cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5161306.v1
title: Supplementary Material for: Limited Role of Random Skin Biopsy in the Diagnosis of Intravascular Lymphoma in Adult Patients with Hemophagocytic Lymphohistiocytosis

description: <strong><em>Background/Aims:</em></strong> This study examined the role of random normal skin biopsy in the diagnosis of intravascular lymphoma (IVL) in adult Western patients with clinically diagnosed hemophagocytic lymphohistiocytosis (HLH). <b><i>Methods:</i></b> In a retrospective chart review study, we analyzed a total of 59 skin biopsies that were performed to diagnose IVL in 21 adult patients with HLH seen at Stanford Hospital between 2004 and 2016. <b><i>Results:</i></b> Out of the 59 skin biopsies, 42 were taken from clinically normal-appearing skin and 17 from clinically abnormal-appearing skin. None of the 59 biopsies revealed a diagnosis of primary or metastatic malignancy, regardless of the malignancy history, clinical presentation, and biopsy and histopathologic characteristics. A review of 8 positive IVL cases at Stanford Hospital including 1 case associated with HLH showed 1 positive diagnosis by a targeted skin biopsy and other positive diagnoses by bone marrow (<i>n</i> = 4), lung (<i>n</i> = 2), brain (<i>n</i> = 2), muscle (<i>n</i> = 1), and nerve (<i>n</i> = 1). <b><i>Conclusion:</i></b> Random skin biopsies have a limited role in diagnosing IVL in adult patients with HLH, in the setting of a single academic institution in the USA. A review of the literature emphasizes the role of a full body skin exam with a selective skin biopsy in these patients.
DOI: 10.6084/m9.figshare.5161228
title: Fluorescence in situ hybridization (FISH) images of methanotrophic (MOX, MITC849 probe double-labelled with 594 dye) symbionts in 10 μm sections of I. methanophila sponge (Chapopote Knoll).

description: We double-labelled MTC849 (5` – CGTTAGCTCCACCACTAAG – 3) with Atto594 dye (Biomers, Ulm, Germany), and hybridized it with sponge tissue in 20% formamide buffer using standard protocol (Duperron <i>et al.</i>, 2008). Photomicrographs were acquired with confocal laser-scanning microscope (LSM 780, Carl Zeiss, Germany) - named CLSM*** or with Zeiss Axioplan 2 epifluorescence microscope (Zeiss, Jena, Germany) - named 7-108-ROV17*** . Three channels were acquired - 594, DAPI and 488/FITC (autofluoresence). Five images that had been acquired with 10x magnification have been used to reconstruct the overview representation.
DOI: 10.6084/m9.figshare.5161222
title: Additional FISH images of methanotrophic (MOX, MITC849 probe double-labelled with 594 dye) symbionts in 10 μm sections of H. (S.) methanophila sponge (Mictlan Knoll individual), epifluorescence microscpopy

description: We double-labelled MTC849 (5` – CGTTAGCTCCACCACTAAG – 3`) with Atto594 dye (Biomers, Ulm, Germany), and hybridized it with sponge tissue in 20% formamide buffer using standard protocol (Duperron <i>et al.</i>, 2008). Photomicrographs were acquired with Zeiss Axioplan 2 epifluorescence microscope (Zeiss, Jena, Germany), 40x or 100x lenses (see file name). Three channels were used - 594 (MITC849), DAPI and FITC(autofluoresence).
DOI: 10.6084/m9.figshare.5161222.v1
title: Additional FISH images of methanotrophic (MOX, MITC849 probe double-labelled with 594 dye) symbionts in 10 μm sections of H. (S.) methanophila sponge (Mictlan Knoll individual), epifluorescence microscpopy

