cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3382966
title: A Minimal DNA Methylation Signature in Oral Tongue Squamous Cell Carcinoma Links Altered Methylation with Tumor Attributes.

description: AbstractOral tongue squamous cell carcinomas (OTSCCs) are a homogenous group of aggressive tumors in the head and neck region that spread early to lymph nodes and have a higher incidence of regional failure. Additionally, there is a rising incidence of oral tongue cancer in younger populations. Studies on functional DNA methylation changes linked with altered gene expression are critical for understanding the mechanisms underlying tumor development and metastasis. Such studies also provide important insight into biomarkers linked with viral infection, tumor metastasis and patient survival in OTSCC. Therefore, we performed genome-wide methylation analysis of tumors (N = 52) and correlated altered methylation with differential gene expression. The minimal tumor-specific DNA 5-methycytosine (5mc) signature identified genes near 16 different differentially methylated regions (DMRs), which were validated using genomic data from The Cancer Genome Atlas (TCGA) cohort. In our cohort, hypermethylation of miR-10b was significantly associated with the differential expression of its target genes NR4A3 and BCL2L11 (P = 0.0125 and P = 0.014 respectively), which was inversely correlated with disease-free survival (P = 9E-15 and P = 2E-15 respectively) in patients. Finally, differential methylation in FUT3, TRIM5, TSPAN7, MAP3K8, RPS6KA2, SLC9A9 and NPAS3 genes was found to be predictive of certain clinical and epidemiological parameters.<b>IMPLICATIONS:</b><br>This study reveals a functional minimal methylation profile in oral tongue tumors with associated risk habits, clinical and epidemiological outcomes. In addition, NR4A3 down-regulation and correlation with patient survival suggests a potential target for therapeutic intervention in oral tongue tumors. Data from the current study are deposited in the NCBI Geo database (Accession number GSE75540).
DOI: 10.6084/m9.figshare.3382966.v1
title: A minimal DNA 5-methylcytosine signature of oral tongue squamous cell carcinoma links altered methylation with tumor characteristics

description: Oral tongue squamous cell carcinomas (OTSCC) are a homogenous group of aggressive tumors in the head and neck region that spread early to lymph nodes and have a higher incidence of regional failure. Additionally, there is a rising incidence of oral tongue cancer among younger population. Studies on functional DNA methylation changes linked with altered gene expression are important towards understanding of tumor development and metastasis. Such studies may provide insights into biomarkers linked with viral infection, tumor metastasis and patient survival in OTSCC. We performed genome-wide methylation analysis of tumors (<i>N</i> = 52) and correlated altered methylation with differential gene expression. The minimal tumor-specific DNA methylation signature identified genes near 16 different differentially methylated regions (DMRs), which were validated using data from the cancer genome atlas (TCGA) cohort. In our cohort, hypermethylation of the microRNA <i>MiR-10B</i> was significantly associated with the differential expression of its target genes <i>NR4A3</i> and <i>BCL2L11</i> (<i>P</i> = 0.0125 and <i>P</i> = 0.014 respectively), which was inversely correlated with disease-free survival (<i>P</i> = 9E-15 and <i>P </i>= 2E-15 respectively) in patients. We found differential methylation in <i>FUT3</i>,<i> TRIM5</i>, <i>TSPAN7</i>,<i> MAP3K8,</i> <i>RPS6KA2, SLC9A9 </i>and<i> NPAS3</i> genes to be predictive of certain clinical and epidemiological parameters. <b>Implications</b>: Our study identified a functional minimal methylation signature in oral tongue tumors and linked various signatures with risk habits, clinical and epidemiological parameters. Down-regulation of <i>NR4A3 </i>and its correlation with patient survival makes it a potential target for therapeutic intervention in oral tongue tumors. Data from the current study are deposited in the NCBI Geo database (Accession number GSE75540).
DOI: 10.6084/m9.figshare.3382966.v3
title: A Minimal DNA Methylation Signature in Oral Tongue Squamous Cell Carcinoma Links Altered Methylation with Tumor Attributes.

