrophoresis and liquid chromatography coupled with mass spectrometry. A total of 120 proteins were identified, and 7 of them were classified as putative uncharacterized proteins and analyzed in silico for structural and functional characterization. An interesting finding was the possibility of the uncharacterized sequence Q8BIS2 being an enzyme involved in the degradation of matrix proteins. Thus, the results provide a comprehensive view of the structure and function for putative uncharacterized proteins found in the enamel matrix that could help to elucidate the mechanisms involved in enamel biomineralization and genetic susceptibility to dental fluorosis.
DOI: 10.6084/m9.figshare.5705437.v1
title: Supplementary Material for: Proteomic Mapping of Dental Enamel Matrix from Inbred Mouse Strains: Unraveling Potential New Players in Enamel

description: Enamel formation is a complex 2-step process by which proteins are secreted to form an extracellular matrix, followed by massive protein degradation and subsequent mineralization. Excessive systemic exposure to fluoride can disrupt this process and lead to a condition known as dental fluorosis. The genetic background influences the responses of mineralized tissues to fluoride, such as dental fluorosis, observed in A/J and 129P3/J mice. The aim of the present study was to map the protein profile of enamel matrix from A/J and 129P3/J strains. Enamel matrix samples were obtained from A/J and 129P3/J mice and analyzed by 2-dimensional electrophoresis and liquid chromatography coupled with mass spectrometry. A total of 120 proteins were identified, and 7 of them were classified as putative uncharacterized proteins and analyzed in silico for structural and functional characterization. An interesting finding was the possibility of the uncharacterized sequence Q8BIS2 being an enzyme involved in the degradation of matrix proteins. Thus, the results provide a comprehensive view of the structure and function for putative uncharacterized proteins found in the enamel matrix that could help to elucidate the mechanisms involved in enamel biomineralization and genetic susceptibility to dental fluorosis.
DOI: 10.6084/m9.figshare.5705314
title: Bovine milk microbiome sequence data

description: MiSeq sequence data plus additional files of processed data.Paired end (PE) DNA sequence files from MiSeq sequencing of 16s rRNA gene V4 PCR amplicons from 21 dairy cow milk samples.<br><br>The filenames ending in qf.fastq.gz are fastq files that have been quality filtered using Trimmomatic.<br>Files beginning AEEYU_PCR-Neg contain sequence from PCR and MiSeq sequence steps where water was used in place of microbial DNA from milk (all other ingredients the same as +DNA samples).<br>Sample identifiers in the fastq filenames refer to these cows:ID cowmsb001334 c400msb001335 c604msb001336 c644msb001337 c659msb001338 c666msb001339 c675msb001340 c690msb001342 c774msb001343 c807msb001344 c854msb001345 c1029msb001347 c5601msb001348 c5621msb001349 c6808msb001350 c8192msb001351 c7905msb001353 c8421msb001354 c9501msb001355 c9504msb001356 c9510msb001357 c9536<br>Also a file of the unique (dereplicated) 16s v4 sequences closely related to Faecalibacterium, together with the list and membership of swarm clusters of those sequences and a fasta file of the swarm seeds. Also 2 sample x abundance tables (space delimited) for cows vs microbial families and cows vs Greengenes OTU.<br>
DOI: 10.6084/m9.figshare.5705314.v1
title: Bovine milk microbiome sequence data

description: MiSeq sequence data plus additional files of processed data.Paired end (PE) DNA sequence files from MiSeq sequencing of 16s rRNA gene V4 PCR amplicons from 21 dairy cow milk samples.<br><br>The filenames ending in qf.fastq.gz are fastq files that have been quality filtered using Trimmomatic.<br>Files beginning AEEYU_PCR-Neg contain sequence from PCR and MiSeq sequence steps where water was used in place of microbial DNA from milk (all other ingredients the same as +DNA samples).<br>Sample identifiers in the fastq filenames refer to these cows:ID cowmsb001334 c400msb001335 c604msb001336 c644msb001337 c659msb001338 c666msb001339 c675msb001340 c690msb001342 c774msb001343 c807msb001344 c854msb001345 c1029msb001347 c5601msb001348 c5621msb001349 c6808msb001350 c8192msb001351 c7905msb001353 c8421msb001354 c9501msb001355 c9504msb001356 c9510msb001357 c9536<br>Also a file of the unique (dereplicated) 16s v4 sequences closely related to Faecalibacterium, together with the list and membership of swarm clusters of those sequences and a fasta file of the swarm seeds. Also 2 sample x abundance tables (space delimited) for cows vs microbial families and cows vs Greengenes OTU.<br>
DOI: 10.6084/m9.figshare.5705275
title: Wax Lake Delta Channel Data (Winter 2013-2014)