description: We double-labelled MTC849 (5` – CGTTAGCTCCACCACTAAG – 3`) with Atto594 dye (Biomers, Ulm, Germany), and hybridized it with sponge tissue in 20% formamide buffer using standard protocol (Duperron <i>et al.</i>, 2008). Photomicrographs were acquired with Zeiss Axioplan 2 epifluorescence microscope (Zeiss, Jena, Germany), 40x or 100x lenses (see file name). Three channels were used - 594 (MITC849), DAPI and FITC(autofluoresence).
DOI: 10.6084/m9.figshare.5161201
title: CLSM reconstruction of methanotrophic bacteria in embryo tissue of deep-sea sponge H. (S.) methanophila, MTC849 probe

description: We double-labelled MTC849 (5` – CGTTAGCTCCACCACTAAG – 3) with Atto594 dye (Biomers, Ulm, Germany), and hybridized it with sponge tissue in 20% formamide buffer using standard protocol (Duperron <i>et al.</i>, 2008). Photomicrographs were acquired with confocal laser-scanning microscope (LSM 780, Carl Zeiss, Germany). Three channels were used - 594, DAPI and 488 (autofluoresence). 3D representation of image stacks was reconstructed with Fiji 3D project option (interpolated)..
DOI: 10.6084/m9.figshare.5161192
title: Mycobiomes of tomato plants with vine decline

description: Tomato vine decline (TVD) in south-western Ontario is a disease with symptoms that include premature plant senescence, root browning and rotting, and fruit yield reduction. Soilborne fungi cause similar vine decline symptoms in melons and potatoes. To identify which potential pathogens might be associated with TVD, we undertook both a DNA and culture based survey of the fungi found in roots and rhizospheres of field and lab grown plants. DNA finger printing revealed that roots are colonized by significantly different fungal populations than those found in rhizospheres or the soil in which they are grown. The fungal species associated with TVD resistant ‘Beaufort’ and ‘RST-04–105-T’ rootstocks were also consistently different from those in the TVD susceptible commercial variety ‘Heinz 2401ʹ. Mycobiomes in ‘Heinz 2401ʹ roots and rhizospheres changed significantly when plants were grown in sterile sand, TVD infested soil, or in the same soil that had been amended with molasses. Internal transcribed spacer (ITS) region sequences derived from PCR product clones or fungal cultures isolated from roots identified 53 different fungal species. Annotated DNA fingerprints showed that roots of all plants grown in soil contained <i>Verticillium dahliae</i>, a destructive vascular pathogen of tomatoes, while only susceptible ‘Heinz 2401ʹ roots were infected with the obligate parasite <i>Olpidium virulentus</i>. While these two pathogens may both be reducing tomato yields in Ontario, it appears that existing tomato rootstock varieties may be resistant to infection by <i>O. virulentus</i>. This poorly characterized soil-transmitted Chrytidiomycete may be contributing to TVD.
DOI: 10.6084/m9.figshare.5161195
title: Protector effect of α-thalassaemia on cholecystitis and cholecystectomy in sickle cell disease

description: <b>Objectives:</b> Cholecystitis is one of the complications of symptomatic cholelithiasis responsible for high levels of morbidity of sickle cell disease (SCD) patients. Here, we investigated the possible protective role of single gene deletions of α-thalassaemia in the occurrence of cholelithiasis and cholecystitis in SCD patients, as well as the cholecystectomy requirements. <b>Methods:</b> The α-globin genotype was determined in 83 SCD patients using the multiplex-polymerase chain reaction and compared with clinical events. <b>Results:</b> Overall, in 23% of patients, -α<sup>3.7</sup> deletion was found. α-Thalassaemia concomitant to SCD was an independent protective factor to cholecystitis (OR = 0.07; 95% CI: 0.01–0.66; <i>p</i> = 0.020) and cholecystectomy requirement (OR = 0.14; 95% CI: 0.03–0.60; <i>p</i> = 0.008). The risk of cholelithiasis was not affected by the α-thalassaemia concomitance. <b>Conclusions:</b> To the best our knowledge, our study is the first to show the protective effect of α-thalassaemia on cholecystitis and cholecystectomy requirements in SCD, which may be due to an improved splenic function.
DOI: 10.6084/m9.figshare.5161198
title: A systematic review of the published literature on team-based learning in health professions education

