cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9976775
title: SM Table 1. Mineral chemistry. Analytical methods. Mid-crustal deformation in a continental margin orogen: structural evolution and timing of the Famatinian Orogeny, NW Argentina

description: SM Table 1. Mineral chemistry.
DOI: 10.6084/m9.figshare.9976778
title: SM Table 2. Monazite composition and EPMA geochronologic data. Mid-crustal deformation in a continental margin orogen: structural evolution and timing of the Famatinian Orogeny, NW Argentina

description: SM Table 2. Monazite composition and EPMA geochronologic data.
DOI: 10.6084/m9.figshare.9976781
title: S2. Phase equilibria analysis. Mid-crustal deformation in a continental margin orogen: structural evolution and timing of the Famatinian Orogeny, NW Argentina

description: S2. Supplementary material. Phase equilibria analysis.
DOI: 10.6084/m9.figshare.9976781.v1
title: S2. Phase equilibria analysis. Mid-crustal deformation in a continental margin orogen: structural evolution and timing of the Famatinian Orogeny, NW Argentina

description: S2. Supplementary material. Phase equilibria analysis.
DOI: 10.6084/m9.figshare.9976775.v1
title: SM Table 1. Mineral chemistry. Analytical methods. Mid-crustal deformation in a continental margin orogen: structural evolution and timing of the Famatinian Orogeny, NW Argentina

description: SM Table 1. Mineral chemistry.
DOI: 10.6084/m9.figshare.9976778.v1
title: SM Table 2. Monazite composition and EPMA geochronologic data. Mid-crustal deformation in a continental margin orogen: structural evolution and timing of the Famatinian Orogeny, NW Argentina

description: SM Table 2. Monazite composition and EPMA geochronologic data.
DOI: 10.6084/m9.figshare.9976670
title: Chronostratigraphy and terrestrial palaeoclimatology of Berriasian–Hauterivian strata of the Cedar Mountain Formation, Utah, USA

description: A supplementary data table summarising LA-ICP-MS U-Pb data on a 50 zircon from sample PSMA 11.71 (data sorted by ascending 206Pb/238U age)
DOI: 10.6084/m9.figshare.9976670.v1
title: Chronostratigraphy and terrestrial palaeoclimatology of Berriasian–Hauterivian strata of the Cedar Mountain Formation, Utah, USA

description: A supplementary data table summarising LA-ICP-MS U-Pb data on a 50 zircon from sample PSMA 11.71 (data sorted by ascending 206Pb/238U age)
DOI: 10.6084/m9.figshare.9976571
title: peak_annotation.zip

description: Peaks from ATAC analysis for exemplary dataset Hendrikson et al. 2017, including annotations<br>
DOI: 10.6084/m9.figshare.9976415
title: Benchmarking single-arm studies against historical controls from non-small cell lung cancer trials – an empirical analysis of bias

description: <b>Background:</b> Recent trials of novel agents in ‘rare’ molecular subtypes of non-small cell lung cancer (NSCLC) have used single-arm trial designs and benchmarked outcomes against historical controls. We assessed the consistency of historical control outcomes using docetaxel data from published NSCLC randomized controlled trials (RCTs). <b>Material and methods:</b> Advanced NSCLC RCTs including a docetaxel monotherapy arm were included. Heterogeneity in tumor objective response rates (ORRs), progression-free survival (PFS) and overall survival (OS), and correlations between outcomes and year of trial commencement were assessed. <b>Results:</b> Among 63 trials (<i>N</i> = 10,633) conducted between 2000 and 2017, ORR ranged from 0% to 26% (<i>I</i><sup>2</sup> = 76.1%, <i>p</i><sub>heterogeneity</sub> I<sup>2</sup> = 86.0%, <i>p</i><sub>heterogeneity</sub> I<sup>2</sup> = 83.0%, <i>p</i><sub>heterogeneity</sub> p = .046), 0.5% (<i>p</i> = .11) and 0.9% (<i>p</i> = .001) improvement in ORR, 3-month PFS and 9-month OS rates, respectively. <b>Conclusions:</b> There was significant heterogeneity and an improving trend in docetaxel outcomes across trials conducted over 20 years. Benchmarking biomarker-targeted agents against historical controls may not be a valid approach to replace RCTs. Innovative study designs involving a concurrent control arm should be considered.
DOI: 10.6084/m9.figshare.9976415.v1
title: Benchmarking single-arm studies against historical controls from non-small cell lung cancer trials – an empirical analysis of bias

description: <b>Background:</b> Recent trials of novel agents in ‘rare’ molecular subtypes of non-small cell lung cancer (NSCLC) have used single-arm trial designs and benchmarked outcomes against historical controls. We assessed the consistency of historical control outcomes using docetaxel data from published NSCLC randomized controlled trials (RCTs). <b>Material and methods:</b> Advanced NSCLC RCTs including a docetaxel monotherapy arm were included. Heterogeneity in tumor objective response rates (ORRs), progression-free survival (PFS) and overall survival (OS), and correlations between outcomes and year of trial commencement were assessed. <b>Results:</b> Among 63 trials (<i>N</i> = 10,633) conducted between 2000 and 2017, ORR ranged from 0% to 26% (<i>I</i><sup>2</sup> = 76.1%, <i>p</i><sub>heterogeneity</sub> I<sup>2</sup> = 86.0%, <i>p</i><sub>heterogeneity</sub> I<sup>2</sup> = 83.0%, <i>p</i><sub>heterogeneity</sub> p = .046), 0.5% (<i>p</i> = .11) and 0.9% (<i>p</i> = .001) improvement in ORR, 3-month PFS and 9-month OS rates, respectively. <b>Conclusions:</b> There was significant heterogeneity and an improving trend in docetaxel outcomes across trials conducted over 20 years. Benchmarking biomarker-targeted agents against historical controls may not be a valid approach to replace RCTs. Innovative study designs involving a concurrent control arm should be considered.
DOI: 10.6084/m9.figshare.9976316
title: 3D reconstruction from A new specimen of Ziphiidae (Cetacea, Odontoceti) from the late Miocene of Denmark with morphological evidence for suction feeding behaviour

description: Pdf file containing a 3D reconstruction of the genus and sp. indet. NHMD 189993.
DOI: 10.6084/m9.figshare.9976316.v1
title: 3D reconstruction from A new specimen of Ziphiidae (Cetacea, Odontoceti) from the late Miocene of Denmark with morphological evidence for suction feeding behaviour

description: Pdf file containing a 3D reconstruction of the genus and sp. indet. NHMD 189993.
DOI: 10.6084/m9.figshare.9976274
title: Argiope Microbiome: fastq Files

description: This folder contains all of the raw reads output from Illumina 16S sequencing, in fastq format. Sequence were processed using dada2 in R, and the script is available here as well.<br>
DOI: 10.6084/m9.figshare.9976274.v1
title: Argiope Microbiome: fastq Files

description: This folder contains all of the raw reads output from Illumina 16S sequencing, in fastq format. Sequence were processed using dada2 in R, and the script is available here as well.<br>
DOI: 10.6084/m9.figshare.9976208
title: Preventing Relapse with Personalised Smart-Messaging After Cognitive Behavioural Therapy: A Proof of Concept Evaluation

description: Objectives. Cognitive Behavioural Therapy (CBT) can improve symptoms of anxiety and depression, but also reduces the risk of future relapse after therapy completion. However, current CBT relapse prevention methods are resource intensive and can be limited in clinical practice. This paper investigates a personalised means of reducing relapse using smart-messaging in two settings; research and routine care. Design. Study 1 presents a cohort study comparing a cohort of smart-messaging users versus non-users. Study 2 presents time series follow up data from a case series of smart-messaging users from clinical practice. Methods. Fifteen of 56 CBT completers who participated in a trial for the treatment of health anxiety wrote advice they would want if in future they were doing well, experiencing early warning signs of relapse, or experiencing full relapse. Following CBT, participants received weekly text-message requests to rate their wellbeing. Dependent upon their response, participants received tailored advice they had written, appropriate to the wellbeing level reported after recovery from health anxiety. Smart-messaging was also trialled in a routine practice sample of 14 CBT completers with anxiety and depression. Results. Across a 12-month follow-up, participants receiving smart-messaging showed greater health improvements than those who did not. Wellbeing scores showed stability between CBT completion and six-month follow-up among routine care patients. Conclusions. These findings suggest that a low-intensity, personalised relapse prevention method can have a clinical benefit following CBT for common mental health problems.
DOI: 10.6084/m9.figshare.9976217
title: Argiope Microbiome: Analysis Files

description: Supplementary data from publication.<br>The seq file consists of bacterial consensus sequences (columns) and spider tissue samples (rows). Raw read numbers fill the table.<br>The meta file has the same row names as the seq files (spider tissue samples), with three columns representing the tissue type, the country of origin, and the individual.<br>The tax file row names correspond to the column names of the seq file. The columns give taxonomic identification from the level of kingdom to species, derived from taxonomic classification with the Silva database.<br>The seq, meta, and tax files were analyzed in R, and the script is available here as well.
DOI: 10.6084/m9.figshare.9976217.v1
title: Argiope Microbiome: Analysis Files

description: Supplementary data from publication.<br>The seq file consists of bacterial consensus sequences (columns) and spider tissue samples (rows). Raw read numbers fill the table.<br>The meta file has the same row names as the seq files (spider tissue samples), with three columns representing the tissue type, the country of origin, and the individual.<br>The tax file row names correspond to the column names of the seq file. The columns give taxonomic identification from the level of kingdom to species, derived from taxonomic classification with the Silva database.<br>The seq, meta, and tax files were analyzed in R, and the script is available here as well.
DOI: 10.5522/04/9976187
title: Proteomics of matrix production - FRCs

description: Data to accompany figure S2Proteomics of FRC-derived matricesIn vitro FRC cell line-derived matrices generated after 5 days in culture were subjected to proteomic analysis by mass spectrometry. Summary data in xls spreadsheet. <br><br>SWATH dataset uploaded to PRIDE repository ID=PXD015816<br>http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD015816<br><br><br>Abstract<br>Lymph nodes (LNs) work as filtering organs, constantly sampling peripheral cues. This is facilitated by the conduit network, a parenchymal tubular-like structure formed of bundles of aligned extracellular matrix (ECM) fibrils ensheathed by fibroblastic reticular cells (FRCs). LNs undergo 5-fold expansion with every adaptive immune response and yet these ECM-rich structures are not permanently damaged. Whether conduit integrity and filtering functions are affected during cycles of LN expansion and resolution is not known. Here we show that the conduit structure is disrupted during acute LN expansion but FRC-FRC contacts remain intact. In homeostasis, polarised FRCs adhere to the underlying substrate to deposit ECM ba-solaterally. ECM production by FRCs is regulated by the C-type lectin CLEC-2, expressed by dendritic cells (DCs), at transcriptional and secretory levels. Inflamed LNs maintain conduit size-exclusion, but flow becomes leaky, which allows soluble antigens to reach more antigen-presenting cells. We show how dynamic communication between peripheral tissues and LNs changes during immune responses, and describe a mechanism that enables LNs to prevent inflammation-induced fibrosis.<br>Highlights<br>FRCs use polarized microtubule networks to guide matrix deposition<br>CLEC-2/PDPN controls matrix production at transcriptional and post-transcriptional levels<br>FRCs halt matrix production and decouple from conduits during acute LN expansion<br>Conduits leak soluble antigen during acute LN expansion
DOI: 10.5522/04/9976187.v1
title: Proteomics of matrix production - FRCs

description: Data to accompany figure S2Proteomics of FRC-derived matricesIn vitro FRC cell line-derived matrices generated after 5 days in culture were subjected to proteomic analysis by mass spectrometry. Summary data in xls spreadsheet. <br><br>SWATH dataset uploaded to PRIDE repository ID=PXD015816<br>http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD015816<br><br><br>Abstract<br>Lymph nodes (LNs) work as filtering organs, constantly sampling peripheral cues. This is facilitated by the conduit network, a parenchymal tubular-like structure formed of bundles of aligned extracellular matrix (ECM) fibrils ensheathed by fibroblastic reticular cells (FRCs). LNs undergo 5-fold expansion with every adaptive immune response and yet these ECM-rich structures are not permanently damaged. Whether conduit integrity and filtering functions are affected during cycles of LN expansion and resolution is not known. Here we show that the conduit structure is disrupted during acute LN expansion but FRC-FRC contacts remain intact. In homeostasis, polarised FRCs adhere to the underlying substrate to deposit ECM ba-solaterally. ECM production by FRCs is regulated by the C-type lectin CLEC-2, expressed by dendritic cells (DCs), at transcriptional and secretory levels. Inflamed LNs maintain conduit size-exclusion, but flow becomes leaky, which allows soluble antigens to reach more antigen-presenting cells. We show how dynamic communication between peripheral tissues and LNs changes during immune responses, and describe a mechanism that enables LNs to prevent inflammation-induced fibrosis.<br>Highlights<br>FRCs use polarized microtubule networks to guide matrix deposition<br>CLEC-2/PDPN controls matrix production at transcriptional and post-transcriptional levels<br>FRCs halt matrix production and decouple from conduits during acute LN expansion<br>Conduits leak soluble antigen during acute LN expansion
DOI: 10.6084/m9.figshare.9976190
title: Wind-Tunnel Simulation of Stable Atmospheric Boundary Layers with an imposed inversion

description: Supporting data for Wind-Tunnel Simulation of Stable Atmospheric Boundary Layers with an imposed inversion
DOI: 10.6084/m9.figshare.9976190.v1
title: Wind-Tunnel Simulation of Stable Atmospheric Boundary Layers with an imposed inversion

description: Supporting data for Wind-Tunnel Simulation of Stable Atmospheric Boundary Layers with an imposed inversion
DOI: 10.6084/m9.figshare.9976154
title: Supplementary Material for: Are There Disparities in Surgical Treatment for Breast Cancer Patients with Prior Physical Disability? A Path Analysis

description: <b><i>Introduction:</i></b> Cancer care for patients with prior physical disability has hardly been researched in clinical research, health services research, or special education. This article aims to compare the severity of disease and the surgical treatment of diagnosed breast cancer patients with and without prior physical disability. <b><i>Methods:</i></b> A total of 4,194 patients with primary breast cancer who underwent surgery in a breast cancer center in North Rhine-Westphalia, Germany, participated in an annual postoperative postal survey, which was complemented by clinical data. Latent class analysis and logit path models were applied to study (1) differences in terms of UICC staging and local cancer treatment between patients with and without prior physical disability and (2) respective differences by disability severity. <b><i>Results:</i></b> Patients with physical disability (<i>n</i> = 780; 18.7%) had a higher chance of receiving mastectomy compared to breast-conserving therapy, even after controlling for socioeconomic status and UICC staging. Disability severity is directly and indirectly associated with receiving a mastectomy. <b><i>Conclusion:</i></b> In light of the research gap on disability and cancer, this work indicates disparities in care for breast cancer patients with prior physical disability. Inequalities might be attributable to (1) unequal access to care, (2) individual preferences and difficulties, or (3) medical difficulties.
DOI: 10.6084/m9.figshare.9976142
title: Wind-Tunnel Simulation of Weakly and Moderately Stable Atmospheric Boundary Layers

description: Supporting Data for<br> Wind-Tunnel Simulation of Weakly and Moderately Stable Atmospheric Boundary Layers https://doi.org/10.1007/s10546-018-0337-7
DOI: 10.6084/m9.figshare.9976154.v1
title: Supplementary Material for: Are There Disparities in Surgical Treatment for Breast Cancer Patients with Prior Physical Disability? A Path Analysis

description: <b><i>Introduction:</i></b> Cancer care for patients with prior physical disability has hardly been researched in clinical research, health services research, or special education. This article aims to compare the severity of disease and the surgical treatment of diagnosed breast cancer patients with and without prior physical disability. <b><i>Methods:</i></b> A total of 4,194 patients with primary breast cancer who underwent surgery in a breast cancer center in North Rhine-Westphalia, Germany, participated in an annual postoperative postal survey, which was complemented by clinical data. Latent class analysis and logit path models were applied to study (1) differences in terms of UICC staging and local cancer treatment between patients with and without prior physical disability and (2) respective differences by disability severity. <b><i>Results:</i></b> Patients with physical disability (<i>n</i> = 780; 18.7%) had a higher chance of receiving mastectomy compared to breast-conserving therapy, even after controlling for socioeconomic status and UICC staging. Disability severity is directly and indirectly associated with receiving a mastectomy. <b><i>Conclusion:</i></b> In light of the research gap on disability and cancer, this work indicates disparities in care for breast cancer patients with prior physical disability. Inequalities might be attributable to (1) unequal access to care, (2) individual preferences and difficulties, or (3) medical difficulties.
DOI: 10.6084/m9.figshare.9976121
title: Screening tests: a review with examples

description: Screening tests are widely used in medicine to assess the likelihood that members of a defined population have a particular disease. This article presents an overview of such tests including the definitions of key technical (sensitivity and specificity) and population characteristics necessary to assess the benefits and limitations of such tests. Several examples are used to illustrate calculations, including the characteristics of low dose computed tomography as a lung cancer screen, choice of an optimal PSA cutoff and selection of the population to undergo mammography. The importance of careful consideration of the consequences of both false positives and negatives is highlighted. Receiver operating characteristic curves are explained as is the need to carefully select the population group to be tested.
DOI: 10.6084/m9.figshare.9976127
title: Perspectives on refractory ceramic fiber (RCF) carcinogenicity: comparisons with other fibers

description: In 2011, SCOEL classified RCF as a secondary genotoxic carcinogen and supported a practical threshold. Inflammation was considered the predominant manifestation of RCF toxicity. Intrapleural and intraperitoneal implantation induced mesotheliomas and sarcomas in laboratory animals. Chronic nose-only inhalation bioassays indicated that RCF exposure in rats increased the incidence of lung cancer and similar exposures resulted in mesothelioma in hamsters, but these studies may have been compromised by overload. Epidemiological studies in the US and Europe showed an association between exposure and prevalence of respiratory symptoms and pleural plaques, but no interstitial fibrosis, mesotheliomas, or increased numbers of lung tumors were observed. As the latency of asbestos induced mesotheliomas can be up to 50 years, the relationship between RCF exposure and respiratory malignances has not been fully determined. Nonetheless, it is possible to offer useful perspectives. RCF and rock wool have similar airborne fiber dimensions and biopersistence. Therefore, it is likely that these fibers have similar toxicology. Traditional rock wool has been the subject of numerous cohort and case control studies. For rock wool, IARC () concluded that the epidemiological studies did not provide evidence of carcinogenicity. Based on analogies with rock wool (read across), it is reasonable to believe that increases in lung cancer or any mesotheliomas are unlikely to be found in the RCF-exposed cohort. RCF producers have developed a product stewardship program to measure and control fiber concentrations and to further understand the health status of their workers.
DOI: 10.6084/m9.figshare.9976142.v1
title: Wind-Tunnel Simulation of Weakly and Moderately Stable Atmospheric Boundary Layers

description: Supporting Data for<br> Wind-Tunnel Simulation of Weakly and Moderately Stable Atmospheric Boundary Layers https://doi.org/10.1007/s10546-018-0337-7
DOI: 10.6084/m9.figshare.9976124
title: A comparative study of the toxicological aspects of vanadium pentoxide and vanadium oxide nanoparticles

description: Indiscriminate use of vanadium oxide nanoparticles (NPs) in steel industries and their release during combustion of fossil fuels makes it essential to study their toxic potential. Herein, we assessed the toxicological effects of two types of in-house synthesized vanadium oxide NPs in Wistar rats exposed to NPs through inhalation route. V<sub>2</sub>O<sub>5</sub> and VO<sub>2</sub> NPs exhibited rod and spherical symmetry, respectively with a mean diameter of 50 ± 20 and 30 ± 10 nm. Assessment of bronchoalveolar lavage fluid parameters demonstrated that VO<sub>2</sub> NP-exposed animals had higher levels of lactate dehydrogenase, gamma-glutamyl transpeptidase and alkaline phosphatase as compared to V<sub>2</sub>O<sub>5</sub> NP-exposed animals. The levels of oxidative stress markers malondialdehyde and reduced glutathione also indicated higher toxic potential of VO<sub>2</sub> NPs. Moreover, after 7-day recovery, the levels of the above parameters were closer to normal levels only in V<sub>2</sub>O<sub>5</sub>-exposed animals. Interestingly, histopathological and immune-histopathology analysis (TNF-α) of lung tissue showed higher damage and inflammatory response in VO<sub>2</sub> NP-exposed animals, which persisted even after 7 days of recovery period. Surprisingly, the carcinogenic potential of vanadium oxide NPs came into light which was indicated by terminal deoxynucleotidyl transferase dUTP nick-end labeling assay as well as the decreased levels of p53 and Bax, in lung tissue of NP-exposed animals. Notably, the physiochemical characterization of NPs, especially the shape and the size, play a central role in shaping the toxicity of these NPs and thus should be extensively evaluated for outlining the regulatory guidelines.