cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7284/125324
title: Hygrometer data collected during research cruise CB1066 using a RM Young 41382 instrument system onboard the platform RV Clifford A. Barnes

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/125326
title: Radiometer data collected during research cruise CB1066 using a Biospherical QSP-2150 instrument system onboard the platform RV Clifford A. Barnes

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/125327
title: Singlebeam Echosounder data collected during research cruise CB1066 using a Knudsen 320M instrument system onboard the platform RV Clifford A. Barnes

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/125328
title: TSG (Thermosalinograph) data collected during research cruise CB1066 using a Sea-Bird SBE-21 instrument system onboard the platform RV Clifford A. Barnes

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7664717
title: MOESM2 of Epigenomic signatures in liver and blood of Wilson disease patients include hypermethylation of liver-specific enhancers

description: Additional file 2. Â Additional Tables S2â S4, S6, S8, S9, and S11â S15.
DOI: 10.6084/m9.figshare.7664717.v1
title: MOESM2 of Epigenomic signatures in liver and blood of Wilson disease patients include hypermethylation of liver-specific enhancers

description: Additional file 2. Â Additional Tables S2â S4, S6, S8, S9, and S11â S15.
DOI: 10.7284/106553
title: GNSS (Global Navigation Satellite System) data collected during research cruise CB939 using a Northstar 951X instrument system onboard the platform RV Clifford A. Barnes

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/106554
title: GNSS (Global Navigation Satellite System) data collected during research cruise CB940 using a Northstar 951X instrument system onboard the platform RV Clifford A. Barnes

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7663127
title: Figures_Johnson et al.

description: Figures were created from simulations of various monitoring scenarios. Original data used for simulations were empirical (see Wallace et al. 2016, PLOS One).
DOI: 10.6084/m9.figshare.7663127.v1
title: Figures_Johnson et al.

description: Figures were created from simulations of various monitoring scenarios. Original data used for simulations were empirical (see Wallace et al. 2016, PLOS One).
DOI: 10.7284/106555
title: GNSS (Global Navigation Satellite System) data collected during research cruise CB942 using a Northstar 951X instrument system onboard the platform RV Clifford A. Barnes

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/106556
title: GNSS (Global Navigation Satellite System) data collected during research cruise CB944 using a Northstar 951X instrument system onboard the platform RV Clifford A. Barnes

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.12883463.v1
title: RAW CSV from GT3X Duplicate

description: The data is from https://springernature.figshare.com/collections/Upper_limb_activity_of_twenty_myoelectric_prosthesis_users_and_twenty_healthy_anatomically_intact_adults_/4457855. Specifically, it is the RAW CSV files zipped from https://springernature.figshare.com/articles/dataset/Unprocessed_raw_30Hz_acceleration_data_stored_as_csv/7946186. It is simply repackaged so that individual files can be downloaded. Please cite the respective data there.
DOI: 10.6084/m9.figshare.7663010
title: Spatial and temporal localization of immune transcripts defines hallmarks and diversity in the tuberculosis granuloma