description: <b>Purpose:</b> Summarize the published literature on team-based learning (TBL) in health professions education (HPE) using the TBL conceptual framework to identify gaps that can guide future research <b>Methods:</b> PubMed, Web of Science, ERIC, and Google Scholar were searched through May 2016 for English-language articles regarding the use of TBL in HPE. Reviewers independently extracted data and coded for the seven elements in Michaelsen’s Model of TBL. <b>Results:</b> A total of 118 articles met inclusion criteria. The number of articles published yearly on TBL has grown steadily, more than tripling between 2011 and 2016. Most studies (55; 47%) involved undergraduate medical students and took place in the US (72; 61%). The most commonly studied framework component was Teacher and Learner Attitudes (97; 82%). Other commonly studied elements included Learning Outcomes (85; 72%) and Team Characteristics (25; 21%). Contextual Factors affecting TBL was addressed in one study. <b>Conclusions:</b> A substantial body of literature examines the effect that TBL has on traditional measures of achievement. However, many dimensions of TBL have not been well studied, including Teacher Decisions about TBL, Contextual Factors that affect TBL, Learners’ Engagement, and Pattern of Engagement within Teams. Future research in these areas could determine the best use of TBL in HPE.
DOI: 10.6084/m9.figshare.5161198.v1
title: A systematic review of the published literature on team-based learning in health professions education

description: <b>Purpose:</b> Summarize the published literature on team-based learning (TBL) in health professions education (HPE) using the TBL conceptual framework to identify gaps that can guide future research <b>Methods:</b> PubMed, Web of Science, ERIC, and Google Scholar were searched through May 2016 for English-language articles regarding the use of TBL in HPE. Reviewers independently extracted data and coded for the seven elements in Michaelsen’s Model of TBL. <b>Results:</b> A total of 118 articles met inclusion criteria. The number of articles published yearly on TBL has grown steadily, more than tripling between 2011 and 2016. Most studies (55; 47%) involved undergraduate medical students and took place in the US (72; 61%). The most commonly studied framework component was Teacher and Learner Attitudes (97; 82%). Other commonly studied elements included Learning Outcomes (85; 72%) and Team Characteristics (25; 21%). Contextual Factors affecting TBL was addressed in one study. <b>Conclusions:</b> A substantial body of literature examines the effect that TBL has on traditional measures of achievement. However, many dimensions of TBL have not been well studied, including Teacher Decisions about TBL, Contextual Factors that affect TBL, Learners’ Engagement, and Pattern of Engagement within Teams. Future research in these areas could determine the best use of TBL in HPE.
DOI: 10.6084/m9.figshare.5161201.v1
title: CLSM reconstruction of methanotrophic bacteria in embryo tissue of deep-sea sponge H. (S.) methanophila, MTC849 probe

description: We double-labelled MTC849 (5` – CGTTAGCTCCACCACTAAG – 3) with Atto594 dye (Biomers, Ulm, Germany), and hybridized it with sponge tissue in 20% formamide buffer using standard protocol (Duperron <i>et al.</i>, 2008). Photomicrographs were acquired with confocal laser-scanning microscope (LSM 780, Carl Zeiss, Germany). Three channels were used - 594, DAPI and 488 (autofluoresence). 3D representation of image stacks was reconstructed with Fiji 3D project option (interpolated)..
DOI: 10.6084/m9.figshare.5161195.v1
title: Protector effect of α-thalassaemia on cholecystitis and cholecystectomy in sickle cell disease

