cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7398527
title: Supplementary Material for: Long Non-Coding RNA H19 Acts as an Estrogen Receptor Modulator that is Required for Endocrine Therapy Resistance in ER<sup>+</sup> Breast Cancer Cells

description: <b><i>Background/Aims:</i></b> Blocking estrogen signaling with endocrine therapies (Tamoxifen or Fulverstrant) is an effective treatment for Estrogen Receptor-<i>α</i> positive (ER<sup>+</sup>) breast cancer tumours. Unfortunately, development of endocrine therapy resistance (ETR) is a frequent event resulting in disease relapse and decreased overall patient survival. The long noncoding RNA, <i>H19</i>, was previously shown to play a significant role in estrogen-induced proliferation of both normal and malignant ER<sup>+</sup> breast epithelial cells. We hypothesized that <i>H19</i> expression is also important for the proliferation and survival of ETR cells<i>.</i> <b><i>Methods:</i></b> Here we utilized established ETR cell models; the Tamoxifen (Tam)-resistant LCC2 and the Fulvestrant and Tam cross-resistant LCC9 cells. Gain and loss of <i>H19</i> function were achieved through lentiviral transduction as well as pharmacological inhibitors of the Notch and c-Met receptor signaling pathways. The effects of altered <i>H19</i> expression on cell viability and ETR were assessed using three-dimensional (3D) organoid cultures and 2D co-cultures with low passage tumour-associated fbroblasts (TAFs). <b><i>Results:</i></b> Here we report that treating ETR cells with Tam or Fulvestrant increases <i>H19</i> expression and that it’s decreased expression overcomes resistance to Tam and Fulvestrant in these cells. Interestingly, <i>H19</i> expression is regulated by Notch and HGF signaling in the ETR cells and pharmacological inhibitors of Notch and c-MET signaling together significantly reverse resistance to Tam and Fulvestrant in an <i>H19</i>-dependent manner in these cells. Lastly, we demonstrate that <i>H19</i> regulates <i>ERα</i> expression at the transcript and protein levels in the ETR cells and that <i>H19</i> protects ERα against Fulvestrant-mediated downregulation of ERα protein. We also observed that blocking Notch and the c-MET receptor signaling also overcomes Fulvestrant and Tam resistance in 3D organoid cultures by decreasing ERα and <i>H19</i> expression in the ETR cells. <b><i>Conclusion:</i></b> In endocrine therapy resistant breast cancer cells Fulvestrant is ineffective in decreasing ERα levels. Our data suggest that in the ETR cells, <i>H19</i> expression acts as an ER modulator and that its levels and subsequently ERα levels can be substantially decreased by blocking Notch and c-MET receptor signaling. Consequently, treating ETR cells with these pharmacological inhibitors helps overcome resistance to Fulvestrant and Tamoxifen.
DOI: 10.6084/m9.figshare.7398530
title: Mecillinam susceptible and resistant isolates (annotated genomes)

description: Mecillinam susceptible isolate, MEC-S (EC38) prior to mecillinam treatmentmecillinam resistant isolate, MEC-R (EC39) after pivmecillinam treatment
DOI: 10.6084/m9.figshare.7398530.v1
title: Mecillinam susceptible and resistant isolates (annotated genomes)

description: Mecillinam susceptible isolate, MEC-S (EC38) prior to mecillinam treatmentmecillinam resistant isolate, MEC-R (EC39) after pivmecillinam treatment
DOI: 10.7284/119969
title: Rain Gauge data collected during research cruise OC1405B using a RM Young 50202 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7398524
title: Nonlinear regression models for heterogeneous data with massive outliers

