cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3172540.v1
title: Epigenetic and genetic burden measures are associated with tumor characteristics in invasive breast carcinoma

description: The development and progression of invasive breast cancer is characterized by alterations to the genome and epigenome. However, the relationship between breast tumor characteristics, disease subtypes, and patient outcomes with the cumulative burden of these molecular alterations are not well characterized. We determined the average departure of tumor DNA methylation from adjacent normal breast DNA methylation using Illumina 450K methylation data from 700 invasive breast tumors and 90 adjacent normal breast tissues in The Cancer Genome Atlas. From this we generated a novel summary measure of altered DNA methylation, the DNA methylation dysregulation index (MDI), and examined the relation of MDI with tumor characteristics and summary measures that quantify cumulative burden of genetic mutation and copy number alterations. Our analysis revealed that MDI was significantly associated with tumor stage (<i>P</i> = 0.017). Across invasive breast tumor subtypes we observed significant differences in genome-wide DNA MDIs (<i>P</i> = 4.9E–09) and in a fraction of the genome with copy number alterations (FGA) (<i>P</i> = 4.6E–03). Results from a linear regression adjusted for subject age, tumor stage, and estimated tumor purity indicated a positive significant association of MDI with both MCB and FGA (<i>P</i> = 0.036 and <i>P</i> &lt; 2.2E–16). A recursively partitioned mixture model of all 3 somatic alteration burden measures resulted in classes of tumors whose epigenetic and genetic burden profile were associated with the PAM50 subtype and mutations in <i>TP53, PIK3CA, and CDH1</i>. Together, our work presents a novel framework for characterizing the epigenetic burden and adds to the understanding of the aggregate impact of epigenetic and genetic alterations in breast cancer.
DOI: 10.6084/m9.figshare.3172519
title: hfAIM: A reliable bioinformatics approach for in silico genome-wide identification of autophagy-associated Atg8-interacting motifs in various organisms

description: Most of the proteins that are specifically turned over by selective autophagy are recognized by the presence of short Atg8 interacting motifs (AIMs) that facilitate their association with the autophagy apparatus. Such AIMs can be identified by bioinformatics methods based on their defined degenerate consensus F/W/Y-X-X-L/I/V sequences in which X represents any amino acid. Achieving reliability and/or fidelity of the prediction of such AIMs on a genome-wide scale represents a major challenge. Here, we present a bioinformatics approach, high fidelity AIM (hfAIM), which uses additional sequence requirements—the presence of acidic amino acids and the absence of positively charged amino acids in certain positions—to reliably identify AIMs in proteins. We demonstrate that the use of the hfAIM method allows for in silico high fidelity prediction of AIMs in AIM-containing proteins (ACPs) on a genome-wide scale in various organisms. Furthermore, by using hfAIM to identify putative AIMs in the <i>Arabidopsis</i> proteome, we illustrate a potential contribution of selective autophagy to various biological processes. More specifically, we identified 9 peroxisomal PEX proteins that contain hfAIM motifs, among which AtPEX1, AtPEX6 and AtPEX10 possess evolutionary-conserved AIMs. Bimolecular fluorescence complementation (BiFC) results verified that AtPEX6 and AtPEX10 indeed interact with Atg8 <i>in planta</i>. In addition, we show that mutations occurring within or nearby hfAIMs in PEX1, PEX6 and PEX10 caused defects in the growth and development of various organisms. Taken together, the above results suggest that the hfAIM tool can be used to effectively perform genome-wide in silico screens of proteins that are potentially regulated by selective autophagy. The hfAIM system is a web tool that can be accessed at link: http://bioinformatics.psb.ugent.be/hfAIM/.
DOI: 10.6084/m9.figshare.3172519.v1
title: hfAIM: A reliable bioinformatics approach for in silico genome-wide identification of autophagy-associated Atg8-interacting motifs in various organisms

