cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4234160
title: Kinetic data for manuscript describing the AutoTST algorithm for automated Transition State Theory calculations of chemical reaction rates.

description: isoButanolModel.tgz contains the kinetic model for isobutanol from http://dx.doi.org/10.1016/j.combustflame.2011.12.017 with the chemical structures of the species identified, and a script used to parse the model, categorize reactions, and attempt transition state searches. <br> CanThermInputOutput.tgz contains files for 781 reactions in the above mechanism belonging to the reaction families Hydrogen Abstraction, Intramolecular Hydrogen Migration, and Radical Addition to a Multiple Bond, and the 282 species they involve. For each is provided the Gaussian '09 log file (which includes the input file) for the species or transition state calculation with M062X/MG3S, and input files for CanTherm package to process these log files and calculate the reaction kinetics. Also provided, in the form of a README file, is a shell script which will install the necessary software and run all the calculations, reproducing the output files (which are also included).
DOI: 10.6084/m9.figshare.4234160.v1
title: Kinetic data for manuscript describing the AutoTST algorithm for automated Transition State Theory calculations of chemical reaction rates.

description: isoButanolModel.tgz contains the kinetic model for isobutanol from http://dx.doi.org/10.1016/j.combustflame.2011.12.017 with the chemical structures of the species identified, and a script used to parse the model, categorize reactions, and attempt transition state searches. <br> CanThermInputOutput.tgz contains files for 781 reactions in the above mechanism belonging to the reaction families Hydrogen Abstraction, Intramolecular Hydrogen Migration, and Radical Addition to a Multiple Bond, and the 282 species they involve. For each is provided the Gaussian '09 log file (which includes the input file) for the species or transition state calculation with M062X/MG3S, and input files for CanTherm package to process these log files and calculate the reaction kinetics. Also provided, in the form of a README file, is a shell script which will install the necessary software and run all the calculations, reproducing the output files (which are also included).
DOI: 10.6084/m9.figshare.4234133.v1
title: Game Bakery Express - Ashri Dinimaharwati

description: RPP, Poster , Game, Mockup
DOI: 10.6084/m9.figshare.4234133.v2
title: Game Skala dan Perbandingan- Bakery Express - Ashri Dinimaharwati

description: RPP, Poster , Game, Mockup
DOI: 10.6084/m9.figshare.4234133.v3
title: Game Skala dan Perbandingan- Ashri Dinimaharwati

description: RPP, Poster , Game, Mockup
DOI: 10.6084/m9.figshare.4233986
title: Improved Outcomes with Robotic Ventral Hernia Repair

description: Data analysis of a single-institution, single-surgeon, retrospective study of 109 laparoscopic ventral hernia cases vs 106 robotic cases based on operative times, blood loss, liength of hospital stay, reoperations, readmissions, intraoperative complications, postoperative complications, pain medicine in the recovery room, conversions and recurrence rates.
DOI: 10.6084/m9.figshare.4234133.v4
title: Game Skala dan Perbandingan- Ashri Dinimaharwati

description: RPP, Poster , Game, Mockup
DOI: 10.6084/m9.figshare.4233986.v1
title: Improved Outcomes with Robotic Ventral Hernia Repair

description: Data analysis of a single-institution, single-surgeon, retrospective study of 109 laparoscopic ventral hernia cases vs 106 robotic cases based on operative times, blood loss, liength of hospital stay, reoperations, readmissions, intraoperative complications, postoperative complications, pain medicine in the recovery room, conversions and recurrence rates.
DOI: 10.6084/m9.figshare.4233983
title: Compiled transcripts for data sharing.docx

description: Transcripts for in-depth interviews
DOI: 10.6084/m9.figshare.4233983.v2
title: Compiled transcripts for data sharing.docx

description: Transcripts for in-depth interviews
DOI: 10.6084/m9.figshare.4233983.v1
title: Compiled transcripts for data sharing.docx

description: Transcripts for in-depth interviews
DOI: 10.6084/m9.figshare.4233887
title: ALFF value of patients and HCs

description: ALFF data
DOI: 10.6084/m9.figshare.4233887.v2
title: ALFF value of patients and HCs

description: ALFF data
DOI: 10.6084/m9.figshare.4233887.v1
title: ALFF value.xlsx

description: ALFF data
DOI: 10.6084/m9.figshare.4233878
title: BIO205 2016 Tut0109 Census 3 Data.xlsx

description: Data set collected at University of Toronto Mississauga (UTM) campus, following protocol posted at http://www.campusecology.network/protcol/
DOI: 10.6084/m9.figshare.4233878.v1
title: BIO205 2016 Tut0109 Census 3 Data.xlsx