description: AbstractOral tongue squamous cell carcinomas (OTSCCs) are a homogenous group of aggressive tumors in the head and neck region that spread early to lymph nodes and have a higher incidence of regional failure. Additionally, there is a rising incidence of oral tongue cancer in younger populations. Studies on functional DNA methylation changes linked with altered gene expression are critical for understanding the mechanisms underlying tumor development and metastasis. Such studies also provide important insight into biomarkers linked with viral infection, tumor metastasis and patient survival in OTSCC. Therefore, we performed genome-wide methylation analysis of tumors (N = 52) and correlated altered methylation with differential gene expression. The minimal tumor-specific DNA 5-methycytosine (5mc) signature identified genes near 16 different differentially methylated regions (DMRs), which were validated using genomic data from The Cancer Genome Atlas (TCGA) cohort. In our cohort, hypermethylation of miR-10b was significantly associated with the differential expression of its target genes NR4A3 and BCL2L11 (P = 0.0125 and P = 0.014 respectively), which was inversely correlated with disease-free survival (P = 9E-15 and P = 2E-15 respectively) in patients. Finally, differential methylation in FUT3, TRIM5, TSPAN7, MAP3K8, RPS6KA2, SLC9A9 and NPAS3 genes was found to be predictive of certain clinical and epidemiological parameters.<b>IMPLICATIONS:</b><br>This study reveals a functional minimal methylation profile in oral tongue tumors with associated risk habits, clinical and epidemiological outcomes. In addition, NR4A3 down-regulation and correlation with patient survival suggests a potential target for therapeutic intervention in oral tongue tumors. Data from the current study are deposited in the NCBI Geo database (Accession number GSE75540).
DOI: 10.6084/m9.figshare.3382966.v2
title: A Minimal DNA Methylation Signature in Oral Tongue Squamous Cell Carcinoma Links Altered Methylation with Tumor Attributes.

description: AbstractOral tongue squamous cell carcinomas (OTSCCs) are a homogenous group of aggressive tumors in the head and neck region that spread early to lymph nodes and have a higher incidence of regional failure. Additionally, there is a rising incidence of oral tongue cancer in younger populations. Studies on functional DNA methylation changes linked with altered gene expression are critical for understanding the mechanisms underlying tumor development and metastasis. Such studies also provide important insight into biomarkers linked with viral infection, tumor metastasis and patient survival in OTSCC. Therefore, we performed genome-wide methylation analysis of tumors (N = 52) and correlated altered methylation with differential gene expression. The minimal tumor-specific DNA 5-methycytosine (5mc) signature identified genes near 16 different differentially methylated regions (DMRs), which were validated using genomic data from The Cancer Genome Atlas (TCGA) cohort. In our cohort, hypermethylation of miR-10b was significantly associated with the differential expression of its target genes NR4A3 and BCL2L11 (P = 0.0125 and P = 0.014 respectively), which was inversely correlated with disease-free survival (P = 9E-15 and P = 2E-15 respectively) in patients. Finally, differential methylation in FUT3, TRIM5, TSPAN7, MAP3K8, RPS6KA2, SLC9A9 and NPAS3 genes was found to be predictive of certain clinical and epidemiological parameters.<b>IMPLICATIONS:</b><br>This study reveals a functional minimal methylation profile in oral tongue tumors with associated risk habits, clinical and epidemiological outcomes. In addition, NR4A3 down-regulation and correlation with patient survival suggests a potential target for therapeutic intervention in oral tongue tumors. Data from the current study are deposited in the NCBI Geo database (Accession number GSE75540).
DOI: 10.6084/m9.figshare.3382921
title: 第1回LODセミナー「実践SPARQL」

description: 日本オラクル株式会社にて2016年5月17日開催の第1回LODセミナー「実践SPARQL」で利用した資料です。
DOI: 10.6084/m9.figshare.3382921.v1
title: 第1回LODセミナー「実践SPARQL」

description: 日本オラクル株式会社にて2016年5月17日開催の第1回LODセミナー「実践SPARQL」で利用した資料です。
DOI: 10.6084/m9.figshare.3382906
title: birth-death-dispersion cellular automata model with different spatial and temporal updating

description: <pre>C++ code for birth-death-dispersion cellular automata model with different spatial and temporal updating.</pre><pre><br></pre><pre><pre>Please cite the article if you use it: Ruxton, G. D. and Saravia, L. A. 1998. The need for biological realism in the updating of cellular automata models. - Ecological Modelling 107: 105-112. </pre><br></pre>
DOI: 10.6084/m9.figshare.3382876
title: Risk Analysis of Plausible Incidental Exploitation Rates for the Pacific Sleeper Shark, a Data-Poor Species in the Gulf of Alaska

