cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7370150.v1
title: Additional file 10: Figure S6

description: Raw data used for creating Additional file 10: Figure S6 of the paper "A Label-free Multicolor Optical Surface Tomography (ALMOST) imaging method for nontransparent 3D samples". Files are combined in compressed 7-Zip archive(s).
DOI: 10.7284/130127
title: Anemometer data collected during research cruise OC1810A 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.7370135
title: Data from Better than expected: the influence of option expectations during decision-making

description: Our choices often arise from a consideration of options presented in a sequence (e.g. the products in a supermarket row). However, whether the precise sequential order of option presentation affects decision-making remains poorly understood. A recent model of choice proposes that, in a set of options presented sequentially, those that are better than expected will be perceived as more valuable, even when options are objectively equivalent within the set. Inspired by this proposal, we devised a novel decision-making task where we manipulated the order of option presentation together with expectations about option value. Even when we compared trials that were exactly equivalent except for option order, we observed a striking preference for options that were better than expected. Our findings show that expectations about options affect which option will be favoured within a sequence, an influence which is manifested as a preference for better-than-expected options. The findings have potential practical implications, as for example they may help policymakers in devising nudge strategies that rely on <i>ad-hoc</i> option orders.
DOI: 10.7284/130123
title: Fluorometer data collected during research cruise OC1810A using a WET Labs WETStar instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130128
title: GNSS (Global Navigation Satellite System) data collected during research cruise OC1810A using a Furuno GP-90 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7370090
title: Dam_data.xlsx

description: This is a original dam deformation data.
DOI: 10.6084/m9.figshare.7370093
title: Deciphering the molecular effects of romidepsin on germ cell tumors: DHRS2 involved in cell cycle arrest but not apoptosis or induction of romidepsin effectors

description: Testicular germ cell tumors mostly affect young men at age 17 – 40. Although high cure rates can be achieved by orchiectomy and chemotherapy, germ cell tumors can still be a lethal threat to young patients with metastases or therapy resistance. Thus, alternative treatment options are needed. Based on studies utilizing germ cell tumor cell lines, the histone deacetylase inhibitor romidepsin is a promising therapeutic option, showing high toxicity at very low doses towards cisplatin-resistant germ cell tumor cells, but not fibroblasts or Sertoli cells. In this study, we extended our analysis of the molecular effects of romidepsin to deepen our understanding of the underlying mechanisms. Patients will benefit from these analyses, since detailed knowledge of the romidepsin effects allows for a better risk and side-effect assessment.We screened for changes in histone acetylation of specific lysine residues and analyzed changes in the DNA methylation landscape after romidepsin treatment of the germ cell tumor proxy cell lines TCam-2, 2102EP, NCCIT and JAR, while human fibroblasts were used as controls. Additionally, we focused on the role of the dehydrogenase/reductase <i>DHRS2</i>, which was strongly upregulated in romidepsin treated cells, by generating <i>DHRS2</i>-deficient TCam-2 cells using CRISPR/Cas9 gene editing. We show that DHRS2 is dispensable for upregulation of romidepsin effectors (<i>GADD45B</i>,<i>DUSP1</i>, <i>ZFP36</i>, <i>ATF3</i>, <i>FOS</i>, <i>CDKN1A</i>,<i>ID2</i>) but contributes to induction of cell cycle arrest. Finally, we show that a combinatory treatment of romidepsin plus the gluccocorticoid dexamethasone further boosts expression of the romidepsin effectors and reduces viability of germ cell tumor cells more strongly than under single agent treatment. Thus, romidepsin and dexamethasone might represent a new combinatorial approach for treatment of GCT.
DOI: 10.7284/130134
title: GNSS (Global Navigation Satellite System) data collected during research cruise OC1810A 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.7370093.v1
title: Deciphering the molecular effects of romidepsin on germ cell tumors: DHRS2 involved in cell cycle arrest but not apoptosis or induction of romidepsin effectors