description: Data set collected at University of Toronto Mississauga (UTM) campus, following protocol posted at http://www.campusecology.network/protcol/
DOI: 10.6084/m9.figshare.4233824
title: Kymographs from plasmids

description: DNA barcodes used in 'Noise Reduction in Single Time Frame Optical DNA Maps' (2017), PLOS One. <br>DNA kymographs from plasmids obtained from nano-channel based competitive binding assays. The set consists of 32 kymograph from three types of plasmids: pUUH239.2 (8 kymographs), pEC005A (11 kymographs) and pEC005B (13 kymographs). Each kymograph corresponds to one molecule and contains 200 single time frames of 0.1s each (6400 single time frames in total).<br>The 32 raw kymographs are in named 'plasmidName_moleculeNumber'. <br>
DOI: 10.6084/m9.figshare.4233824.v2
title: Kymographs from plasmids

description: DNA barcodes used in 'Noise Reduction in Single Time Frame Optical DNA Maps' (2017), PLOS One. <br>DNA kymographs from plasmids obtained from nano-channel based competitive binding assays. The set consists of 32 kymograph from three types of plasmids: pUUH239.2 (8 kymographs), pEC005A (11 kymographs) and pEC005B (13 kymographs). Each kymograph corresponds to one molecule and contains 200 single time frames of 0.1s each (6400 single time frames in total).<br>The 32 raw kymographs are in named 'plasmidName_moleculeNumber'. <br>
DOI: 10.6084/m9.figshare.4233824.v1
title: Kymographs from plasmids

description: DNA barcodes used in 'Noise Reduction in Single Time Frame Optical DNA Maps' (2017), PLOS One. <br>DNA kymographs from plasmids obtained from nano-channel based competitive binding assays. The set consists of 32 kymograph from three types of plasmids: pUUH239.2 (8 kymographs), pEC005A (11 kymographs) and pEC005B (13 kymographs). Each kymograph corresponds to one molecule and contains 200 single time frames of 0.1s each (6400 single time frames in total).<br>The 32 raw kymographs are in format .tif and .dat named 'plasmidName_moleculeNumber'. <br>The aligned kymographs (using WPAlign method) are in format .dat and named 'plasmidName-Aligned_moleculeNumber'.
DOI: 10.6084/m9.figshare.4233791
title: H- and C-NMR spectra of (−)-(M)-1-aza1-methyl[6]helicene tetrafluoroborate in CD2Cl2

description: zip files of H- and C-NMR spectra of (−)-(M)-1-aza1-methyl[6]helicene tetrafluoroborate in CD2Cl2, 50 mM, 24 C
DOI: 10.6084/m9.figshare.4233791.v1
title: H- and C-NMR spectra of (−)-(M)-1-aza1-methyl[6]helicene tetrafluoroborate in CD2Cl2

description: zip files of H- and C-NMR spectra of (−)-(M)-1-aza1-methyl[6]helicene tetrafluoroborate in CD2Cl2, 50 mM, 24 C
DOI: 10.6084/m9.figshare.4233782
title: Representation of the German transmission grid for Renewable Energy Sources impact analysis

description: This file is presented here as a zipped directory. The directory itself contains 5 other directories, one for each value of renewable energy penetration as described in the associated data descriptor.
DOI: 10.6084/m9.figshare.4233782.v1
title: Germany_grid_data.7z

description: This file is presented here as a zipped directory. The directory itself contains 5 other directories, one for each value of renewable energy penetration as described in the associated data descriptor.
DOI: 10.6084/m9.figshare.4233776
title: Kasprak_SFM_Lab.zip

description: A set of photographs (courtesy of Rebecca Rossi at Utah State University) and a brief laboratory exercise I wrote to conduct some basic structure-from-motion photogrammetry and point cloud editing.
DOI: 10.6084/m9.figshare.4233776.v1
title: Kasprak_SFM_Lab.zip

description: A set of photographs (courtesy of Rebecca Rossi at Utah State University) and a brief laboratory exercise I wrote to conduct some basic structure-from-motion photogrammetry and point cloud editing.
DOI: 10.6084/m9.figshare.4233767
title: PETrA: a Software-based Tool for Estimating the Energy Profile of Android Applications

description: Energy efficiency is a vital characteristic of any mobile application, and indeed it is becoming an important factor for user satisfaction. For this reason, in the recent years several approaches and tools for measuring the energy consumption of mobile devices have been proposed. Hardware-based solutions are highly precise, but at the same time they require costly hardware toolkits. Model-based techniques require a possibly difficult calibration of the parameters needed to correctly create a model on a specific hardware device. Finally, software-based solutions are easier to use, but they are possibly less precise than hardware-based solution. In this demo, we present PETrA, a novel software based tool for measuring the energy consumption of Android apps. We also provide evidence that our tool is able to perform similarly to hardware-based solutions.
DOI: 10.6084/m9.figshare.4233722
title: Medical Words Network: Point-wise mutual information matrix