description: The 'RBR' MATLAB files are data from an RBRconcerto CTD with OBS. The data includes the conductivity, temperature, depth, and turbidity from the Wax Lake Delta from the winter of 2013-2014. <br>The ADCP MATLAB files are data from East (Location 2) and Main (Location 1) Passes covering the same period. These ADCPs were Teledyne RDI Workhorse Monitors. I have attached the commands used to program the ADCPs for this deployment.<br>Please see attached file (WLD_BC_settings_and_locations) for meta-data.
DOI: 10.6084/m9.figshare.5705275.v2
title: Wax Lake Delta Channel Data (Winter 2013-2014)

description: The 'RBR' MATLAB files are data from an RBRconcerto CTD with OBS. The data includes the conductivity, temperature, depth, and turbidity from the Wax Lake Delta from the winter of 2013-2014. <br>The ADCP MATLAB files are data from East (Location 2) and Main (Location 1) Passes covering the same period. These ADCPs were Teledyne RDI Workhorse Monitors. I have attached the commands used to program the ADCPs for this deployment.<br>Please see attached file (WLD_BC_settings_and_locations) for meta-data.
DOI: 10.6084/m9.figshare.5705269
title: First draft genome sequence of the rock bream in the family Oplegnathidae

description: The rock bream (<i>Oplegnathus fasciatus</i>) is one of the most economically valuable marine fish in East Asia. Various factors including temperature changes, pathogenic infections, and disorders related to hereditary and somatic mutations have led to huge revenue losses in production. In order to attempt to overcome these issues on the molecular scale, reference genome sequences are needed. In this study, we constructed the first draft genome for the family <i>Oplegnathidae (O. fasciatus) </i>to develop genetic bio-markers for the above-mentioned problems. The <i>O. fasciatus </i>genome size was estimated to be 780 Mb based on 235 Gb of fragmented sequences that were assembled into a 766-Mb draft genome. From the draft genome, 23,338 genes were predicted and the gene coverage was estimated by comparing the core eukaryotic genes. In total, 81.9% of core eukaryote genes were present in the total gene contents. Moreover, 97% of the genes were obtained the functional terms from similar fish genomes. To the best of our knowledge this is the first draft genome for the family <i>Oplegnathidae</i>.
DOI: 10.6084/m9.figshare.5705269.v2
title: First draft genome sequence of the rock bream in the family Oplegnathidae

description: The rock bream (<i>Oplegnathus fasciatus</i>) is one of the most economically valuable marine fish in East Asia. Various factors including temperature changes, pathogenic infections, and disorders related to hereditary and somatic mutations have led to huge revenue losses in production. In order to attempt to overcome these issues on the molecular scale, reference genome sequences are needed. In this study, we constructed the first draft genome for the family <i>Oplegnathidae (O. fasciatus) </i>to develop genetic bio-markers for the above-mentioned problems. The <i>O. fasciatus </i>genome size was estimated to be 780 Mb based on 235 Gb of fragmented sequences that were assembled into a 766-Mb draft genome. From the draft genome, 23,338 genes were predicted and the gene coverage was estimated by comparing the core eukaryotic genes. In total, 81.9% of core eukaryote genes were present in the total gene contents. Moreover, 97% of the genes were obtained the functional terms from similar fish genomes. To the best of our knowledge this is the first draft genome for the family <i>Oplegnathidae</i>.
DOI: 10.6084/m9.figshare.5705269.v1
title: First draft genome sequence of the rock bream in the family Oplegnathidae

