cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9976118
title: Effect of recombinant human keratinocyte growth factor in inducing Ras–Raf–Erk pathway-mediated cell proliferation in emphysematous mice lung

description: <i>Context</i>: Pulmonary emphysema is resulted due to destruction of the structure of the alveoli. Recently, exogenous recombinant human Keratinocyte growth factor (rHuKGF) has been reported to induce the regeneration of gas exchange structures. However, the molecular mechanisms governing this process are so far unknown. <i>Objective</i>: The objective of this study was to investigate the effect of rHuKGF in the lungs of emphysema-challenged mice on Ras–Raf–Erk (Erk, extracellular signal-regulated kinase) mediated signaling pathway that regulates alveolar epithelial cell proliferation. <i>Methods</i>: Three experimental groups (i.e. emphysema, therapy and control group) were prepared. Lungs of mice were therapeutically treated at three occasions by oropharyngeal instillation of 10 mg rHuKGF per kg body weight after induction of emphysema by porcine pancreatic elastase (PPE). Subsequently, lung tissues from each mouse were collected for histopathology and molecular biology studies. <i>Results and discussion</i>: Histopathology photomicrographs and Destructive Index analysis have shown that elastase induced airspace enlargement and loss of alveoli were recovered in therapy group. Moreover, proliferating cell nuclear antigen (PCNA) at mRNA and protein expression level was markedly increased in therapy group than emphysema group. Upon validation at mRNA level, expressions of FGF-7, FGF-R, Ras, c-Raf, Erk-1, Erk-2, c-Myc and were significantly increased, whereas Elk-1 was notably decreased in therapy group when compared with emphysema group and were well comparable with the control group. <i>Conclusion</i>: Therapeutic supplementation of rHuKGF rectifies the deregulated Ras–Raf–Erk pathway in emphysema condition, resulting in alveolar epithelium regeneration. Hence, rHuKGF may prove to be a potential drug in the treatment of emphysema.
DOI: 10.6084/m9.figshare.9976121.v2
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.v2
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: 10.5522/04/9976112
title: RNA seq - PDPN/CLEC-2 transcription in FRCs

description: Raw data to accompany figure 2 - Effects of CLEC-2 on ECM production by FRCsIncludes sample list in all format and and fastq files from RNAseq runs.Data set 28GB<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.9976121.v1
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.9976124.v2
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.
DOI: 10.6084/m9.figshare.9976127.v1
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.9976118.v2
title: Effect of recombinant human keratinocyte growth factor in inducing Ras–Raf–Erk pathway-mediated cell proliferation in emphysematous mice lung

description: <i>Context</i>: Pulmonary emphysema is resulted due to destruction of the structure of the alveoli. Recently, exogenous recombinant human Keratinocyte growth factor (rHuKGF) has been reported to induce the regeneration of gas exchange structures. However, the molecular mechanisms governing this process are so far unknown. <i>Objective</i>: The objective of this study was to investigate the effect of rHuKGF in the lungs of emphysema-challenged mice on Ras–Raf–Erk (Erk, extracellular signal-regulated kinase) mediated signaling pathway that regulates alveolar epithelial cell proliferation. <i>Methods</i>: Three experimental groups (i.e. emphysema, therapy and control group) were prepared. Lungs of mice were therapeutically treated at three occasions by oropharyngeal instillation of 10 mg rHuKGF per kg body weight after induction of emphysema by porcine pancreatic elastase (PPE). Subsequently, lung tissues from each mouse were collected for histopathology and molecular biology studies. <i>Results and discussion</i>: Histopathology photomicrographs and Destructive Index analysis have shown that elastase induced airspace enlargement and loss of alveoli were recovered in therapy group. Moreover, proliferating cell nuclear antigen (PCNA) at mRNA and protein expression level was markedly increased in therapy group than emphysema group. Upon validation at mRNA level, expressions of FGF-7, FGF-R, Ras, c-Raf, Erk-1, Erk-2, c-Myc and were significantly increased, whereas Elk-1 was notably decreased in therapy group when compared with emphysema group and were well comparable with the control group. <i>Conclusion</i>: Therapeutic supplementation of rHuKGF rectifies the deregulated Ras–Raf–Erk pathway in emphysema condition, resulting in alveolar epithelium regeneration. Hence, rHuKGF may prove to be a potential drug in the treatment of emphysema.
DOI: 10.6084/m9.figshare.9976124.v1
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.
DOI: 10.6084/m9.figshare.9976103
title: Morphological data of Mangrove warbler in Costa Rica

