cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1569020.v2
title: Adaptive radiotherapy for locally advanced non-small cell lung cancer, can we predict when and for whom?

description: ABSTRACT<b>Background.</b> Adaptive radiotherapy (ART) could be a tool to reduce toxicity and to facilitate dose escalation in stage III NSCLC. Our aim was to identify the most appropriate time and potential benefit of ART.<b>Material and methods.</b> We analyzed volume reduction and dosimetric consequences of 41 patients who were treated with concurrent (cCRT) (n = 21) or sequential (sCRT) chemoradiotherapy to a median dose of 70 Gy, 2 Gy/F. At every treatment fraction a cone-beam CT (CBCT) was performed. The gross tumor volume (GTV-T) was adapted (exclusion of lymph nodes) to create the GTV-T-F1. Every fifth fraction (F5–F30), the GTV-T-F1 was adapted on the CBCT to create a GTV-T-Fx. Dose volume histograms were recalculated for every GTV-T-Fx, enabling to create lookup tables to predict the theoretical dosimetric advantage on common lung dose constraints.<b>Results.</b> The average GTV reduction was 42.1% (range 4.0–69.3%); 50.1% and 33.7% for the cCRT and sCRT patients, respectively. A linear relationship between GTV-T-F1 volume and absolute volume decrease was found for both groups. The mean V5, V20, V30 and mean lung dose increased by 0.8, 3.1, 5.2 and 3.4%, respectively. A larger increase (p &lt; 0.05) was observed for peripheral tumors and cCRT. Lookup tables were generated.<b>Conclusion.</b> ART offers the most beneficial dosimetric effects when performed around fraction 15, especially for patients with a large initial GTV-T treated by cCRT.
DOI: 10.6084/m9.figshare.1569020.v1
title: Adaptive radiotherapy for locally advanced non-small cell lung cancer, can we predict when and for whom?

description: <b>Background.</b> Adaptive radiotherapy (ART) could be a tool to reduce toxicity and to facilitate dose escalation in stage III NSCLC. Our aim was to identify the most appropriate time and potential benefit of ART.<b>Material and methods.</b> We analyzed volume reduction and dosimetric consequences of 41 patients who were treated with concurrent (cCRT) (n = 21) or sequential (sCRT) chemoradiotherapy to a median dose of 70 Gy, 2 Gy/F. At every treatment fraction a cone-beam CT (CBCT) was performed. The gross tumor volume (GTV-T) was adapted (exclusion of lymph nodes) to create the GTV-T-F1. Every fifth fraction (F5–F30), the GTV-T-F1 was adapted on the CBCT to create a GTV-T-Fx. Dose volume histograms were recalculated for every GTV-T-Fx, enabling to create lookup tables to predict the theoretical dosimetric advantage on common lung dose constraints.<b>Results.</b> The average GTV reduction was 42.1% (range 4.0–69.3%); 50.1% and 33.7% for the cCRT and sCRT patients, respectively. A linear relationship between GTV-T-F1 volume and absolute volume decrease was found for both groups. The mean V5, V20, V30 and mean lung dose increased by 0.8, 3.1, 5.2 and 3.4%, respectively. A larger increase (p &lt; 0.05) was observed for peripheral tumors and cCRT. Lookup tables were generated. <i>Conclusion.</i> ART offers the most beneficial dosimetric effects when performed around fraction 15, especially for patients with a large initial GTV-T treated by cCRT.
DOI: 10.6084/m9.figshare.1568993
title: Weed Control Data with TDZ analogs

description: Weed Control data with analogs of TDZ synthesized at the University of Tennessee
DOI: 10.6084/m9.figshare.1568991
title: Identification of functional networks associated with cell death in the retina of OXYS rats during the development of retinopathy

description: Age-related macular degeneration (AMD) is a major cause of blindness in developed countries, and the molecular pathogenesis of early events in AMD is poorly understood. Senescence-accelerated OXYS rats develop AMD-like retinopathy. The aim of this study was to explore the differences in retinal gene expression between OXYS and Wistar (control) rats at age 20 d and to identify the pathways of retinal cell death involved in the OXYS retinopathy initiation and progression. Retinal mRNA profiles of 20-day-old OXYS and Wistar rats were generated at the sequencing read depth 40 mln, in triplicate, using Illumina GAIIx. A terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate nick end labeling (TUNEL) assay was performed to measure the apoptosis level. GeneMANIA was used to construct interaction networks for differentially expressed (DE) apoptosis-related genes at ages 20 d and 3 and 18 months. Functional analysis was suggestive of a developmental process, signal transduction, and cell differentiation as the most enriched biological processes among 245 DE genes at age 20 d An increased level of apoptosis was observed in OXYS rats at age 20 d but not at advanced stages. We identified functional clusters in the constructed interaction networks and possible hub genes (<i>Rasa1, cFLAR, Birc3, Cdk1, Hspa1b, Erbb3</i>, and <i>Ntf3)</i>. We also demonstrated the significance of the extrinsic apoptotic pathway at preclinical, early, and advanced stages of retinopathy development. Besides the cell death signaling pathways, immune system-related processes and lipid-metabolic processes showed overrepresentation in the clusters of all networks. These characteristics of the expression profile of the genes functionally associated with apoptosis may contribute to the pathogenesis of AMD-like retinopathy in senescence-accelerated OXYS rats.
DOI: 10.6084/m9.figshare.1568993.v1
title: Weed Control Data with TDZ analogs

description: Weed Control data with analogs of TDZ synthesized at the University of Tennessee
DOI: 10.6084/m9.figshare.1568988
title: A wavelet-based approach to the analysis and modelling of financial time series exhibiting strong long-range dependence: the case of Southeast Europe

description: This paper demonstrates the utilization of wavelet-based tools for the analysis and prediction of financial time series exhibiting strong long-range dependence (LRD). Commonly emerging markets' stock returns are characterized by LRD. Therefore, we track the LRD evolvement for the return series of six Southeast European stock indices through the application of a wavelet-based semi-parametric method. We further engage the á trous wavelet transform in order to extract deeper knowledge on the returns term structure and utilize it for prediction purposes. In particular, a multiscale autoregressive (MAR) model is fitted and its out-of-sample forecast performance is benchmarked to that of ARMA. Additionally, a data-driven MAR feature selection procedure is outlined. We find that the wavelet-based method captures adequately LRD dynamics both in calm as well as in turmoil periods detecting the presence of transitional changes. At the same time, the MAR model handles with the complicated autocorrelation structure implied by the LRD in a parsimonious way achieving better performance.
DOI: 10.6084/m9.figshare.1568991.v2
title: Identification of functional networks associated with cell death in the retina of OXYS rats during the development of retinopathy

description: Age-related macular degeneration (AMD) is a major cause of blindness in developed countries, and the molecular pathogenesis of early events in AMD is poorly understood. Senescence-accelerated OXYS rats develop AMD-like retinopathy. The aim of this study was to explore the differences in retinal gene expression between OXYS and Wistar (control) rats at age 20 d and to identify the pathways of retinal cell death involved in the OXYS retinopathy initiation and progression. Retinal mRNA profiles of 20-day-old OXYS and Wistar rats were generated at the sequencing read depth 40 mln, in triplicate, using Illumina GAIIx. A terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate nick end labeling (TUNEL) assay was performed to measure the apoptosis level. GeneMANIA was used to construct interaction networks for differentially expressed (DE) apoptosis-related genes at ages 20 d and 3 and 18 months. Functional analysis was suggestive of a developmental process, signal transduction, and cell differentiation as the most enriched biological processes among 245 DE genes at age 20 d An increased level of apoptosis was observed in OXYS rats at age 20 d but not at advanced stages. We identified functional clusters in the constructed interaction networks and possible hub genes (<i>Rasa1, cFLAR, Birc3, Cdk1, Hspa1b, Erbb3</i>, and <i>Ntf3)</i>. We also demonstrated the significance of the extrinsic apoptotic pathway at preclinical, early, and advanced stages of retinopathy development. Besides the cell death signaling pathways, immune system-related processes and lipid-metabolic processes showed overrepresentation in the clusters of all networks. These characteristics of the expression profile of the genes functionally associated with apoptosis may contribute to the pathogenesis of AMD-like retinopathy in senescence-accelerated OXYS rats.
DOI: 10.6084/m9.figshare.1568991.v1
title: Identification of functional networks associated with cell death in the retina of OXYS rats during the development of retinopathy

description: ABSTRACT<b>Purpose</b>: Age-related macular degeneration (AMD) is a major cause of blindness in developed countries, and the molecular pathogenesis of early events in AMD is poorly understood. Senescence-accelerated OXYS rats develop AMD-like retinopathy. The aim of this study was to explore the differences in retinal gene expression between OXYS and Wistar (control) rats at age 20 days and to identify the pathways of retinal cell death involved in the OXYS retinopathy initiation and progression.<b>Methods</b>: Retinal mRNA profiles of 20-day-old OXYS and Wistar rats were generated at the sequencing read depth 40 mln, in triplicate, using Illumina GAIIx. A terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate nick end labeling (TUNEL) assay was performed to measure the apoptosis level. GeneMANIA was used to construct interaction networks for differentially expressed (DE) apoptosis-related genes at ages 20 days and three and 18 months.<b>Results</b>: Functional analysis was suggestive of a developmental process, signal transduction, and cell differentiation as the most enriched biological processes among 245 DE genes at age 20 days. An increased level of apoptosis was observed in OXYS rats at age 20 days but not at advanced stages. We identified functional clusters in the constructed interaction networks and possible hub genes (<i>Rasa1, cFLAR, Birc3, Cdk1, Hspa1b, Erbb3</i>, and <i>Ntf3</i>). We also demonstrated the significance of the extrinsic apoptotic pathway at preclinical, early, and advanced stages of retinopathy development. Besides the cell death signaling pathways, immune system-related processes and lipid-metabolic processes showed overrepresentation in the clusters of all networks.<b>Conclusions</b>: These characteristics of the expression profile of the genes functionally associated with apoptosis may contribute to the pathogenesis of AMD-like retinopathy in senescence-accelerated OXYS rats.
DOI: 10.6084/m9.figshare.1568985
title: Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions?

description: We introduce a representative benchmark database of 20 cycloreversion reaction energies obtained by means of the high-level W1 thermochemical protocol. We use these benchmark values to assess the performance of a variety of contemporary DFT, double-hybrid DFT (DHDFT), standard ab initio, and compound thermochemistry methods. We show that this set of reaction energies provides an extremely challenging test for nearly all of the considered DFT and DHDFT methods. For example, about 80% of the considered functionals result in root-mean-square deviations (RMSDs) above 10 kJ mol<sup>−1</sup>. The best DFT and DHDFT procedures are ωB97X and DSD-PBEP86-D3, with RMSDs of 4.7 and 7.9 kJ mol<sup>−1</sup>, respectively. Coupled with the fact that the barrier heights for these reactions also pose a significant challenge for many DFT methods, this work shows that only a handful of functionals can quantitatively describe all aspects of the potential energy surface of this important class of reactions. In addition, this work shows that London dispersion effects are particularly large for this class of reactions. For example, empirical D3 dispersion corrections reduce the RMSDs for the DFT and DHDFT procedures by amounts ranging from 3.5 (PBE and B2K-PLYP) to 22.0 (BLYP) kJ mol<sup>−1</sup>.
DOI: 10.6084/m9.figshare.1568988.v1
title: A wavelet-based approach to the analysis and modelling of financial time series exhibiting strong long-range dependence: the case of Southeast Europe

description: This paper demonstrates the utilization of wavelet-based tools for the analysis and prediction of financial time series exhibiting strong long-range dependence (LRD). Commonly emerging markets' stock returns are characterized by LRD. Therefore, we track the LRD evolvement for the return series of six Southeast European stock indices through the application of a wavelet-based semi-parametric method. We further engage the á trous wavelet transform in order to extract deeper knowledge on the returns term structure and utilize it for prediction purposes. In particular, a multiscale autoregressive (MAR) model is fitted and its out-of-sample forecast performance is benchmarked to that of ARMA. Additionally, a data-driven MAR feature selection procedure is outlined. We find that the wavelet-based method captures adequately LRD dynamics both in calm as well as in turmoil periods detecting the presence of transitional changes. At the same time, the MAR model handles with the complicated autocorrelation structure implied by the LRD in a parsimonious way achieving better performance.
DOI: 10.6084/m9.figshare.1568983
title: Identification of ACE-inhibitory peptides from <i>Phaseolus vulgaris</i> after <i>in vitro</i> gastrointestinal digestion

description: The objective of this study was to identify the angiotensin I-converting enzyme (ACE)-inhibitory peptides released from thermally treated <i>Phaseolus vulgaris</i> (pinto) whole beans after <i>in vitro</i> gastrointestinal digestion. The degree of hydrolysis increased during digestion reaching a value of 50% at the end of the pancreatic digestion. The &lt;3 kDa fraction of the postpancreatic sample showed high ACE-inhibitory activity (<i>IC</i><sub>50</sub> = 105.6 ± 2.1 μg of peptides/mL). Peptides responsible for the ACE-inhibitory activity were isolated by reverse-phase high-performance liquid chromatography (HPLC). Three fractions, showing the highest inhibitory activity, were selected for tandem mass spectrometry (MS/MS) experiments. Eleven of the identified sequences have previously been described as ACE-inhibitors. Most of the identified bioactive peptides have a hydrophobic amino acid, (iso)leucine or phenylalanine, or proline at the C-terminal position, which is crucial for their ACE-inhibitory activity. The sequence of some peptides allowed us to anticipate the presence of ACE-inhibitory activity.
DOI: 10.6084/m9.figshare.1568985.v1
title: Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions?

description: We introduce a representative benchmark database of 20 cycloreversion reaction energies obtained by means of the high-level W1 thermochemical protocol. We use these benchmark values to assess the performance of a variety of contemporary DFT, double-hybrid DFT (DHDFT), standard ab initio, and compound thermochemistry methods. We show that this set of reaction energies provides an extremely challenging test for nearly all of the considered DFT and DHDFT methods. For example, about 80% of the considered functionals result in root-mean-square deviations (RMSDs) above 10 kJ mol<sup>−1</sup>. The best DFT and DHDFT procedures are ωB97X and DSD-PBEP86-D3, with RMSDs of 4.7 and 7.9 kJ mol<sup>−1</sup>, respectively. Coupled with the fact that the barrier heights for these reactions also pose a significant challenge for many DFT methods, this work shows that only a handful of functionals can quantitatively describe all aspects of the potential energy surface of this important class of reactions. In addition, this work shows that London dispersion effects are particularly large for this class of reactions. For example, empirical D3 dispersion corrections reduce the RMSDs for the DFT and DHDFT procedures by amounts ranging from 3.5 (PBE and B2K-PLYP) to 22.0 (BLYP) kJ mol<sup>−1</sup>.
DOI: 10.6084/m9.figshare.1568983.v2
title: Identification of ACE-inhibitory peptides from <i>Phaseolus vulgaris</i> after <i>in vitro</i> gastrointestinal digestion

description: The objective of this study was to identify the angiotensin I-converting enzyme (ACE)-inhibitory peptides released from thermally treated <i>Phaseolus vulgaris</i> (pinto) whole beans after <i>in vitro</i> gastrointestinal digestion. The degree of hydrolysis increased during digestion reaching a value of 50% at the end of the pancreatic digestion. The &lt;3 kDa fraction of the postpancreatic sample showed high ACE-inhibitory activity (<i>IC</i><sub>50</sub> = 105.6 ± 2.1 μg of peptides/mL). Peptides responsible for the ACE-inhibitory activity were isolated by reverse-phase high-performance liquid chromatography (HPLC). Three fractions, showing the highest inhibitory activity, were selected for tandem mass spectrometry (MS/MS) experiments. Eleven of the identified sequences have previously been described as ACE-inhibitors. Most of the identified bioactive peptides have a hydrophobic amino acid, (iso)leucine or phenylalanine, or proline at the C-terminal position, which is crucial for their ACE-inhibitory activity. The sequence of some peptides allowed us to anticipate the presence of ACE-inhibitory activity.
DOI: 10.6084/m9.figshare.1568983.v1
title: Identification of ACE-inhibitory peptides from <i>Phaseolus vulgaris</i> after <i>in vitro</i> gastrointestinal digestion

description: The objective of this study was to identify the angiotensin I-converting enzyme (ACE)-inhibitory peptides released from thermally treated <i>Phaseolus vulgaris</i> (pinto) whole beans after <i>in vitro</i> gastrointestinal digestion. The degree of hydrolysis increased during digestion reaching a value of 50% at the end of the pancreatic digestion. The &lt;3 kDa fraction of the postpancreatic sample showed high ACE-inhibitory activity (<i>IC</i><sub>50</sub> = 105.6 ± 2.1 μg of peptides/mL). Peptides responsible for the ACE-inhibitory activity were isolated by reverse-phase high-performance liquid chromatography (HPLC). Three fractions, showing the highest inhibitory activity, were selected for tandem mass spectrometry (MS/MS) experiments. Eleven of the identified sequences have previously been described as ACE-inhibitors. Most of the identified bioactive peptides have a hydrophobic amino acid, (iso)leucine or phenylalanine, or proline at the C-terminal position, which is crucial for their ACE-inhibitory activity. The sequence of some peptides allowed us to anticipate the presence of ACE-inhibitory activity.
DOI: 10.6084/m9.figshare.1568979
title: Root zone of a continental rift: the Neoproterozoic Kebnekaise Intrusive Complex, northern Swedish Caledonides

description: Mafic magmatic rocks formed between ca. 615 and 560 Ma along the Neoproterozoic margins of Baltica and Laurentia are classically attributed to continental rifting heralding the opening of the Iapetus Ocean. We report new data for the Kebnekaise Intrusive Complex (KIC) exposed in the Seve Nappes in northern Sweden. The KIC consists of sheeted dolerite dykes and gabbroic bodies with mutually intrusive relations. Major and trace element data exhibit a transitional- to normal-mid-ocean-ridge basalt-type geochemical signature. Differentiation processes and late-stage liquid immiscibility of a tholeiitic melt are considered to account for the compositional range exhibited by the KIC igneous rocks. U/Pb SIMS geochronological data from zircon rims yield an emplacement age of 578 ± 9 Ma. The KIC is thus younger and more depleted than coeval mafic rocks found in the Seve Nappe, and is interpreted to represent a high-level magma plumbing system in a late-stage continental rift. The composition and volume of rift-related igneous rocks in the Seve Nappes are inconsistent with a mantle plume origin, but are thought to record progressive lithospheric thinning and increasing involvement of an asthenospheric mantle component.
DOI: 10.6084/m9.figshare.1568979.v1
title: Root zone of a continental rift: the Neoproterozoic Kebnekaise Intrusive Complex, northern Swedish Caledonides

description: Mafic magmatic rocks formed between ca. 615 and 560 Ma along the Neoproterozoic margins of Baltica and Laurentia are classically attributed to continental rifting heralding the opening of the Iapetus Ocean. We report new data for the Kebnekaise Intrusive Complex (KIC) exposed in the Seve Nappes in northern Sweden. The KIC consists of sheeted dolerite dykes and gabbroic bodies with mutually intrusive relations. Major and trace element data exhibit a transitional- to normal-mid-ocean-ridge basalt-type geochemical signature. Differentiation processes and late-stage liquid immiscibility of a tholeiitic melt are considered to account for the compositional range exhibited by the KIC igneous rocks. U/Pb SIMS geochronological data from zircon rims yield an emplacement age of 578 ± 9 Ma. The KIC is thus younger and more depleted than coeval mafic rocks found in the Seve Nappe, and is interpreted to represent a high-level magma plumbing system in a late-stage continental rift. The composition and volume of rift-related igneous rocks in the Seve Nappes are inconsistent with a mantle plume origin, but are thought to record progressive lithospheric thinning and increasing involvement of an asthenospheric mantle component.
DOI: 10.6084/m9.figshare.1568974
title: Exploring the association between working memory and driving performance in Parkinson's disease

description: <b>Objective:</b> The aim of this study was to explore whether varying levels of operational and tactical driving task demand differentially affect drivers with Parkinson's disease (PD) and control drivers in their sign recall. <b>Methods:</b> Study participants aged between 50 and 70 years included a group of drivers with PD (<i>n</i> = 10) and a group of age- and sex-matched control drivers (<i>n</i> = 10). Their performance in a sign recall task was measured using a driving simulator. <b>Results:</b> Drivers in the control group performed better than drivers with PD in a sign recall task, but this trend was not statistically significant (<i>P</i> =.43). In addition, regardless of group membership, subjects' performance differed according to varying levels of task demand. Performance in the sign recall task was more likely to drop with increasing task demand (<i>P</i> =.03). This difference was significant when the variation in task demand was associated with a cognitive task; that is, when drivers were required to apply the instructions from working memory. <b>Conclusions:</b> Although the conclusions drawn from this study are tentative, the evidence presented here is encouraging with regard to the use of a driving simulator to examine isolated cognitive functions underlying driving performance in PD. With an understanding of its limitations, such driving simulation in combination with functional assessment batteries measuring physical, visual, and cognitive abilities could comprise one component of a multitiered system to evaluate medical fitness to drive.