cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19336691
title: Supplementary Material for: Optimal Value for Serum Anti-PLA2R Antibody in Primary Membranous Nephropathy: A Multicenter Observational Study

description: <b><i>Introduction:</i></b> Anti-phospholipase A2 receptor antibody (PLA2R-Ab) is highly specific for primary membranous nephropathy (PMN). Here, we compare the diagnostic value of different circulating PLA2R-Ab cutoff titers in multicenter cohorts, with particular focus on determining the optimal cutoff value for Chinese patients. <b><i>Methods:</i></b> In total, 288 patients with PMN and 301 with other nephropathies were recruited retrospectively from five hospitals in China between September 2011 and October 2018. PLA2R-Ab in serum obtained at renal biopsy was determined by enzyme-linked immunosorbent assay. The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and receiver operating characteristic (ROC) curve of PLA2R-Ab in diagnosing PMN were assessed. Diagnostic efficiency was evaluated by internal validation. <b><i>Results:</i></b> The sensitivity, specificity, PPV, NPV, and Youden index for PMN diagnosis were 71%, 90%, 88%, 75%, and 0.61 at the cutoff of 3.8 RU/mL; 74%, 86%, 84%, 76%, and 0.60 at 2.7 RU/mL; 68%, 92%, 90%, 73%, and 0.60 at 5.2 RU/mL; 64%, 95%, 93%, 72%, and 0.59 at 9.0 RU/mL; 57%, 96%, 94%, 68%, and 0.54 at 14.0 RU/mL; 51%, 97%, 95%, 66%, and 0.49 at 20.0 RU/mL; 47%, 98%, 96%, 64%, and 0.45 at 40.0 RU/mL, respectively. The area under the ROC curve was 0.83. <b><i>Conclusion:</i></b> By comprehensively considering specificity and sensitivity, we show that 3.8 RU/mL is the optimal cutoff of PLA2R-Ab in Chinese PMN patients, with a sensitivity of 71% and a specificity of 90%. The cutoff values were 5.2 RU/mL and 9.0 RU/mL when the diagnostic specificity was increased to 92% and 95%, respectively.
DOI: 10.6084/m9.figshare.19336691.v1
title: Supplementary Material for: Optimal Value for Serum Anti-PLA2R Antibody in Primary Membranous Nephropathy: A Multicenter Observational Study

description: <b><i>Introduction:</i></b> Anti-phospholipase A2 receptor antibody (PLA2R-Ab) is highly specific for primary membranous nephropathy (PMN). Here, we compare the diagnostic value of different circulating PLA2R-Ab cutoff titers in multicenter cohorts, with particular focus on determining the optimal cutoff value for Chinese patients. <b><i>Methods:</i></b> In total, 288 patients with PMN and 301 with other nephropathies were recruited retrospectively from five hospitals in China between September 2011 and October 2018. PLA2R-Ab in serum obtained at renal biopsy was determined by enzyme-linked immunosorbent assay. The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and receiver operating characteristic (ROC) curve of PLA2R-Ab in diagnosing PMN were assessed. Diagnostic efficiency was evaluated by internal validation. <b><i>Results:</i></b> The sensitivity, specificity, PPV, NPV, and Youden index for PMN diagnosis were 71%, 90%, 88%, 75%, and 0.61 at the cutoff of 3.8 RU/mL; 74%, 86%, 84%, 76%, and 0.60 at 2.7 RU/mL; 68%, 92%, 90%, 73%, and 0.60 at 5.2 RU/mL; 64%, 95%, 93%, 72%, and 0.59 at 9.0 RU/mL; 57%, 96%, 94%, 68%, and 0.54 at 14.0 RU/mL; 51%, 97%, 95%, 66%, and 0.49 at 20.0 RU/mL; 47%, 98%, 96%, 64%, and 0.45 at 40.0 RU/mL, respectively. The area under the ROC curve was 0.83. <b><i>Conclusion:</i></b> By comprehensively considering specificity and sensitivity, we show that 3.8 RU/mL is the optimal cutoff of PLA2R-Ab in Chinese PMN patients, with a sensitivity of 71% and a specificity of 90%. The cutoff values were 5.2 RU/mL and 9.0 RU/mL when the diagnostic specificity was increased to 92% and 95%, respectively.
DOI: 10.25934/pr00000842.0
title: Available IPD datapackage for study 'Multicenter, Pivotal Phase III Study of Iodine-131 Anti-B1 Antibody (Murine) Radioimmunotherapy for Chemotherapy Refractory Low Grade B Cell Lymphomas and Low Grade Lymphomas That Have Transformed to Higher Grade Histologies'

