cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5477062.v1
title: ALDH1A1 and HLTF modulate the activity of lysosomal autophagy inhibitors in cancer cells

description: Lysosomal autophagy inhibitors (LAI) such as hydroxychloroquine (HCQ) have significant activity in a subset of cancer cell lines. LAIs are being evaluated in cancer clinical trials, but genetic determinants of sensitivity to LAIs are unknown, making it difficult to predict which tumors would be most susceptible. Here we characterize differentially expressed genes in HCQ-sensitive (-S) and -resistant (-R) cancer cells. Notably, expression of canonical macroautophagy/autophagy genes was not associated with sensitivity to HCQ. Expression patterns of ALDH1A1 (aldehyde dehydrogenase 1 family member A1) and HLTF (helicase like transcription factor) identified HCQ-S (ALDH1A1<sub>high</sub> HLTF<sub>low</sub>; ALDH1A1<sub>low</sub> HLTF<sub>low</sub>) and HCQ-R (ALDH1A1<sub>low</sub> HLTF<sub>high</sub>) cells. ALDH1A1 overexpression was found to enhance LAI cell entry and cytotoxicity without directly affecting lysosome function or autophagic flux. Expression of HLTF allows repair of DNA damage caused by LAI-induced reactive oxygen species, leading to HCQ resistance. Sensitivity to HCQ is increased in cells where <i>HLTF</i> is silenced by promoter methylation. HLTF overexpression blunted the antitumor efficacy of chloroquine derivatives in vitro and in vivo. Analysis of tumor RNA sequencing data from &gt;700 patients in the Cancer Genome Atlas identified cancers including colon cancer, renal cell carcinoma, and gastric cancers, that were enriched for the HCQ-S or HCQ-R signature. These results provide mechanistic insights into LAI efficacy, and guidance for LAI clinical development.
DOI: 10.6084/m9.figshare.5477212.v1
title: Waste activated sludge (7 - 13 wt%) flow curves at elevated temperature conditions (80 - 140 °C)

description: This submission contains the raw rheometer outputs from flow curve measurements of waste activated sludge (7, 9, 12 and 13 wt% total solids) at high temperature conditions (80, 100, 120, 130 and 140 °C).<br>The measurements were carried out on a DHR-3 rheometer (TA-Instruments), equipped with a pressure cell geometry. <br>Measurement protocol summary:<br>1) Waste activated sludge samples loaded into pressure cell.2) Nitrogen gas used to purge air from pressure cell.3) Nitrogen gas used to pressurise pressure cell to 5 bar.4) Flow curve generated for sample at 25 °C. Flow curves were generated by presetting a decreasing logarithmic shear-rate sweep.5) Sample heated to desired set point (80 °C).6) Once reached, flow curves were generated periodically at constant temperature (80 °C) over a 60 minute period.7) Sample cooled down to 25 °C and final flow curve generated.8) Sample replaced and repeat at new desired temperature (80 - 140 °C).<br>Detailed experimental protocol is recorded in the .tri (TRIOS) file attached with each data set. This file can be read using the TRIOS software made available on TA-Instruments website (http://www.tainstruments.com/support/software-downloads-support/downloads/). Rheometer geometry dimensions and other details are also obtainable from these files. <br>Please contact authors for access to files.<br><br>Contact:<br><br>nicky.eshtiaghi@rmit.edu.au RMITrheologygroup@gmail.com <br><br><br><br>Licence:<br>CC BY-NC<br><br>
DOI: 10.6084/m9.figshare.5476966
title: RefSoil genbank file annotated by RAST

description: Reference soil Database
DOI: 10.6084/m9.figshare.5476993
title: Time-varying logistic model code

description: This is code to run a time-varying logistic population growth model presented in the following paper: McMullen, LE, DeLeenheer, P, Tonkin JD, and Lytle, DA. (2017) High mortality and enhanced recovery: modelling the countervailing effects of disturbance on population dynamics. Ecology Letters. doi: 10.1111/ele.12866.<br>The code uses the logistic model to create flood–population response surfaces for three taxa with contrasting life histories after a single-flood event (Figure 1 in the paper).
DOI: 10.6084/m9.figshare.5477059.v2
title: A study of fatal pedestrian crashes at rural low-volume road intersections in southwest China