description: Network analysis was used to explore how the medical sciences have evolved between 1980 and 2015 based on the shared words contained in more than 9 million PubMed abstracts. <br>All abstracts in PubMed until January 2015 inclusive were uploaded using contact with Application Programming Interface (API) of the National Library of Medicine (http://www.nlm.nih.gov/api/). We only included entities with English abstracts for the analysis (9,592,193 in total). <br>Words that were used more than 2000 times were considered for further analysis and the point-wise mutual information (PMI) between all permutations of two words were calculated. Attached files contain the PMI of medical words used more than 2000 times in each time period. <br>
DOI: 10.6084/m9.figshare.4233722.v1
title: Medical Words Network: Point-wise mutual information matrix

description: Network analysis was used to explore how the medical sciences have evolved between 1980 and 2015 based on the shared words contained in more than 9 million PubMed abstracts. <br>All abstracts in PubMed until January 2015 inclusive were uploaded using contact with Application Programming Interface (API) of the National Library of Medicine (http://www.nlm.nih.gov/api/). We only included entities with English abstracts for the analysis (9,592,193 in total). <br>Words that were used more than 2000 times were considered for further analysis and the point-wise mutual information (PMI) between all permutations of two words were calculated. Attached files contain the PMI of medical words used more than 2000 times in each time period. <br>
DOI: 10.6084/m9.figshare.4233767.v2
title: PETrA: a Software-based Tool for Estimating the Energy Profile of Android Applications

description: Energy efficiency is a vital characteristic of any mobile application, and indeed it is becoming an important factor for user satisfaction. For this reason, in the recent years several approaches and tools for measuring the energy consumption of mobile devices have been proposed. Hardware-based solutions are highly precise, but at the same time they require costly hardware toolkits. Model-based techniques require a possibly difficult calibration of the parameters needed to correctly create a model on a specific hardware device. Finally, software-based solutions are easier to use, but they are possibly less precise than hardware-based solution. In this demo, we present PETrA, a novel software based tool for measuring the energy consumption of Android apps. We also provide evidence that our tool is able to perform similarly to hardware-based solutions.
DOI: 10.6084/m9.figshare.4233707
title: IR spectrum of (−)-(M)-1-aza1-methyl[6]helicene tetrafluoroborate

description: IR spectrum of (−)-(<i>M</i>)-1-aza1-methyl[6]helicene tetrafluoroborate
DOI: 10.6084/m9.figshare.4233707.v1
title: IR spectrum of (−)-(M)-1-aza1-methyl[6]helicene tetrafluoroborate

description: IR spectrum of (−)-(<i>M</i>)-1-aza1-methyl[6]helicene tetrafluoroborate
DOI: 10.6084/m9.figshare.4233716.v1
title: Game Relasi - Matematika Kelas VIII.rar

description: Game ini ditujukan untuk memvisualisasikan materi relasi pada matematika kelas VIII. Siswa diharapkan lebih mudah dalam memahami materi terkait relasi dengan menarik
DOI: 10.6084/m9.figshare.4233701
title: .xyz files of optimised helicene dimer structures

description: .xyz files obtained from optimisation at the at the DFT-D3(BJ)-TPSS-D3/def2-TZVP level.
DOI: 10.6084/m9.figshare.4233716.v2
title: Game Relasi - Matematika Kelas VIII.rar

description: Game ini ditujukan untuk memvisualisasikan materi relasi pada matematika kelas VIII. Siswa diharapkan lebih mudah dalam memahami materi terkait relasi dengan menarik
DOI: 10.6084/m9.figshare.4233695
title: Immediate-early alcohol-responsive miRNA expression in <i>Drosophila</i>