description: The results from Phase 1/2 (RIT-I-000) and Phase 2 (RIT-II-001) studies of Tositumomab and Iodine I 131 Tositumomab (TST/I-131 TST) demonstrated that TST/ I-131 TST produced a high response rate in patients with chemotherapy-relapsed/refractory, low-grade or transformed low-grade Non-Hodgkin's Lymphoma (NHL). On the basis of these results this study was designed to compare the efficacy of TST/ I-131 TST to the last qualifying chemotherapy regimen in patients with chemotherapy-refractory, low-grade or transformed low-grade NHL.
DOI: 10.5281/zenodo.6341815
title: Cancer Paper 2019 - UTX-RNAseq.part3

description: Cancer Paper 2019 - UTX-RNAseq.part3
DOI: 10.5281/zenodo.6341814
title: Cancer Paper 2019 - UTX-RNAseq.part3

description: Cancer Paper 2019 - UTX-RNAseq.part3
DOI: 10.25934/pr00000093.0
title: Available IPD datapackage for study 'Phase II Study of Iodine-131 Anti-B1 Antibody for Non Hodgkin's Lymphoma Patients Who Have Previously Received Rituximab'

description: This is a single-arm, open-label, multicenter study of Iodine I-131 Anti B1 Antibody (Tositumomab and Iodine I 131 Tositumomab) for treatment of non-Hodgkin's lymphoma (NHL) who were previously treated with rituximab antibody. Patients must have been treated with at least 4 doses of rituximab and have progressed during or following rituximab therapy. Patients will undergo two dosing phases of study. In the first phase, termed the "dosimetric dose", patients will receive an infusion of unlabeled Anti-B1 Antibody (450 mg) over 70 minutes immediately followed by a 30-minute infusion of Anti-B1 Antibody (35 mg) which has been radiolabeled with 5 mCi of Iodine-131. Whole body gamma camera scans will be obtained on Day 0; Day 2, 3, or 4; and Day 6 or 7 following the dosimetric dose. Using the dosimetric data from three imaging timepoints, a patient-specific dose of Iodine-131 will be calculated to deliver the desired total body dose of radiotherapy. In the second phase, termed the "therapeutic dose", patients will receive a 70-minute infusion of unlabeled Anti-B1 Antibody (450 mg) immediately followed by a 30-minute infusion of 35 mg Anti-B1 Antibody labeled with a patient-specific dose of Iodine-131 to deliver a whole body dose of 75 cGy to patients with no hematologic risk factors. Patients who have platelet counts of 100,001-149,999 cells/mm3 will receive 65 cGy and patients who are obese will be dosed based upon 137% of their lean body mass. Patients will be treated with either saturated solution potassium iodide (SSKI), Lugol's solution, or potassium iodide tablets starting at least 24 hours prior to the first infusion of the Iodine-131 Anti-B1 Antibody (i.e., dosimetric dose) and continuing for 14 days following the last infusion of Iodine-131 Anti-B1 Antibody (i.e., therapeutic dose). The endpoints of the study are to determine the response rate, complete response rate, duration of response, and time to progression or death, based on both a Masked Independent Randomized Radiographic and Oncologic Review (MIRROR) panel and the Investigators, and the Investigators' assessment of safety and survival of survival of Iodine-131 Anti-B1 Antibody therapy in NHL patients who have previously been treated with rituximab.
DOI: 10.6084/m9.figshare.19336694
title: Source Data.xlsx