description: This repository contains raw data and all scripts for the in situ sequencing processing pipeline (Mats Nilsson Lab, Stockholm University) and downstream analysis applied in the manuscript “<b>Spatial and temporal localization of immune transcripts defines hallmarks and diversity in the tuberculosis granuloma”. </b><b><br></b><b>Raw images:</b>All 16bit tiff images are for 12 weeks_section1Format is baseX_cY_ORGX indicates the hybridization round (1-4)Y indicates the channel: 1: DAPI2: FITC (T)3: Cy3 (G)4: TexR (C)5: Cy5 (A)6: AF750 (Anchor primer)<br> <b><i></i><i></i>Raw data in folders:</b> Lung csv files Bacteria csv files DAPI for plotting HE folder<br> <b>Scripts folder:</b> Matlab scripts Cellprofiler pipelines<br> <b>Identification and plotting of transcripts:</b> For all matlab scripts: Download the “Matlab scripts” folder, add lib to MATLAB path. Except MATLAB, no additional Mathworks product is required. Tested on R2017b. <br> <b>InSituSequencing.m</b> is the top-level script processing sequencing images to positional visualization of decoded transcripts. Use raw images for 12weeks_section1 as input images (others are available on request) . After Tiling in "InsituSequencing.m", process tiled images in the cell profiler pipeline “Blob identification”. Run decode and threshold in "InSituSequencing.m" to generate csv files containing position and intensity of each identified signal.<br>csv files for all lung scans (3 per time point) are in “lung csv files” folder and can be plotted on DAPI images (10% of original size) found in “DAPI for plotting” folder using Plotting global in "InSituSequencing.m". High resolution H&E scans of in situ-sequenced lungs for lung section per time point are in the “HE folder” at 50% of original size. For all images 1 pixel corresponds to 0.325 mm.<br> <b>Identification and plotting of transcripts in given proximity to bacteria:</b> Use the cellprofiler pipeline “Bacteria identification” instead of “Blob identification” to identify signal in indicated distances from identified bacteria. The folder “bacteria csv files” contains identified signals in the indicated distances to identified bacteria. Input images are available on request.<br> <b>Downstream analysis (Matlab Scripts folder)</b> <b>DensityEstimation.m</b> was used to display not absolute reads but a kernel density estimation of a certain gene in a 2log scale. <b>ROI_draw_onImage.m</b> was applied to extract reads from annotated regions. Pictures of annotations can be found in the manuscript supplementary figure S1. <b>HexbinClustering.m </b>performed an unsupervised clustering (kmeans) of spatial data with a given number of distinct clusters in a given radius.<br><b>Table 1-3 </b>contain sequences of used specific primers, padlock probes and detection oligos. <br>
DOI: 10.6084/m9.figshare.7663115.v1
title: Dynamic Vector Mode Regression

description: We study the semi-parametric estimation of the conditional mode of a random vector that has a continuous conditional joint density with a well-defined global mode. A novel full-system estimator is proposed and its asymptotic properties are studied. We specifically consider the estimation of vector autoregressive conditional mode models and of systems of linear simultaneous equations defined by mode restrictions. The proposed estimator is easy to implement and simulations suggest that it is reasonably behaved in finite samples. An empirical example illustrates the application of the proposed methods, including its use to obtain multi-step forecasts and to construct impulse response functions.
DOI: 10.7284/106557
title: GNSS (Global Navigation Satellite System) data collected during research cruise CB946 using a Northstar 951X instrument system onboard the platform RV Clifford A. Barnes

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.25373/ctsnet.7662950
title: Management of Chronic Neglected Traumatic Diaphragmatic Hernia

description: A 45-year-old man came to the emergency department complaining of progressive shortness of breath for 10 days. He also complained of vomiting and absolute constipation for four days. He had a past history of left stab to the chest for 1.5 years. Examination revealed the patient was hemodynamically unstable, with severe respiratory distress, cyanosis, fever, and absent air entry on the left side of the chest. The patient had a chest x-ray suggestive of tension pneumothorax, however a chest computed tomography scan was suggestive of diaphragmatic hernia.<br>An emergency left posterolateral thoracotomy was performed. There was a gangrenous perforated transverse colon inside the chest. The authors widened the diaphragmatic defect, and they performed a transthoracic transverse colectomy and reanastomosis, as well as a right iliac ileostomy. The authors repaired the diaphragmatic defect. The patient was discharged at postoperative day 30 in a good general condition.<br><b>Conclusion</b>History-taking and high index of suspicion is important for the diagnosis of neglected traumatic diaphragmatic injuries. In this case, the authors performed the repair totally transthoracically, with no need for an abdominal incision.
DOI: 10.25373/ctsnet.7662950.v1
title: Management of Chronic Neglected Traumatic Diaphragmatic Hernia

