cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7334633
title: Supplementary Material for: Mismatch Repair Deficiency Drives Durable Complete Remission by Targeting Programmed Death Receptor 1 in a Metastatic Luminal Breast Cancer Patient

description: <b><i>Background:</i></b> In the field of breast cancer tumor biology, triple-negative breast cancer patients are the main focus of current clinical trials exploring the use of immune checkpoint inhibitors due to higher frequencies of somatic mutations, neoantigens, and resulting tumor-specific T-cell reactivity. <b><i>Case Report:</i></b> Here, we present the case of a 66-year-old woman with metastatic luminal breast cancer that rapidly responded to monotherapy with pembrolizumab, a monoclonal anti-PD-1 antibody. This patient obtained a partial clinical response within the first cycle of treatment and an ongoing durable complete remission after 12 weeks. Except for a transient immune-related thyreoiditis, there were no side effects observed offering remarkable quality of life to the patient. To evaluate the underlying mechanisms, we performed immunohistochemistry, explored the mutational landscape by whole-exome sequencing, and identified potential T-cell epitopes by prediction of neoantigens with high affinity binding to one of the patient's HLA. Briefly, we found a strong infiltration of CD8+ T cells without staining for PD-L1 in the tumor stroma. Exome sequencing revealed an enormous frequency of somatic and tumor-specific alterations, mainly C&gt;T/G&gt;A transitions. The mutational pattern was further linked to genome instability and deficient mismatch repair supported by the loss of MSH6 protein expression and therefore leading to susceptibility to immune checkpoint blockade. <b><i>Conclusion:</i></b> Within the overall goal to establish operating procedures for breast cancer immunotherapy, we propose to re-evaluate testing for deficient mismatch repair and to further intensify the search for biomarkers predictive for the success of immune checkpoint modulation including all tumor biologic subtypes of breast cancer.
DOI: 10.6084/m9.figshare.7334633.v1
title: Supplementary Material for: Mismatch Repair Deficiency Drives Durable Complete Remission by Targeting Programmed Death Receptor 1 in a Metastatic Luminal Breast Cancer Patient

description: <b><i>Background:</i></b> In the field of breast cancer tumor biology, triple-negative breast cancer patients are the main focus of current clinical trials exploring the use of immune checkpoint inhibitors due to higher frequencies of somatic mutations, neoantigens, and resulting tumor-specific T-cell reactivity. <b><i>Case Report:</i></b> Here, we present the case of a 66-year-old woman with metastatic luminal breast cancer that rapidly responded to monotherapy with pembrolizumab, a monoclonal anti-PD-1 antibody. This patient obtained a partial clinical response within the first cycle of treatment and an ongoing durable complete remission after 12 weeks. Except for a transient immune-related thyreoiditis, there were no side effects observed offering remarkable quality of life to the patient. To evaluate the underlying mechanisms, we performed immunohistochemistry, explored the mutational landscape by whole-exome sequencing, and identified potential T-cell epitopes by prediction of neoantigens with high affinity binding to one of the patient's HLA. Briefly, we found a strong infiltration of CD8+ T cells without staining for PD-L1 in the tumor stroma. Exome sequencing revealed an enormous frequency of somatic and tumor-specific alterations, mainly C&gt;T/G&gt;A transitions. The mutational pattern was further linked to genome instability and deficient mismatch repair supported by the loss of MSH6 protein expression and therefore leading to susceptibility to immune checkpoint blockade. <b><i>Conclusion:</i></b> Within the overall goal to establish operating procedures for breast cancer immunotherapy, we propose to re-evaluate testing for deficient mismatch repair and to further intensify the search for biomarkers predictive for the success of immune checkpoint modulation including all tumor biologic subtypes of breast cancer.
DOI: 10.6084/m9.figshare.7334618
title: Comparative transcriptome profiles of Lindian chicken eyelids identify melanin genes controlling eyelid pigmentation