description: source data
DOI: 10.6084/m9.figshare.4742104.v1
title: Determinants of cyanobacterial species composition in the splash zone of two Croatian islands

description: Cyanobacterial communities of the splash zone of two Croatian islands, Veruda and Ugljan, were surveyed. At each island, we studied eight localities with different aspects. From all 336 samples, a total of 42 cyanobacterial species, one green alga, and one red alga were found. In both islands <i>Hyella</i> spp. and <i>Gloeocapsopsis crepidinum</i> dominated and <i>Entophysalis deusta, Solentia</i> spp., <i>Kyrtuthrix dalmatica</i> and <i>Mastigocoleus testarum</i> were found frequently. Multivariate statistical analysis of species composition shows that the vertical gradient is the strongest determinant of species composition and that there are statistically significant but not very pronounced differences in species composition between the two islands. Species composition among individual sites within islands differed slightly, and between localities decreased rather slowly with the distance of individual samples (i.e. the similarity distance decay was very slow), showing that even close samples can have quite different species composition. The species accumulation curves do not reach their asymptote, indicating that many samples are needed to reasonably cover the species richness of a site. This study highlights the importance of in-depth species counts and high density sampling along vertical gradients for satisfactory cyanobacterial community assessments in marine coastal splash zones.
DOI: 10.6084/m9.figshare.4872833
title: The freshwater red alga <i>Batrachospermum turfosum</i> (Florideophyceae) can acclimate to a wide range of light and temperature conditions

description: <i>Batrachospermum turfosum</i> Bory is one of the generalists among the few red algae that have adapted to freshwater habitats, occurring in a variety of primarily shaded, nutrient-poor micro-habitats with lotic (running) or lentic (standing) waters. Seasonal variations in water level and canopy cover can expose this sessile alga to widely fluctuating temperatures, solar irradiation and nutrient availability. Here we report on the ecophysiology of <i>B. turfosum</i> collected from an ultra-oligotrophic bog pool in the Austrian Alps. Photosynthesis as a function of photon fluence density (PFD) and temperature was studied by measuring oxygen evolution in combination with chlorophyll fluorescence. In addition, the effects of ultraviolet radiation (UVR) on photosynthetic pigments were analysed using HPLC and spectrophotometric methods, and cellular ultrastructure was studied using transmission electron microscopy. We found that <i>B. turfosum</i> is adapted to low light, with a light compensation point (<i>I</i><sub>c</sub>) and a light saturation point (<i>I</i><sub>k</sub>) of 8.4 and 29.7 µmol photons m<sup>–2</sup> s<sup>–1</sup>, respectively, but also tolerates higher PFDs of ~1000 µmol photons m<sup>–2</sup> s<sup>–1</sup>, and is capable of net photosynthesis at temperatures between 5°C and 35°C. Exposure to either UV-A or UV-AB for 102 h led to a strong transient drop in effective quantum yield (ΔF/F<sub>M</sub>’), followed by an acclimation to about 70% of initial ΔF/F<sub>M</sub>’ values. Ultrastructural changes included the accumulation of plastoglobules and dilated membranes after UVR treatment. Although all photosynthetic pigments strongly decreased upon UVR exposure and no UV-photoprotectants (e.g. mycosporine-like amino acids) could be detected, the alga was capable of recovering ΔF/F<sub>M</sub>’ and phycobiliproteins after UVR treatment. In summary, <i>B. turfosum</i> tolerates a wide range of irradiation and temperature regimes, and these traits may be the basis for its successful adaptation to challenging environments.
DOI: 10.6084/m9.figshare.4742104
title: Determinants of cyanobacterial species composition in the splash zone of two Croatian islands