description: Morphological data of Mangrove warbler populations along an environmental gradient in Costa Rica
DOI: 10.6084/m9.figshare.9976106
title: Chapter2 data

description: This is the dataset based on the tree map from CERA and work with QGIS
DOI: 10.6084/m9.figshare.9976118.v1
title: Effect of recombinant human keratinocyte growth factor in inducing Ras–Raf–Erk pathway-mediated cell proliferation in emphysematous mice lung

description: <i>Context</i>: Pulmonary emphysema is resulted due to destruction of the structure of the alveoli. Recently, exogenous recombinant human Keratinocyte growth factor (rHuKGF) has been reported to induce the regeneration of gas exchange structures. However, the molecular mechanisms governing this process are so far unknown. <i>Objective</i>: The objective of this study was to investigate the effect of rHuKGF in the lungs of emphysema-challenged mice on Ras–Raf–Erk (Erk, extracellular signal-regulated kinase) mediated signaling pathway that regulates alveolar epithelial cell proliferation. <i>Methods</i>: Three experimental groups (i.e. emphysema, therapy and control group) were prepared. Lungs of mice were therapeutically treated at three occasions by oropharyngeal instillation of 10 mg rHuKGF per kg body weight after induction of emphysema by porcine pancreatic elastase (PPE). Subsequently, lung tissues from each mouse were collected for histopathology and molecular biology studies. <i>Results and discussion</i>: Histopathology photomicrographs and Destructive Index analysis have shown that elastase induced airspace enlargement and loss of alveoli were recovered in therapy group. Moreover, proliferating cell nuclear antigen (PCNA) at mRNA and protein expression level was markedly increased in therapy group than emphysema group. Upon validation at mRNA level, expressions of FGF-7, FGF-R, Ras, c-Raf, Erk-1, Erk-2, c-Myc and were significantly increased, whereas Elk-1 was notably decreased in therapy group when compared with emphysema group and were well comparable with the control group. <i>Conclusion</i>: Therapeutic supplementation of rHuKGF rectifies the deregulated Ras–Raf–Erk pathway in emphysema condition, resulting in alveolar epithelium regeneration. Hence, rHuKGF may prove to be a potential drug in the treatment of emphysema.
DOI: 10.6084/m9.figshare.9976091
title: lineations.xls

description: Mineral stretching lineation measurements from the southern Western Gneiss Region of Norway. Supplement to manuscript submitted to Tectonics:Wiest, J.D, Osmundsen, P.T., Jacobs, J., Fossen, H., Deep crustal flow within post-orogenic metamorphic core complexes – Insights from the southern Western Gneiss Region of Norway
DOI: 10.6084/m9.figshare.9976088
title: fold_axes.xls

description: Fold axes measurements from the southern Western Gneiss Region of Norway. Supplement to manuscript submitted to Tectonics:Wiest, J.D, Osmundsen, P.T., Jacobs, J., Fossen, H., Deep crustal flow within post-orogenic metamorphic core complexes – Insights from the southern Western Gneiss Region of Norway
DOI: 10.6084/m9.figshare.9976106.v1
title: Chapter2 data

description: This is the dataset based on the tree map from CERA and work with QGIS
DOI: 10.6084/m9.figshare.9976079
title: foliations.xls

description: Foliation measurements from the southern Western Gneiss Region of Norway. Supplement to manuscript submitted to Tectonics:Wiest, J.D, Osmundsen, P.T., Jacobs, J., Fossen, H., Deep crustal flow within post-orogenic metamorphic core complexes – Insights from the southern Western Gneiss Region of Norway
DOI: 10.6084/m9.figshare.9976085
title: Images.zip