description: The income or expenditure-related data sets are often nonlinear, heteroscedastic, skewed even after the transformation, and contain numerous outliers. We propose a class of robust nonlinear models that treat outlying observations effectively without removing them. For this purpose, case-specific parameters and a related penalty are employed to detect and modify the outliers systematically. We show how the existing nonlinear models such as smoothing splines and generalized additive models can be robustified by the case-specific parameters. Next, we extend the proposed methods to the heterogeneous models by incorporating unequal weights. The details of estimating the weights are provided. Two real data sets and simulated data sets show the potential of the proposed methods when the nature of the data is nonlinear with outlying observations.
DOI: 10.6084/m9.figshare.7398524.v1
title: Nonlinear regression models for heterogeneous data with massive outliers

description: The income or expenditure-related data sets are often nonlinear, heteroscedastic, skewed even after the transformation, and contain numerous outliers. We propose a class of robust nonlinear models that treat outlying observations effectively without removing them. For this purpose, case-specific parameters and a related penalty are employed to detect and modify the outliers systematically. We show how the existing nonlinear models such as smoothing splines and generalized additive models can be robustified by the case-specific parameters. Next, we extend the proposed methods to the heterogeneous models by incorporating unequal weights. The details of estimating the weights are provided. Two real data sets and simulated data sets show the potential of the proposed methods when the nature of the data is nonlinear with outlying observations.
DOI: 10.7284/119960
title: Singlebeam Echosounder data collected during research cruise OC1405B using a Knudsen 3260 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7398503
title: Appendix 1

description: This dataset contains: 'Appendix 1.0: Newsreel Data', 'Appendix 1.1: Primary Categories', 'Appendix 1.2: Secondary Categories'.
DOI: 10.6084/m9.figshare.7398503.v1
title: Appendix 1

description: This dataset contains: 'Appendix 1.0: Newsreel Data', 'Appendix 1.1: Primary Categories', 'Appendix 1.2: Secondary Categories'.
DOI: 10.7284/119962
title: Singlebeam Echosounder data collected during research cruise OC1405B using a Knudsen 3260 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7398476
title: Managing the severely impaired arm after stroke: a mixed-methods study with qualitative emphasis

description: <b>Purpose:</b> There is a paucity of research into self-management strategies employed by stroke survivors outside of formal rehabilitation. This study aimed to explore stroke survivors’ experiences of, and strategies for self-managing their severely impaired upper limb. <b>Materials and methods:</b> English-speaking stroke survivors whose upper limb had been non-functional at 3 months post-stroke took part in interviews (<i>n</i> = 16), a focus group (<i>n</i> = 6) and a survey (<i>n</i> = 20). Quantitative data were analysed descriptively. Qualitative data were analysed through thematic framework analysis using NVivo<sup>©</sup> software. <b>Results:</b> Participants’ median (range) age group was 50–59 years (30–39, 70+). Median (range) time post-stroke was 39 months (4 months, 46 years). The overarching theme across the data was “choosing and expanding.” Participants enacted professionally driven management strategies for their affected arm, and then chose to continue with what worked for them. Strategies were expanded through self-discovery and interaction with peers. There were sadness and frustration at the loss of arm function, but also satisfaction and self-confidence when progress was being made. Participants described an attitude of not giving up and remaining hopeful. <b>Conclusions:</b> These findings extend our understanding about how individuals manage their severely impaired upper limb and can be used to inform a novel stroke self-management intervention.Implications for rehabilitationStroke survivors’ experiences of managing the severely affected upper limb may inform rehabilitation practice to foster self-management.Rehabilitation professionals may actively support stroke survivors in choosing from, and expanding on professionals’ advice and guidance.Maintaining a positive and hopeful outlook is important to many stroke survivors. Professionals should be mindful of the potential impact of their interactions and negative predictions.Stroke survivors’ experiences of managing the severely affected upper limb may inform the development of a novel tailored self-management intervention. Stroke survivors’ experiences of managing the severely affected upper limb may inform rehabilitation practice to foster self-management. Rehabilitation professionals may actively support stroke survivors in choosing from, and expanding on professionals’ advice and guidance. Maintaining a positive and hopeful outlook is important to many stroke survivors. Professionals should be mindful of the potential impact of their interactions and negative predictions. Stroke survivors’ experiences of managing the severely affected upper limb may inform the development of a novel tailored self-management intervention.
DOI: 10.6084/m9.figshare.7398476.v1
title: Managing the severely impaired arm after stroke: a mixed-methods study with qualitative emphasis