description: Cyanobacterial communities of the splash zone of two Croatian islands, Veruda and Ugljan, were surveyed. At each island, we studied eight localities with different aspects. From all 336 samples, a total of 42 cyanobacterial species, one green alga, and one red alga were found. In both islands <i>Hyella</i> spp. and <i>Gloeocapsopsis crepidinum</i> dominated and <i>Entophysalis deusta, Solentia</i> spp., <i>Kyrtuthrix dalmatica</i> and <i>Mastigocoleus testarum</i> were found frequently. Multivariate statistical analysis of species composition shows that the vertical gradient is the strongest determinant of species composition and that there are statistically significant but not very pronounced differences in species composition between the two islands. Species composition among individual sites within islands differed slightly, and between localities decreased rather slowly with the distance of individual samples (i.e. the similarity distance decay was very slow), showing that even close samples can have quite different species composition. The species accumulation curves do not reach their asymptote, indicating that many samples are needed to reasonably cover the species richness of a site. This study highlights the importance of in-depth species counts and high density sampling along vertical gradients for satisfactory cyanobacterial community assessments in marine coastal splash zones.
DOI: 10.6084/m9.figshare.4872830
title: Ultrastructure and molecular phylogenetic position of a new marine sand-dwelling dinoflagellate from British Columbia, Canada: <i>Pseudadenoides polypyrenoides</i> sp. nov. (Dinophyceae)

description: Two monospecific genera of marine benthic dinoflagellates, <i>Adenoides</i> and <i>Pseudadenoides</i>, have unusual thecal tabulation patterns (lack of cingular plates in the former; and no precingular plates and a complete posterior intercalary plate series in the latter) and are thus difficult to place within a phylogenetic framework. Although both genera share morphological similarities, they have not formed sister taxa in previous molecular phylogenetic analyses. We discovered and characterized a new species of <i>Pseudadenoides, P. polypyrenoides</i> sp. nov., at both the ultrastructural and molecular phylogenetic levels. Molecular phylogenetic analyses of SSU and LSU rDNA sequences demonstrated a close relationship between <i>P. polypyrenoides</i> sp. nov. and <i>Pseudadenoides kofoidii</i>, and <i>Adenoides</i> and <i>Pseudadenoides</i> formed sister taxa in phylogenetic trees inferred from LSU rDNA sequences. Comparisons of morphological traits, such as the apical pore complex (APC), demonstrated similarities between <i>Adenoides, Pseudadenoides</i> and several planktonic genera (e.g. <i>Heterocapsa, Azadinium</i> and <i>Amphidoma</i>). Molecular phylogenetic analyses of SSU and LSU rDNA sequences also demonstrated an undescribed species within <i>Adenoides.</i>
DOI: 10.6084/m9.figshare.4872830.v2
title: Ultrastructure and molecular phylogenetic position of a new marine sand-dwelling dinoflagellate from British Columbia, Canada: <i>Pseudadenoides polypyrenoides</i> sp. nov. (Dinophyceae)

description: Two monospecific genera of marine benthic dinoflagellates, <i>Adenoides</i> and <i>Pseudadenoides</i>, have unusual thecal tabulation patterns (lack of cingular plates in the former; and no precingular plates and a complete posterior intercalary plate series in the latter) and are thus difficult to place within a phylogenetic framework. Although both genera share morphological similarities, they have not formed sister taxa in previous molecular phylogenetic analyses. We discovered and characterized a new species of <i>Pseudadenoides, P. polypyrenoides</i> sp. nov., at both the ultrastructural and molecular phylogenetic levels. Molecular phylogenetic analyses of SSU and LSU rDNA sequences demonstrated a close relationship between <i>P. polypyrenoides</i> sp. nov. and <i>Pseudadenoides kofoidii</i>, and <i>Adenoides</i> and <i>Pseudadenoides</i> formed sister taxa in phylogenetic trees inferred from LSU rDNA sequences. Comparisons of morphological traits, such as the apical pore complex (APC), demonstrated similarities between <i>Adenoides, Pseudadenoides</i> and several planktonic genera (e.g. <i>Heterocapsa, Azadinium</i> and <i>Amphidoma</i>). Molecular phylogenetic analyses of SSU and LSU rDNA sequences also demonstrated an undescribed species within <i>Adenoides.</i>
DOI: 10.6084/m9.figshare.4872836
title: Pathogens of brown algae: culture studies of <i>Anisolpidium ectocarpii</i> and <i>A. rosenvingei</i> reveal that the Anisolpidiales are uniflagellated oomycetes