description: The rock bream (<i>Oplegnathus fasciatus</i>) is one of the most economically valuable marine fish in East Asia. Various factors including temperature changes, pathogenic infections, and disorders related to hereditary and somatic mutations have led to huge revenue losses in production. In order to attempt to overcome these issues on the molecular scale, reference genome sequences are needed. In this study, we constructed the first draft genome for the family <i>Oplegnathidae (O. fasciatus) </i>to develop genetic bio-markers for the above-mentioned problems. The <i>O. fasciatus </i>genome size was estimated to be 780 Mb based on 235 Gb of fragmented sequences that were assembled into a 766-Mb draft genome. From the draft genome, 23,338 genes were predicted and the gene coverage was estimated by comparing the core eukaryotic genes. In total, 81.9% of core eukaryote genes were present in the total gene contents. Moreover, 97% of the genes were obtained the functional terms from similar fish genomes. To the best of our knowledge this is the first draft genome for the family <i>Oplegnathidae</i>.
DOI: 10.17608/k6.auckland.5705239
title: Metabolomic profiling of maternal hair suggests rapid development of Intrahepatic Cholestasis of Pregnancy

description: Case control study of pregnant women recruited in Chongqing, China at 26-28 weeks' gestation (38 women that developed intrahepatic cholestasis of pregnancy (ICP) and 46 healthy controls). Ethics approval received from Chongqing Medical University (date: 2014-01-06) and informed consent was obtained from all participants. Aim of the study was to identify ICP biomarkers in maternal hair that could be used clinically for identifying women at risk of ICP development prior to disease onset/progression.Metabolomic profiling was conducted using gas chromatography-mass spectrometry. The samples were normalised by an internal standard (d4-alanine) and hair biomass before statistical analysis. The data available is the normalised metabolite data and corresponding metadata for each participant.
DOI: 10.17608/k6.auckland.5705239.v1
title: Metabolomic profiling of maternal hair suggests rapid development of Intrahepatic Cholestasis of Pregnancy

description: Case control study of pregnant women recruited in Chongqing, China at 26-28 weeks' gestation (38 women that developed intrahepatic cholestasis of pregnancy (ICP) and 46 healthy controls). Ethics approval received from Chongqing Medical University (date: 2014-01-06) and informed consent was obtained from all participants. Aim of the study was to identify ICP biomarkers in maternal hair that could be used clinically for identifying women at risk of ICP development prior to disease onset/progression.Metabolomic profiling was conducted using gas chromatography-mass spectrometry. The samples were normalised by an internal standard (d4-alanine) and hair biomass before statistical analysis. The data available is the normalised metabolite data and corresponding metadata for each participant.
DOI: 10.6084/m9.figshare.5705236
title: 1000Gphase3.5superpopulations.hg19

description: a bgzipped version of the allele frequencies of 1000G variants mapped to hg19 and aggregated by 5 continental super populations.
DOI: 10.6084/m9.figshare.5705236.v1
title: 1000Gphase3.5superpopulations.hg19

description: a bgzipped version of the allele frequencies of 1000G variants mapped to hg19 and aggregated by 5 continental super populations.
DOI: 10.6084/m9.figshare.5705203
title: Systematics, biogeography and evolution of <i>Asaccus gallagheri</i> (Squamata, Phyllodactylidae) with the description of a new endemic species from Oman

description: The Hajar Mountains are the highest mountain range in eastern Arabia. Despite being classified as a mountain desert, it is considered one of the top biodiversity hotspots of Arabia. As a result of its relatively old geological origin, complex topography, environmental heterogeneity and geographic isolation from other mountain ranges, its fauna and flora have diversified significantly producing high levels of endemicity, particularly amongst reptiles. Several genetic studies indicate that this diversity may still be underestimated, especially within some groups containing morphologically similar species like the nocturnal geckos of the genus <i>Asaccus</i>. These have radiated extensively on both sides of the Gulf of Oman, in the Hajar Mountains and the Zagros Mountains of south-west Asia, and are a good example of the faunal affinities between these two mountain ranges. In the present work, we analyse <i>A. gallagheri</i>, the smallest species of the Arabian radiation, using an unprecedented sampling across its entire distribution range and an integrative approach combining morphological, macroecological and multilocus molecular data with the objective of clarifying its systematics and phylogeography. The results support the presence of two allopatric species within <i>A. gallagheri</i> that split approximately 6 Ma. The newly discovered species is endemic to the Eastern Hajars and is described herein mainly on the basis of its smaller size and high genetic divergence from <i>A. gallagheri</i>. The molecular analyses also uncovered remarkable levels of genetic diversity within both species. The present study highlights the diversity of the genus <i>Asaccus</i> in south-east Arabia and stresses its relevance from a conservation point of view. http://www.zoobank.org/urn:lsid:zoobank.org:pub:62EB3146-9F79-4857-8CC6-36FE235D84D4
DOI: 10.6084/m9.figshare.5705203.v1
title: Systematics, biogeography and evolution of <i>Asaccus gallagheri</i> (Squamata, Phyllodactylidae) with the description of a new endemic species from Oman

