cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5331241.v2
title: The influence of breathing motion and a variable relative biological effectiveness in proton therapy of left-sided breast cancer

description: <b>Background:</b> Proton breast radiotherapy has been suggested to improve target coverage as well as reduce cardiopulmonary and integral dose compared with photon therapy. This study aims to assess this potential when accounting for breathing motion and a variable relative biological effectiveness (RBE). <b>Methods:</b> Photon and robustly optimized proton plans were generated to deliver 50 Gy (RBE) in 25 fractions (RBE = 1.1) to the CTV (whole left breast) for 12 patients. The plan evaluation was performed using the constant RBE and a variable RBE model. Robustness against breathing motion, setup, range and RBE uncertainties was analyzed using CT data obtained at free-breathing, breath-hold-at-inhalation and breath-hold-at-exhalation. <b>Results:</b> All photon and proton plans (RBE = 1.1) met the clinical goals. The variable RBE model predicted an average RBE of 1.18 for the CTVs (range 1.14–1.21) and even higher RBEs in organs at risk (OARs). However, the dosimetric impact of this latter aspect was minor due to low OAR doses. The normal tissue complication probability (NTCP) for the lungs was low for all patients (&lt;1%), and similar for photons and protons. The proton plans were generally considered robust for all patients. However, in the most extreme scenarios, the lowest dose received by 98% of the CTV dropped from 96 to 99% of the prescribed dose to around 92–94% for both protons and photons. Including RBE uncertainties in the robustness analysis resulted in substantially higher worst-case OAR doses. <b>Conclusions:</b> Breathing motion seems to have a minor effect on the plan quality for breast cancer. The variable RBE might impact the potential benefit of protons, but could probably be neglected in most cases where the physical OAR doses are low. However, to be able to identify outlier cases at risk for high OAR doses, the biological evaluation of proton plans taking into account the variable RBE is recommended.
DOI: 10.6084/m9.figshare.5331214
title: MR Instruments

description: This file contains the list of all used instruments in Robert Porsch's PhD thesis. These genetic instruments were used in a Mendelian Randomization framework.
DOI: 10.6084/m9.figshare.5331253.v3
title: Feature selection methodology for longitudinal cone-beam CT radiomics

description: <b>Background:</b> Cone-beam CT (CBCT) scans are typically acquired daily for positioning verification of non-small cell lung cancer (NSCLC) patients. Quantitative information, derived using radiomics, can potentially contribute to (early) treatment adaptation. The aims of this study were to (1) describe and investigate a methodology for feature selection of a longitudinal radiomics approach (2) investigate which time-point during treatment is potentially useful for early treatment response assessment. <b>Material and methods:</b> For 90 NSCLC patients CBCT scans of the first two fractions of treatment (considered as ‘test-retest’ scans) were analyzed, as well as weekly CBCT images. One hundred and sixteen radiomic features were extracted from the GTV of all scans and subsequently absolute and relative differences were calculated between weekly CBCT images and the CBCT of the first fraction. Test-retest scans were used to determine the smallest detectable change (C = 1.96 * SD) allowing for feature selection by choosing a minimum number of patients for which a feature should change more than ‘C’ to be considered as relevant. Analysis of which features change at which moment during treatment was used to investigate which time-point is potentially relevant to extract longitudinal radiomics information for early treatment response assessment. <b>Results:</b> A total of six absolute delta features changed for at least ten patients at week 2 of treatment and increased to 61 at week 3, 79 at week 4 and 85 at week 5. There was 93% overlap between features selected at week 3 and the other weeks. <b>Conclusions:</b> This study describes a feature selection methodology for longitudinal radiomics that is able to select reproducible delta radiomics features that are informative due to their change during treatment, which can potentially be used for treatment decisions concerning adaptive radiotherapy. Nonetheless, the prognostic value of the selected delta radiomic features should be investigated in future studies.
DOI: 10.6084/m9.figshare.5331214.v1
title: MR Instruments

description: This file contains the list of all used instruments in Robert Porsch's PhD thesis. These genetic instruments were used in a Mendelian Randomization framework.
DOI: 10.6084/m9.figshare.5331199
title: Larmic_paper30-Data.docx