description: A 45-year-old man came to the emergency department complaining of progressive shortness of breath for 10 days. He also complained of vomiting and absolute constipation for four days. He had a past history of left stab to the chest for 1.5 years. Examination revealed the patient was hemodynamically unstable, with severe respiratory distress, cyanosis, fever, and absent air entry on the left side of the chest. The patient had a chest x-ray suggestive of tension pneumothorax, however a chest computed tomography scan was suggestive of diaphragmatic hernia.<br>An emergency left posterolateral thoracotomy was performed. There was a gangrenous perforated transverse colon inside the chest. The authors widened the diaphragmatic defect, and they performed a transthoracic transverse colectomy and reanastomosis, as well as a right iliac ileostomy. The authors repaired the diaphragmatic defect. The patient was discharged at postoperative day 30 in a good general condition.<br><b>Conclusion</b>History-taking and high index of suspicion is important for the diagnosis of neglected traumatic diaphragmatic injuries. In this case, the authors performed the repair totally transthoracically, with no need for an abdominal incision.
DOI: 10.7284/106558
title: GNSS (Global Navigation Satellite System) data collected during research cruise CB947 using a Northstar 951X instrument system onboard the platform RV Clifford A. Barnes

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7663010.v1
title: Spatial and temporal localization of immune transcripts defines hallmarks and diversity in the tuberculosis granuloma

description: This repository contains raw data and all scripts for the in situ sequencing processing pipeline (Mats Nilsson Lab, Stockholm University) and downstream analysis applied in the manuscript “<b>Spatial and temporal localization of immune transcripts defines hallmarks and diversity in the tuberculosis granuloma”.</b> <b>Raw data in folders:</b> Lung csv files Bacteria csv files DAPI for plotting HE folder <b>Scripts folder:</b> Matlab scripts Cellprofiler pipelines <b>Identification and plotting of transcripts:</b> For all matlab scripts: Download the “Matlab scripts” folder, add lib to MATLAB path. Except MATLAB, no additional Mathworks product is required. Tested on R2017b. <b>InSituSequencing.m</b> is the top-level script processing sequencing images to positional visualization of decoded transcripts. Input images are available on request, those were tiled and then processed in the cell profiler pipeline “Blob identification” generating csv files containing position and intensity of each identified signal.csv files for all lung scans (3 per time point) are in “lung csv files” folder and can be plotted on high resolution DAPI images (10% of original size) found in “DAPI for plotting” folder using InSituSequencing.m. High resolution H&E scans of in situ-sequenced lungs for lung section per time point are in the “HE folder” at 50% of original size. For all images 1 pixel corresponds to 0.325 mm. <b>Identification and plotting of transcripts in given proximity to bacteria:</b> Use the cellprofiler pipeline “Bacteria identification” instead of “Blob identification” to identify signal in indicated distances from identified bacteria. The folder “bacteria csv files” contains identified signals in the indicated distances to identified bacteria. Input images are available on request. <b>Downstream analysis (Matlab Scripts folder)</b> <b>DensityEstimation.m</b> was used to display not absolute reads but a kernel density estimation of a certain gene in a 2log scale. <b>ROI_draw_onImage.m</b> was applied to extract reads from annotated regions. Pictures of annotations can be found in the manuscript supplementary figure S1. <b>HexbinClustering.m </b>performed an unsupervised clustering (kmeans) of spatial data with a given number of distinct clusters in a given radius. <br>
DOI: 10.6084/m9.figshare.7661447
title: Description of the first sclerogibbid wasp (Hymenoptera: Sclerogibbidae) from Burmese (Myanmar) amber and its phylogenetic significance