description: At the core of the changes characteristic of alcoholism are alterations in gene expression in the brain of the addicted individual. These changes are believed to underlie some of the neuroadaptations that promote compulsive drinking. Unfortunately, the mechanisms by which alcohol consumption produces changes in gene expression remain poorly understood. MicroRNAs (miRNAs) have emerged as important regulators of gene expression because they can coordinately modulate the translation efficiency of large sets of specific mRNAs. Here, we investigate the early miRNA responses elicited by an acute sedating dose of alcohol in the <i>Drosophila</i> model organism. In our analysis, we combine the power of next-generation sequencing with <i>Drosophila</i> genetics to identify alcohol-sensitive miRNAs and to functionally test them for a role in modulating alcohol sensitivity. We identified 14 known <i>Drosophila</i> miRNAs, and 13 putative novel miRNAs that respond to an acute sedative exposure to alcohol. Using the GeneSwitch Gal4/UAS system, a subset of these ethanol-responsive miRNAs was functionally tested to determine their individual contribution in modulating ethanol sensitivity. We identified two microRNAs that when overexpressed significantly increased ethanol sensitivity: miR-6 and miR-310. MicroRNA target prediction analysis revealed that the different alcohol-responsive miRNAs target-overlapping sets of mRNAs. Alcoholism is the product of accumulated cellular changes produced by chronic ethanol consumption. Although all of the changes described herein are extremely rapid responses evoked by a single ethanol exposure, understanding the gene expression changes that occur in the first few minutes after ethanol exposure will help us to categorize ethanol responses into those that are near instantaneous and those that are emergent responses produced only by repeated ethanol exposure.
DOI: 10.6084/m9.figshare.4233695.v1
title: Immediate-early alcohol-responsive miRNA expression in <i>Drosophila</i>

description: At the core of the changes characteristic of alcoholism are alterations in gene expression in the brain of the addicted individual. These changes are believed to underlie some of the neuroadaptations that promote compulsive drinking. Unfortunately, the mechanisms by which alcohol consumption produces changes in gene expression remain poorly understood. MicroRNAs (miRNAs) have emerged as important regulators of gene expression because they can coordinately modulate the translation efficiency of large sets of specific mRNAs. Here, we investigate the early miRNA responses elicited by an acute sedating dose of alcohol in the <i>Drosophila</i> model organism. In our analysis, we combine the power of next-generation sequencing with <i>Drosophila</i> genetics to identify alcohol-sensitive miRNAs and to functionally test them for a role in modulating alcohol sensitivity. We identified 14 known <i>Drosophila</i> miRNAs, and 13 putative novel miRNAs that respond to an acute sedative exposure to alcohol. Using the GeneSwitch Gal4/UAS system, a subset of these ethanol-responsive miRNAs was functionally tested to determine their individual contribution in modulating ethanol sensitivity. We identified two microRNAs that when overexpressed significantly increased ethanol sensitivity: miR-6 and miR-310. MicroRNA target prediction analysis revealed that the different alcohol-responsive miRNAs target-overlapping sets of mRNAs. Alcoholism is the product of accumulated cellular changes produced by chronic ethanol consumption. Although all of the changes described herein are extremely rapid responses evoked by a single ethanol exposure, understanding the gene expression changes that occur in the first few minutes after ethanol exposure will help us to categorize ethanol responses into those that are near instantaneous and those that are emergent responses produced only by repeated ethanol exposure.
DOI: 10.6084/m9.figshare.4233608
title: Supplementary Material for: Vitamin K Metabolism in a Rat Model of Chronic Kidney Disease

description: <b><i>Background:</i></b> Patients with chronic kidney disease (CKD) have very high levels of uncarboxylated, inactive, extra-hepatic vitamin K-dependent proteins measured in circulation, putting them at risk for complications of vitamin K deficiency. The major form of vitamin K found in the liver is phylloquinone (K1). Menaquinone-4 (MK-4) is the form of vitamin K that is preferentially found in extra-hepatic tissues. <b><i>Methods:</i></b> In the present study, we assessed tissue concentrations of K1 and MK-4 and the expression of vitamin K-related genes in a rat model of adenine-induced CKD. <b><i>Results:</i></b> It was found that rats with both mild and severe CKD had significantly lower amounts of K1 measured in liver, spleen and heart and higher levels of MK-4 measured in kidney cortex and medulla. All animals treated with high dietary K1 had an increase in tissue levels of both K1 and MK-4; however, the relative increase in K1 differed suggesting that the conversion of K1 to MK-4 may be a regulated/limiting process in some tissues. There was a decrease in the thoracic aorta expression of vitamin K recycling (<i>Vkor</i>) and utilization (<i>Ggcx</i>) enzymes, and a decrease in the kidney level of vitamin K1 to MK-4 bioconversion enzyme <i>Ubiad1</i> in CKD. <b><i>Conclusion:</i></b> Taken together, these findings suggest that CKD impacts vitamin K metabolism, and this occurs early in the disease course. Our findings that vitamin K metabolism is altered in the presence of CKD provides further support that sub-clinical vitamin K deficiency may represent a modifiable risk factor for vascular and bone health in this population.
DOI: 10.6084/m9.figshare.4233584
title: Mackey-Glass time series