description: The Hajar Mountains are the highest mountain range in eastern Arabia. Despite being classified as a mountain desert, it is considered one of the top biodiversity hotspots of Arabia. As a result of its relatively old geological origin, complex topography, environmental heterogeneity and geographic isolation from other mountain ranges, its fauna and flora have diversified significantly producing high levels of endemicity, particularly amongst reptiles. Several genetic studies indicate that this diversity may still be underestimated, especially within some groups containing morphologically similar species like the nocturnal geckos of the genus <i>Asaccus</i>. These have radiated extensively on both sides of the Gulf of Oman, in the Hajar Mountains and the Zagros Mountains of south-west Asia, and are a good example of the faunal affinities between these two mountain ranges. In the present work, we analyse <i>A. gallagheri</i>, the smallest species of the Arabian radiation, using an unprecedented sampling across its entire distribution range and an integrative approach combining morphological, macroecological and multilocus molecular data with the objective of clarifying its systematics and phylogeography. The results support the presence of two allopatric species within <i>A. gallagheri</i> that split approximately 6 Ma. The newly discovered species is endemic to the Eastern Hajars and is described herein mainly on the basis of its smaller size and high genetic divergence from <i>A. gallagheri</i>. The molecular analyses also uncovered remarkable levels of genetic diversity within both species. The present study highlights the diversity of the genus <i>Asaccus</i> in south-east Arabia and stresses its relevance from a conservation point of view. http://www.zoobank.org/urn:lsid:zoobank.org:pub:62EB3146-9F79-4857-8CC6-36FE235D84D4
DOI: 10.6084/m9.figshare.5705200
title: New York Harbor environmental DNA detection of fish, 12 month update

description: Updated dataset for "Aquatic environmental DNA detects seasonal fish abundance and habitat preference in an urban estuary (PLOS ONE 2017 e0175186). <br><br>33 additional water samples (109 total) were collected from August through December 2016, extending the original six-month study to twelve months. <br><br>Samples were analyzed as described in the original study. Briefly, one-liter water samples were filtered through a 0.45μM nylon filter, DNA was isolated using MoBio PowerSoil kit, amplified with broad-range vertebrate 12S primers, indexed with Nextera tags, and submitted to GENEWIZ for 2x150bp MiSeq sequencing. Fastq files were analyzed using DADA2 and unique sequences were submitted to GenBank using BLAST. Sequences matching fish species were selected for further analysis. The complete set of fastq files and associated data are deposited together with original dataset in NCBI Sequence Read Archive under BioProject ID PRJNA358446. New findings include 1) fall decrease in species per sample; 2) seasonal species counts roughly paralleled water temperature in the estuary; and 3) six additional species detected (Fig. 1). The fall decrease in species counts strengthens the original finding, namely, eDNA detectability is coincident with known seasonal movements of fish populations in and out of the lower Hudson estuary. The complete data set further supports eDNA localization within the estuary: nearshore marine species eDNAs were more common in East River (Atlantic silverside, cunner, rock gunnel, scup, seaboard goby), and brackish estuary species eDNAs were more common in the Hudson River (American eel, hogchoker, naked goby) (Fig. 1). At both sites, rarefaction analysis, new to this update, revealed a relatively small proportion of species produced the great majority of eDNA reads (Fig. 2). In particular, about 20% of species accounted for about 90% of reads at both sites; the predominant species differed by site consistent with known habitat preferences.<br> Table 1. Fish amplicon reads by sample. <br>Table 2. Fish 12s amplicon sequences. <br>