description: DATASET: Earthworms as an alternative feeding resource after landfill closure in a breeding Yellow-legged gull population. Behavioral Ecology and Sociobiology.
DOI: 10.6084/m9.figshare.5331193
title: ASL and SWI in TIA

description: The dataset concerns a prospective cohort of patients with clinical time-based transient ischemic attack and holds per patient and per lesion data describing basic demographics, risk factors and imaging features.
DOI: 10.6084/m9.figshare.5331193.v1
title: ASL and SWI in TIA

description: The dataset concerns a prospective cohort of patients with clinical time-based transient ischemic attack and holds per patient and per lesion data describing basic demographics, risk factors and imaging features.
DOI: 10.6084/m9.figshare.5331199.v1
title: Larmic_paper30-Data.docx

description: DATASET: Earthworms as an alternative feeding resource after landfill closure in a breeding Yellow-legged gull population. Behavioral Ecology and Sociobiology.
DOI: 10.17608/k6.auckland.5331166
title: Population Cartogram for District Health Boards of New Zealand

description: The fileset containing a Readme.pdf file, a population cartogram shapefile, and a Chatham Islands reference frame shape file. The cartogram is at the District Health Board (DHB) level. It was designed to represent social and health information with the size of each DHB proportionate to its 2013 census population. This makes DHBs with densely populated urban areas more visible. This read me file describes how to use the population cartogram. It also provides citation and contribution information and the contact details of the author.
DOI: 10.17608/k6.auckland.5331166.v1
title: Population Cartogram for District Health Boards of New Zealand

description: The fileset containing a Readme.pdf file, a population cartogram shapefile, and a Chatham Islands reference frame shape file. The cartogram is at the District Health Board (DHB) level. It was designed to represent social and health information with the size of each DHB proportionate to its 2013 census population. This makes DHBs with densely populated urban areas more visible. This read me file describes how to use the population cartogram. It also provides citation and contribution information and the contact details of the author.
DOI: 10.6084/m9.figshare.5331148
title: WB Proteins.pzf

description: Data set for western blots, contractile and histological data.<br>
DOI: 10.6084/m9.figshare.5330944
title: An urban energy network data

description: This is the data of day-ahead dispatch for unban energy systems. Please refer to my paper "Adaptive Robust Day-ahead Dispatch for Urban Energy Systems" if available online.
DOI: 10.6084/m9.figshare.5330944.v1
title: An urban energy network data

description: This is the data of day-ahead dispatch for unban energy systems. Please refer to my paper "Adaptive Robust Day-ahead Dispatch for Urban Energy Systems" if available online.
DOI: 10.6084/m9.figshare.5330911
title: Tabela de Clusters

description: Analise dos clusters utilizando a ferramenta R. A identificação de cada cluster está listada na ultima coluna da tabela.
DOI: 10.6084/m9.figshare.5330917
title: Holocene evolution of the southern Tauranga Harbour

description: Tauranga Harbour is a major economic centre and home to New Zealand’s largest port. Despite the importance of the harbour basin, and especially of the shipping channel, the subsurface stratigraphy of this area has not been studied in detail. We use sediment cores retrieved in support of a recent dredging campaign to characterise the subsurface stratigraphy and interpret the sediments in terms of paleoenvironment. Four main facies (volcanic sand, lithic silt, coarse sand and pumiceous sand) were identified using textural, mineralogical and geochemical characteristics. They represent distinct depositional environments at different stages of the Holocene marine transgression (HMT). The oldest facies, deposited prior to the HMT (volcanic sand and lithic silt facies), represent the channel and overbank deposits of an aggrading river system with rapidly migrating channels. During the deposition of this facies, a change in sediment source is evident from geochemical data. This preceded a transition to a predominantly offshore sediment source (coarse sand facies), likely supplied by longshore drift from the Kaituna River, which was associated with the development of Mt Maunganui tombolo and Matakana barrier island. During the Holocene stillstand, the barrier island and tombolo restricted sediment input from offshore, resulting in the deposition of a predominantly locally derived unit (pumiceous sand facies), which still dominates sedimentation in the harbour today.
DOI: 10.6084/m9.figshare.5330908
title: MicroCT files from 'A new species of Xenoturbella from the western Pacific Ocean and the evolution of Xenoturbella'