description: Most of the proteins that are specifically turned over by selective autophagy are recognized by the presence of short Atg8 interacting motifs (AIMs) that facilitate their association with the autophagy apparatus. Such AIMs can be identified by bioinformatics methods based on their defined degenerate consensus F/W/Y-X-X-L/I/V sequences in which X represents any amino acid. Achieving reliability and/or fidelity of the prediction of such AIMs on a genome-wide scale represents a major challenge. Here, we present a bioinformatics approach, high fidelity AIM (hfAIM), which uses additional sequence requirements—the presence of acidic amino acids and the absence of positively charged amino acids in certain positions—to reliably identify AIMs in proteins. We demonstrate that the use of the hfAIM method allows for in silico high fidelity prediction of AIMs in AIM-containing proteins (ACPs) on a genome-wide scale in various organisms. Furthermore, by using hfAIM to identify putative AIMs in the <i>Arabidopsis</i> proteome, we illustrate a potential contribution of selective autophagy to various biological processes. More specifically, we identified 9 peroxisomal PEX proteins that contain hfAIM motifs, among which AtPEX1, AtPEX6 and AtPEX10 possess evolutionary-conserved AIMs. Bimolecular fluorescence complementation (BiFC) results verified that AtPEX6 and AtPEX10 indeed interact with Atg8 <i>in planta</i>. In addition, we show that mutations occurring within or nearby hfAIMs in PEX1, PEX6 and PEX10 caused defects in the growth and development of various organisms. Taken together, the above results suggest that the hfAIM tool can be used to effectively perform genome-wide in silico screens of proteins that are potentially regulated by selective autophagy. The hfAIM system is a web tool that can be accessed at link: http://bioinformatics.psb.ugent.be/hfAIM/.
DOI: 10.6084/m9.figshare.3172450
title: Persistent asymmetrical priority effects in a California grassland restoration experiment

description: This priority experiment between native California grasses and forbs is reported on in the <i>Ecological Applications</i> paper, "Persistent asymmetrical priority effects in a California grassland restoration experiment" <b><br></b><br>
DOI: 10.6084/m9.figshare.3172468
title: Decreased snowpack and warmer temperatures reduce the negative effects of interspecific competitors on regenerating conifers

description: Data for survival and size of conifer seedlings in a competition by weather experiment. Data collected from ibuttons to establish snowpack duration. R markdown file used for data analysis and figures in article.
DOI: 10.6084/m9.figshare.3172468.v1
title: Decreased snowpack and warmer temperatures reduce the negative effects of interspecific competitors on regenerating conifers

description: Data for survival and size of conifer seedlings in a competition by weather experiment. Data collected from ibuttons to establish snowpack duration. R markdown file used for data analysis and figures in article.
DOI: 10.6084/m9.figshare.3172297
title: Splenectomised patients in the ED: Do you adequatly adress these patients? http://www.egms.de/static/de/journals/gms/2016-14/000237.shtml

description: This figure illustrates the article: The sword of Damokles for the splenectomised: death by OPSI.<br>
DOI: 10.6084/m9.figshare.3172450.v1
title: Treatment_Through_Time.xls

description: Grass/Forb priority experiment planted in 2008. <br>Treatments are forb only (F), grass only (G), grasses and forbs planted simultaneously (B), forbs then grasses added one year later (FG), grass then forbs added one year later (GF), and an unseeded control (C). <br>Year is the number of years after the initial seeding when the survey took place. Data was collected 1, 2, 3, and 8 years after initial seeding. <br>The rest of the columns are visual estimates of species cover. SP (Stipa pulchra), PS (Poa secunda), KM (Koeleria macrantha), HB (Hordeum brachyantherum), AM (Achillea millefolium), CC (Calandrinia ciliata), LP (Lotus purshianus), LF (Lupinus formosus).<br><br>
DOI: 10.6084/m9.figshare.3172297.v1
title: Splenectomised patients in the ED: Do you adequatly adress these patients? http://www.egms.de/static/de/journals/gms/2016-14/000237.shtml

description: This figure illustrates the article: The sword of Damokles for the splenectomised: death by OPSI.<br>
DOI: 10.6084/m9.figshare.3172291
title: Improving the reproducibility of voluntary deep inspiration breath hold technique during adjuvant left-sided breast cancer radiotherapy