description: Sclerogibbid wasps (Hymenoptera: Chrysidoidea: Sclerogibbidae) are the obligate parasitoids of webspinners (Embiidina) in extant fauna; fossil sclerogibbids are very rare, while fossil webspinners are more abundant. Burmese amber is the oldest Lagerstätte where both diverse webspinners and sclerogibbids are found. In this paper, <i>Sclerogibba cretacica</i> sp. nov. is described from Late Cretaceous Burmese (Myanmar) amber. The new species, assigned to the extant genus <i>Sclerogibba</i> Riggio & De Stefani-Perez, 1888, is the fourth known fossil species of Sclerogibbidae and the first known fossil male of this family. Moreover, this is the first described sclerogibbid wasp from Burmese amber and the first known fossil species of <i>Sclerogibba. Sclerogibba cretacica</i> is similar to extant sclerogibbid wasps with a closed discoidal cell from South-East Asia, but differs in the shape of the discoidal cell and small number of antennomeres (19 only). The phylogenetic significance of this species is discussed. Evolutionary trends in the antennal polymorphism of sclerogibbid wasps since the Cretaceous are outlined. The records of fossil webspinners, their ancestors (Alexrasniidae) and sclerogibbids suggest a Laurasian origin of Sclerogibbidae. The genus <i>Protosclerogibba</i> Olmi, Marletta, Guglielmino & Speranza, 2016 is synonymized with <i>Herpetosphex</i> Arnold, 1940 (Pompilidae) and <i>Protosclerogibba australis</i> Olmi, Marletta, Guglielmino & Speranza, 2016 is synonymized with <i>Herpetosphex staphylinoides</i> Arnold, 1940 (new synonyms). http://zoobank.org/urn:lsid:zoobank.org:pub:8742C684-7937-401C-9958-C6106DB5C378
DOI: 10.6084/m9.figshare.7661450
title: Taxonomic harmonization of Neogene and Quaternary candonid genera (Crustacea, Ostracoda) of the Paratethys

description: During the Cenozoic, the constant northward movement of the African plate led to the division of the Tethys Ocean into two: the Palaeomediterranean and the Paratethyan branches. The latter was represented by a huge epicontinental sea and brackish to freshwater lakes that extended across central Europe and western Asia. Neogene and Quaternary ostracods from the Paratethys originated through major adaptive radiations, which gave rise to endemic brackish taxa. Unfortunately, much confusion surrounds their taxonomy, due to the quality of descriptions and images in the original literature and the incompleteness of the type material, making necessary a taxonomic revision. In this paper, we propose a systematic revision of several Paratethyan endemic candonid genera based on the analysis of the type material, new material collected from the type localities, and new fossil material from the Ponto-Caspian area. The study focuses on the description of the valve morphology and particularly on the geometric morphometric analysis of the valve outline. Thirty-three genera were taken into account of which four (<i>Advenocypris</i>, <i>Candoniella</i>, <i>Graviacypris</i>, <i>Telekia</i>) were considered to be junior synonyms of <i>Typhlocypris</i>, <i>Pseudocandona</i> or <i>Candona</i>. <i>Moesiella</i> is considered a <i>nomen nudum</i>. In the case of <i>Caspiollina</i>, <i>Dacicandona</i>, <i>Liventalina</i> and <i>Turkmenella</i> the scarcity of material and/or the poor descriptions reported in the literature prevented us from performing a full revision. The monospecific genus <i>Thaminocypris</i> possibly includes a teratological form. The remaining 23 genera were merged into nine valid, endemic, genera (<i>Bakunella</i>, <i>Camptocypria</i>, <i>Caspiocypris</i>, <i>Hastacandona</i>, <i>Lineocypris</i>, <i>Pontoniella</i>, <i>Propontoniella</i>, <i>Typhlocyprella</i> and <i>Zalanyiella</i>). Emended diagnoses and descriptions are proposed for these genera and a new species, <i>Bakunella anae</i> sp. nov., is described. This study considerably reduces the taxonomic uncertainty within the Paratethyan candonids, providing new data for the evaluation of the palaeobiodiversity of the Paratethyan domain. Finally, the palaeobiogeography of Paratethyan candonids during the Neogene and Quaternary is also discussed. http://zoobank.org/urn:lsid:zoobank.org:pub:EB9EC2D4-AFD2-428E-9958-C97F36ED7FF2
DOI: 10.6084/m9.figshare.7661450.v1
title: Taxonomic harmonization of Neogene and Quaternary candonid genera (Crustacea, Ostracoda) of the Paratethys