description: Testicular germ cell tumors mostly affect young men at age 17 – 40. Although high cure rates can be achieved by orchiectomy and chemotherapy, germ cell tumors can still be a lethal threat to young patients with metastases or therapy resistance. Thus, alternative treatment options are needed. Based on studies utilizing germ cell tumor cell lines, the histone deacetylase inhibitor romidepsin is a promising therapeutic option, showing high toxicity at very low doses towards cisplatin-resistant germ cell tumor cells, but not fibroblasts or Sertoli cells. In this study, we extended our analysis of the molecular effects of romidepsin to deepen our understanding of the underlying mechanisms. Patients will benefit from these analyses, since detailed knowledge of the romidepsin effects allows for a better risk and side-effect assessment.We screened for changes in histone acetylation of specific lysine residues and analyzed changes in the DNA methylation landscape after romidepsin treatment of the germ cell tumor proxy cell lines TCam-2, 2102EP, NCCIT and JAR, while human fibroblasts were used as controls. Additionally, we focused on the role of the dehydrogenase/reductase <i>DHRS2</i>, which was strongly upregulated in romidepsin treated cells, by generating <i>DHRS2</i>-deficient TCam-2 cells using CRISPR/Cas9 gene editing. We show that DHRS2 is dispensable for upregulation of romidepsin effectors (<i>GADD45B</i>,<i>DUSP1</i>, <i>ZFP36</i>, <i>ATF3</i>, <i>FOS</i>, <i>CDKN1A</i>,<i>ID2</i>) but contributes to induction of cell cycle arrest. Finally, we show that a combinatory treatment of romidepsin plus the gluccocorticoid dexamethasone further boosts expression of the romidepsin effectors and reduces viability of germ cell tumor cells more strongly than under single agent treatment. Thus, romidepsin and dexamethasone might represent a new combinatorial approach for treatment of GCT.
DOI: 10.6084/m9.figshare.7370081
title: Endosperm enzyme activity is responsible for texture and eating quality of cooked rice grains in Japanese cultivars

description: Eating quality of cooked rice grains is an important determinant of its market price and consumer acceptance. To comprehensively assess the variation of eating-quality traits in 152 Japanese rice cultivars, we evaluated activities of eight endosperm enzymes related to degradation of starch and cell-wall polysaccharides. Endosperm enzyme activities showed a wide range of variations and were lower in recently developed cultivars than in landraces and old improved cultivars. Activities of most endosperm enzymes correlated significantly with the eating-quality score and surface texture of cooked rice grains. Principal component analysis revealed that rice cultivars with high eating-quality scores had high stickiness of the grain surface and low levels of endosperm enzyme activities. These results suggest that endosperm enzyme activities control texture and eating quality of cooked rice grains in Japanese rice cultivars. Japanese rice cultivars with low endosperm enzyme activities showed high eating-quality scores and high stickiness of the surface of cooked grains.
DOI: 10.6084/m9.figshare.7370081.v1
title: Endosperm enzyme activity is responsible for texture and eating quality of cooked rice grains in Japanese cultivars

description: Eating quality of cooked rice grains is an important determinant of its market price and consumer acceptance. To comprehensively assess the variation of eating-quality traits in 152 Japanese rice cultivars, we evaluated activities of eight endosperm enzymes related to degradation of starch and cell-wall polysaccharides. Endosperm enzyme activities showed a wide range of variations and were lower in recently developed cultivars than in landraces and old improved cultivars. Activities of most endosperm enzymes correlated significantly with the eating-quality score and surface texture of cooked rice grains. Principal component analysis revealed that rice cultivars with high eating-quality scores had high stickiness of the grain surface and low levels of endosperm enzyme activities. These results suggest that endosperm enzyme activities control texture and eating quality of cooked rice grains in Japanese rice cultivars. Japanese rice cultivars with low endosperm enzyme activities showed high eating-quality scores and high stickiness of the surface of cooked grains.
DOI: 10.7284/130121
title: Gyrocompass data collected during research cruise OC1810A using a Sperry MK-37 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130122
title: PTU (Pressure, Temperature, Humidity) data collected during research cruise OC1810A using a Vaisala PTU300 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130125
title: Radiometer data collected during research cruise OC1810A using a RMR Co. PRP instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7370057
title: Methods documents for Livelihood Assessments in Trinidad and Tobago