description: <b>Background</b>: Adjuvant radiotherapy (RT) of left-sided breast cancer (LSBC) with voluntary deep inspiration breath hold (vDIBH) technique reduces the cardiac dose. In this study, the effect of marker block position and the efficacy of breath hold level (BHL) correction based on lateral kV setup images are evaluated to improve the daily reproducibility. <b>Material and methods</b>: A total of 148 consecutive LSBC patients treated with vDIBH RT were included in this study. The real-time position management (RPM) marker block was placed on the abdominal wall in 63 patients (group A) and on the sternum in 85 patients (group S). Acquired 900 (group A) + 1040 (group S) orthogonal image pairs were retrospectively analyzed. The actual BHL was determined from the lateral kV images. The height of the BHL gating window in RPM was corrected if errors of the actual BHL exceeded 4 mm. Setup margins were calculated for the chest wall and for bony surrogates of the lymph node regions. <b>Results</b>: The sternal marker block reduced the random residual errors in the actual BHL (p Conclusions: Reproducibility of the BHL can be improved by placing the marker block on the sternum and correcting the height of the BHL window based on lateral kV setup images. Acquisition of lateral kV images in the first 3 fractions and once a week during RT is recommended.
DOI: 10.6084/m9.figshare.3172450.v2
title: Treatment_Through_Time.xls

description: This priority experiment between native California grasses and forbs is reported on in the <i>Ecological Applications</i> paper, "Persistent asymmetrical priority effects in a California grassland restoration experiment" <b><br></b><b>Treatment_Through_Time.xls</b>[Note that this dataset overlaps with Survey2015.xls, but includes only one starting planting year (2008) and monitoring surveys in 2009, 2010, 2011, and 2015.]<br><br>Treatment is forb only (F), grass only (G), grasses and forbs planted simultaneously (B), forbs then grasses added one year later (FG), grass then forbs added one year later (GF), and an unseeded control (C). <br>Year is the number of years after the initial seeding when the survey took place. Data was collected 1, 2, 3, and 8 years after initial seeding. <br>The rest of the columns are visual estimates of species cover. SP (Stipa pulchra), PS (Poa secunda), KM (Koeleria macrantha), HB (Hordeum brachyantherum), AM (Achillea millefolium), CC (Calandrinia ciliata), LP (Lotus purshianus), LF (Lupinus formosus).<br><b>Survey2015.xls</b>[Note: this dataset overlaps with that in Treatment_Through_Time, but includes all three planting years (2008, 2009, 2010) and only has survey data from 2015 (6-8 years after initial planting)]<br>Treatment is forb only (F), grass only (G), grasses and forbs planted simultaneously (B), forbs then grasses added one year later (FG), grass then forbs added one year later (GF), and an unseeded control (C). <br>PlantingYear is the year of experiment initiation (1 = 2008, 2 = 2009, 3 = 2010, 0 = unseeded control). <br>The rest of the columns are visual estimates of species cover. SP (Stipa pulchra), PS (Poa secunda), KM (Koeleria macrantha), HB (Hordeum brachyantherum), AM (Achillea millefolium), CC (Calandrinia ciliata), LP (Lotus purshianus), LF (Lupinus formosus). Weed is any exotic grass or forb, and Bare is bare ground. <br>
DOI: 10.6084/m9.figshare.3172291.v1
title: Improving the reproducibility of voluntary deep inspiration breath hold technique during adjuvant left-sided breast cancer radiotherapy

description: <b>Background</b>: Adjuvant radiotherapy (RT) of left-sided breast cancer (LSBC) with voluntary deep inspiration breath hold (vDIBH) technique reduces the cardiac dose. In this study, the effect of marker block position and the efficacy of breath hold level (BHL) correction based on lateral kV setup images are evaluated to improve the daily reproducibility. <b>Material and methods</b>: A total of 148 consecutive LSBC patients treated with vDIBH RT were included in this study. The real-time position management (RPM) marker block was placed on the abdominal wall in 63 patients (group A) and on the sternum in 85 patients (group S). Acquired 900 (group A) + 1040 (group S) orthogonal image pairs were retrospectively analyzed. The actual BHL was determined from the lateral kV images. The height of the BHL gating window in RPM was corrected if errors of the actual BHL exceeded 4 mm. Setup margins were calculated for the chest wall and for bony surrogates of the lymph node regions. <b>Results</b>: The sternal marker block reduced the random residual errors in the actual BHL (p Conclusions: Reproducibility of the BHL can be improved by placing the marker block on the sternum and correcting the height of the BHL window based on lateral kV setup images. Acquisition of lateral kV images in the first 3 fractions and once a week during RT is recommended.
DOI: 10.6084/m9.figshare.3172450.v4
title: Persistent asymmetrical priority effects in a California grassland restoration experiment