description: 1. During the long history of chicken domestication, eyelid colour, like skin colour and shank colour, has been one of the physical traits of Chinese indigenous chickens that influence consumer buying behaviour. In China, the Lindian chicken, which has coloured feathers, is renowned for the appetizing flavour of its meat and eggs, and its eyelid colours vary from deep (black) to light shades (light yellow). 2. To investigate genes involved in eyelid colour, the expression profiles of black and light-yellow eyelids of Lindian chickens were analysed with transcriptome sequencing. 3. A total of 13 466 genes were detected in the eyelids, among which 14 were differentially expressed. Among these differentially expressed genes (DEGs), three key genes, premelanosome protein (<i>PMEL</i>), dopachrome tautomerase (<i>DCT</i>), and tyrosinase (<i>TYR</i>), encoded proteins that positively regulate melanogenesis and melanin deposition. <i>PMEL, DCT</i> and <i>TYR</i> were expressed much more strongly in the black eyelids than in the light-yellow eyelids. A Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that tyrosine metabolism and melanogenesis genes were significantly enriched among these DEGs (corrected <i>P</i> 4. In conclusion, melanin may be one of the main factors involved in Lindian chicken eyelid colour. Furthermore, these results provide a valuable resource for the future study of the physical traits of Lindian chicken.
DOI: 10.7284/104680
title: Gyrocompass data collected during research cruise RR1115 using a iXSea Hydrins instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.23645/epacomptox.7334603
title: Neurotoxicant literature

description: This Excel macro-enabled workbook contains a list of chemicals affecting the nervous system. The construction of the file is described in the manuscript “Connecting Environmental Exposure and Neurodegeneration using Cheminformatics and High Resolution Mass Spectrometry: Potential and Challenges” available at http://doi.org/10.1039/C9EM00068B. The chemicals are MeSH terms and the links to the nervous system are determined by co-occurrences of MeSH terms in PubMed. DSSToxIDs and CAS are added where available.
DOI: 10.23645/epacomptox.7334603.v1
title: Neurotoxicant literature

description: This Excel macro-enabled workbook contains a list of chemicals affecting the nervous system. The construction of the file is described in the manuscript “Connecting Environmental Exposure and Neurodegeneration using Cheminformatics and High Resolution Mass Spectrometry: Potential and Challenges” available at http://doi.org/10.1039/C9EM00068B. The chemicals are MeSH terms and the links to the nervous system are determined by co-occurrences of MeSH terms in PubMed. DSSToxIDs and CAS are added where available.
DOI: 10.6084/m9.figshare.7334618.v2
title: Comparative transcriptome profiles of Lindian chicken eyelids identify melanin genes controlling eyelid pigmentation

description: 1. During the long history of chicken domestication, eyelid colour, like skin colour and shank colour, has been one of the physical traits of Chinese indigenous chickens that influence consumer buying behaviour. In China, the Lindian chicken, which has coloured feathers, is renowned for the appetizing flavour of its meat and eggs, and its eyelid colours vary from deep (black) to light shades (light yellow). 2. To investigate genes involved in eyelid colour, the expression profiles of black and light-yellow eyelids of Lindian chickens were analysed with transcriptome sequencing. 3. A total of 13 466 genes were detected in the eyelids, among which 14 were differentially expressed. Among these differentially expressed genes (DEGs), three key genes, premelanosome protein (<i>PMEL</i>), dopachrome tautomerase (<i>DCT</i>), and tyrosinase (<i>TYR</i>), encoded proteins that positively regulate melanogenesis and melanin deposition. <i>PMEL, DCT</i> and <i>TYR</i> were expressed much more strongly in the black eyelids than in the light-yellow eyelids. A Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that tyrosine metabolism and melanogenesis genes were significantly enriched among these DEGs (corrected <i>P</i> 4. In conclusion, melanin may be one of the main factors involved in Lindian chicken eyelid colour. Furthermore, these results provide a valuable resource for the future study of the physical traits of Lindian chicken.
DOI: 10.7284/104684
title: Gyrocompass data collected during research cruise RR1115 using a iXSea Phins instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/103778
title: Meteorological Station data collected during research cruise RR1115 using a SIO MET-System instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7334549
title: Primary repellents review

description: We surveyed the Web of Science database using the keywords “repellent”, “deterrent”, “deter” and “repel”. We focused on terrestrial mammals and included publications dealing with the use or development of chemical or semiochemical primary repellents to deal with herbivore and carnivore mammals, excluding reviews and commentaries. First, as a measure of repellents efficacy, we collected all available empirical data measuring a) the amount of food consumed by target species exposed to a repellent, b) the number of trespassing events in an area treated with a repellent, and c) the approach distance to a repellent source or the time spent in a treated area, with a BACI approach, before and after a chemical or semiochemical repellent was applied. Then weadded 0.1 to every value and calculated a repellency ratio between measures using the repellent over the control situation (repellent/control) and standardized it by using ln in order to avoid over dispersion (after Moreira-Arce et al. 2018)
DOI: 10.7284/103782
title: Multibeam Echosounder data collected during research cruise RR1115 using a Kongsberg EM122 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7334549.v1
title: Primary repellents review