description: Using laboratory cultures, we have documented the life cycle of <i>Anisolpidium ectocarpii</i>, a pathogen of <i>Ectocarpus</i> and other filamentous brown algae, and presented preliminary observations on <i>Anisolpidium rosenvingei</i>, a pathogen of <i>Pylaiella littoralis</i>. Consistent with earlier reports, the zoospores of both species have a single anterior flagellum, which justified the placement of <i>Anisolpidium</i> amongst the Hyphochytriales (Hyphochytridiomycota). We have also shown that <i>A. ectocarpii</i> can complete its infection cycle in a broad selection of species from various brown algal orders, whereas <i>A. rosenvingei</i> seemingly exhibits a strict specificity for unilocular sporangia of <i>P. littoralis</i>. Unexpectedly, nuclear (18S rRNA) and mitochondrial (<i>cox</i>1, <i>cox</i>2) markers regroup <i>A. ectocarpii</i> and <i>A. rosenvingei</i>, into a hitherto unrecognized monophyletic clade within the oomycetes (Oomycota), most closely related to the Olpidiopsidales. The <i>Anisolpidium</i> genus is therefore entirely distinct from the Hyphochytridiomycota and represents the first confirmed instance of an anteriorly uniciliate oomycete. Finally, we suggest that a valid morphological criterion to separate true hyphochytrids from oomycetes is the timing of zoospore cleavage. Given the evidence, we propose to transfer the Anisolpidiales from the Hyphochytriales to the Oomycetes.
DOI: 10.6084/m9.figshare.4872833.v1
title: The freshwater red alga <i>Batrachospermum turfosum</i> (Florideophyceae) can acclimate to a wide range of light and temperature conditions

description: <i>Batrachospermum turfosum</i> Bory is one of the generalists among the few red algae that have adapted to freshwater habitats, occurring in a variety of primarily shaded, nutrient-poor micro-habitats with lotic (running) or lentic (standing) waters. Seasonal variations in water level and canopy cover can expose this sessile alga to widely fluctuating temperatures, solar irradiation and nutrient availability. Here we report on the ecophysiology of <i>B. turfosum</i> collected from an ultra-oligotrophic bog pool in the Austrian Alps. Photosynthesis as a function of photon fluence density (PFD) and temperature was studied by measuring oxygen evolution in combination with chlorophyll fluorescence. In addition, the effects of ultraviolet radiation (UVR) on photosynthetic pigments were analysed using HPLC and spectrophotometric methods, and cellular ultrastructure was studied using transmission electron microscopy. We found that <i>B. turfosum</i> is adapted to low light, with a light compensation point (<i>I</i><sub>c</sub>) and a light saturation point (<i>I</i><sub>k</sub>) of 8.4 and 29.7 µmol photons m<sup>–2</sup> s<sup>–1</sup>, respectively, but also tolerates higher PFDs of ~1000 µmol photons m<sup>–2</sup> s<sup>–1</sup>, and is capable of net photosynthesis at temperatures between 5°C and 35°C. Exposure to either UV-A or UV-AB for 102 h led to a strong transient drop in effective quantum yield (ΔF/F<sub>M</sub>’), followed by an acclimation to about 70% of initial ΔF/F<sub>M</sub>’ values. Ultrastructural changes included the accumulation of plastoglobules and dilated membranes after UVR treatment. Although all photosynthetic pigments strongly decreased upon UVR exposure and no UV-photoprotectants (e.g. mycosporine-like amino acids) could be detected, the alga was capable of recovering ΔF/F<sub>M</sub>’ and phycobiliproteins after UVR treatment. In summary, <i>B. turfosum</i> tolerates a wide range of irradiation and temperature regimes, and these traits may be the basis for its successful adaptation to challenging environments.
DOI: 10.6084/m9.figshare.4872836.v1
title: Pathogens of brown algae: culture studies of <i>Anisolpidium ectocarpii</i> and <i>A. rosenvingei</i> reveal that the Anisolpidiales are uniflagellated oomycetes