description: Monte Carlo simulation was used to investigate the sustainability of incidental exploitation rates (<i>U</i>) for Pacific Sleeper Sharks <i>Somniosus pacificus</i> in the Gulf of Alaska (GOA) under status quo management. Monte Carlo simulations were implemented with a standard, length-based, age-structured model that was evaluated with forward projection. Given the paucity of relevant data, we investigated the sensitivity of simulation results to a range of assumptions about key model parameters by using 24 alternative model configurations, each simulated 1,000 times. The risk analysis results were most sensitive to Pacific Sleeper Shark <i>U</i>-values. The aggregate fraction of simulations ending in an overfished condition increased from 0% under the low-<i>U</i> scenario to 59% under the high-<i>U</i> scenario. Risk analysis results were also sensitive to the assumed shape of the length-based selectivity curve (asymptotic or dome shaped) but were less sensitive to the range of assumptions about other key model parameters, including maximum age and stock productivity. These results indicate that a priority for Pacific Sleeper Shark management is to reduce the uncertainty in <i>U</i>. This major uncertainty will be decreased by an observer program that is now in place to monitor the historically unobserved GOA Pacific Halibut <i>Hippoglossus stenolepis</i> fishery, which incidentally catches Pacific Sleeper Sharks. Received March 19, 2015; accepted December 7, 2015 Published online May 16, 2016
DOI: 10.6084/m9.figshare.3382876.v1
title: Risk Analysis of Plausible Incidental Exploitation Rates for the Pacific Sleeper Shark, a Data-Poor Species in the Gulf of Alaska

description: Monte Carlo simulation was used to investigate the sustainability of incidental exploitation rates (<i>U</i>) for Pacific Sleeper Sharks <i>Somniosus pacificus</i> in the Gulf of Alaska (GOA) under status quo management. Monte Carlo simulations were implemented with a standard, length-based, age-structured model that was evaluated with forward projection. Given the paucity of relevant data, we investigated the sensitivity of simulation results to a range of assumptions about key model parameters by using 24 alternative model configurations, each simulated 1,000 times. The risk analysis results were most sensitive to Pacific Sleeper Shark <i>U</i>-values. The aggregate fraction of simulations ending in an overfished condition increased from 0% under the low-<i>U</i> scenario to 59% under the high-<i>U</i> scenario. Risk analysis results were also sensitive to the assumed shape of the length-based selectivity curve (asymptotic or dome shaped) but were less sensitive to the range of assumptions about other key model parameters, including maximum age and stock productivity. These results indicate that a priority for Pacific Sleeper Shark management is to reduce the uncertainty in <i>U</i>. This major uncertainty will be decreased by an observer program that is now in place to monitor the historically unobserved GOA Pacific Halibut <i>Hippoglossus stenolepis</i> fishery, which incidentally catches Pacific Sleeper Sharks. Received March 19, 2015; accepted December 7, 2015 Published online May 16, 2016
DOI: 10.4119/unibi/2945513
title: Natural and synthetic CHO-K1 time-lapse suspension cell microscopy images (bright-field and phase-contrast)

description: Collection of natural and synthetic CHO-K1 time-lapse suspension cell images. The data set contains bright-field (BF) and phase-contrast (PC) microscopy images. The BF set contains 12 scenarios and accumulates to 5202 images, of which 1.4 percent are labeled. The PC set contains 37 scenarios and accumulates to 11.189 images, of which 5.9 percent are labeled. The labels were created in a regular interval over the data sets. Images with more than 30 cells put in a nested archive beforehand, due to loss in relevance for the cultivation experiments with this data.
DOI: 10.6084/m9.figshare.3382855
title: Vascular endothelial growth factor expression in pediatric non-Hodgkin lymphoma: A prospective study

description: Vascular endothelial growth factor expression in pediatric non-Hodgkin lymphoma: A prospective study
DOI: 10.6084/m9.figshare.3382855.v1
title: Vascular endothelial growth factor expression in pediatric non-Hodgkin lymphoma: A prospective study

description: Vascular endothelial growth factor expression in pediatric non-Hodgkin lymphoma: A prospective study
DOI: 10.6084/m9.figshare.3382846
title: Final.xlsx

description: FNA biopsy data
DOI: 10.6084/m9.figshare.3382846.v2
title: Final.xlsx

description: FNA biopsy data
DOI: 10.6084/m9.figshare.3382846.v1
title: Final.xlsx

description: FNA biopsy data
DOI: 10.6084/m9.figshare.3382837
title: Data_Unconventional U-Turn Design Evaluation.xls