description: <b>Purpose:</b> There is a paucity of research into self-management strategies employed by stroke survivors outside of formal rehabilitation. This study aimed to explore stroke survivors’ experiences of, and strategies for self-managing their severely impaired upper limb. <b>Materials and methods:</b> English-speaking stroke survivors whose upper limb had been non-functional at 3 months post-stroke took part in interviews (<i>n</i> = 16), a focus group (<i>n</i> = 6) and a survey (<i>n</i> = 20). Quantitative data were analysed descriptively. Qualitative data were analysed through thematic framework analysis using NVivo<sup>©</sup> software. <b>Results:</b> Participants’ median (range) age group was 50–59 years (30–39, 70+). Median (range) time post-stroke was 39 months (4 months, 46 years). The overarching theme across the data was “choosing and expanding.” Participants enacted professionally driven management strategies for their affected arm, and then chose to continue with what worked for them. Strategies were expanded through self-discovery and interaction with peers. There were sadness and frustration at the loss of arm function, but also satisfaction and self-confidence when progress was being made. Participants described an attitude of not giving up and remaining hopeful. <b>Conclusions:</b> These findings extend our understanding about how individuals manage their severely impaired upper limb and can be used to inform a novel stroke self-management intervention.Implications for rehabilitationStroke survivors’ experiences of managing the severely affected upper limb may inform rehabilitation practice to foster self-management.Rehabilitation professionals may actively support stroke survivors in choosing from, and expanding on professionals’ advice and guidance.Maintaining a positive and hopeful outlook is important to many stroke survivors. Professionals should be mindful of the potential impact of their interactions and negative predictions.Stroke survivors’ experiences of managing the severely affected upper limb may inform the development of a novel tailored self-management intervention. Stroke survivors’ experiences of managing the severely affected upper limb may inform rehabilitation practice to foster self-management. Rehabilitation professionals may actively support stroke survivors in choosing from, and expanding on professionals’ advice and guidance. Maintaining a positive and hopeful outlook is important to many stroke survivors. Professionals should be mindful of the potential impact of their interactions and negative predictions. Stroke survivors’ experiences of managing the severely affected upper limb may inform the development of a novel tailored self-management intervention.
DOI: 10.7284/119970
title: Speedlog data collected during research cruise OC1405B using a Furuno DS-50 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/119958
title: Water Temperature data collected during research cruise OC1405B using a Sea-Bird SBE-48 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7398458
title: Additional file 8: of Comparative genomics of downy mildews reveals potential adaptations to biotrophy

description: ORF annotation results. Summary of the results from hmm search and regular expression string searches when applied to all open reading frames of both P. effusa isolates. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.7398458.v1
title: Additional file 8: of Comparative genomics of downy mildews reveals potential adaptations to biotrophy

description: ORF annotation results. Summary of the results from hmm search and regular expression string searches when applied to all open reading frames of both P. effusa isolates. (XLSX 8 kb)
DOI: 10.7284/119971
title: Water Temperature data collected during research cruise OC1405B using a Sea-Bird SBE-38 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7398446
title: Additional file 6: of Comparative genomics of downy mildews reveals potential adaptations to biotrophy

description: Intermediate annotation results. Summary of maker runs bootstrapping SNAP hidden markov model. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.7398449
title: Additional file 7: of High-throughput sequencing of small RNAs revealed the diversified cold-responsive pathways during cold stress in the wild banana (Musa itinerans)

description: Table S6. ta-siRNA mapped to Banana Genome A. (XLS 42 kb)
DOI: 10.6084/m9.figshare.7398443
title: Additional file 6: of High-throughput sequencing of small RNAs revealed the diversified cold-responsive pathways during cold stress in the wild banana (Musa itinerans)