description: <b>Objectives:</b> Cholecystitis is one of the complications of symptomatic cholelithiasis responsible for high levels of morbidity of sickle cell disease (SCD) patients. Here, we investigated the possible protective role of single gene deletions of α-thalassaemia in the occurrence of cholelithiasis and cholecystitis in SCD patients, as well as the cholecystectomy requirements. <b>Methods:</b> The α-globin genotype was determined in 83 SCD patients using the multiplex-polymerase chain reaction and compared with clinical events. <b>Results:</b> Overall, in 23% of patients, -α<sup>3.7</sup> deletion was found. α-Thalassaemia concomitant to SCD was an independent protective factor to cholecystitis (OR = 0.07; 95% CI: 0.01–0.66; <i>p</i> = 0.020) and cholecystectomy requirement (OR = 0.14; 95% CI: 0.03–0.60; <i>p</i> = 0.008). The risk of cholelithiasis was not affected by the α-thalassaemia concomitance. <b>Conclusions:</b> To the best our knowledge, our study is the first to show the protective effect of α-thalassaemia on cholecystitis and cholecystectomy requirements in SCD, which may be due to an improved splenic function.
DOI: 10.6084/m9.figshare.5161174
title: Treatment of peritoneal metastases from small bowel adenocarcinoma

description: <b>Background/purpose:</b> Peritoneal metastases (PM) affect approximately one third of patients with metastatic small bowel adenocarcinoma (SBA). Treatment options are (1) systemic therapy ± palliative surgery and (2) cytoreductive surgery with intraperitoneal chemotherapy (CRS + IPC). Due to scarce evidence, PM from SBA represents a therapeutic challenge. This narrative review summarised and discussed the evidence that investigated available treatment options. <b>Methods:</b> Studies were discussed if they investigated first line systemic therapy for advanced SBA or CRS + IPC for PM from SBA. Extracted outcomes were objective response rate (ORR), disease control rate (DCR), progression-free survival (PFS), disease-free survival (DFS), overall survival (OS), and grade III–V toxicity/morbidity. <b>Results:</b> Eighteen studies (15 observational, 3 phase II) that investigated systemic therapy and six observational studies that investigated CRS + IPC were reviewed. In studies that investigated systemic therapy, ORR, DCR, median PFS, median OS, and grade III–V toxicity ranged from 6% to 50%, 50% to 90%, 3 to 11 months, 8 to 20 months, and 10% to 68%, respectively. Fluoropyrimidine–oxaliplatin revealed favourable survival outcomes compared to fluoropyrimidine–irinotecan, fluoropyrimidine–cisplatin, fluoropyrimidine monotherapy, and other regimens. In studies that investigated CRS + IPC, median DFS, median OS, and grade III–V morbidity ranged from 10 to 12 months, 16 to 47 months, and 12% to 35%, respectively. <b>Conclusion:</b> Based on available evidence, fluoropyrimidine–oxaliplatin should be regarded as optimal first line systemic treatment. In selected patients, CRS + IPC appears safe and may be more effective than systemic therapy as single treatment. Future studies should evaluate survival and morbidity of CRS + IPC in larger cohorts, as well as the value of chemotherapy with targeted agents in metastatic SBA with subgroup analysis for PM from SBA.
DOI: 10.6084/m9.figshare.5161174.v1
title: Treatment of peritoneal metastases from small bowel adenocarcinoma