description: The data file includes two parts of data: 1) the field data collection at two intersections to calibrate the simulation model; and 2) the simulation results for the unconventional U-turn design. In the first part, data were collected from two sites in Nanchang, China. In sheet "Field data collection1", the data are used to calibrate the vehicle maneuvers at intersections in the Vissim. The data contains the following variables: No. (which is the vehicle number); Vehicle type; Turning start time; Turning end time; Turning time; Average distance of turning; Speed of turning; Type of maneuver (i.e., U-turn to left-most lane, U-turn to 2nd lane, or U-turn to 3rd lane); U-turn mode choice (i.e., straight-&gt;U-turn-&gt;turn right, or turn right-&gt;U-turn-&gt;straight). In the sheet "Field data collection2", the data are used as inputs in the simulation model. Those data are traffic parameters such as vehicle count and type in each turning-direction (i.e., left, straight, right) at each of the four intersection approaches. In the second part, data are those obtained from the simulation. Key information such as travel time, delay, and number of stops are provided. The comparison between UUT and DLT are also provided. We provide those data so that interested authors can better understand our U-turn design performance when combining the data with the contexts and figures/tables provided in the manuscript.
DOI: 10.6084/m9.figshare.3382774
title: HTRC Extracted Features [v.0.2] `langid`

description: This archive contains the results of computing `langid` for the OCR tokens of each page in every volume of the HathiTrust HTRC Extracted Features [v.0.2] dataset. Each file is a CSV file of ISO639-1 language code and probability pairs for each page, where the filename is `[HTRC-volume-identifier].basic.json.csv`. Version 1.1.5 of `langid` was used for processing.<br><b>Warning:</b> this archive will decompress to a ~25GB directory containing 4,805,434 files.
DOI: 10.6084/m9.figshare.3382774.v1
title: HTRC Extracted Features [v.0.2] `langid`

description: This archive contains the results of computing `langid` for the OCR tokens of each page in every volume of the HathiTrust HTRC Extracted Features [v.0.2] dataset. Each file is a CSV file of ISO639-1 language code and probability pairs for each page, where the filename is `[HTRC-volume-identifier].basic.json.csv`. Version 1.1.5 of `langid` was used for processing.<br><b>Warning:</b> this archive will decompress to a ~25GB directory containing 4,805,434 files.
DOI: 10.6084/m9.figshare.3382768
title: Altimetric_data_Volcanic_volcano.xls

description: Original dataset downloaded from Altmetrics in July 2015. Top 100 papers published with keywords 'volcano' and 'volcanic'. Added to by Jenni Barclay with Google Scholar citations (May 2016) and with her own classification of paper type.
DOI: 10.6084/m9.figshare.3382759
title: Statistical supplement to: Visual guidance of forward flight in hummingbirds reveals control based on image features instead of pattern velocity

description: Data and R script of analyses in support of the study: "Visual guidance of forward flight in hummingbirds reveals control based on image features instead of pattern velocity"<br>Study authors: Roslyn Dakin, Tyee K. Fellows, and Douglas L. Altshuler<br><br><br>
DOI: 10.6084/m9.figshare.3382759.v1
title: statistical_supplement_flight_course_control.R

description: Data and R script of analyses in support of the study: "Visual guidance of forward flight in hummingbirds reveals control based on image features instead of pattern velocity"<br>Study authors: Roslyn Dakin, Tyee K. Fellows, and Douglas L. Altshuler<br><br><br>
DOI: 10.6084/m9.figshare.3382759.v2
title: Visual guidance of forward flight in hummingbirds reveals control based on image features instead of pattern velocity

description: Data and R script of analyses in support of the study: "Visual guidance of forward flight in hummingbirds reveals control based on image features instead of pattern velocity"<br>Study authors: Roslyn Dakin, Tyee K. Fellows, and Douglas L. Altshuler<br><br><br>
DOI: 10.6084/m9.figshare.3382759.v4
title: Statistical supplement to: Visual guidance of forward flight in hummingbirds reveals control based on image features instead of pattern velocity

description: Data and R script of analyses in support of the study: "Visual guidance of forward flight in hummingbirds reveals control based on image features instead of pattern velocity"<br>Study authors: Roslyn Dakin, Tyee K. Fellows, and Douglas L. Altshuler<br><br><br>
DOI: 10.6084/m9.figshare.3382759.v3
title: Statistical supplement to: "Visual guidance of forward flight in hummingbirds reveals control based on image features instead of pattern velocity"

description: Data and R script of analyses in support of the study: "Visual guidance of forward flight in hummingbirds reveals control based on image features instead of pattern velocity"<br>Study authors: Roslyn Dakin, Tyee K. Fellows, and Douglas L. Altshuler<br><br><br>
DOI: 10.6084/m9.figshare.3382756
title: Antibiotic resistance and corruption regression table