description: Household questionnaires, community meeting discussion topics list and topics list for interviews with community-based organisations, used for the livelihoods assessment in communities surrounding protected areas in Trinidad and Tobago.
DOI: 10.6084/m9.figshare.7370057.v1
title: Methods documents for Livelihood Assessments in Trinidad and Tobago

description: Household questionnaires, community meeting discussion topics list and topics list for interviews with community-based organisations, used for the livelihoods assessment in communities surrounding protected areas in Trinidad and Tobago.
DOI: 10.7284/130126
title: Water Temperature data collected during research cruise OC1810A using a Sea-Bird SBE-38 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130132
title: Water Temperature data collected during research cruise OC1810A using a Sea-Bird SBE-48 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130131
title: Timeserver data collected during research cruise OC1810A using a Microsemi SyncServer S350 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130138
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise OC1810B 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.7369967.v1
title: Physiological and Genomic Analysis Reveals Candidate Genes Involved in Anthocyanin Biosynthesis in Colored-leaf Poplar ‘Caihong’ (Populus deltoides)

description: Leaf color is an important agronomic trait that contributes to the ornamental value of plants. However, the molecular mechanism of leaf coloration is still unclear. In our study, a colored-leaf poplar ‘Caihong’ (CHP, bright red leaves) and wild-type L2025 (green leaves) were used to explore the mechanism of leaf coloration by physiological and genomic analysis. Compared with leaves of L2025, leaves of CHP had a higher content of anthocyanins and a lower content of total Chl and carotenoids, and the ratio of anthocyanins to total Chl in CHP was more than 10 times of those in L2025, which may be the physiological reason why they show red leaf color. Based on the whole genome resequencing and bioinformatics analysis, eight structural genes and 20 regulatory genes associated with anthocyanin biosynthesis carrying more than five non-synonymous SNPs in coding regions were screened. These candidate genes were also identified according to the qRT-PCR analysis, and eight structural genes and three MYB family genes might play important roles in the leaf coloration of CHP. The above results could provide reference to explore the molecular regulation mechanism of leaf coloration in <i>Populus deltoids</i>, and also provided insight into coloration of other woody plants.
DOI: 10.7284/130141
title: Anemometer data collected during research cruise OC1810B 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.7369964
title: Sludge bioreactor microcosm study on complex bacterial communities and ecosystem function using 3-CA disturbance at varying frequencies for 35 days

description: Disturbance is known to affect ecosystem structure, but predicting its outcomes remains elusive. Similarly, community diversity is believed to relate to ecosystem functions, yet the underlying mechanisms are poorly understood. Here, we tested the effect of disturbance on the structure, assembly, and ecosystem function of complex microbial communities within an engineered system. We carried out a microcosm experiment where activated sludge bioreactors operated in daily cycles were subjected to eight different frequency levels of augmentation with a toxic pollutant, from never (undisturbed) to everyday (press-disturbed), for 35 days. Microbial communities were assessed by combining distance-based methods, general linear multivariate models, a-diversity indices, and null model analyses on metagenomics and 16S rRNA gene amplicon data. A stronger temporal decrease in a-diversity at the extreme, undisturbed and press-disturbed, ends of the disturbance range led to a hump-backed pattern, with the highest diversity found at intermediate levels of disturbance. Undisturbed and press-disturbed levels displayed the highest community and functional similarity across replicates, suggesting deterministic processes were dominating. The opposite was observed amongst intermediately disturbed levels, indicating stronger stochastic assembly mechanisms. Trade-offs were observed in ecosystem function between organic carbon removal and both nitrification and biomass productivity, as well as between diversity and these functions. Hence, not every ecosystem function was favoured by higher community diversity. Our results show that the assessment of changes in diversity, along with the underlying stochastic-deterministic assembly processes, is essential to understanding the impact of disturbance in complex microbial communities.
DOI: 10.6084/m9.figshare.7369943
title: Multi-drug resistance protein 2 (MRP2) expression, adjuvant tamoxifen therapy, and risk of breast cancer recurrence: a Danish population-based nested case-control study