description: The fileset contains the original microCT files used in the manuscript entitled 'A new species of <i>Xenoturbella</i> from the western Pacific Ocean and the evolution of <i>Xenoturbella</i>'.
DOI: 10.6084/m9.figshare.5330908.v1
title: MicroCT files from 'A new species of Xenoturbella from the western Pacific Ocean and the evolution of Xenoturbella'

description: The fileset contains the original microCT files used in the manuscript entitled 'A new species of <i>Xenoturbella</i> from the western Pacific Ocean and the evolution of <i>Xenoturbella</i>'.
DOI: 10.6084/m9.figshare.5330911.v1
title: Tabela de Clusters

description: Analise dos clusters utilizando a ferramenta R. A identificação de cada cluster está listada na ultima coluna da tabela.
DOI: 10.6084/m9.figshare.5330917.v1
title: Holocene evolution of the southern Tauranga Harbour

description: Tauranga Harbour is a major economic centre and home to New Zealand’s largest port. Despite the importance of the harbour basin, and especially of the shipping channel, the subsurface stratigraphy of this area has not been studied in detail. We use sediment cores retrieved in support of a recent dredging campaign to characterise the subsurface stratigraphy and interpret the sediments in terms of paleoenvironment. Four main facies (volcanic sand, lithic silt, coarse sand and pumiceous sand) were identified using textural, mineralogical and geochemical characteristics. They represent distinct depositional environments at different stages of the Holocene marine transgression (HMT). The oldest facies, deposited prior to the HMT (volcanic sand and lithic silt facies), represent the channel and overbank deposits of an aggrading river system with rapidly migrating channels. During the deposition of this facies, a change in sediment source is evident from geochemical data. This preceded a transition to a predominantly offshore sediment source (coarse sand facies), likely supplied by longshore drift from the Kaituna River, which was associated with the development of Mt Maunganui tombolo and Matakana barrier island. During the Holocene stillstand, the barrier island and tombolo restricted sediment input from offshore, resulting in the deposition of a predominantly locally derived unit (pumiceous sand facies), which still dominates sedimentation in the harbour today.
DOI: 10.6084/m9.figshare.5330824
title: fluency data storing

description: It is a visual display of data showing the number of correct intraverbals emitted by each participant in two treatment conditions.
DOI: 10.6084/m9.figshare.5330824.v1
title: fluency data storing

description: It is a visual display of data showing the number of correct intraverbals emitted by each participant in two treatment conditions.
DOI: 10.6084/m9.figshare.5330593
title: Unified RNA-seq datasets in human cancers and normal tissues - normalized data

description: Normalized gene expression levels
DOI: 10.6084/m9.figshare.5330620
title: Geochemistry and petrogenesis of post-collisional alkaline and peralkaline granites of the Arabian-Nubian Shield: a case study from the southern tip of Sinai Peninsula, Egypt

description: The southern Sinai Peninsula, underlain by the northernmost extension of the Arabian-Nubian Shield, exposes post-collisional calc-alkaline and alkaline granites that represent the youngest phase of late Neoproterozoic igneous activity. We report a petrographic, mineralogical and geochemical investigation of post-collisional plutons of alkaline and, in some cases, peralkaline granite. These granites intrude metamorphosed country rocks as well as syn- and post-collisional calc-alkaline granitoids. The alkaline and peralkaline granites of the southern tip of Sinai divide into three subgroups: syenogranite, alkali feldspar granite and riebeckite granite. The rocks of these subgroups essentially consist of alkali feldspar and quartz with variable amounts of plagioclase and mafic minerals. The syenogranite and alkali feldspar granite contain small amounts of calcic amphibole and biotite, often less than 3%, while the riebeckite granite is distinguished by sodic amphibole (5–10%). These plutons have geochemical signatures typical of post-collisional A-type granites and were most likely emplaced during a transition between orogenic and anorogenic settings. The parental mafic magma may be linked to lithospheric delamination and upwelling of asthenospheric mantle material. Differentiation of the underplated basaltic magma with contributions from the juvenile crust eventually yielded the post-collisional alkaline granites. Petrogenetic modelling of the studied granitic suite shows that pure fractional crystallization cannot quantitatively explain chemical variations with the observed suite, with both major oxides and several trace elements displaying trends opposite to those required by the equilibrium phase assemblage. Instead, we show that compositional variation from syenogranite through alkali feldspar granite to riebeckite granite is dominated by mixing between a low-SiO<sub>2</sub> liquid as primitive or more primitive than the lowest-SiO<sub>2</sub> syenogranite and an evolved, high-SiO<sub>2</sub> liquid that might be a high-degree partial melt of lower crust.
DOI: 10.6084/m9.figshare.5330575
title: Unified RNA-seq datasets in human cancers and normal tissues - unnormalized data