description: <b>Background/purpose:</b> Peritoneal metastases (PM) affect approximately one third of patients with metastatic small bowel adenocarcinoma (SBA). Treatment options are (1) systemic therapy ± palliative surgery and (2) cytoreductive surgery with intraperitoneal chemotherapy (CRS + IPC). Due to scarce evidence, PM from SBA represents a therapeutic challenge. This narrative review summarised and discussed the evidence that investigated available treatment options. <b>Methods:</b> Studies were discussed if they investigated first line systemic therapy for advanced SBA or CRS + IPC for PM from SBA. Extracted outcomes were objective response rate (ORR), disease control rate (DCR), progression-free survival (PFS), disease-free survival (DFS), overall survival (OS), and grade III–V toxicity/morbidity. <b>Results:</b> Eighteen studies (15 observational, 3 phase II) that investigated systemic therapy and six observational studies that investigated CRS + IPC were reviewed. In studies that investigated systemic therapy, ORR, DCR, median PFS, median OS, and grade III–V toxicity ranged from 6% to 50%, 50% to 90%, 3 to 11 months, 8 to 20 months, and 10% to 68%, respectively. Fluoropyrimidine–oxaliplatin revealed favourable survival outcomes compared to fluoropyrimidine–irinotecan, fluoropyrimidine–cisplatin, fluoropyrimidine monotherapy, and other regimens. In studies that investigated CRS + IPC, median DFS, median OS, and grade III–V morbidity ranged from 10 to 12 months, 16 to 47 months, and 12% to 35%, respectively. <b>Conclusion:</b> Based on available evidence, fluoropyrimidine–oxaliplatin should be regarded as optimal first line systemic treatment. In selected patients, CRS + IPC appears safe and may be more effective than systemic therapy as single treatment. Future studies should evaluate survival and morbidity of CRS + IPC in larger cohorts, as well as the value of chemotherapy with targeted agents in metastatic SBA with subgroup analysis for PM from SBA.
DOI: 10.6084/m9.figshare.5161168
title: CLSM reconstruction of bacteria in embryo tissue of deep-sea sponge H. (S.) methanophila, EUB probe

description: Catalyzed reporter deposition (CARD)-FISH with horseradish peroxidase-labeled probes (Biomers, Ulm, Germany), EUB338 (Amann et al.,1990) was performed on 8 μm sections of sponge tissue. Photomicrographs were acquired with confocal laser-scanning microscope (LSM 780, Carl Zeiss, Germany). Three channels were used - cy3, EUB probe, DAPI and 488 (autofluoresence). 3D representation of image stacks was reconstructed with Fiji 3D project option (interpolated)..
DOI: 10.6084/m9.figshare.5161153
title: Fluorescence in situ hybridization (FISH) images of methanotrophic (MOX, MITC849 probe double-labelled with 594 dye) symbionts in 10 μm sections of H. (S.) methanophila sponge (Mictlan Knoll individual).

description: Twenty 3-channel images were acquired with Zeiss Axioplan 2 epifluorescence microscope (Zeiss, Jena, Germany) with 10x magnification. Color legend is: MOX, magenta; DNA (DAPI), blue; autofluoresence at ~520 nm with ~490 nm excitation (FITC filter), green. These images were aligned with FIJI Grid/collection stitching plugin to produce the resulting mosaic. <br>
DOI: 10.6084/m9.figshare.5161156
title: Data accompanying the article "Space-by-time decomposition for single-trial decoding of M/EEG activity"

description: This is an EEG dataset recorded during the performance of a visual categorization task. We used this dataset to illustrate the effectiveness of the space-by-time M/EEG decomposition which we introduced in the linked article.
DOI: 10.6084/m9.figshare.5161168.v1
title: CLSM reconstruction of bacteria in embryo tissue of deep-sea sponge H. (S.) methanophila, EUB probe

description: Catalyzed reporter deposition (CARD)-FISH with horseradish peroxidase-labeled probes (Biomers, Ulm, Germany), EUB338 (Amann et al.,1990) was performed on 8 μm sections of sponge tissue. Photomicrographs were acquired with confocal laser-scanning microscope (LSM 780, Carl Zeiss, Germany). Three channels were used - cy3, EUB probe, DAPI and 488 (autofluoresence). 3D representation of image stacks was reconstructed with Fiji 3D project option (interpolated)..
DOI: 10.6084/m9.figshare.5161156.v1
title: Data accompanying the article "Space-by-time decomposition for single-trial decoding of M/EEG activity"

description: This is an EEG dataset recorded during the performance of a visual categorization task. We used this dataset to illustrate the effectiveness of the space-by-time M/EEG decomposition which we introduced in the linked article.
DOI: 10.6084/m9.figshare.5161099
title: max-front2-data.zip

description: <br>zip file containing data files associated to the paper:<br>"Petrological Geodynamics of Mantle Melting II. AlphaMELTS + Multiphase Flow: Dynamic Fractional Melting"<br>by Max Tirone<br>Front. Earth Sci. DOI: 10.3389/feart.2018.00018<br>
DOI: 10.6084/m9.figshare.5161099.v1
title: max-front2-data.zip