description: Geotagged field photos from the southern Western Gneiss Region of Norway. The photos in the ZIP-folder can be linked geographically through the field "image_file" in the file "images.xls" using GIS software.Supplement to manuscript submitted to Tectonics:Wiest, J.D, Osmundsen, P.T., Jacobs, J., Fossen, H., Deep crustal flow within post-orogenic metamorphic core complexes – Insights from the southern Western Gneiss Region of Norway
DOI: 10.6084/m9.figshare.9976091.v1
title: lineations.xls

description: Mineral stretching lineation measurements from the southern Western Gneiss Region of Norway. Supplement to manuscript submitted to Tectonics:Wiest, J.D, Osmundsen, P.T., Jacobs, J., Fossen, H., Deep crustal flow within post-orogenic metamorphic core complexes – Insights from the southern Western Gneiss Region of Norway
DOI: 10.6084/m9.figshare.9976082
title: images.xls

description: Comments and locations of geotagged field photos from the southern Western Gneiss Region of Norway. The photos in the ZIP-folder can be linked through the field "image_file" in GIS software.Supplement to manuscript submitted to Tectonics:Wiest, J.D, Osmundsen, P.T., Jacobs, J., Fossen, H., Deep crustal flow within post-orogenic metamorphic core complexes – Insights from the southern Western Gneiss Region of Norway
DOI: 10.6084/m9.figshare.9976076
title: eclogite_localities.xls

description: Eclogite localities in the southern Western Gneiss Region of Norway. Supplement to manuscript submitted to Tectonics:Wiest, J.D, Osmundsen, P.T., Jacobs, J., Fossen, H., Deep crustal flow within post-orogenic metamorphic core complexes – Insights from the southern Western Gneiss Region of Norway
DOI: 10.6084/m9.figshare.9976082.v1
title: images.xls

description: Comments and locations of geotagged field photos from the southern Western Gneiss Region of Norway. The photos in the ZIP-folder can be linked through the field "image_file" in GIS software.Supplement to manuscript submitted to Tectonics:Wiest, J.D, Osmundsen, P.T., Jacobs, J., Fossen, H., Deep crustal flow within post-orogenic metamorphic core complexes – Insights from the southern Western Gneiss Region of Norway
DOI: 10.6084/m9.figshare.9976085.v1
title: Images.zip

description: Geotagged field photos from the southern Western Gneiss Region of Norway. The photos in the ZIP-folder can be linked geographically through the field "image_file" in the file "images.xls" using GIS software.Supplement to manuscript submitted to Tectonics:Wiest, J.D, Osmundsen, P.T., Jacobs, J., Fossen, H., Deep crustal flow within post-orogenic metamorphic core complexes – Insights from the southern Western Gneiss Region of Norway
DOI: 10.6084/m9.figshare.9976088.v1
title: fold_axes.xls

description: Fold axes measurements from the southern Western Gneiss Region of Norway. Supplement to manuscript submitted to Tectonics:Wiest, J.D, Osmundsen, P.T., Jacobs, J., Fossen, H., Deep crustal flow within post-orogenic metamorphic core complexes – Insights from the southern Western Gneiss Region of Norway
DOI: 10.6084/m9.figshare.9976073
title: DISK.xls

description: Dataset of semi-quantitative strain mapping in the southern Western Gneiss Region of Norway. Supplement to manuscript submitted to Tectonics:Wiest, J.D, Osmundsen, P.T., Jacobs, J., Fossen, H., Deep crustal flow within post-orogenic metamorphic core complexes – Insights from the southern Western Gneiss Region of Norway<br>
DOI: 10.6084/m9.figshare.9976076.v1
title: eclogite_localities.xls

description: Eclogite localities in the southern Western Gneiss Region of Norway. Supplement to manuscript submitted to Tectonics:Wiest, J.D, Osmundsen, P.T., Jacobs, J., Fossen, H., Deep crustal flow within post-orogenic metamorphic core complexes – Insights from the southern Western Gneiss Region of Norway