description: <b>Background:</b> Adjuvant tamoxifen therapy approximately halves the risk of recurrence in estrogen receptor-positive (ER+) breast cancer patients, but many women respond insufficiently to therapy. Expression of multi-drug resistance protein 2 (MRP2) in breast cancer may potentiate tamoxifen resistance. Thus, we investigated the expression of MRP2 in breast cancer as a predictor of tamoxifen therapy effectiveness. <b>Material and methods:</b> We conducted a case-control study nested in the Danish Breast Cancer Group clinical database. The study included women aged 35–69 years diagnosed with stage l–lll breast cancer during 1985–2001, in Jutland, Denmark. We identified 541 recurrent breast cancers (cases) among women with estrogen receptor positive (ER+) disease treated with tamoxifen for at least 1 year (ER+/TAM+) and 300 cases among women with estrogen receptor-negative (ER−) disease, never treated with tamoxifen (ER−/TAM−). We matched one recurrence-free control to each recurrent case. We retrieved paraffin-embedded primary tumor tissue for all patients, and all available recurrent tumor tissue from pathology archives. MRP2 expression was evaluated using immunohistochemistry. We computed odds ratios (ORs) and 95% confidence intervals (95% CIs) associating MRP2 expression (positive vs. none) with breast cancer recurrence in conditional logistic regression models. We compared MRP2 expression in paired primary- and recurrent tumors. <b>Results:</b> MRP2 expression was more prevalent in the ER+/TAM + group, than in the ER−/TAM − group. No predictive utility of MRP2 for breast cancer recurrence was found in the ER+/TAM + group (OR<sub>adj</sub> = 0.96, 95% CI 0.70, 1.33). Further, no prognostic utility was found in the ER−/TAM − group (OR<sub>adj</sub> = 0.81, 95% CI 0.53, 1.23). MRP2 expression was not increased in recurrent versus primary tumors. <b>Conclusions:</b> MRP2 expression is neither a predictive marker of tamoxifen effectiveness nor a prognostic marker in breast cancer.
DOI: 10.26180/5c04756e7f1c0
title: participant 15 EEG.zip

description: Participant 15, day 1 and 2 EEG data
DOI: 10.7284/130137
title: Fluorometer data collected during research cruise OC1810B using a WET Labs WETStar instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130142
title: GNSS (Global Navigation Satellite System) data collected during research cruise OC1810B using a Furuno GP-90 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7369943.v2
title: Multi-drug resistance protein 2 (MRP2) expression, adjuvant tamoxifen therapy, and risk of breast cancer recurrence: a Danish population-based nested case-control study