description: <b>Objective</b>: Although intersections correspond to a small proportion of the entire roadway system, they account for a disproportionally high number of fatal pedestrian crashes, especially on rural roads situated in low- and middle-income countries. This article examines pedestrian safety at rural intersections and suggests applicable accident prevention treatments by providing an in-depth analysis of 28 fatal pedestrian crashes from 8 low-volume roads in southwest China. <b>Methods</b>: The driving reliability and error analysis method (DREAM) is a method to support a systematic classification of accident causation information and to facilitate aggregation of that information into patterns of contributing factors. This is the first time that DREAM was used to analyze pedestrian–vehicle crashes and provide suggestions for road improvements in China. <b>Results</b>: The key issues adversely affecting pedestrian safety can be organized in 4 distinctive thematic categories, namely, deficient intersection safety infrastructure, lack of pedestrian safety education, inadequate driver training, and insufficient traffic law enforcement. Given that resources for traffic safety investments in rural areas are limited, it is determined that the potential countermeasures should focus on low-cost, easily implementable, and long-lasting measures increasing the visibility and predictability of pedestrian movement and reducing speeding and irresponsible driving among drivers and risk-taking behaviors among pedestrians. <b>Conclusions</b>: Accident prevention treatments are suggested based on their suitability for rural areas in southwest China. These countermeasures include introducing better access management and traffic calming treatments, providing more opportunities for pedestrian education, and enhancing the quality of driver training and traffic law enforcement.
DOI: 10.6084/m9.figshare.5477059.v1
title: A Study of Fatal Pedestrian Crashes at Rural Low Volume Road Intersections in Southwest China

description: <b>Objective</b>: Although intersections correspond to a small proportion of the entire roadway system, they account for a disproportionally high number of fatal pedestrian crashes, especially in rural roads situated in low- and middle-income countries. This paper examines pedestrian safety at rural intersections and suggests applicable accident prevention treatments by providing an in-depth analysis of 28 fatal pedestrian crashes from eight low volume roads in Southwest China. <b>Methods</b>: The Driving Reliability and Error Analysis Method (DREAM) is a method to support a systematic classification of accident causation information and to facilitate aggregation of that information into patterns of contributing factors. This is the first time DREAM was used to analyze pedestrian-vehicle crashes and provide suggestions for road improvements in China. <b>Results</b>: The key issues adversely affecting pedestrian safety can be organized in four distinctive thematic categories, namely <i>deficient intersection safety infrastructure, lack of pedestrian safety education, inadequate driver training</i> and <i>insufficient traffic law enforcement</i>. Given that resources for traffic safety investments in rural areas are limited, it is determined that the potential countermeasures should focus on low-cost, easily implementable and long-lasting measures increasing the visibility and predictability of pedestrian movement and reducing speeding and irresponsible driving for drivers and risk-taking behaviors for pedestrians. <b>Conclusions</b>: Accident prevention treatments are suggested based on their suitability for rural areas in Southwest China. These countermeasures include introducing better access management and traffic calming treatments, providing more opportunities for pedestrian education and enhancing the quality of driver training and traffic law enforcement.
DOI: 10.6084/m9.figshare.5476966.v1
title: RefSoil genbank file annotated by RAST

description: Reference soil Database
DOI: 10.6084/m9.figshare.5476909
title: VirusDataV2

description: Virus trait dataset used in our analysis.
DOI: 10.6084/m9.figshare.5476909.v1
title: VirusDataV2

description: Virus trait dataset used in our analysis.
DOI: 10.6084/m9.figshare.5473252
title: PEGylated magnetic nanoparticles (PEG@Fe3O4) as cost effectivealternative for oxidative cyanation of tertiary amines via C H activation

description: An efficient, cost effective and environmental friendly PEGylated magnetic nanoparticle catalyzed oxida-tive cyanation via CH activation of tertiary amines to corresponding -aminonitriles using hydrogenperoxide as oxidant and sodium cyanide as cyanide source is described. The synthesized nanocatalyst waseasily recovered with the help of external magnet and was successfully reused for several runs withoutany significant loss in catalytic activity.
DOI: 10.6084/m9.figshare.5473246
title: Visible light assisted photocatalytic reduction of CO2 using a graphene oxide supported heteroleptic ruthenium complex

description: A new heteroleptic ruthenium complex containing 2-thiophenyl benzimidazole ligands was synthesizedusing a microwave technique and was immobilized to graphene oxide via covalent attachment. The synthesizedcatalyst was used for the photoreduction of carbon dioxide under visible light irradiation withoutusing a sacrificial agent, which gave 2050 μmol g−1 cat methanol after 24 h of irradiation
DOI: 10.6084/m9.figshare.5473243
title: Octahedral rhenium K4[Re6S8(CN)6] and Cu(OH)2cluster modifiedTiO2for the photoreduction of CO2under visible light irradiation

description: tOctahedral hexacyano rhenium K4[Re6S8(CN)6] cluster complexes were grafted onto photoactive Cu(OH)2cluster modified TiO2{Cu(OH)2/TiO2} support. The rhenium and copper cluster modified TiO2photocata-lyst combines the advantages of heterogeneous catalyst (facile recovery, recycling ability of the catalyst)with the reactivity, selectivity of the soluble molecular catalyst. The synthesized heterogeneous cata-lyst was found to be highly efficient photoredox catalyst for the reduction of CO2under visible lightirradiation. Methanol was found to be the major liquid product with the formation of hydrogen as a byproduct as determined with GC-FID and GC-TCD, respectively. The methanol yield after 24 h irradiationwas found to be 149 mol/0.1 g cat. for Re-cluster@Cu(OH)2/TiO2photocatalyst that is much higher than35 mol/0.1 g cat. for Cu(OH)2/TiO2and 75 mol/0.1 g cat. for equimolar rhenium cluster in the presenceof triethanolamine (TEOA) as a sacrificial donor. The quantum yields ( MeOH) of Re-cluster@Cu(OH)2/TiO2and Cu(OH)2/TiO2were found to be 0.018 and 0.004 mol einstein−1, respectively. These values are muchhigher than those reported for other heterogeneous catalysts for six electron transfer reaction.
DOI: 10.6084/m9.figshare.5473252.v2
title: PEGylated magnetic nanoparticles (PEG@Fe3O4) as cost effectivealternative for oxidative cyanation of tertiary amines via C H activation

description: An efficient, cost effective and environmental friendly PEGylated magnetic nanoparticle catalyzed oxida-tive cyanation via CH activation of tertiary amines to corresponding -aminonitriles using hydrogenperoxide as oxidant and sodium cyanide as cyanide source is described. The synthesized nanocatalyst waseasily recovered with the help of external magnet and was successfully reused for several runs withoutany significant loss in catalytic activity.
DOI: 10.6084/m9.figshare.5473237
title: Nitrogen-doped graphene-supported copper complex: a novel photocatalyst for CO2 reduction under visible light irradiation

description: A copper(II) complex grafted to nitrogen-doped graphene (GrN700–CuC) was synthesized and thendemonstrated as an efficient photocatalyst for CO2 reduction into methanol under visible light irradiationusing a DMF/water mixture. The chemical and microstructural features of GrN700–CuC nanosheets werestudied by FTIR, XPS, XRD and HRTEM analyses. Owing to its truly heterogeneous nature, GrN700–CuCcould be easily recovered after the photocatalytic reaction and showed efficient recyclability forsubsequent runs
DOI: 10.6084/m9.figshare.5473240
title: A graphene/hemin hybrid material as an efficient green catalyst for stereoselective olefination of aldehydes

description: A hemin/graphene composite, prepared by mixing an aqueous solution of graphene oxide (GO) with heminand sonicating the suspension for 5 h at room temperature, was investigated for olefination of aldehydesusing ethyl diazoacetate in the presence of triphenylphosphine. Efficient olefination of aromaticaldehydes with high (E)-selectivity was obtained, revealing that rGO/hemin is a promising heterogeneouscatalyst for the olefination reaction. The as-synthesized catalyst could easily be recovered from thereaction mixture and was subsequently used for several runs without any significantly loss in activity andselectivity.
DOI: 10.6084/m9.figshare.5473243.v2
title: Octahedral rhenium K4[Re6S8(CN)6] and Cu(OH)2cluster modifiedTiO2for the photoreduction of CO2under visible light irradiation

description: tOctahedral hexacyano rhenium K4[Re6S8(CN)6] cluster complexes were grafted onto photoactive Cu(OH)2cluster modified TiO2{Cu(OH)2/TiO2} support. The rhenium and copper cluster modified TiO2photocata-lyst combines the advantages of heterogeneous catalyst (facile recovery, recycling ability of the catalyst)with the reactivity, selectivity of the soluble molecular catalyst. The synthesized heterogeneous cata-lyst was found to be highly efficient photoredox catalyst for the reduction of CO2under visible lightirradiation. Methanol was found to be the major liquid product with the formation of hydrogen as a byproduct as determined with GC-FID and GC-TCD, respectively. The methanol yield after 24 h irradiationwas found to be 149 mol/0.1 g cat. for Re-cluster@Cu(OH)2/TiO2photocatalyst that is much higher than35 mol/0.1 g cat. for Cu(OH)2/TiO2and 75 mol/0.1 g cat. for equimolar rhenium cluster in the presenceof triethanolamine (TEOA) as a sacrificial donor. The quantum yields ( MeOH) of Re-cluster@Cu(OH)2/TiO2and Cu(OH)2/TiO2were found to be 0.018 and 0.004 mol einstein−1, respectively. These values are muchhigher than those reported for other heterogeneous catalysts for six electron transfer reaction.
DOI: 10.6084/m9.figshare.5473225
title: Index-Match function.xlsx

description: yeshgff
DOI: 10.6084/m9.figshare.5473186
title: metaphlan_species_comparisons.zip

description: These are the statistical comparison reports of significant species abundance differences in environmental stream and wastewater samples. Fold change and p values are shown.
DOI: 10.6084/m9.figshare.5473225.v1
title: Index-Match function.xlsx

description: yeshgff
DOI: 10.6084/m9.figshare.5473186.v1
title: metaphlan_species_comparisons.zip

description: These are the statistical comparison reports of significant species abundance differences in environmental stream and wastewater samples. Fold change and p values are shown.
DOI: 10.6084/m9.figshare.5473156
title: Aphid_count_data

description: This is the same aphid abundance data set available from KBS LTER database
DOI: 10.6084/m9.figshare.5473153
title: CHCs of gamma-irradiated tsetse flies

description: Cuticular hydrocarbon profiles of tsetse flies which were subjected to gamma-irradiation as early (22day), late (29day) pupae and 5day old adults.
DOI: 10.6084/m9.figshare.5473153.v1
title: CHCs of gamma-irradiated tsetse flies

description: Cuticular hydrocarbon profiles of tsetse flies which were subjected to gamma-irradiation as early (22day), late (29day) pupae and 5day old adults.
DOI: 10.6084/m9.figshare.5472997
title: Artificial neural network modeling of cross-shore profile on sand beaches: The coast of the province of Valencia (Spain)

description: The paper describes the training, validation, testing, and application of models of artificial neural networks (ANN) for computing the cross-shore beach profile of the sand beaches of the province of Valencia (Spain). Sixty ANN models were generated by modifying both the input variables as the number of neurons in the hidden layer. The input variables consist of wave data and sedimentological data. To select and evaluate the performance of the optimal model, the following parameters were used: <i>R</i><sup>2</sup>, absolute error, mean absolute percentage error, and percentage relative error. Finally, the results are compared with the numerical model proposed by Aragonés et al. (2016b) for the equilibrium profile in the study area. The results show a mean absolute error of 0.21 m compared to 0.33 m Aragones’ model, significantly improving the results of the numerical model in the bar area around de Valencia Port. In addition, when comparing the results with other methods currently used (Dean’s or Vellinga formulation), the errors of these compared to ANN are of the order of 167 and 1538% higher, respectively.
DOI: 10.6084/m9.figshare.5472970
title: datasets

description: Datasets for practising in class<br>
DOI: 10.6084/m9.figshare.5472997.v2
title: Artificial neural network modeling of cross-shore profile on sand beaches: The coast of the province of Valencia (Spain)

description: The paper describes the training, validation, testing, and application of models of artificial neural networks (ANN) for computing the cross-shore beach profile of the sand beaches of the province of Valencia (Spain). Sixty ANN models were generated by modifying both the input variables as the number of neurons in the hidden layer. The input variables consist of wave data and sedimentological data. To select and evaluate the performance of the optimal model, the following parameters were used: <i>R</i><sup>2</sup>, absolute error, mean absolute percentage error, and percentage relative error. Finally, the results are compared with the numerical model proposed by Aragonés et al. (2016b) for the equilibrium profile in the study area. The results show a mean absolute error of 0.21 m compared to 0.33 m Aragones’ model, significantly improving the results of the numerical model in the bar area around de Valencia Port. In addition, when comparing the results with other methods currently used (Dean’s or Vellinga formulation), the errors of these compared to ANN are of the order of 167 and 1538% higher, respectively.
DOI: 10.6084/m9.figshare.5472976
title: shortbred_comparison_reports.zip

description: These are the statistical comparison reports of significant antibiotic gene resistance abundance differences in environmental stream and wastewater samples. Fold change and p values are shown.
DOI: 10.6084/m9.figshare.5472997.v1
title: Artificial neural network modelling of cross-shore profile on sand beaches: The coast of the province of Valencia (Spain)

description: The paper describes the training, validation, testing and application of models of artificial neural networks (ANN) for computing the cross-shore beach profile of the sand beaches of the province of Valencia (Spain). Sixty ANN models were generated by modifying both the input variables as the number of neurons in the hidden layer. The input variables consist of wave data and sedimentological data. To select and evaluate the performance of the optimal model, the following parameters were used: R<sup>2</sup>, absolute error, mean absolute percentage error and percentage relative error. Finally, the results are compared with the numerical model proposed by Aragonés et al. (2016b) for the equilibrium profile in the study area. The results show a mean absolute error of 0.21 m compared to 0.33 m Aragones’ model, significantly improving the results of the numerical model in the bar area around de Valencia Port. In addition, when comparing the results with other methods currently used (Dean’s or Vellinga formulation), the errors of these compared to ANN are of the order of 167% and 1538% higher, respectively.
DOI: 10.6084/m9.figshare.5472967
title: Inherited DNA lesions determine G1 duration in the next cell cycle

description: Replication stress is a major source of DNA damage and an important driver of cancer development. Replication intermediates that occur upon mild forms of replication stress frequently escape cell cycle checkpoints and can be transmitted through mitosis into the next cell cycle. The consequences of such inherited DNA lesions for cell fate and survival are poorly understood. By using time-lapse microscopy and quantitative image-based cytometry to simultaneously monitor inherited DNA lesions marked by the genome caretaker protein 53BP1 and cell cycle progression, we show that inheritance of 53BP1-marked lesions from the previous S-phase is associated with a prolonged G1 duration in the next cell cycle. These results suggest that cell-to-cell variation in S-phase commitment is determined, at least partially, by the amount of replication-born inherited DNA damage in individual cells. We further show that loss of the tumor suppressor protein p53 overrides replication stress-induced G1 prolongation and allows S-phase entry with excessive amounts of inherited DNA lesions. Thus, replication stress and p53 loss may synergize during cancer development by promoting cell cycle re-entry with unrepaired mutagenic DNA lesions originating from the previous cell cycle.
DOI: 10.6084/m9.figshare.5472976.v1
title: shortbred_comparison_reports.zip

description: These are the statistical comparison reports of significant antibiotic gene resistance abundance differences in environmental stream and wastewater samples. Fold change and p values are shown.
DOI: 10.6084/m9.figshare.5472967.v2
title: Inherited DNA lesions determine G1 duration in the next cell cycle

description: Replication stress is a major source of DNA damage and an important driver of cancer development. Replication intermediates that occur upon mild forms of replication stress frequently escape cell cycle checkpoints and can be transmitted through mitosis into the next cell cycle. The consequences of such inherited DNA lesions for cell fate and survival are poorly understood. By using time-lapse microscopy and quantitative image-based cytometry to simultaneously monitor inherited DNA lesions marked by the genome caretaker protein 53BP1 and cell cycle progression, we show that inheritance of 53BP1-marked lesions from the previous S-phase is associated with a prolonged G1 duration in the next cell cycle. These results suggest that cell-to-cell variation in S-phase commitment is determined, at least partially, by the amount of replication-born inherited DNA damage in individual cells. We further show that loss of the tumor suppressor protein p53 overrides replication stress-induced G1 prolongation and allows S-phase entry with excessive amounts of inherited DNA lesions. Thus, replication stress and p53 loss may synergize during cancer development by promoting cell cycle re-entry with unrepaired mutagenic DNA lesions originating from the previous cell cycle.
DOI: 10.6084/m9.figshare.5472874
title: Supplementary Material for: IMRT, IGRT, SBRT

description: <strong>Online Supplementary Material</strong><strong>IMRT, IGRT, SBRT – Advances in the Treatment Planning and Delivery of Radiotherapy<br><br></strong> 2nd, revised and extended edition<br> Frontiers of Radiation Therapy and Oncology, Vol. 43
DOI: 10.6084/m9.figshare.5472820
title: likert.xlsx

description: this dataset is to be moved to datasets
DOI: 10.6084/m9.figshare.5472874.v1
title: Supplementary Material for: IMRT, IGRT, SBRT

description: <strong>Online Supplementary Material</strong><strong>IMRT, IGRT, SBRT – Advances in the Treatment Planning and Delivery of Radiotherapy<br><br></strong> 2nd, revised and extended edition<br> Frontiers of Radiation Therapy and Oncology, Vol. 43