description: Using laboratory cultures, we have documented the life cycle of <i>Anisolpidium ectocarpii</i>, a pathogen of <i>Ectocarpus</i> and other filamentous brown algae, and presented preliminary observations on <i>Anisolpidium rosenvingei</i>, a pathogen of <i>Pylaiella littoralis</i>. Consistent with earlier reports, the zoospores of both species have a single anterior flagellum, which justified the placement of <i>Anisolpidium</i> amongst the Hyphochytriales (Hyphochytridiomycota). We have also shown that <i>A. ectocarpii</i> can complete its infection cycle in a broad selection of species from various brown algal orders, whereas <i>A. rosenvingei</i> seemingly exhibits a strict specificity for unilocular sporangia of <i>P. littoralis</i>. Unexpectedly, nuclear (18S rRNA) and mitochondrial (<i>cox</i>1, <i>cox</i>2) markers regroup <i>A. ectocarpii</i> and <i>A. rosenvingei</i>, into a hitherto unrecognized monophyletic clade within the oomycetes (Oomycota), most closely related to the Olpidiopsidales. The <i>Anisolpidium</i> genus is therefore entirely distinct from the Hyphochytridiomycota and represents the first confirmed instance of an anteriorly uniciliate oomycete. Finally, we suggest that a valid morphological criterion to separate true hyphochytrids from oomycetes is the timing of zoospore cleavage. Given the evidence, we propose to transfer the Anisolpidiales from the Hyphochytriales to the Oomycetes.
DOI: 10.6084/m9.figshare.4872830.v1
title: Ultrastructure and molecular phylogenetic position of a new marine sand-dwelling dinoflagellate from British Columbia, Canada: <i>Pseudadenoides polypyrenoides</i> sp. nov. (Dinophyceae)

description: Two monospecific genera of marine benthic dinoflagellates, <i>Adenoides</i> and <i>Pseudadenoides</i>, have unusual thecal tabulation patterns (lack of cingular plates in the former; and no precingular plates and a complete posterior intercalary plate series in the latter) and are thus difficult to place within a phylogenetic framework. Although both genera share morphological similarities, they have not formed sister taxa in previous molecular phylogenetic analyses. We discovered and characterized a new species of <i>Pseudadenoides, P. polypyrenoides</i> sp. nov., at both the ultrastructural and molecular phylogenetic levels. Molecular phylogenetic analyses of SSU and LSU rDNA sequences demonstrated a close relationship between <i>P. polypyrenoides</i> sp. nov. and <i>Pseudadenoides kofoidii</i>, and <i>Adenoides</i> and <i>Pseudadenoides</i> formed sister taxa in phylogenetic trees inferred from LSU rDNA sequences. Comparisons of morphological traits, such as the apical pore complex (APC), demonstrated similarities between <i>Adenoides, Pseudadenoides</i> and several planktonic genera (e.g. <i>Heterocapsa, Azadinium</i> and <i>Amphidoma</i>). Molecular phylogenetic analyses of SSU and LSU rDNA sequences also demonstrated an undescribed species within <i>Adenoides.</i>