description: <b>Background:</b> Adjuvant tamoxifen therapy approximately halves the risk of recurrence in estrogen receptor-positive (ER+) breast cancer patients, but many women respond insufficiently to therapy. Expression of multi-drug resistance protein 2 (MRP2) in breast cancer may potentiate tamoxifen resistance. Thus, we investigated the expression of MRP2 in breast cancer as a predictor of tamoxifen therapy effectiveness. <b>Material and methods:</b> We conducted a case-control study nested in the Danish Breast Cancer Group clinical database. The study included women aged 35–69 years diagnosed with stage l–lll breast cancer during 1985–2001, in Jutland, Denmark. We identified 541 recurrent breast cancers (cases) among women with estrogen receptor positive (ER+) disease treated with tamoxifen for at least 1 year (ER+/TAM+) and 300 cases among women with estrogen receptor-negative (ER−) disease, never treated with tamoxifen (ER−/TAM−). We matched one recurrence-free control to each recurrent case. We retrieved paraffin-embedded primary tumor tissue for all patients, and all available recurrent tumor tissue from pathology archives. MRP2 expression was evaluated using immunohistochemistry. We computed odds ratios (ORs) and 95% confidence intervals (95% CIs) associating MRP2 expression (positive vs. none) with breast cancer recurrence in conditional logistic regression models. We compared MRP2 expression in paired primary- and recurrent tumors. <b>Results:</b> MRP2 expression was more prevalent in the ER+/TAM + group, than in the ER−/TAM − group. No predictive utility of MRP2 for breast cancer recurrence was found in the ER+/TAM + group (OR<sub>adj</sub> = 0.96, 95% CI 0.70, 1.33). Further, no prognostic utility was found in the ER−/TAM − group (OR<sub>adj</sub> = 0.81, 95% CI 0.53, 1.23). MRP2 expression was not increased in recurrent versus primary tumors. <b>Conclusions:</b> MRP2 expression is neither a predictive marker of tamoxifen effectiveness nor a prognostic marker in breast cancer.
DOI: 10.6084/m9.figshare.7369943.v1
title: Multi-drug resistance protein 2 (MRP2) expression, adjuvant tamoxifen therapy, and risk of breast cancer recurrence: a Danish population-based nested case-control study

description: <b>Background:</b> Adjuvant tamoxifen therapy approximately halves the risk of recurrence in estrogen receptor-positive (ER+) breast cancer patients, but many women respond insufficiently to therapy. Expression of multi-drug resistance protein 2 (MRP2) in breast cancer may potentiate tamoxifen resistance. Thus, we investigated the expression of MRP2 in breast cancer as a predictor of tamoxifen therapy effectiveness. <b>Material and methods:</b> We conducted a case-control study nested in the Danish Breast Cancer Group clinical database. The study included women aged 35–69 years diagnosed with stage l–lll breast cancer during 1985–2001, in Jutland, Denmark. We identified 541 recurrent breast cancers (cases) among women with estrogen receptor positive (ER+) disease treated with tamoxifen for at least 1 year (ER+/TAM+) and 300 cases among women with estrogen receptor-negative (ER−) disease, never treated with tamoxifen (ER−/TAM−). We matched one recurrence-free control to each recurrent case. We retrieved paraffin-embedded primary tumor tissue for all patients, and all available recurrent tumor tissue from pathology archives. MRP2 expression was evaluated using immunohistochemistry. We computed odds ratios (ORs) and 95% confidence intervals (95% CIs) associating MRP2 expression (positive vs. none) with breast cancer recurrence in conditional logistic regression models. We compared MRP2 expression in paired primary- and recurrent tumors. <b>Results:</b> MRP2 expression was more prevalent in the ER+/TAM + group, than in the ER−/TAM − group. No predictive utility of MRP2 for breast cancer recurrence was found in the ER+/TAM + group (OR<sub>adj</sub> = 0.96, 95% CI 0.70, 1.33). Further, no prognostic utility was found in the ER−/TAM − group (OR<sub>adj</sub> = 0.81, 95% CI 0.53, 1.23). MRP2 expression was not increased in recurrent versus primary tumors. <b>Conclusions:</b> MRP2 expression is neither a predictive marker of tamoxifen effectiveness nor a prognostic marker in breast cancer.
DOI: 10.7284/130148
title: GNSS (Global Navigation Satellite System) data collected during research cruise OC1810B using a Ashtech ADU5 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130135
title: Gyrocompass data collected during research cruise OC1810B using a Sperry MK-37 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition