cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.4010560
title: Quantitative Nanoscale Absorption Mapping: A Novel Technique To Probe Optical Absorption of Two-Dimensional Materials

description: Two-dimensional semiconductors, in particular transition metal dichalcogenides and related heterostructures, have gained increasing interest as they constitute potential new building blocks for the next generation of electronic and optoelectronic applications. In this work, we develop a novel nondestructive and noncontact technique for mapping the absorption properties of 2D materials, by taking advantage of the underlying substrate cathodoluminescence emission. We map the quantitative absorption of MoS<sub>2</sub> and MoSe<sub>2</sub> monolayers, obtained on sapphire and oxidized silicon, with nanoscale resolution. We extend our technique to the characterization of the absorption properties of MoS<sub>2</sub>/MoSe<sub>2</sub> van der Waals heterostructures. We demonstrate that interlayer excitonic phenomena enhance the absorption in the UV range. Our technique also highlights the presence of defects such as grain boundaries and ad-layers. We provide measurements on the absorption of grain boundaries in monolayer MoS<sub>2</sub> at different merging angles. We observe a higher absorption yield of randomly oriented monolayers with respect to 60° rotated monolayers. This work opens up a new possibility for characterizing the functional properties two-dimensional semiconductors at the nanoscale. This dataset contains some of the raw data for Figures 1 and 2.
description: L.F. and A.F.i.M. are thankful for the funding from SNSF via the NCCR QSIT. D.D. and A.K. acknowledge funding from Swiss SNF Sinergia Grant 147607, Marie Curie ITN network "MoWSeS" (grant 317451), and the CCMX Materials Challenge grant "Large Area Growth of 2D Materials for device integration". M.N., M.B., and F.F. want to thank G.Attolini and F. Rossi (IMEM-CNR) for the useful discussions.
DOI: 10.6084/m9.figshare.5331550
title: What affects power to estimate speciation rate shifts?

description: The development of methods to estimate rates of speciation and extinction from time-calibrated phylogenies has revolutionized evolutionary biology by allowing researchers to correlate diversification rate shifts with causal factors. A growing number of researchers are interested in testing whether the evolution of a trait or a trait variant has influenced speciation rates, and three modelling methods – BiSSE, MEDUSA and BAMM – have been widely used in such studies. We simulated phylogenies with a single speciation rate shift each, and evaluated the power of the three methods to detect these shifts. We varied the degree of increase in speciation rate (rate asymmetry), the number of tips, the tip-ratio bias (ratio of number of tips with each character state) and the relative age in relation to overall tree age when the rate shift occurred. All methods had good power to detect rate shifts when the rate asymmetry was strong and the sizes of the two lineages with the distinct speciation rates were large. Even when lineage size was small, power was good when rate asymmetry was high. In our simulated scenarios, small lineage sizes appear to affect BAMM most strongly. Tip-ratio bias influenced the accuracy of speciation rate estimation but did not have a strong effect on power to detect rate shifts. Based on our results, we provide some suggestions to users of these methods.
DOI: 10.6084/m9.figshare.5331550.v1
title: What affects power to estimate speciation rate shifts?

description: The development of methods to estimate rates of speciation and extinction from time-calibrated phylogenies has revolutionized evolutionary biology by allowing researchers to correlate diversification rate shifts with causal factors. A growing number of researchers are interested in testing whether the evolution of a trait or a trait variant has influenced speciation rates, and three modelling methods – BiSSE, MEDUSA and BAMM – have been widely used in such studies. We simulated phylogenies with a single speciation rate shift each, and evaluated the power of the three methods to detect these shifts. We varied the degree of increase in speciation rate (rate asymmetry), the number of tips, the tip-ratio bias (ratio of number of tips with each character state) and the relative age in relation to overall tree age when the rate shift occurred. All methods had good power to detect rate shifts when the rate asymmetry was strong and the sizes of the two lineages with the distinct speciation rates were large. Even when lineage size was small, power was good when rate asymmetry was high. In our simulated scenarios, small lineage sizes appear to affect BAMM most strongly. Tip-ratio bias influenced the accuracy of speciation rate estimation but did not have a strong effect on power to detect rate shifts. Based on our results, we provide some suggestions to users of these methods.
DOI: 10.15131/shef.data.5331628.v1
title: Full dataset - Insomnia, negative affect and paranoia

description: This is the full dataset for a manuscript describing a structural equation model of the relationship between insomnia, negative affect and paranoia in the general population. <br>This data set was used as the basis for the PLoS One paper; specifically the cross-sectional mediation analysis (path analysis) and the regression analysis of objective sleep as a predictor of negative affect and paranoid thinking.<br>Scott, A.J., Rowse, G. and Webb, T.L. (2017) A structural equation model of the relationship between insomnia, negative affect, and paranoid thinking. PLoS One, 12 (10). e0186233. DOI:10.1371/journal.pone.0186233<br>
DOI: 10.5281/zenodo.4010559
title: Quantitative Nanoscale Absorption Mapping: A Novel Technique To Probe Optical Absorption of Two-Dimensional Materials

description: Two-dimensional semiconductors, in particular transition metal dichalcogenides and related heterostructures, have gained increasing interest as they constitute potential new building blocks for the next generation of electronic and optoelectronic applications. In this work, we develop a novel nondestructive and noncontact technique for mapping the absorption properties of 2D materials, by taking advantage of the underlying substrate cathodoluminescence emission. We map the quantitative absorption of MoS<sub>2</sub> and MoSe<sub>2</sub> monolayers, obtained on sapphire and oxidized silicon, with nanoscale resolution. We extend our technique to the characterization of the absorption properties of MoS<sub>2</sub>/MoSe<sub>2</sub> van der Waals heterostructures. We demonstrate that interlayer excitonic phenomena enhance the absorption in the UV range. Our technique also highlights the presence of defects such as grain boundaries and ad-layers. We provide measurements on the absorption of grain boundaries in monolayer MoS<sub>2</sub> at different merging angles. We observe a higher absorption yield of randomly oriented monolayers with respect to 60° rotated monolayers. This work opens up a new possibility for characterizing the functional properties two-dimensional semiconductors at the nanoscale. This dataset contains some of the raw data for Figures 1 and 2.
description: L.F. and A.F.i.M. are thankful for the funding from SNSF via the NCCR QSIT. D.D. and A.K. acknowledge funding from Swiss SNF Sinergia Grant 147607, Marie Curie ITN network "MoWSeS" (grant 317451), and the CCMX Materials Challenge grant "Large Area Growth of 2D Materials for device integration". M.N., M.B., and F.F. want to thank G.Attolini and F. Rossi (IMEM-CNR) for the useful discussions.
DOI: 10.6084/m9.figshare.5331697.v1
title: A novel form of stereo vision in the praying mantis: DATA

description: The data support the research described in the unpublished paper entitle: 'A novel form of biological stereopsis'. The data are from experiments investigated stereopsis in mantises (<i>Sphodromantis lineola</i>) and humans in different experiments as detailed in the paper. The datafiles for the mantises detail the occurence and number of strikes in response to different disparity, correlation and motion conditions. The datafiles for the human participants detail their judgement of whether a 3D target was near or far in response to different disparity, correlation and motion conditions.
DOI: 10.6084/m9.figshare.5331499
title: The activity and safety of novel proteasome inhibitors strategies (single, doublet and triplet) for relapsed/refractory multiple myeloma

description: <b>Purpose:</b> We sought to evaluate the activity and safety of these novel proteasome inhibitors (PIs) (carfilzomib, ixazomib, oprozomib and marizomib) containing regimens (single, doublet and triplet) for relapsed/refractory multiple myeloma (R/RMM). <b>Methods:</b> We searched published reports including these novel PIs containing regimens for R/RMM. <b>Results:</b> Finally, we identified 28 prospective studies that evaluated 4123 patients. Pooled analysis showed that novel PIs doublet combinations attained an impressive overall response rate (ORR) of 67%, which was higher than that of 22% from novel PIs single-agent (<i>p</i> p = .54). And, there were no difference between them in ≥VGPR and CBR analysis. Compared to standard therapy, novel PIs combinations clearly benefited patients with R/RMM in terms of overall survival (HR, 0.79; <i>p</i>= .01), progression free survival(HR, 0.64; <i>p</i> = .01), overall response rate (RR = 1.21 <i>p</i> <b>Conclusions:</b> Novel PIs doublet combinations attained superior response outcomes over novel PIs single-agent in patients with R/RMM. Meanwhile, novel PIs triplet combinations had similar response outcomes with novel PIs doublet combinations. Compared to standard therapy, novel PIs combinations clearly prolonged survival for patients with R/RMM.
DOI: 10.6084/m9.figshare.5331499.v1
title: The activity and safety of novel proteasome inhibitors strategies (single, doublet and triplet) for relapsed/refractory multiple myeloma

description: <b>Purpose:</b> We sought to evaluate the activity and safety of these novel proteasome inhibitors (PIs) (carfilzomib, ixazomib, oprozomib and marizomib) containing regimens (single, doublet and triplet) for relapsed/refractory multiple myeloma (R/RMM). <b>Methods:</b> We searched published reports including these novel PIs containing regimens for R/RMM. <b>Results:</b> Finally, we identified 28 prospective studies that evaluated 4123 patients. Pooled analysis showed that novel PIs doublet combinations attained an impressive overall response rate (ORR) of 67%, which was higher than that of 22% from novel PIs single-agent (<i>p</i> p = .54). And, there were no difference between them in ≥VGPR and CBR analysis. Compared to standard therapy, novel PIs combinations clearly benefited patients with R/RMM in terms of overall survival (HR, 0.79; <i>p</i>= .01), progression free survival(HR, 0.64; <i>p</i> = .01), overall response rate (RR = 1.21 <i>p</i> <b>Conclusions:</b> Novel PIs doublet combinations attained superior response outcomes over novel PIs single-agent in patients with R/RMM. Meanwhile, novel PIs triplet combinations had similar response outcomes with novel PIs doublet combinations. Compared to standard therapy, novel PIs combinations clearly prolonged survival for patients with R/RMM.
DOI: 10.6084/m9.figshare.5331418
title: FRM4STS Namibia - LST FICE Photos

description: FRM4STS Namibia pictures
DOI: 10.6084/m9.figshare.5331478.v2
title: Impact of model and dose uncertainty on model-based selection of oropharyngeal cancer patients for proton therapy

description: <b>Background:</b> Proton therapy is becoming increasingly available, so it is important to apply objective and individualized patient selection to identify those who are expected to benefit most from proton therapy compared to conventional intensity modulated radiation therapy (IMRT). Comparative treatment planning using normal tissue complication probability (NTCP) evaluation has recently been proposed. This work investigates the impact of NTCP model and dose uncertainties on model-based patient selection. <b>Material and Methods:</b> We used IMRT and intensity modulated proton therapy (IMPT) treatment plans of 78 oropharyngeal cancer patients, which were generated based on automated treatment planning and evaluated based on three published NTCP models. A reduction in NTCP of more than a certain threshold (e.g. 10% lower NTCP) leads to patient selection for IMPT, referred to as ‘nominal’ selection. To simulate the effect of uncertainties in NTCP-model coefficients (based on reported confidence intervals) and planned doses on the accuracy of model-based patient selection, the Monte Carlo method was used to sample NTCP-model coefficients and doses from a probability distribution centered at their nominal values. Patient selection accuracy within a certain sample was defined as the fraction of patients which had similar selection in both the ‘nominal’ and ‘sampled’ scenario. <b>Results:</b> For all three NTCP models, the median patient selection accuracy was found to be above 70% when only NTCP-model uncertainty was considered. Selection accuracy decreased with increasing uncertainty resulting from differences between planned and delivered dose. In case of excessive dose uncertainty, selection accuracy decreased to 60%. <b>Conclusion:</b> Model and dose uncertainty highly influence the accuracy of model-based patient selection for proton therapy. A reduction of NTCP-model uncertainty is necessary to reach more accurate model-based patient selection.
DOI: 10.6084/m9.figshare.5331418.v1
title: FRM4STS Namibia - LST FICE Photos

description: FRM4STS Namibia pictures
DOI: 10.6084/m9.figshare.5331442
title: Impact of respiratory motion on variable relative biological effectiveness in 4D-dose distributions of proton therapy

description: <b>Background:</b> Organ motion during radiation therapy with scanned protons leads to deviations between the planned and the delivered physical dose. Using a constant relative biological effectiveness (RBE) of 1.1 linearly maps these deviations into RBE-weighted dose. However, a constant value cannot account for potential nonlinear variations in RBE suggested by variable RBE models. Here, we study the impact of motion on recalculations of RBE-weighted dose distributions using a phenomenological variable RBE model. <b>Material and methods:</b> 4D-dose calculation including variable RBE was implemented in the open source treatment planning toolkit matRad. Four scenarios were compared for one field and two field proton treatments for a liver cancer patient assuming (<i>α</i>∕<i>β</i>)<i><sub>x</sub></i> = 2 Gy and (<i>α</i>∕<i>β</i>)<i><sub>x</sub></i> = 10 Gy: (A) the optimized static dose distribution with constant RBE, (B) a static recalculation with variable RBE, (C) a 4D-dose recalculation with constant RBE and (D) a 4D-dose recalculation with variable RBE. For (B) and (D), the variable RBE was calculated by the model proposed by McNamara. For (C), the physical dose was accumulated with direct dose mapping; for (D), dose-weighted radio-sensitivity parameters of the linear quadratic model were accumulated to model synergistic irradiation effects on RBE. <b>Results:</b> Dose recalculation with variable RBE led to an elevated biological dose at the end of the proton field, while 4D-dose recalculation exhibited random deviations everywhere in the radiation field depending on the interplay of beam delivery and organ motion. For a single beam treatment assuming (<i>α</i>∕<i>β</i>)<i><sub>x</sub></i> = 2 Gy, D<sub>95</sub><i><sub>%</sub></i> was 1.98 Gy (RBE) (A), 2.15 Gy (RBE) (B), 1.81 Gy (RBE) (C) and 1.98 Gy (RBE) (D). The homogeneity index was 1.04 (A), 1.08 (B), 1.23 (C) and 1.25 (D). <b>Conclusion:</b> For the studied liver case, intrafractional motion did not reduce the modulation of the RBE-weighted dose postulated by variable RBE models for proton treatments.
DOI: 10.6084/m9.figshare.5331391
title: Infrared Spectroscopy Coupled with a Dispersion Model for Quantifying the Real-Time Dynamics of Kanamycin Resistance in Artificial Microbiota

description: Overusage of antibiotics leads to the widespread induction of antibiotic-resistance genes (ARGs). Developing an approach to allow real-time monitoring and fast prediction of ARGs dynamics in clinical or environmental samples has become an urgent matter. Vibrational spectroscopy is potentially an ideal technique for the characterization of the microbial composition of microbiota as it is nondestructive, high-throughput, and label-free. The present study included two strains without kanamycin-resistant-gene,<i> Mycobacterium vanbaalenii </i>PYR-1 (Myco) and<i> Escherichia coli </i>DH5α (<i>E.coli</i>), and one kanamycin-resistant strain <i>Acinetobacter baylyi</i> ADPWH_recA (ADP). The three control groups contained pure <i>M. vanbaalenii </i>PYR-1, <i>E. coli </i>DH5α and <i>A. baylyi</i> ADPWH_recA, respectively. The artificial microbiotas were prepared for both static (M1 to M5) and dynamic (M1 and M2) experiments by gently mixing the cells in the compositions. The <i>A. baylyi</i> ADPWH_recA ratios in static (M1 to M5) and dynamic (M1, M2) were 10%, 25%, 50%, 75%, 90% and 20%, 50% respectively. The tested exposure time points were 0, 4, 8, 12, 24hrs. This file contains raw and preprocessed data from the static and dynamic experiments. Raw spectra were preprocessed to correct problems associated with data acquisition and further multivariate approaches were applied to study the respective datasets. The preprocessing of the raw spectra was performed within MATLAB software, using an in-house-developed IRootLab toolbox (http://trevisanj.github.io/irootlab/). <br>
DOI: 10.6084/m9.figshare.5331442.v1
title: Impact of respiratory motion on variable relative biological effectiveness in 4D-dose distributions of proton therapy

description: <b>Background:</b> Organ motion during radiation therapy with scanned protons leads to deviations between the planned and the delivered physical dose. Using a constant relative biological effectiveness (RBE) of 1.1 linearly maps these deviations into RBE-weighted dose. However, a constant value cannot account for potential nonlinear variations in RBE suggested by variable RBE models. Here, we study the impact of motion on recalculations of RBE-weighted dose distributions using a phenomenological variable RBE model. <b>Material and methods:</b> 4D-dose calculation including variable RBE was implemented in the open source treatment planning toolkit matRad. Four scenarios were compared for one field and two field proton treatments for a liver cancer patient assuming (<i>α</i>∕<i>β</i>)<i><sub>x</sub></i> = 2 Gy and (<i>α</i>∕<i>β</i>)<i><sub>x</sub></i> = 10 Gy: (A) the optimized static dose distribution with constant RBE, (B) a static recalculation with variable RBE, (C) a 4D-dose recalculation with constant RBE and (D) a 4D-dose recalculation with variable RBE. For (B) and (D), the variable RBE was calculated by the model proposed by McNamara. For (C), the physical dose was accumulated with direct dose mapping; for (D), dose-weighted radio-sensitivity parameters of the linear quadratic model were accumulated to model synergistic irradiation effects on RBE. <b>Results:</b> Dose recalculation with variable RBE led to an elevated biological dose at the end of the proton field, while 4D-dose recalculation exhibited random deviations everywhere in the radiation field depending on the interplay of beam delivery and organ motion. For a single beam treatment assuming (<i>α</i>∕<i>β</i>)<i><sub>x</sub></i> = 2 Gy, D<sub>95</sub><i><sub>%</sub></i> was 1.98 Gy (RBE) (A), 2.15 Gy (RBE) (B), 1.81 Gy (RBE) (C) and 1.98 Gy (RBE) (D). The homogeneity index was 1.04 (A), 1.08 (B), 1.23 (C) and 1.25 (D). <b>Conclusion:</b> For the studied liver case, intrafractional motion did not reduce the modulation of the RBE-weighted dose postulated by variable RBE models for proton treatments.
DOI: 10.6084/m9.figshare.5331442.v3
title: Impact of respiratory motion on variable relative biological effectiveness in 4D-dose distributions of proton therapy

description: <b>Background:</b> Organ motion during radiation therapy with scanned protons leads to deviations between the planned and the delivered physical dose. Using a constant relative biological effectiveness (RBE) of 1.1 linearly maps these deviations into RBE-weighted dose. However, a constant value cannot account for potential nonlinear variations in RBE suggested by variable RBE models. Here, we study the impact of motion on recalculations of RBE-weighted dose distributions using a phenomenological variable RBE model. <b>Material and methods:</b> 4D-dose calculation including variable RBE was implemented in the open source treatment planning toolkit matRad. Four scenarios were compared for one field and two field proton treatments for a liver cancer patient assuming (<i>α</i>∕<i>β</i>)<i><sub>x</sub></i> = 2 Gy and (<i>α</i>∕<i>β</i>)<i><sub>x</sub></i> = 10 Gy: (A) the optimized static dose distribution with constant RBE, (B) a static recalculation with variable RBE, (C) a 4D-dose recalculation with constant RBE and (D) a 4D-dose recalculation with variable RBE. For (B) and (D), the variable RBE was calculated by the model proposed by McNamara. For (C), the physical dose was accumulated with direct dose mapping; for (D), dose-weighted radio-sensitivity parameters of the linear quadratic model were accumulated to model synergistic irradiation effects on RBE. <b>Results:</b> Dose recalculation with variable RBE led to an elevated biological dose at the end of the proton field, while 4D-dose recalculation exhibited random deviations everywhere in the radiation field depending on the interplay of beam delivery and organ motion. For a single beam treatment assuming (<i>α</i>∕<i>β</i>)<i><sub>x</sub></i> = 2 Gy, D<sub>95</sub><i><sub>%</sub></i> was 1.98 Gy (RBE) (A), 2.15 Gy (RBE) (B), 1.81 Gy (RBE) (C) and 1.98 Gy (RBE) (D). The homogeneity index was 1.04 (A), 1.08 (B), 1.23 (C) and 1.25 (D). <b>Conclusion:</b> For the studied liver case, intrafractional motion did not reduce the modulation of the RBE-weighted dose postulated by variable RBE models for proton treatments.
DOI: 10.6084/m9.figshare.5331391.v1
title: Infrared Spectroscopy Coupled with a Dispersion Model for Quantifying the Real-Time Dynamics of Kanamycin Resistance in Artificial Microbiota

description: Overusage of antibiotics leads to the widespread induction of antibiotic-resistance genes (ARGs). Developing an approach to allow real-time monitoring and fast prediction of ARGs dynamics in clinical or environmental samples has become an urgent matter. Vibrational spectroscopy is potentially an ideal technique for the characterization of the microbial composition of microbiota as it is nondestructive, high-throughput, and label-free. The present study included two strains without kanamycin-resistant-gene,<i> Mycobacterium vanbaalenii </i>PYR-1 (Myco) and<i> Escherichia coli </i>DH5α (<i>E.coli</i>), and one kanamycin-resistant strain <i>Acinetobacter baylyi</i> ADPWH_recA (ADP). The three control groups contained pure <i>M. vanbaalenii </i>PYR-1, <i>E. coli </i>DH5α and <i>A. baylyi</i> ADPWH_recA, respectively. The artificial microbiotas were prepared for both static (M1 to M5) and dynamic (M1 and M2) experiments by gently mixing the cells in the compositions. The <i>A. baylyi</i> ADPWH_recA ratios in static (M1 to M5) and dynamic (M1, M2) were 10%, 25%, 50%, 75%, 90% and 20%, 50% respectively. The tested exposure time points were 0, 4, 8, 12, 24hrs. This file contains raw and preprocessed data from the static and dynamic experiments. Raw spectra were preprocessed to correct problems associated with data acquisition and further multivariate approaches were applied to study the respective datasets. The preprocessing of the raw spectra was performed within MATLAB software, using an in-house-developed IRootLab toolbox (http://trevisanj.github.io/irootlab/). <br>