description: Gene expression levels calculated from RSEM’s fpkm
DOI: 10.6084/m9.figshare.5330593.v1
title: Data record 3

description: Normalized gene expression levels
DOI: 10.6084/m9.figshare.5330575.v1
title: Data record 2

description: Gene expression levels calculated from RSEM’s fpkm
DOI: 10.6084/m9.figshare.5330539
title: Unified RNA-seq datasets in human cancers and normal tissues - expected count

description: The expected_count in RSEM's output<br>
DOI: 10.6084/m9.figshare.5330452
title: Data aggregation at the level of molecular pathways improves stability of experimental transcriptomic and proteomic data

description: High throughput technologies opened a new era in biomedicine by enabling massive analysis of gene expression at both RNA and protein levels. Unfortunately, expression data obtained in different experiments are often poorly compatible, even for the same biologic samples. Here, using experimental and bioinformatic investigation of major experimental platforms, we show that aggregation of gene expression data at the level of molecular pathways helps to diminish cross- and intra-platform bias otherwise clearly seen at the level of individual genes. We created a mathematical model of cumulative suppression of data variation that predicts the ideal parameters and the optimal size of a molecular pathway. We compared the abilities to aggregate experimental molecular data for the 5 alternative methods, also evaluated by their capacity to retain meaningful features of biologic samples. The bioinformatic method OncoFinder showed optimal performance in both tests and should be very useful for future cross-platform data analyses.
DOI: 10.6084/m9.figshare.5330452.v1
title: Data aggregation at the level of molecular pathways improves stability of experimental transcriptomic and proteomic data

description: High throughput technologies opened a new era in biomedicine by enabling massive analysis of gene expression at both RNA and protein levels. Unfortunately, expression data obtained in different experiments are often poorly compatible, even for the same biologic samples. Here, using experimental and bioinformatic investigation of major experimental platforms, we show that aggregation of gene expression data at the level of molecular pathways helps to diminish cross- and intra-platform bias otherwise clearly seen at the level of individual genes. We created a mathematical model of cumulative suppression of data variation that predicts the ideal parameters and the optimal size of a molecular pathway. We compared the abilities to aggregate experimental molecular data for the 5 alternative methods, also evaluated by their capacity to retain meaningful features of biologic samples. The bioinformatic method OncoFinder showed optimal performance in both tests and should be very useful for future cross-platform data analyses.
DOI: 10.6084/m9.figshare.5330539.v1
title: Data record 1

description: The expected_count in RSEM's output<br>
DOI: 10.6084/m9.figshare.5329660
title: BORC coordinates encounter and fusion of lysosomes with autophagosomes

description: Whereas the mechanisms involved in autophagosome formation have been extensively studied for the past 2 decades, those responsible for autophagosome-lysosome fusion have only recently begun to garner attention. In this study, we report that the multisubunit BORC complex, previously implicated in kinesin-dependent movement of lysosomes toward the cell periphery, is required for efficient autophagosome-lysosome fusion. Knockout (KO) of <i>BORC</i> subunits causes not only juxtanuclear clustering of lysosomes, but also increased levels of the autophagy protein LC3B-II and the receptor SQSTM1. Increases in LC3B-II occur without changes in basal MTORC1 activity and autophagy initiation. Instead, LC3B-II accumulation largely results from decreased lysosomal degradation. Further experiments show that <i>BORC</i> KO impairs both the encounter and fusion of autophagosomes with lysosomes. Reduced encounters result from an inability of lysosomes to move toward the peripheral cytoplasm, where many autophagosomes are formed. However, <i>BORC</i> KO also reduces the recruitment of the HOPS tethering complex to lysosomes and assembly of the STX17-VAMP8-SNAP29 <i>trans</i>-SNARE complex involved in autophagosome-lysosome fusion. Through these dual roles, BORC integrates the kinesin-dependent movement of lysosomes toward autophagosomes with HOPS-dependent autophagosome-lysosome fusion. These findings reveal a requirement for lysosome dispersal in autophagy that is independent of changes in MTORC1 signaling, and identify BORC as a novel regulator of autophagosome-lysosome fusion.
DOI: 10.6084/m9.figshare.5329660.v2
title: BORC coordinates encounter and fusion of lysosomes with autophagosomes

description: Whereas the mechanisms involved in autophagosome formation have been extensively studied for the past 2 decades, those responsible for autophagosome-lysosome fusion have only recently begun to garner attention. In this study, we report that the multisubunit BORC complex, previously implicated in kinesin-dependent movement of lysosomes toward the cell periphery, is required for efficient autophagosome-lysosome fusion. Knockout (KO) of <i>BORC</i> subunits causes not only juxtanuclear clustering of lysosomes, but also increased levels of the autophagy protein LC3B-II and the receptor SQSTM1. Increases in LC3B-II occur without changes in basal MTORC1 activity and autophagy initiation. Instead, LC3B-II accumulation largely results from decreased lysosomal degradation. Further experiments show that <i>BORC</i> KO impairs both the encounter and fusion of autophagosomes with lysosomes. Reduced encounters result from an inability of lysosomes to move toward the peripheral cytoplasm, where many autophagosomes are formed. However, <i>BORC</i> KO also reduces the recruitment of the HOPS tethering complex to lysosomes and assembly of the STX17-VAMP8-SNAP29 <i>trans</i>-SNARE complex involved in autophagosome-lysosome fusion. Through these dual roles, BORC integrates the kinesin-dependent movement of lysosomes toward autophagosomes with HOPS-dependent autophagosome-lysosome fusion. These findings reveal a requirement for lysosome dispersal in autophagy that is independent of changes in MTORC1 signaling, and identify BORC as a novel regulator of autophagosome-lysosome fusion.
DOI: 10.6084/m9.figshare.5329660.v1
title: BORC Coordinates Encounter and Fusion of Lysosomes with Autophagosomes

description: Whereas the mechanisms involved in autophagosome formation have been extensively studied for the past 2 decades, those responsible for autophagosome-lysosome fusion have only recently begun to garner attention. In this study, we report that the multisubunit BORC complex, previously implicated in kinesin-dependent movement of lysosomes toward the cell periphery, is required for efficient autophagosome-lysosome fusion. Knockout (KO) of <i>BORC</i> subunits causes not only juxtanuclear clustering of lysosomes, but also increased levels of the autophagy protein LC3B-II and the receptor SQSTM1. Increases in LC3B-II occur without changes in basal MTORC1 activity and autophagy initiation. Instead, LC3B-II accumulation largely results from decreased lysosomal degradation. Further experiments show that <i>BORC</i> KO impairs both the encounter and fusion of autophagosomes with lysosomes. Reduced encounters result from an inability of lysosomes to move toward the peripheral cytoplasm, where many autophagosomes are formed. However, <i>BORC</i> KO also reduces the recruitment of the HOPS tethering complex to lysosomes and assembly of the STX17-VAMP8-SNAP29 <i>trans</i>-SNARE complex involved in autophagosome-lysosome fusion. Through these dual roles, BORC integrates the kinesin-dependent movement of lysosomes toward autophagosomes with HOPS-dependent autophagosome-lysosome fusion. These findings reveal a requirement for lysosome dispersal in autophagy that is independent of changes in MTORC1 signaling, and identify BORC as a novel regulator of autophagosome-lysosome fusion.