description: Table S5. Detailed information of identified novel miRNAs mapped to Banana Genome A. (XLS 56 kb)
DOI: 10.6084/m9.figshare.7398446.v1
title: Additional file 6: of Comparative genomics of downy mildews reveals potential adaptations to biotrophy

description: Intermediate annotation results. Summary of maker runs bootstrapping SNAP hidden markov model. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.7398449.v1
title: Additional file 7: of High-throughput sequencing of small RNAs revealed the diversified cold-responsive pathways during cold stress in the wild banana (Musa itinerans)

description: Table S6. ta-siRNA mapped to Banana Genome A. (XLS 42 kb)
DOI: 10.7284/119972
title: Transmissometer data collected during research cruise OC1405B using a WET Labs C-Star instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7398437
title: Additional file 5: of High-throughput sequencing of small RNAs revealed the diversified cold-responsive pathways during cold stress in the wild banana (Musa itinerans)

description: Table S4. Detailed information of the known miRNAs mapped to Banana Genome A. (XLS 156 kb)
DOI: 10.6084/m9.figshare.7398443.v1
title: Additional file 6: of High-throughput sequencing of small RNAs revealed the diversified cold-responsive pathways during cold stress in the wild banana (Musa itinerans)

description: Table S5. Detailed information of identified novel miRNAs mapped to Banana Genome A. (XLS 56 kb)
DOI: 10.7284/119973
title: TSG (Thermosalinograph) data collected during research cruise OC1405B using a Sea-Bird SBE-45 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7398431
title: Additional file 4: of High-throughput sequencing of small RNAs revealed the diversified cold-responsive pathways during cold stress in the wild banana (Musa itinerans)

description: Table S3. The length distribution of sequencing reads from the 4 small RNA libraries. (XLS 24 kb)
DOI: 10.6084/m9.figshare.7398434
title: Additional file 4: of Comparative genomics of downy mildews reveals potential adaptations to biotrophy

description: RepeatModeler summary of outputs. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.7398437.v1
title: Additional file 5: of High-throughput sequencing of small RNAs revealed the diversified cold-responsive pathways during cold stress in the wild banana (Musa itinerans)

description: Table S4. Detailed information of the known miRNAs mapped to Banana Genome A. (XLS 156 kb)
DOI: 10.6084/m9.figshare.7398434.v1
title: Additional file 4: of Comparative genomics of downy mildews reveals potential adaptations to biotrophy

description: RepeatModeler summary of outputs. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.7398425
title: Additional file 3: of High-throughput sequencing of small RNAs revealed the diversified cold-responsive pathways during cold stress in the wild banana (Musa itinerans)

description: Table S2. Numbers of reads for each small RNA classification identified, the map of known, novel miRNA. (XLS 16 kb)
DOI: 10.6084/m9.figshare.7398431.v1
title: Additional file 4: of High-throughput sequencing of small RNAs revealed the diversified cold-responsive pathways during cold stress in the wild banana (Musa itinerans)

description: Table S3. The length distribution of sequencing reads from the 4 small RNA libraries. (XLS 24 kb)
DOI: 10.7284/119991
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise OC1406A using a Hawaii UHDAS instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7398422
title: Additional file 3: of Comparative genomics of downy mildews reveals potential adaptations to biotrophy

description: JELLYFISH histogram outputs and line plots. (7Z 171 kb)
DOI: 10.6084/m9.figshare.7398425.v1
title: Additional file 3: of High-throughput sequencing of small RNAs revealed the diversified cold-responsive pathways during cold stress in the wild banana (Musa itinerans)

description: Table S2. Numbers of reads for each small RNA classification identified, the map of known, novel miRNA. (XLS 16 kb)
DOI: 10.6084/m9.figshare.7398419
title: Additional file 2: of Comparative genomics of downy mildews reveals potential adaptations to biotrophy

description: Intermediate assembly statistics and REAPR scores. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.7398419.v1
title: Additional file 2: of Comparative genomics of downy mildews reveals potential adaptations to biotrophy