description: During the Cenozoic, the constant northward movement of the African plate led to the division of the Tethys Ocean into two: the Palaeomediterranean and the Paratethyan branches. The latter was represented by a huge epicontinental sea and brackish to freshwater lakes that extended across central Europe and western Asia. Neogene and Quaternary ostracods from the Paratethys originated through major adaptive radiations, which gave rise to endemic brackish taxa. Unfortunately, much confusion surrounds their taxonomy, due to the quality of descriptions and images in the original literature and the incompleteness of the type material, making necessary a taxonomic revision. In this paper, we propose a systematic revision of several Paratethyan endemic candonid genera based on the analysis of the type material, new material collected from the type localities, and new fossil material from the Ponto-Caspian area. The study focuses on the description of the valve morphology and particularly on the geometric morphometric analysis of the valve outline. Thirty-three genera were taken into account of which four (<i>Advenocypris</i>, <i>Candoniella</i>, <i>Graviacypris</i>, <i>Telekia</i>) were considered to be junior synonyms of <i>Typhlocypris</i>, <i>Pseudocandona</i> or <i>Candona</i>. <i>Moesiella</i> is considered a <i>nomen nudum</i>. In the case of <i>Caspiollina</i>, <i>Dacicandona</i>, <i>Liventalina</i> and <i>Turkmenella</i> the scarcity of material and/or the poor descriptions reported in the literature prevented us from performing a full revision. The monospecific genus <i>Thaminocypris</i> possibly includes a teratological form. The remaining 23 genera were merged into nine valid, endemic, genera (<i>Bakunella</i>, <i>Camptocypria</i>, <i>Caspiocypris</i>, <i>Hastacandona</i>, <i>Lineocypris</i>, <i>Pontoniella</i>, <i>Propontoniella</i>, <i>Typhlocyprella</i> and <i>Zalanyiella</i>). Emended diagnoses and descriptions are proposed for these genera and a new species, <i>Bakunella anae</i> sp. nov., is described. This study considerably reduces the taxonomic uncertainty within the Paratethyan candonids, providing new data for the evaluation of the palaeobiodiversity of the Paratethyan domain. Finally, the palaeobiogeography of Paratethyan candonids during the Neogene and Quaternary is also discussed. http://zoobank.org/urn:lsid:zoobank.org:pub:EB9EC2D4-AFD2-428E-9958-C97F36ED7FF2
DOI: 10.7284/106559
title: GNSS (Global Navigation Satellite System) data collected during research cruise CB948 using a Northstar 951X instrument system onboard the platform RV Clifford A. Barnes

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7661447.v1
title: Description of the first sclerogibbid wasp (Hymenoptera: Sclerogibbidae) from Burmese (Myanmar) amber and its phylogenetic significance

description: Sclerogibbid wasps (Hymenoptera: Chrysidoidea: Sclerogibbidae) are the obligate parasitoids of webspinners (Embiidina) in extant fauna; fossil sclerogibbids are very rare, while fossil webspinners are more abundant. Burmese amber is the oldest Lagerstätte where both diverse webspinners and sclerogibbids are found. In this paper, <i>Sclerogibba cretacica</i> sp. nov. is described from Late Cretaceous Burmese (Myanmar) amber. The new species, assigned to the extant genus <i>Sclerogibba</i> Riggio & De Stefani-Perez, 1888, is the fourth known fossil species of Sclerogibbidae and the first known fossil male of this family. Moreover, this is the first described sclerogibbid wasp from Burmese amber and the first known fossil species of <i>Sclerogibba. Sclerogibba cretacica</i> is similar to extant sclerogibbid wasps with a closed discoidal cell from South-East Asia, but differs in the shape of the discoidal cell and small number of antennomeres (19 only). The phylogenetic significance of this species is discussed. Evolutionary trends in the antennal polymorphism of sclerogibbid wasps since the Cretaceous are outlined. The records of fossil webspinners, their ancestors (Alexrasniidae) and sclerogibbids suggest a Laurasian origin of Sclerogibbidae. The genus <i>Protosclerogibba</i> Olmi, Marletta, Guglielmino & Speranza, 2016 is synonymized with <i>Herpetosphex</i> Arnold, 1940 (Pompilidae) and <i>Protosclerogibba australis</i> Olmi, Marletta, Guglielmino & Speranza, 2016 is synonymized with <i>Herpetosphex staphylinoides</i> Arnold, 1940 (new synonyms). http://zoobank.org/urn:lsid:zoobank.org:pub:8742C684-7937-401C-9958-C6106DB5C378