description: <br>zip file containing data files associated to the paper:<br>"Petrological Geodynamics of Mantle Melting II. AlphaMELTS + Multiphase Flow: Dynamic Fractional Melting"<br>by Max Tirone<br>Front. Earth Sci. DOI: 10.3389/feart.2018.00018<br>
DOI: 10.6084/m9.figshare.5161003
title: High- but not low-grade histologic chorioamnionitis is associated with spontaneous preterm birth in a Swedish cohort

description: <b>Objective:</b> To examine whether different grades of placenta inflammation are associated with risk for spontaneous preterm birth, taking into consideration maternal and delivery factors. Placentas from spontaneous preterm births were compared with a control group from full-term deliveries. <b>Methods:</b> Placentas from 98 full-term, 71 late preterm (gestational week 34–37), and 65 early preterm (gestational week 22–33) singleton deliveries were analysed from the Karolinska University Hospital in Stockholm. The placentas were examined for histologic chorioamnionitis (HCA) grade 1 (low) and 2 (high). Mother, child, and delivery parameters were collected from maternity centre and delivery forms. <b>Results:</b> There was a relatively low incidence of HCA in the preterm groups (26.7% and 38.5% in the late and early preterm groups, respectively). HCA 2 was most common in the early preterm group and HCA 1 was most common in the full-term group. The odds of early preterm birth was <i>lower</i> for placentas with HCA 1 compared to HCA 2 (OR = 0.17) and higher for placentas with HCA 2 compared to no HCA (OR = 2.17). <b>Conclusions:</b> Despite a relatively low incidence of HCA in the preterm groups, HCA 2 seems to be associated with early preterm birth whereas HCA 1 seems to be part of the full-term delivery.
DOI: 10.6084/m9.figshare.5160997
title: Numerical modelling on deformation and recrystallisation in ice

description: This dataset contains 16 movies showing the results of numerically modelling deformation and recrystallisation in ice on the microscopic scale using the modelling platform Elle. The movies illustrate the 2D microstructure evolution under pure shear deformation in terms of crystallographic preferred orientations, dislocation densities and local strain rates. The numerical simulations are used to investigate the relevance of the process of grain dissection for ice microdynamics. Further information is provided in the related publication “The relevance of grain dissection for grain size reduction in polar ice: insights from numerical models and ice core microstructure analysis” by Steinbach et al. (2017).
DOI: 10.6084/m9.figshare.5161003.v1
title: High- but not low-grade histologic chorioamnionitis is associated with spontaneous preterm birth in a Swedish cohort

description: <b>Objective:</b> To examine whether different grades of placenta inflammation are associated with risk for spontaneous preterm birth, taking into consideration maternal and delivery factors. Placentas from spontaneous preterm births were compared with a control group from full-term deliveries. <b>Methods:</b> Placentas from 98 full-term, 71 late preterm (gestational week 34–37), and 65 early preterm (gestational week 22–33) singleton deliveries were analysed from the Karolinska University Hospital in Stockholm. The placentas were examined for histologic chorioamnionitis (HCA) grade 1 (low) and 2 (high). Mother, child, and delivery parameters were collected from maternity centre and delivery forms. <b>Results:</b> There was a relatively low incidence of HCA in the preterm groups (26.7% and 38.5% in the late and early preterm groups, respectively). HCA 2 was most common in the early preterm group and HCA 1 was most common in the full-term group. The odds of early preterm birth was <i>lower</i> for placentas with HCA 1 compared to HCA 2 (OR = 0.17) and higher for placentas with HCA 2 compared to no HCA (OR = 2.17). <b>Conclusions:</b> Despite a relatively low incidence of HCA in the preterm groups, HCA 2 seems to be associated with early preterm birth whereas HCA 1 seems to be part of the full-term delivery.