description: We surveyed the Web of Science database using the keywords “repellent”, “deterrent”, “deter” and “repel”. We focused on terrestrial mammals and included publications dealing with the use or development of chemical or semiochemical primary repellents to deal with herbivore and carnivore mammals, excluding reviews and commentaries. First, as a measure of repellents efficacy, we collected all available empirical data measuring a) the amount of food consumed by target species exposed to a repellent, b) the number of trespassing events in an area treated with a repellent, and c) the approach distance to a repellent source or the time spent in a treated area, with a BACI approach, before and after a chemical or semiochemical repellent was applied. Then weadded 0.1 to every value and calculated a repellency ratio between measures using the repellent over the control situation (repellent/control) and standardized it by using ln in order to avoid over dispersion (after Moreira-Arce et al. 2018)
DOI: 10.6084/m9.figshare.7334546
title: Raw data -LncRNA Analysis of Lung Tissues after hUC-MSCandFTY720 Treatment of Lipopolysaccharide-induced Acute Lung Injury in Mice

description: <b>Methods</b>. We built a lipopolysaccharide (LPS)-induced ALI model in mice. After treatment with hUC-MSCs, FTY720, or a combination of hUC-MSCs and FTY207, the lung inflammatory response was apparently attenuated. To understand the mechanism underlying MSC treatment of ALI at the genetic level, significant differentially expressed long non-coding RNAs (lncRNAs) between the treatment and model groups were analyzed using microarray technology. Moreover, genetic gene prediction, gene ontology (GO) analysis, pathway analysis, and transcription factor (TF) prediction were carried out.The research procedures were approved by the Affiliated Hospital of Military Medical Science Scientific Research Ethics Committee.（IRB Approval number: ky-2015-3-7）
DOI: 10.6084/m9.figshare.7334546.v1
title: Raw data -LncRNA Analysis of Lung Tissues after hUC-MSCandFTY720 Treatment of Lipopolysaccharide-induced Acute Lung Injury in Mice

description: <b>Methods</b>. We built a lipopolysaccharide (LPS)-induced ALI model in mice. After treatment with hUC-MSCs, FTY720, or a combination of hUC-MSCs and FTY207, the lung inflammatory response was apparently attenuated. To understand the mechanism underlying MSC treatment of ALI at the genetic level, significant differentially expressed long non-coding RNAs (lncRNAs) between the treatment and model groups were analyzed using microarray technology. Moreover, genetic gene prediction, gene ontology (GO) analysis, pathway analysis, and transcription factor (TF) prediction were carried out.The research procedures were approved by the Affiliated Hospital of Military Medical Science Scientific Research Ethics Committee.（IRB Approval number: ky-2015-3-7）
DOI: 10.7284/103783
title: Singlebeam Echosounder data collected during research cruise RR1115 using a Knudsen 3260 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/104707
title: Winch data collected during research cruise RR1115 using a Markey DUSH-5 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/104717
title: Winch data collected during research cruise RR1115 using a Markey DUTW-9-11 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/103790
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise RR1116 using a Hawaii UHDAS instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/103789
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise RR1116 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/110555
title: Expendable Probe data collected during research cruise RR1116 using a Turo Quoll instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7334447
title: MAASAI_GAIT_PERCEPTION

description: Maasai male and female strength and attractiveness ratings of strong and weak British male walkers<br>
DOI: 10.7284/103785
title: GNSS (Global Navigation Satellite System) data collected during research cruise RR1116 using a Ashtech ADU2 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7334447.v1
title: MAASAI_GAIT_PERCEPTION.xlsx

description: Maasai male and female strength and attractiveness ratings of strong and weak British male walkers<br>
DOI: 10.6084/m9.figshare.7334435
title: The Role of Interleukin-1 in the Pathogenesis of Cancer and its Potential as a Therapeutic Target in Clinical Practice

description: Full copyright for enhanced digital features is owned by the authors. <strong>Article full text</strong> <br> The full text of this article can be found <b>here</b>. <br> <br> <strong>Provide enhanced digital features for this article</strong><br> If you are an author of this publication and would like to provide additional enhanced digital features for your article then please contact adisrapidplus@springer.com.<br> <br> The journal offers a range of additional features designed to increase visibility and readership. All features will be thoroughly peer reviewed to ensure the content is of the highest scientific standard and all features are marked as ‘peer reviewed’ to ensure readers are aware that the content has been reviewed to the same level as the articles they are being presented alongside. Moreover, all sponsorship and disclosure information is included to provide complete transparency and adherence to good publication practices. This ensures that however the content is reached the reader has a full understanding of its origin. No fees are charged for hosting additional open access content.<br> <br> Other enhanced features include, but are not limited to:<br> • Slide decks<br> • Videos and animations<br> • Audio abstracts<br> • Audio slides <b> </b>
DOI: 10.6084/m9.figshare.7334435.v1
title: The Role of Interleukin-1 in the Pathogenesis of Cancer and its Potential as a Therapeutic Target in Clinical Practice