description: This priority experiment between native California grasses and forbs is reported on in the <i>Ecological Applications</i> paper, "Persistent asymmetrical priority effects in a California grassland restoration experiment" <b><br></b><br>
DOI: 10.6084/m9.figshare.3172450.v3
title: Persistent asymmetrical priority effects in a California grassland restoration experiment

description: This priority experiment between native California grasses and forbs is reported on in the <i>Ecological Applications</i> paper, "Persistent asymmetrical priority effects in a California grassland restoration experiment" <b><br></b><b>Treatment_Through_Time.xls</b>[Note that this dataset overlaps with Survey2015.xls, but includes only one starting planting year (2008) and monitoring surveys in 2009, 2010, 2011, and 2015.]<br><br>Treatment is forb only (F), grass only (G), grasses and forbs planted simultaneously (B), forbs then grasses added one year later (FG), grass then forbs added one year later (GF), and an unseeded control (C). <br>Year is the number of years after the initial seeding when the survey took place. Data was collected 1, 2, 3, and 8 years after initial seeding. <br>The rest of the columns are visual estimates of species cover. SP (Stipa pulchra), PS (Poa secunda), KM (Koeleria macrantha), HB (Hordeum brachyantherum), AM (Achillea millefolium), CC (Calandrinia ciliata), LP (Lotus purshianus), LF (Lupinus formosus).<br><b>Survey2015.xls</b>[Note: this dataset overlaps with that in Treatment_Through_Time, but includes all three planting years (2008, 2009, 2010) and only has survey data from 2015 (6-8 years after initial planting)]<br>Treatment is forb only (F), grass only (G), grasses and forbs planted simultaneously (B), forbs then grasses added one year later (FG), grass then forbs added one year later (GF), and an unseeded control (C). <br>PlantingYear is the year of experiment initiation (1 = 2008, 2 = 2009, 3 = 2010, 0 = unseeded control). <br>The rest of the columns are visual estimates of species cover. SP (Stipa pulchra), PS (Poa secunda), KM (Koeleria macrantha), HB (Hordeum brachyantherum), AM (Achillea millefolium), CC (Calandrinia ciliata), LP (Lotus purshianus), LF (Lupinus formosus). Weed is any exotic grass or forb, and Bare is bare ground. <br>
DOI: 10.18462/iir.rankine.2020.1151
title: Evaluation of heat recovery heat exchanger design parameters for heat-to-power conversion from metallurgical off-gas.
DOI: 10.6084/m9.figshare.3172057
title: A portable electronic system for in-situ measurements of oil concentration in MetalWorking fluids

description: MetalWorking Fluids (MWFs) are widely used to cool and lubricate machines and tools. By far, the most common MWFs are oil-in-water emulsions with oil concentration (C<sub>oil</sub>) in the range from 1% to 10% , depending on type of oil, material to be worked, etc. In order to optimize emulsion and machine performance, as well as for good waste policy, the right value of C<sub>oil </sub>should be kept (approximately) constant during the MWF’s lifecycle to compensate inevitable changes due to water evaporation, bacterial attack, oil adhesion to metal parts, etc.. This, however, requires periodic measurements, often skipped because they require unhandy operations and produce inaccurate results. In this context, a new system is presented<sub> </sub>that is based on the falling ball principle, normally used for viscosity measurements, shown to be suitable also for accurate C<sub>oil</sub> measurements. In our system, the transit time of the sphere within the instrument is determined by means of inductive proximity sensors, a PT100 sensor is used for temperature whose effects on C<sub>oil</sub> are accounted for by means of an ad-hoc algorithm. A battery-operated electronic board has been designed that allows rapid and user-friendly “in-situ” measurements and a prototype of an whole portable and automatic instrument, suitable for in-situ measurements, has been fabricated.
DOI: 10.6084/m9.figshare.3172057.v1
title: A portable electronic system for in-situ measurements of oil concentration in MetalWorking fluids