description: Mackey-Glass time series<br>
DOI: 10.6084/m9.figshare.4233581
title: Star Brightness time series

description: Star brightness was recorded for 600 successive nights at midnight.
DOI: 10.6084/m9.figshare.4233581.v1
title: Star Brightness time series

description: Star brightness was recorded for 600 successive nights at midnight.
DOI: 10.6084/m9.figshare.4233461
title: Supplementary Material for: Identifying Gene Signature for the Detection of Ovarian Cancer Based on the Achieved Related Genes

description: <i>Background:</i> The overall survival rate of ovarian cancer patients is still poor because of the difficulties encountered in detection, diagnosis and treatment. Here, we aim to systematically identify the genetic factors causing ovarian cancer and find the accurate diagnostic and therapeutic targets for ovarian cancer. <i>Methods:</i> We collected the known archived ovarian cancer-related genes from the databases used as the investigated targets and employed the minimum redundancy maximum relevance and random forest classification to identify the novel ovarian cancer-related genes in addition to the known ones. We further identified candidates as the markers for the detection of the ovarian cancer based on the gene expression data and then confirmed them by quantitative real-time PCR. <i>Results:</i> We found out the genetic terms to interpret the mechanism of ovarian cancer. Based on those terms, we predicted 860 novel related genes as candidates. These candidates can act as expression biomarkers for clinical detection and they achieved a 100% accuracy. We verified 10 of them as the optimal biomarkers for detection in the expression data. <i>Conclusion:</i> We employed the features of achieved ovarian cancer-related genes to identify 860 novel ovarian cancer genes. We further validated 10 genes as biomarkers for detection of ovarian cancer.
DOI: 10.6084/m9.figshare.4233461.v1
title: Supplementary Material for: Identifying Gene Signature for the Detection of Ovarian Cancer Based on the Achieved Related Genes

description: <i>Background:</i> The overall survival rate of ovarian cancer patients is still poor because of the difficulties encountered in detection, diagnosis and treatment. Here, we aim to systematically identify the genetic factors causing ovarian cancer and find the accurate diagnostic and therapeutic targets for ovarian cancer. <i>Methods:</i> We collected the known archived ovarian cancer-related genes from the databases used as the investigated targets and employed the minimum redundancy maximum relevance and random forest classification to identify the novel ovarian cancer-related genes in addition to the known ones. We further identified candidates as the markers for the detection of the ovarian cancer based on the gene expression data and then confirmed them by quantitative real-time PCR. <i>Results:</i> We found out the genetic terms to interpret the mechanism of ovarian cancer. Based on those terms, we predicted 860 novel related genes as candidates. These candidates can act as expression biomarkers for clinical detection and they achieved a 100% accuracy. We verified 10 of them as the optimal biomarkers for detection in the expression data. <i>Conclusion:</i> We employed the features of achieved ovarian cancer-related genes to identify 860 novel ovarian cancer genes. We further validated 10 genes as biomarkers for detection of ovarian cancer.
DOI: 10.6084/m9.figshare.4233428
title: Supplementary Material for: Oncogenic Properties of Candidate Oncogenes in Chromosome Region 17p11.2p12 in Human Osteosarcoma

description: Osteosarcomas are primary tumors of bone that most often develop in adolescents. They are characterized by complex genomic changes including amplifications, deletions, and translocations. The chromosome region 17p11.2p12 is frequently amplified in human high grade osteosarcomas (25% of cases), suggesting the presence of one or more oncogenes. In previous studies, we identified 9 candidate oncogenes in this region <i>(GID4</i>,<i> ARGHAP44</i>,<i> LRRC75A-AS1</i>, <i>TOP3A</i>,<i> COPS3</i>,<i> SHMT1</i>,<i> PRPSAP2</i>,<i> PMP22</i>, and<i> RASD1)</i>. The aim of the present study was to determine their oncogenic properties. Therefore, we generated osteosarcoma cell lines overexpressing these genes, except for <i>LRRC75A-AS1</i> and <i>PRPSAP2</i>, and subjected these to functional oncogenic assays. We found that <i>TOP3A</i>, <i>SHMT1</i>, and <i>RASD1</i> overexpression provided increased proliferation and that <i>ARGHAP44</i>, <i>COPS3</i>, and <i>PMP22</i> overexpression had a stimulatory effect on migration and invasion of the cells. <i>COPS3</i> and <i>PMP22</i> overexpression additionally improved the ability of the cells to form new colonies. No oncogenic effect could be demonstrated for <i>GID4</i> overexpression. We conclude that the concerted amplification-mediated overexpression of these genes in 17p11.2p12 may contribute to the oncogenic process in malignant osteosarcoma.