description: Intermediate assembly statistics and REAPR scores. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.7398422.v1
title: Additional file 3: of Comparative genomics of downy mildews reveals potential adaptations to biotrophy

description: JELLYFISH histogram outputs and line plots. (7Z 171 kb)
DOI: 10.6084/m9.figshare.7398416
title: Additional file 2: of High-throughput sequencing of small RNAs revealed the diversified cold-responsive pathways during cold stress in the wild banana (Musa itinerans)

description: Table S1. The results of sRNA sequences from four wild banana libraries mapped to genome A. (XLS 21 kb)
DOI: 10.7284/119978
title: Anemometer data collected during research cruise OC1406A using a Gill WindObserver II instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7398416.v1
title: Additional file 2: of High-throughput sequencing of small RNAs revealed the diversified cold-responsive pathways during cold stress in the wild banana (Musa itinerans)

description: Table S1. The results of sRNA sequences from four wild banana libraries mapped to genome A. (XLS 21 kb)
DOI: 10.6084/m9.figshare.7398407
title: Additional file 21: of High-throughput sequencing of small RNAs revealed the diversified cold-responsive pathways during cold stress in the wild banana (Musa itinerans)

description: Table S13. The primers used in this study. (XLS 27 kb)
DOI: 10.6084/m9.figshare.7398407.v1
title: Additional file 21: of High-throughput sequencing of small RNAs revealed the diversified cold-responsive pathways during cold stress in the wild banana (Musa itinerans)

description: Table S13. The primers used in this study. (XLS 27 kb)
DOI: 10.7284/119980
title: Fluorometer data collected during research cruise OC1406A using a WET Labs WETStar instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7398398
title: Additional file 15: of Comparative genomics of downy mildews reveals potential adaptations to biotrophy

description: BUSCO alignments used to create Fig. 5. The alignments are not concatenated. Note: .7z files can be accessed by downloading 7zip. This software is free and available at https://www.7-zip.org/ . (7Z 50 kb)
DOI: 10.7284/117343
title: GNSS (Global Navigation Satellite System) data collected during research cruise OC1406A using a Ashtech ADU5 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7398398.v1
title: Additional file 15: of Comparative genomics of downy mildews reveals potential adaptations to biotrophy

description: BUSCO alignments used to create Fig. 5. The alignments are not concatenated. Note: .7z files can be accessed by downloading 7zip. This software is free and available at https://www.7-zip.org/ . (7Z 50 kb)
DOI: 10.7284/119981
title: Gyrocompass data collected during research cruise OC1406A using a Sperry MK-37 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/119983
title: Hygrometer data collected during research cruise OC1406A using a Vaisala HMT300 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7398368
title: Additional file 13: of Comparative genomics of downy mildews reveals potential adaptations to biotrophy

description: Orthogroup overview. Listing all the orthogroups identified and the genes they contain, which were plotted in Fig. 4. To query P. effusa proteins in GenBank, substitute PeffR13 with DD237, PeffR14 with DD238 and remove the -RA suffix. (7Z 21 kb)
DOI: 10.7284/119982
title: PTU (Pressure, Temperature, Humidity) data collected during research cruise OC1406A using a Vaisala PTU300 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7398368.v1
title: Additional file 13: of Comparative genomics of downy mildews reveals potential adaptations to biotrophy

description: Orthogroup overview. Listing all the orthogroups identified and the genes they contain, which were plotted in Fig. 4. To query P. effusa proteins in GenBank, substitute PeffR13 with DD237, PeffR14 with DD238 and remove the -RA suffix. (7Z 21 kb)
DOI: 10.6084/m9.figshare.7398359
title: Additional file 12: of Comparative genomics of downy mildews reveals potential adaptations to biotrophy

description: Orthogroups unique to Peronospora spp. Details sequence names of all proteins inferred as being orthologous only between P. effusa and P. tabacina. To query P. effusa proteins in GenBank, substitute PeffR13 with DD237, PeffR14 with DD238 and remove the -RA suffix. (XLSX 10 kb)