description: MetalWorking Fluids (MWFs) are widely used to cool and lubricate machines and tools. By far, the most common MWFs are oil-in-water emulsions with oil concentration (C<sub>oil</sub>) in the range from 1% to 10% , depending on type of oil, material to be worked, etc. In order to optimize emulsion and machine performance, as well as for good waste policy, the right value of C<sub>oil </sub>should be kept (approximately) constant during the MWF’s lifecycle to compensate inevitable changes due to water evaporation, bacterial attack, oil adhesion to metal parts, etc.. This, however, requires periodic measurements, often skipped because they require unhandy operations and produce inaccurate results. In this context, a new system is presented<sub> </sub>that is based on the falling ball principle, normally used for viscosity measurements, shown to be suitable also for accurate C<sub>oil</sub> measurements. In our system, the transit time of the sphere within the instrument is determined by means of inductive proximity sensors, a PT100 sensor is used for temperature whose effects on C<sub>oil</sub> are accounted for by means of an ad-hoc algorithm. A battery-operated electronic board has been designed that allows rapid and user-friendly “in-situ” measurements and a prototype of an whole portable and automatic instrument, suitable for in-situ measurements, has been fabricated.
DOI: 10.17045/sthlmuni.3171967
title: Tarfala meteorological data 2013

description: This file set contains the complete registered meteorological data from the "Tarfala met" AWS 2013. Included in the file set are the complete set of data split into files for each parameter, the original logger data, the Matlab program that takes the logger data and generates the parameter files and finally the report summarizing the data and any issues or changes made during the year.
DOI: 10.17045/sthlmuni.3171970
title: Tarfala meteorological data 2014

description: This file set contains the complete registered meteorological data from the "Tarfala met" AWS 2014. Included in the file set are the complete set of data split into files for each parameter, the original logger data, the Matlab program that takes the logger data and generates the parameter files and finally the report summarizing the data and any issues or changes made during the year. <br>
DOI: 10.17045/sthlmuni.3171964
title: Tarfala meteorological data 2012

description: This file set contains the complete registered meteorological data from the "Tarfala met" AWS 2012. Included in the file set are the complete set of data split into files for each parameter, the original logger data, the Matlab program that takes the logger data and generates the parameter files and finally the report summarizing the data and any issues or changes made during the year.
DOI: 10.17045/sthlmuni.3171970.v1
title: Tarfala meteorological data 2014

description: This file set contains the complete registered meteorological data from the "Tarfala met" AWS 2014. Included in the file set are the complete set of data split into files for each parameter, the original logger data, the Matlab program that takes the logger data and generates the parameter files and finally the report summarizing the data and any issues or changes made during the year. <br>
DOI: 10.17045/sthlmuni.3171964.v1
title: Tarfala meteorological data 2012

description: This file set contains the complete registered meteorological data from the "Tarfala met" AWS 2012. Included in the file set are the complete set of data split into files for each parameter, the original logger data, the Matlab program that takes the logger data and generates the parameter files and finally the report summarizing the data and any issues or changes made during the year.
DOI: 10.17045/sthlmuni.3171961
title: Tarfala meteorological data 2011

description: This file set contains the complete registered meteorological data from the "Tarfala met" AWS 2011. Included in the file set are the complete set of data split into files for each parameter, the original logger data, the Matlab program that takes the logger data and generates the parameter files and finally the report summarizing the data and any issues or changes made during the year.
DOI: 10.17045/sthlmuni.3171967.v1
title: Tarfala meteorological data 2013

description: This file set contains the complete registered meteorological data from the "Tarfala met" AWS 2013. Included in the file set are the complete set of data split into files for each parameter, the original logger data, the Matlab program that takes the logger data and generates the parameter files and finally the report summarizing the data and any issues or changes made during the year.
DOI: 10.17045/sthlmuni.3171949
title: Tarfala meteorological data 2008

description: This file set contains the complete registered meteorological data from the "Tarfala met" AWS 2008. Included in the file set are the complete set of data split into files for each parameter, the original logger data, the Matlab program that takes the logger data and generates the parameter files and finally the report summarizing the data and any issues or changes made during the year.
DOI: 10.17045/sthlmuni.3171952
title: Tarfala meteorological data 2009

description: This file set contains the complete registered meteorological data from the "Tarfala met" AWS 2009. Included in the file set are the complete set of data split into files for each parameter, the original logger data, the Matlab program that takes the logger data and generates the parameter files and finally the report summarizing the data and any issues or changes made during the year.
DOI: 10.17045/sthlmuni.3171958
title: Tarfala meteorological data 2010

description: This file set contains the complete registered meteorological data from the "Tarfala met" AWS 2010. Included in the file set are the complete set of data split into files for each parameter, the original logger data, the Matlab program that takes the logger data and generates the parameter files and finally the report summarizing the data and any issues or changes made during the year.