description: This Table accompanies our reply to critics of our PLoS paper dealing with the strong association of levels of corruption in countries and the levels of antibiotic resistance seen in those countries
DOI: 10.6084/m9.figshare.3382693
title: Tc1 and WT brains cohort 1 (C1)

description: This dataset corresponds to a PLOS ONE paper, "Fully-automated µMRI morphometric phenotyping of the Tc1 mouse model of Down syndrome".<br><br><b>Corresponding article</b>: Powell NM, Modat M, Cardoso MJ, Ma D, Holmes HE, Yu Y, et al. (2016) Fully-Automated μMRI Morphometric Phenotyping of the Tc1 Mouse Model of Down Syndrome. PLoS ONE 11(9): e0162974. doi:10.1371/journal.pone.0162974 - http://dx.doi.org/10.1371/journal.pone.0162974<br><br><b>See also:</b><br>* Cohort 2: https://figshare.com/s/cb3b7056f0a9a029ee79 doi: <br>10.6084/m9.figshare.3394786<br>* 3-brain holder for ex vivo µMRI scans: https://figshare.com/articles/CABI_Mouse_Brain_Holder_3_brain_/3394783 doi: 10.6084/m9.figshare.3394783 <br>* https://github.com/nmpowell/mousemorph<br>
DOI: 10.6084/m9.figshare.3382693.v1
title: Tc1 and WT brains cohort 1 (C1)

description: This dataset corresponds to a PLOS ONE paper, "Fully-automated µMRI morphometric phenotyping of the Tc1 mouse model of Down syndrome".<br><br><b>Corresponding article</b>: Powell NM, Modat M, Cardoso MJ, Ma D, Holmes HE, Yu Y, et al. (2016) Fully-Automated μMRI Morphometric Phenotyping of the Tc1 Mouse Model of Down Syndrome. PLoS ONE 11(9): e0162974. doi:10.1371/journal.pone.0162974 - http://dx.doi.org/10.1371/journal.pone.0162974<br><br><b>See also:</b><br>* Cohort 2: https://figshare.com/s/cb3b7056f0a9a029ee79 doi: <br>10.6084/m9.figshare.3394786<br>* 3-brain holder for ex vivo µMRI scans: https://figshare.com/articles/CABI_Mouse_Brain_Holder_3_brain_/3394783 doi: 10.6084/m9.figshare.3394783 <br>* https://github.com/nmpowell/mousemorph<br>
DOI: 10.6084/m9.figshare.3382672
title: AÇÕES E MEDIDAS VISANDO A ERRADICAÇÃO DO TRABALHO ESCRAVO NO BRASIL CONTEMPORÂNEO

description: Pur avendo stata abolita la schiavitù per oltre 125 anni e l'attuale Diploma Penale brasiliano tipizzare come reato la splorazione dell'uomo in condizioni di schiavitù, oltre il vasto sistema internazionale e nazionale per la protezione dei lavoratori, la realtà brasiliana contemporanea dimostra che questa pratica si fa presente in Brasile, ferendo sostanzialmente la dignità della persona umana. La presente ricerca obiettiva dimostrare i mezzi che lo Stato brasiliano viene prendendo, attraverso azioni concrete istituzionali e dele Potere Legislativo, Esecutivo e Giudiziario, per combattere duramente questa ferita abusiva che è incorporata nella società, motivo per cui si è considerato dalle organizzazioni internazionali come il paese che di più lotta per la eradicazione della pratica schiavista nelle società contemporanee.
DOI: 10.6084/m9.figshare.3382672.v1
title: AÇÕES E MEDIDAS VISANDO A ERRADICAÇÃO DO TRABALHO ESCRAVO NO BRASIL CONTEMPORÂNEO

description: Pur avendo stata abolita la schiavitù per oltre 125 anni e l'attuale Diploma Penale brasiliano tipizzare come reato la splorazione dell'uomo in condizioni di schiavitù, oltre il vasto sistema internazionale e nazionale per la protezione dei lavoratori, la realtà brasiliana contemporanea dimostra che questa pratica si fa presente in Brasile, ferendo sostanzialmente la dignità della persona umana. La presente ricerca obiettiva dimostrare i mezzi che lo Stato brasiliano viene prendendo, attraverso azioni concrete istituzionali e dele Potere Legislativo, Esecutivo e Giudiziario, per combattere duramente questa ferita abusiva che è incorporata nella società, motivo per cui si è considerato dalle organizzazioni internazionali come il paese che di più lotta per la eradicazione della pratica schiavista nelle società contemporanee.