cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7776827.v1
title: Membrane partitioning of peptide aggregates: coarse-grained molecular dynamics simulations

description: Coarse-grained molecular dynamics (CGMD) simulation technique (MARTINI force field) is applied to monitor the aggregation of helical peptides representing the transmembrane sequence and its extension of bone marrow stromal cell antigen 2 (BST-2). One of the peptides is coupled with a protein transducing domain (PTD) of nine arginine residues (R9) at its <i>N</i>-terminal side as well as a peptide, pep11**, which has been shown to bind to human papilloma virus 16 (HPV16) E6 oncoprotein. A short hydrophobic stretch of the transmembrane domain (TMD) of BST-2 aggregates the fastest and inserts into a lipid membrane. An aggregate of R9-pep11** attaches to the membrane <i>via</i> simultaneous contact of many arginine residues. Monomers from the aggregates of the shortest of the hydrophobic TMDs dissolve into the opposing leaflet when the aggregate spans the bilayer. A ‘flipping’ of the individual monomeric peptides is not observed. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.7776827.v2
title: Membrane partitioning of peptide aggregates: coarse-grained molecular dynamics simulations

description: Coarse-grained molecular dynamics (CGMD) simulation technique (MARTINI force field) is applied to monitor the aggregation of helical peptides representing the transmembrane sequence and its extension of bone marrow stromal cell antigen 2 (BST-2). One of the peptides is coupled with a protein transducing domain (PTD) of nine arginine residues (R9) at its <i>N</i>-terminal side as well as a peptide, pep11**, which has been shown to bind to human papilloma virus 16 (HPV16) E6 oncoprotein. A short hydrophobic stretch of the transmembrane domain (TMD) of BST-2 aggregates the fastest and inserts into a lipid membrane. An aggregate of R9-pep11** attaches to the membrane <i>via</i> simultaneous contact of many arginine residues. Monomers from the aggregates of the shortest of the hydrophobic TMDs dissolve into the opposing leaflet when the aggregate spans the bilayer. A ‘flipping’ of the individual monomeric peptides is not observed. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.7776701
title: Long-term outcomes following stereotactic body radiotherapy boost for oropharyngeal squamous cell carcinoma

description: <b>Background/purpose:</b> To determine the efficacy and toxicity profile of a stereotactic body radiotherapy (SBRT) boost as a first line treatment in patients with oropharyngeal squamous cell carcinoma (OPSCC). <b>Materials and methods:</b> We performed a retrospective cohort study in 195 consecutive OPSCC patients with T1-small T3 disease, treated at Erasmus MC between 2009 and 2016 with a SBRT (3 × 5.5 Gy) boost after 46 Gy IMRT. Primary endpoints were disease-specific survival (DSS) and Grade ≥3 toxicity (Common Terminology Criteria). The Kaplan-Meier method and Cox regression model were applied to determine rates and risk factors. <b>Results:</b> The median follow-up was 4.3 years. Treatment compliance was high (100%). Rates of 5-year DSS and late grade ≥3 toxicity were 85% and 28%, respectively. Five-year overall survival was 67%. The most frequently observed toxicities were mucosal ulceration or soft tissue necrosis (<i>n</i> = 30, 5 year 18%), dysphagia or weight loss (<i>n</i> = 18, 5 year 12%) and osteoradionecrosis (<i>n</i> = 11, 5 year 9%). Current smoker status (hazard ratio [HR] = 2.9, <i>p</i> = .001) and Charlson Comorbidity Index ≥2 (HR = 1.9, <i>p</i> = .03) were was associated with increased toxicity risk. Tooth extraction prior to RT was associated with increased osteoradionecrosis risk (HR = 6.4, <i>p</i> = .006). <b>Conclusion:</b> We reported on outcomes in the largest patient series to date treated with a hypofractionated boost for OPSCC. Efficacy was good with survival rates comparable to conventionally fractionated (chemo)radiotherapy. Grade ≥3 toxicity profiles showed high rates of soft tissue necrosis and osteoradionecrosis. Strategies to mitigate severe toxicity risks are under investigation to improve the tolerability of the SBRT boost.
DOI: 10.6084/m9.figshare.7776695
title: Supplementary Material for: Medial Amygdala <b><i>Kiss1</i></b> Neurons Mediate Female Pheromone Stimulation of Luteinizing Hormone in Male Mice

description: <b><i>Background/Aims:</i></b> The medial amygdala (MeA) responds to olfactory stimuli and alters reproductive physiology. However, the neuronal circuit that relays signals from the MeA to the reproductive axis remains poorly defined. This study aimed to test whether MeA kisspeptin (MeA<sup>Kiss</sup>) neurons in male mice are sensitive to sexually relevant olfactory stimuli and transmit signals to alter reproductive physiology. We also investigated whether MeA<sup>Kiss</sup> neurons have the capacity to elaborate glutamate and GABA neurotransmitters and potentially contribute to reproductive axis regulation. <b><i>Methods:</i></b> Using female urine as a pheromone stimulus, MeA<sup>Kiss</sup> neuronal activity was analysed and serum luteinizing hormone (LH) was measured in male mice. Next, using a chemogenetic approach, MeA<sup>Kiss</sup> neurons were bi-directionally modulated to measure the effect on serum LH and evaluate the activation of the preoptic area. Lastly, using in situ<i></i> hybridization, we identified the proportion of MeA<sup>Kiss</sup> neurons that express markers for GABAergic (Vgat) and glutamatergic (Vglut2) neurotransmission. <b><i>Results:</i></b> Male mice exposed to female urine showed a two-fold increase in the number of c-Fos-positive MeA<sup>Kiss</sup> neurons concomitant with raised LH. Chemogenetic activation of MeA<sup>Kiss</sup> neurons significantly increased LH in the absence of urine exposure, whereas inhibition of MeA<sup>Kiss</sup> neurons did not alter LH. In situ<i></i> hybridization revealed that MeA<sup>Kiss</sup> neurons are a mixed neuronal population in which 71% express Vgat mRNA, 29% express Vglut2 mRNA, and 6% express both. <b><i>Conclusions:</i></b> Our results uncover, for the first time, that MeA<sup>Kiss</sup> neurons process sexually relevant olfactory signals to influence reproductive hormone levels in male mice, likely through a complex interplay of neuropeptide and neurotransmitter signalling.
DOI: 10.6084/m9.figshare.7776701.v1
title: Long-term outcomes following stereotactic body radiotherapy boost for oropharyngeal squamous cell carcinoma

description: <b>Background/purpose:</b> To determine the efficacy and toxicity profile of a stereotactic body radiotherapy (SBRT) boost as a first line treatment in patients with oropharyngeal squamous cell carcinoma (OPSCC). <b>Materials and methods:</b> We performed a retrospective cohort study in 195 consecutive OPSCC patients with T1-small T3 disease, treated at Erasmus MC between 2009 and 2016 with a SBRT (3 × 5.5 Gy) boost after 46 Gy IMRT. Primary endpoints were disease-specific survival (DSS) and Grade ≥3 toxicity (Common Terminology Criteria). The Kaplan-Meier method and Cox regression model were applied to determine rates and risk factors. <b>Results:</b> The median follow-up was 4.3 years. Treatment compliance was high (100%). Rates of 5-year DSS and late grade ≥3 toxicity were 85% and 28%, respectively. Five-year overall survival was 67%. The most frequently observed toxicities were mucosal ulceration or soft tissue necrosis (<i>n</i> = 30, 5 year 18%), dysphagia or weight loss (<i>n</i> = 18, 5 year 12%) and osteoradionecrosis (<i>n</i> = 11, 5 year 9%). Current smoker status (hazard ratio [HR] = 2.9, <i>p</i> = .001) and Charlson Comorbidity Index ≥2 (HR = 1.9, <i>p</i> = .03) were was associated with increased toxicity risk. Tooth extraction prior to RT was associated with increased osteoradionecrosis risk (HR = 6.4, <i>p</i> = .006). <b>Conclusion:</b> We reported on outcomes in the largest patient series to date treated with a hypofractionated boost for OPSCC. Efficacy was good with survival rates comparable to conventionally fractionated (chemo)radiotherapy. Grade ≥3 toxicity profiles showed high rates of soft tissue necrosis and osteoradionecrosis. Strategies to mitigate severe toxicity risks are under investigation to improve the tolerability of the SBRT boost.
DOI: 10.6084/m9.figshare.7776311
title: Egg to adult viability

description: Number of adults from 20 eggs
DOI: 10.6084/m9.figshare.7776311.v1
title: Egg to adult viability

description: Number of adults from 20 eggs
DOI: 10.6084/m9.figshare.7776293
title: Starvation resistance

description: Starvation resistance of male and female flies after feeding regimes
DOI: 10.6084/m9.figshare.7776293.v1
title: Starvation resistance

description: Starvation resistance of male and female flies after feeding regimes
DOI: 10.6084/m9.figshare.7776269
title: Male reproductive output: Mating time and egg hatchability

description: Mating time and the number of eggs laid by the female and the number of eggs that hatched.
DOI: 10.6084/m9.figshare.7776269.v1
title: Male reproductive output: Mating time and egg hatchability

description: Mating time and the number of eggs laid by the female and the number of eggs that hatched.
DOI: 10.23645/epacomptox.7776212
title: CFM-ID Paper Data

description: This upload is a zip containing the following files:<b><br></b><b>Predicted EI-MS Spectra of CompTox Chemicals Dashboard Structures:</b>Predicted EI-MS spectra of ~700,000 chemical structures from the CompTox Chemicals Dashboard were generated using the CFM-ID model developed by Allen, et al. (https://doi.org/10.1021/acs.analchem.6b01622). These data are provided in .dat ASCII format.<b><br></b><b>Predicted MS/MS Spectra in ESI-positive mode of CompTox Chemicals Dashboard Structures:</b>Predicted MS/MS spectra of ~700,000 chemical structures from the CompTox Chemicals Dashboard were generated using the CFM-ID model developed by Allen, et al. (https://doi.org/10.1007/s11306-014-0676-4) in ESI-positive mode. These data are provided in .dat ASCII format.<b><br></b><b>Predicted MS/MS Spectra in ESI-negative mode of CompTox Chemicals Dashboard Structures:</b>Predicted MS/MS spectra of ~700,000 chemical structures from the CompTox Chemicals Dashboard were generated using the CFM-ID model developed by Allen, et al. (https://doi.org/10.1007/s11306-014-0676-4) in ESI-negative mode. These data are provided in .dat ASCII format.<b></b><b><br></b><b>Database of Predicted Spectra of CompTox Chemicals Dashboard Structures:</b>Predicted spectra of ~700,000 chemical structures from the CompTox Chemicals Dashboard were generated using the CFM-ID model developed by Allen, et al. (https://doi.org/10.1007/s11306-014-0676-4 and https://doi.org/10.1007/s11306-014-0676-4) in ESI-positive and negative modes and EI-MS. These data are provided in an SQL relational database.<b><br></b><b>Database Schema File of Predicted Spectra of CompTox Chemicals Dashboard Structures:</b>Predicted spectra of ~700,000 chemical structures from the CompTox Chemicals Dashboard were generated using the CFM-ID model developed by Allen, et al. (https://doi.org/10.1007/s11306-014-0676-4 and https://doi.org/10.1007/s11306-014-0676-4) in ESI-positive and negative modes and EI-MS. These data are provided in an SQL relational database and described in this SQL Schema file.<b><br></b><b>Chemical Metadata from the CompTox Chemicals Dashboard Linked to Predicted Spectra:</b>Chemical metadata from the CompTox Chemicals Dashboard are linked through the unique DSSTox chemical identifier (DTXCID) enabling integration to predicted mass spectral data. Chemical metadata includes CASRN, molecular formula, SMILES, presence in lists, and data source occurrences.<b><br></b><b>Chemical Structures that failed during mass spectral prediction:</b>Predicted spectra of ~700,000 chemical structures from the CompTox Chemicals Dashboard were generated using the CFM-ID model developed by Allen, et al. (https://doi.org/10.1007/s11306-014-0676-4 and https://doi.org/10.1007/s11306-014-0676-4) in ESI-positive and negative modes and EI-MS. Due to structural errors and model constraints, the prediction of all MS modes failed for 56 structures.
DOI: 10.6084/m9.figshare.7776188
title: Psychotherapy or Medication for Depression? Using Individual Symptom Meta-analyses to Derive a Symptom-Oriented Therapy (SOrT) Metric for a Personalised Psychiatry [Registered Report Stage 1 Protocol]

description: <b>Abstract</b><b><br></b>Major Depressive Disorder (MDD) is a highly prevalent and debilitating disease leading to great economic burden. While antidepressant medication (ADM) and psychotherapy constitute effective main treatments, established guidelines provide only unspecific advice on which form of treatment to apply (e.g., based on symptom severity and chronicity). Recent approaches towards a more personalised psychiatry attempt to create algorithms for treatment allocation. Although promising, these attempts focus on sum-scores of depression scales, which neglect illness heterogeneity. In the current project, we extract information from depression symptom profiles, which might offer important information on treatment selection. We aim to develop what we term Symptom-Oriented Therapy (SOrT) metric, which quantifies patients’ treatment suitability for ADM or psychotherapy on the individual patient level. To this end, the current investigation follows a two-step approach. First, we wish to conduct a systematic review and meta-analyses of randomised controlled trials (RCTs) comparing ADM and psychotherapy on the individual symptom level. We will search PubMed Medline, PsycINFO, and Cochrane Central Register of Controlled Trials databases, search a database specific for psychotherapy RCTs, and look for unpublished RCTs. Applying random-effects meta-analyses on individual depressive symptoms will create an overview on whether specific symptoms might be better treated by ADM or psychotherapy. Second, we will compute the SOrT metric from meta-analyses results and validate it using data from the Munich Antidepressant Response Signature (MARS) study and the Emory Predictors of Remission in Depression to Individual and Combined Treatments (PReDICT) study. This will allow us to determine consistency of the metric, its clinical and demographic correlates, and test its potential clinical utility by comparing optimally versus non-optimally allocated patients. Ultimately, we hope that our results will provide an evidence-based means of personalising treatment for depression by utilising the symptom heterogeneity of the disease in a pragmatic and clinically straightforward method. <br><br>
DOI: 10.23645/epacomptox.7776212.v1
title: CFM-ID Paper Data

description: This upload is a zip containing the following files:<b><br></b><b>Predicted EI-MS Spectra of CompTox Chemicals Dashboard Structures:</b>Predicted EI-MS spectra of ~700,000 chemical structures from the CompTox Chemicals Dashboard were generated using the CFM-ID model developed by Allen, et al. (https://doi.org/10.1021/acs.analchem.6b01622). These data are provided in .dat ASCII format.<b><br></b><b>Predicted MS/MS Spectra in ESI-positive mode of CompTox Chemicals Dashboard Structures:</b>Predicted MS/MS spectra of ~700,000 chemical structures from the CompTox Chemicals Dashboard were generated using the CFM-ID model developed by Allen, et al. (https://doi.org/10.1007/s11306-014-0676-4) in ESI-positive mode. These data are provided in .dat ASCII format.<b><br></b><b>Predicted MS/MS Spectra in ESI-negative mode of CompTox Chemicals Dashboard Structures:</b>Predicted MS/MS spectra of ~700,000 chemical structures from the CompTox Chemicals Dashboard were generated using the CFM-ID model developed by Allen, et al. (https://doi.org/10.1007/s11306-014-0676-4) in ESI-negative mode. These data are provided in .dat ASCII format.<b></b><b><br></b><b>Database of Predicted Spectra of CompTox Chemicals Dashboard Structures:</b>Predicted spectra of ~700,000 chemical structures from the CompTox Chemicals Dashboard were generated using the CFM-ID model developed by Allen, et al. (https://doi.org/10.1007/s11306-014-0676-4 and https://doi.org/10.1007/s11306-014-0676-4) in ESI-positive and negative modes and EI-MS. These data are provided in an SQL relational database.<b><br></b><b>Database Schema File of Predicted Spectra of CompTox Chemicals Dashboard Structures:</b>Predicted spectra of ~700,000 chemical structures from the CompTox Chemicals Dashboard were generated using the CFM-ID model developed by Allen, et al. (https://doi.org/10.1007/s11306-014-0676-4 and https://doi.org/10.1007/s11306-014-0676-4) in ESI-positive and negative modes and EI-MS. These data are provided in an SQL relational database and described in this SQL Schema file.<b><br></b><b>Chemical Metadata from the CompTox Chemicals Dashboard Linked to Predicted Spectra:</b>Chemical metadata from the CompTox Chemicals Dashboard are linked through the unique DSSTox chemical identifier (DTXCID) enabling integration to predicted mass spectral data. Chemical metadata includes CASRN, molecular formula, SMILES, presence in lists, and data source occurrences.<b><br></b><b>Chemical Structures that failed during mass spectral prediction:</b>Predicted spectra of ~700,000 chemical structures from the CompTox Chemicals Dashboard were generated using the CFM-ID model developed by Allen, et al. (https://doi.org/10.1007/s11306-014-0676-4 and https://doi.org/10.1007/s11306-014-0676-4) in ESI-positive and negative modes and EI-MS. Due to structural errors and model constraints, the prediction of all MS modes failed for 56 structures.
DOI: 10.6084/m9.figshare.7776188.v1
title: Psychotherapy or Medication for Depression? Using Individual Symptom Meta-analyses to Derive a Symptom-Oriented Therapy (SOrT) Metric for a Personalised Psychiatry [Registered Report Stage 1 Protocol]

description: <b>Abstract</b><b><br></b>Major Depressive Disorder (MDD) is a highly prevalent and debilitating disease leading to great economic burden. While antidepressant medication (ADM) and psychotherapy constitute effective main treatments, established guidelines provide only unspecific advice on which form of treatment to apply (e.g., based on symptom severity and chronicity). Recent approaches towards a more personalised psychiatry attempt to create algorithms for treatment allocation. Although promising, these attempts focus on sum-scores of depression scales, which neglect illness heterogeneity. In the current project, we extract information from depression symptom profiles, which might offer important information on treatment selection. We aim to develop what we term Symptom-Oriented Therapy (SOrT) metric, which quantifies patients’ treatment suitability for ADM or psychotherapy on the individual patient level. To this end, the current investigation follows a two-step approach. First, we wish to conduct a systematic review and meta-analyses of randomised controlled trials (RCTs) comparing ADM and psychotherapy on the individual symptom level. We will search PubMed Medline, PsycINFO, and Cochrane Central Register of Controlled Trials databases, search a database specific for psychotherapy RCTs, and look for unpublished RCTs. Applying random-effects meta-analyses on individual depressive symptoms will create an overview on whether specific symptoms might be better treated by ADM or psychotherapy. Second, we will compute the SOrT metric from meta-analyses results and validate it using data from the Munich Antidepressant Response Signature (MARS) study and the Emory Predictors of Remission in Depression to Individual and Combined Treatments (PReDICT) study. This will allow us to determine consistency of the metric, its clinical and demographic correlates, and test its potential clinical utility by comparing optimally versus non-optimally allocated patients. Ultimately, we hope that our results will provide an evidence-based means of personalising treatment for depression by utilising the symptom heterogeneity of the disease in a pragmatic and clinically straightforward method. <br><br>
DOI: 10.6084/m9.figshare.7775972
title: YD_SE_DATA.rar

description: The whole database of the Vs measurements mentioned in the article:"Calibrating a new attenuation curve for the Dead Sea region using surface wave dispersion surveys in sites damaged bythe 1927 Jericho earthquake"<br>By Yaniv Darvasi and Amotz AgnonThe Fredy & Nadine Herrmann Institute of Earth Sciences, The Hebrew University of Jerusalem, 9190401 Jerusalem, Israel.<br>
DOI: 10.6084/m9.figshare.7775927
title: Supplementary Material for: The Precuneus – A Witness for Excessive Aβ Gathering in Alzheimer’s Disease Pathology

description: Evidence of cortical beta-amyloid (Aβ) load, assessed by Aβ positron emission tomography (Aβ-PET), is an established in vivo biomarker of Alzheimer’s disease (AD)-related pathophysiology. Qualitative assessment of Aβ-PET provides binary information; meanwhile semiquantitative approaches require a parcellation of PET image either manually or by placement of atlas-based volumes of interest. We supposed that a whole-brain approach with voxel-by-voxel standardized uptake value ratio (SUVr) parametric images may better elucidate the spatial trajectories of Aβ burden along the continuum<i></i> of AD. <b><i>Methods:</i></b> We recruited 32 subjects with a diagnosis of probable AD dementia (ADD, <i>n</i> = 20) and mild cognitive impairment due to AD (MCI-AD, <i>n</i> = 12) according to the NIA-AA 2011 criteria. We also enrolled a control group of 6 cognitively healthy individuals (HCs) with preserved cognitive functions and negative Aβ-PET scan. The PET images were spatially normalized using the AV45 PET template in the MNI brain space. Subsequently, parametric SUVr images were calculated using the whole cerebellum as a reference region. A voxel-wise analysis of covariance was used to compare (between groups) the Αβ distribution pattern considering age as a nuisance covariate. <b><i>Results:</i></b> Both ADD and MCI-AD subjects showed a widespread increase in radiotracer uptake when compared with HC participants (<i>p</i> &lt; 0.001, uncorrected). After applying a multiple comparison correction (<i>p</i> &lt; 0.05, corrected), a relative large cluster of increased [<sup>18</sup>F]-flor­betapir uptake was observed in the precuneus in the ADD and MCI-AD groups compared to HCs. Voxel-wise regression analysis showed a significant positive linear association between the voxel-wise SUVr values and the disease duration. <b><i>Conclusions:</i></b> The voxel-wise semiquantitative analysis shows that the precuneus is a region with higher vulnerability to Aβ depositions when compared to other cortical regions in both MCI-AD and ADD subjects. We think that the precuneus is a promising PET-based outcome measure for clinical trials of drugs targeting brain Aβ. We found a positive association between the overall Aβ-PET SUVr and the disease duration suggesting that the region-specific slow saturation of Aβ deposition continuously takes place as the disease progresses.