description: Full copyright for enhanced digital features is owned by the authors. <strong>Article full text</strong> <br> The full text of this article can be found <b>here</b>. <br> <br> <strong>Provide enhanced digital features for this article</strong><br> If you are an author of this publication and would like to provide additional enhanced digital features for your article then please contact adisrapidplus@springer.com.<br> <br> The journal offers a range of additional features designed to increase visibility and readership. All features will be thoroughly peer reviewed to ensure the content is of the highest scientific standard and all features are marked as ‘peer reviewed’ to ensure readers are aware that the content has been reviewed to the same level as the articles they are being presented alongside. Moreover, all sponsorship and disclosure information is included to provide complete transparency and adherence to good publication practices. This ensures that however the content is reached the reader has a full understanding of its origin. No fees are charged for hosting additional open access content.<br> <br> Other enhanced features include, but are not limited to:<br> • Slide decks<br> • Videos and animations<br> • Audio abstracts<br> • Audio slides <b> </b>
DOI: 10.7284/103793
title: GNSS (Global Navigation Satellite System) data collected during research cruise RR1116 using a Furuno GP-150 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/104687
title: GNSS (Global Navigation Satellite System) data collected during research cruise RR1116 using a Furuno GP-150 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/104690
title: GNSS (Global Navigation Satellite System) data collected during research cruise RR1116 using a Ashtech ADU2 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/104689
title: Gravimeter data collected during research cruise RR1116 using a Bell BGM-3 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/104688
title: Gyrocompass data collected during research cruise RR1116 using a iXSea Hydrins instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/104691
title: Gyrocompass data collected during research cruise RR1116 using a iXSea Phins instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/103787
title: Meteorological Station data collected during research cruise RR1116 using a SIO MET-System instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/103791
title: Multibeam Echosounder data collected during research cruise RR1116 using a Kongsberg EM122 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7334372
title: Supplementary Material for: Microarray Profiling of TGF-β1-Induced Long Non-Coding RNA Expression Patterns in Human Lung Bronchial Epithelial BEAS-2B Cells

description: <b><i>Background/Aims:</i></b> TGF-β1 mediated radiation-induced bystander effects (RIBE) have been linked with malignant transformation and tumorigenesis. However, the underlying mechanisms are not fully understood. <b><i>Methods:</i></b> To reveal new molecules of regulatory functions in this process, lncRNA microarray was performed to profile both lncRNA and mRNA expression patterns in human lung bronchial epithelial BEAS-2B cells treated with TGF-β1 at a concentration measured in the medium conditioned by directly irradiated BEAS-2B cells. The potential functions of the differentially expressed lncRNAs were predicted by GO and KEGG pathway analyses of their co-expressed mRNAs. Cis- and trans-regulation of the lncRNAs were analyzed and the interaction networks were constructed using Cytoscape. qRT-PCR was conducted to validate the results of microarray profiling. CCK-8 assay was employed for functional validation of 3 identified lncRNAs. <b><i>Results:</i></b> 224 lncRNAs were found to be dysregulated, among which 6 lncRNAs were chosen for expression validation by qRT-PCR assay. Pathway analyses showed that differentially expressed lncRNAs are highly correlated with cell proliferation, transformation, migration, <i>etc</i>. Trans-regulation analyses showed that the differentially expressed lncRNAs most likely participate in the pathways regulated by four transcriptional factors, FOS, STAT3, RAD21 and E2F1, which have been identified to be involved in the modulation of oncogenic transformation, cell cycle progression, genomic instability, <i>etc</i>. lnc-THEMIS-2 and lnc-ITGB6-4, predicted to be regulated by STAT3 and E2F1 respectively, were found to rescue the decrease of cell viability induced by TGF-β1 treatment. <b><i>Conclusion:</i></b> Our findings suggest that the differentially expressed lncRNAs induced by TGF-β1 play crucial roles in the oncogenic transformation and tumorigenesis, which provide a better understanding of the underlying mechanisms related to tumorigensis induced by LD/LDR radiations.
DOI: 10.7284/103792
title: Singlebeam Echosounder data collected during research cruise RR1116 using a Knudsen 3260 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/104708
title: Winch data collected during research cruise RR1116 using a Markey DUSH-5 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/104718
title: Winch data collected during research cruise RR1116 using a Markey DUTW-9-11 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition