cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12827189
title: Supplementary Material for: Usefulness of Color Doppler Ultrasonography in the Risk Stratification of Thyroid Nodules

description: <b><i>Introduction:</i></b> Thyroid ultrasound (US) is crucial for clinical decision in the management of thyroid nodules. In this cross-sectional study, we aimed to test if the evaluation of thyroid nodules’ vascularization could improve the risk stratification ability of the American College of Radiology (ACR) TI-RADS classification system. <b><i>Methods:</i></b> A total of 873 thyroid nodules undergoing fine-needle aspiration were classified according to ACR TI-RADS US classification. Three types of vascularization were identified: type 0, no vascular signals; type 1, peripheral vascular signals; type 2, peripheral and intralesional vascular signals. Cytology specimens were evaluated conforming to the Italian Reporting System for Thyroid Cytology, and TIR3b, TIR4, and TIR5 were defined as high risk for malignancy. Odds ratios (ORs) with 95% confidence intervals (CI) and the areas under the receiver operating characteristic curves (ROC-AUC) for high-risk cytology categories were calculated. <b><i>Results:</i></b> The 3 vascular patterns were differently distributed within the cytology categories: 52.4% of TIR1c, 15.9% of TIR2, 5.9% of TIR3a, 6.7% of TIR3b, 12.5% of TIR4, and 28.9% of TIR5 nodules had no vascular signals (<i>p</i> &lt; 0.001). Nodule vascularity alone was not associated with a higher risk of malignant cytology (OR [95% CI] 0.75 [0.43–1.32], <i>p</i> = 0.32), without differences between peripheral (OR [95% CI] 0.65 [0.35–1.20]) and intranodular (OR [95% CI] 0.88 [0.48–1.62]) vascularization (<i>p</i> = 0.22). The ROC-AUC (95% CI) for the diagnosis of malignant cytology was similar when considering TI-RADS classification alone (0.736 [0.684–0.786]) and when considering TI-RADS classification plus the presence/absence of vascular signals (0.736 [0.683–0.789], <i>p</i> value for differences between the ROC-AUCs: 0.91). Among TR1, TR2, and TR3 TI-RADS classes, no nodules without vascular signals showed a malignant cytology, allowing the identification of nodules with benign cytology with 100% specificity within these US classes. <b><i>Conclusions:</i></b> Color Doppler study of thyroid nodules does not improve the risk stratification ability of the ACR TI-RADS US classification system.
DOI: 10.6084/m9.figshare.12827189.v1
title: Supplementary Material for: Usefulness of Color Doppler Ultrasonography in the Risk Stratification of Thyroid Nodules

description: <b><i>Introduction:</i></b> Thyroid ultrasound (US) is crucial for clinical decision in the management of thyroid nodules. In this cross-sectional study, we aimed to test if the evaluation of thyroid nodules’ vascularization could improve the risk stratification ability of the American College of Radiology (ACR) TI-RADS classification system. <b><i>Methods:</i></b> A total of 873 thyroid nodules undergoing fine-needle aspiration were classified according to ACR TI-RADS US classification. Three types of vascularization were identified: type 0, no vascular signals; type 1, peripheral vascular signals; type 2, peripheral and intralesional vascular signals. Cytology specimens were evaluated conforming to the Italian Reporting System for Thyroid Cytology, and TIR3b, TIR4, and TIR5 were defined as high risk for malignancy. Odds ratios (ORs) with 95% confidence intervals (CI) and the areas under the receiver operating characteristic curves (ROC-AUC) for high-risk cytology categories were calculated. <b><i>Results:</i></b> The 3 vascular patterns were differently distributed within the cytology categories: 52.4% of TIR1c, 15.9% of TIR2, 5.9% of TIR3a, 6.7% of TIR3b, 12.5% of TIR4, and 28.9% of TIR5 nodules had no vascular signals (<i>p</i> &lt; 0.001). Nodule vascularity alone was not associated with a higher risk of malignant cytology (OR [95% CI] 0.75 [0.43–1.32], <i>p</i> = 0.32), without differences between peripheral (OR [95% CI] 0.65 [0.35–1.20]) and intranodular (OR [95% CI] 0.88 [0.48–1.62]) vascularization (<i>p</i> = 0.22). The ROC-AUC (95% CI) for the diagnosis of malignant cytology was similar when considering TI-RADS classification alone (0.736 [0.684–0.786]) and when considering TI-RADS classification plus the presence/absence of vascular signals (0.736 [0.683–0.789], <i>p</i> value for differences between the ROC-AUCs: 0.91). Among TR1, TR2, and TR3 TI-RADS classes, no nodules without vascular signals showed a malignant cytology, allowing the identification of nodules with benign cytology with 100% specificity within these US classes. <b><i>Conclusions:</i></b> Color Doppler study of thyroid nodules does not improve the risk stratification ability of the ACR TI-RADS US classification system.
DOI: 10.6084/m9.figshare.12827300.v1
title: R0187_20170919a_videos

description: Rat 0187, skilled reaching data collected on 9/19/2017 in Leventhal laboratory by Alexandra Bova
DOI: 10.6084/m9.figshare.12827129
title: Dataset on the effect of Dendrobium officinale dietary fiber on the gut microbiome in high-fat-diet-induced obese mice

description: Obesity and related metabolic syndromes are becoming a major public health problem due to excess dietary fat intake. <i>Dendrobium officinale</i> is a medicine food homology herb ranked as the head of “nine kinds of precious medicinal herbs” in China and exerts multiple health-promoting effects. In this study, mice were fed with standard chow diet (Chow), high-fat diet (HFD) or HFD plus daily administration of <i>D. officinale</i> dietary fiber (DODF, 1.0 g/kg) by intragastric gavage for 11 weeks. To examine the gut microbial changes, a 16S rRNA gene sequencing approach was used to analyze the gut microbiome in fecal samples of mice fed with Chow, HFD and DODF. To investigate the impact of DODF on host metabolism, a <sup>1</sup>H NMR-based metabolomics approach was applied to analyze metabolic changes in feces, serum, and liver. In addition, to elucidate whether the gut flora acts as a causal factor for mediating the efficacies of DODF, we next transferred the faecal microbiota either from DODF-treated or vehicle-treated HFD-fed donor mice (DODF-R and HFD-R) to HFD-induced obese mice for 14 days.
DOI: 10.6084/m9.figshare.12827090
title: Dataset on the effect of Dendrobium officinale dietary fiber on host metabolism in high-fat-diet-induced obese mice

description: Obesity and related metabolic syndromes are becoming a major public health problem due to excess dietary fat intake. <i>Dendrobium officinale</i> is a medicine food homology herb ranked as the head of “nine kinds of precious medicinal herbs” in China and exerts multiple health-promoting effects. In this study, mice were fed with standard chow diet (Chow), high-fat diet (HFD) or HFD plus daily administration of <i>D. officinale</i> dietary fiber (DODF, 1.0 g/kg) by intragastric gavage for 11 weeks. To examine the gut microbial changes, a 16S rRNA gene sequencing approach was used to analyze the gut microbiome in fecal samples of mice fed with Chow, HFD and DODF. To investigate the impact of DODF on host metabolism, a <sup>1</sup>H NMR-based metabolomics approach was applied to analyze metabolic changes in feces, serum, and liver. In addition, to elucidate whether the gut flora acts as a causal factor for mediating the efficacies of DODF, we next transferred the faecal microbiota either from DODF-treated or vehicle-treated HFD-fed donor mice (DODF-R and HFD-R) to HFD-induced obese mice for 14 days.
DOI: 10.6084/m9.figshare.12827090.v1
title: Dataset on the effect of Dendrobium officinale dietary fiber on host metabolism in high-fat-diet-induced obese mice

description: Obesity and related metabolic syndromes are becoming a major public health problem due to excess dietary fat intake. <i>Dendrobium officinale</i> is a medicine food homology herb ranked as the head of “nine kinds of precious medicinal herbs” in China and exerts multiple health-promoting effects. In this study, mice were fed with standard chow diet (Chow), high-fat diet (HFD) or HFD plus daily administration of <i>D. officinale</i> dietary fiber (DODF, 1.0 g/kg) by intragastric gavage for 11 weeks. To examine the gut microbial changes, a 16S rRNA gene sequencing approach was used to analyze the gut microbiome in fecal samples of mice fed with Chow, HFD and DODF. To investigate the impact of DODF on host metabolism, a <sup>1</sup>H NMR-based metabolomics approach was applied to analyze metabolic changes in feces, serum, and liver. In addition, to elucidate whether the gut flora acts as a causal factor for mediating the efficacies of DODF, we next transferred the faecal microbiota either from DODF-treated or vehicle-treated HFD-fed donor mice (DODF-R and HFD-R) to HFD-induced obese mice for 14 days.
DOI: 10.6084/m9.figshare.12859577
title: Supplementary Material for: Use of Continuous Physiological Monitor Data to Evaluate Doxapram Therapy in Preterm Infants

description: <b><i>Introduction:</i></b> Evaluation of pharmacotherapy during intensive care treatment is commonly based on subjective, intermittent interpretations of physiological parameters. Real-time visualization and analysis may improve drug effect evaluation. We aimed to evaluate the effects of the respiratory stimulant doxapram objectively in preterm infants using continuous physiological parameters. <b><i>Methods:</i></b> In this longitudinal observational study, preterm infants who received doxapram therapy were eligible for inclusion. Physiological data (1 Hz) were used to assess respiration and to evaluate therapy effects. The oxygen saturation (SpO<sub>2</sub>)/fraction of inspired oxygen (FiO<sub>2</sub>) ratio and the area under the 89% SpO<sub>2</sub> curve (duration × saturation depth below target) were calculated as measures of hypoxemia. Regression analyses were performed in 1-h timeframes to discriminate therapy failure (intubation or death) from success (no intubation). <b><i>Results:</i></b> Monitor data of 61 patients with a median postmenstrual age (PMA) at doxapram initiation of 28.7 (IQR 27.6–30.0) weeks were available. The success rate of doxapram therapy was 56%. Doxapram pharmacodynamics were reflected in an increased SpO<sub>2</sub> and SpO<sub>2</sub>/FiO<sub>2</sub> ratio as well as a decrease in episodes with saturations below target (SpO<sub>2</sub> &lt;89%). The SpO<sub>2</sub>/FiO<sub>2</sub> ratio, corrected for PMA and mechanical ventilation before therapy start, discriminated best between therapy failure and success (highest AUC ROC of 0.83). <b><i>Conclusion:</i></b> The use of continuous physiological monitor data enables objective and detailed interpretation of doxapram in preterm infants. The SpO<sub>2</sub>/FiO<sub>2</sub> ratio is the best predictive parameter for therapy failure or success. Further implementation of real-time data analysis and treatment algorithms would provide new opportunities to treat newborns.
DOI: 10.6084/m9.figshare.12826931
title: Müller and Garcia (Biology Letters).tnt from A paraphyletic ‘Silesauridae' as an alternative hypothesis for the initial radiation of ornithischian dinosaurs

description: Whereas ornithischian dinosaurs are well known from Jurassic and Cretaceous deposits, deciphering the origin and early evolution of the group remains one of the hardest challenges for palaeontologists. So far, there are no unequivocal records of ornithischians from Triassic beds. Here, we present an alternative evolutionary hypothesis that suggests consideration of traditional ‘silesaurids' as a group of low-diversity clades representing a stem group leading to core ornithischians (i.e. unambiguous ornithischians, such as <i>Heterodontosaurus tucki</i>). This is particularly interesting because it fills most of the ghost lineages that emerge from the Triassic. Following the present hypothesis, the lineage that encompasses the Jurassic ornithischians evolved from ‘silesaurids' during the Middle to early Late Triassic, while typical ‘silesaurids' shared the land ecosystems with their relatives until the Late Triassic, when the group completely vanished. Therefore, Ornithischia changes from an obscure to a well-documented clade in the Triassic and is represented by records from Gondwana and Laurasia. Furthermore, according to the present hypothesis, Ornithischia was the first group of dinosaurs to adopt an omnivorous/herbivorous diet. However, this behaviour was achieved as a secondary step instead of an ancestral condition for ornithischians, as the earliest member of the clade is a faunivorous taxon. This pattern was subsequently followed by sauropodomorph dinosaurs. Indeed, the present scenario favours the independent acquisition of an herbivorous diet for ornithischians and sauropodomorphs during the Triassic, whereas the previous hypotheses suggested the independent acquisition for sauropodomorphs, ornithischians, and ‘silesaurids'.
DOI: 10.6084/m9.figshare.12826931.v1
title: Müller and Garcia (Biology Letters).tnt from A paraphyletic ‘Silesauridae' as an alternative hypothesis for the initial radiation of ornithischian dinosaurs

description: Whereas ornithischian dinosaurs are well known from Jurassic and Cretaceous deposits, deciphering the origin and early evolution of the group remains one of the hardest challenges for palaeontologists. So far, there are no unequivocal records of ornithischians from Triassic beds. Here, we present an alternative evolutionary hypothesis that suggests consideration of traditional ‘silesaurids' as a group of low-diversity clades representing a stem group leading to core ornithischians (i.e. unambiguous ornithischians, such as <i>Heterodontosaurus tucki</i>). This is particularly interesting because it fills most of the ghost lineages that emerge from the Triassic. Following the present hypothesis, the lineage that encompasses the Jurassic ornithischians evolved from ‘silesaurids' during the Middle to early Late Triassic, while typical ‘silesaurids' shared the land ecosystems with their relatives until the Late Triassic, when the group completely vanished. Therefore, Ornithischia changes from an obscure to a well-documented clade in the Triassic and is represented by records from Gondwana and Laurasia. Furthermore, according to the present hypothesis, Ornithischia was the first group of dinosaurs to adopt an omnivorous/herbivorous diet. However, this behaviour was achieved as a secondary step instead of an ancestral condition for ornithischians, as the earliest member of the clade is a faunivorous taxon. This pattern was subsequently followed by sauropodomorph dinosaurs. Indeed, the present scenario favours the independent acquisition of an herbivorous diet for ornithischians and sauropodomorphs during the Triassic, whereas the previous hypotheses suggested the independent acquisition for sauropodomorphs, ornithischians, and ‘silesaurids'.
DOI: 10.6084/m9.figshare.12826862
title: R0186_20170812a_videos

description: Rat 0186, skilled reaching data collected on 8/12/2017 in Leventhal laboratory by Alexandra Bova
DOI: 10.6084/m9.figshare.12826841
title: Supplementary Material for: Probability of Major Depression Classification Based on the SCID, CIDI, and MINI Diagnostic Interviews: A Synthesis of Three Individual Participant Data Meta-Analyses

description: <b><i>Introduction:</i></b> Three previous individual participant data meta-analyses (IPDMAs) reported that, compared to the Structured Clinical Interview for the DSM (SCID), alternative reference standards, primarily the Composite International Diagnostic Interview (CIDI) and the Mini International Neuropsychiatric Interview (MINI), tended to misclassify major depression status, when controlling for depression symptom severity. However, there was an important lack of precision in the results. <b><i>Objective:</i></b> To compare the odds of the major depression classification based on the SCID, CIDI, and MINI. <b><i>Methods:</i></b> We included and standardized data from 3 IPDMA databases. For each IPDMA, separately, we fitted binomial generalized linear mixed models to compare the adjusted odds ratios (aORs) of major depression classification, controlling for symptom severity and characteristics of participants, and the interaction between interview and symptom severity. Next, we synthesized results using a DerSimonian-Laird random-effects meta-analysis. <b><i>Results:</i></b> In total, 69,405 participants (7,574 [11%] with major depression) from 212 studies were included. Controlling for symptom severity and participant characteristics, the MINI (74 studies; 25,749 participants) classified major depression more often than the SCID (108 studies; 21,953 participants; aOR 1.46; 95% confidence interval [CI] 1.11–1.92]). Classification odds for the CIDI (30 studies; 21,703 participants) and the SCID did not differ overall (aOR 1.19; 95% CI 0.79–1.75); however, as screening scores increased, the aOR increased less for the CIDI than the SCID (interaction aOR 0.64; 95% CI 0.52–0.80). <b><i>Conclusions:</i></b> Compared to the SCID, the MINI classified major depression more often. The odds of the depression classification with the CIDI increased less as symptom levels increased. Interpretation of research that uses diagnostic interviews to classify depression should consider the interview characteristics.
DOI: 10.6084/m9.figshare.12826862.v1
title: R0186_20170812a_videos

description: Rat 0186, skilled reaching data collected on 8/12/2017 in Leventhal laboratory by Alexandra Bova
DOI: 10.6084/m9.figshare.12826820
title: Legacy livestock modelled distributions

description: Legacy modelled livestock distributions, 1km resolution, year 2000, values number per pixel x 10. Files in ESRI Grid format, component files for each species in folders with names as follows: <br>*ct=cattle, *bf=buffalo, *bv=bovines, *sh=sheep, *gt = goats, *sr= small ruminants, *.pg=pigs, *po=poultry<br><br>World2kliv: Raw model numbers corrected at country level so that national totals match official FAO totals for 2000.<br>Worldtotcor: Raw model numbers corrected at subnational polygon level so that polygon totals match input polygon densities for 2000.<br>More recent versions at http://www.fao.org/livestock-systems/global-distributions/en/<br>
DOI: 10.6084/m9.figshare.12826823
title: Supplementary Material for: Short-Term Intravenous Infusion of Cyclophosphamide in the Treatment of Refractory Pemphigus Vulgaris: A Retrospective Study

description: <b><i>Background:</i></b> Pemphigus is an autoimmune disease of the skin and mucous membranes. Glucocorticoids have been the most effective drug for the treatment of pemphigus; however, some patients are insensitive to glucocorticoid therapy. Cyclophosphamide has been extensively used in the treatment of pemphigus. <b><i>Objectives:</i></b> To observe and evaluate the efficacy and safety of high-dose glucocorticoid with weekly intravenous cyclophosphamide in the treatment of refractory pemphigus vulgaris insensitive to glucocorticoids. <b><i>Methods:</i></b> Clinical data of 19 patients with refractory pemphigus vulgaris (insensitive to glucocorticoid) who were treated with high-dose glucocorticoids(1.5 mg/kg/day prednisone) and weekly intravenous infusion of cyclophosphamide, and 24 patients who were sensitive to glucocorticoid therapy received a medium dose of glucocorticoid alone (1 mg/kg/day prednisone) were retrospectively analyzed. <b><i>Results:</i></b> By the time the disease was brought under control, the average total dose of cyclophosphamide was 2.02 g. Comparison between the glucocorticoid-insensitive and glucocorticoid-sensitive groups showed that the average time to disease control was 2.68 vs. 2 weeks, and the average daily dosage of steroid was 1.33 ± 0.53 vs. 0.90 ± 0.28 mg/kg. At the 12- and 18-month follow-ups, the recurrence rate of the glucocorticoid-insensitive group was significantly lower than that of the sensitive group (5.3 vs. 37.5%, 15.8 vs. 45.8%). No serious adverse reactions were observed. <b><i>Conclusion:</i></b> High-dose glucocorticoid plus weekly intravenous infusion of cyclophosphamide safely, effectively, and rapidly controlled the conditions of the patients with refractory pemphigus who were insensitive to glucocorticoids, shortened the duration of hospitalization, avoided the risk of complications that could be caused by further increasing the dose of glucocorticoids (&gt;1.5 mg/kg/day), and lowered the recurrence rate within 18 months.
DOI: 10.6084/m9.figshare.12826820.v1
title: Legacy livestock modelled distributions

description: Legacy modelled livestock distributions, 1km resolution, year 2000, values number per pixel x 10. Files in ESRI Grid format, component files for each species in folders with names as follows: <br>*ct=cattle, *bf=buffalo, *bv=bovines, *sh=sheep, *gt = goats, *sr= small ruminants, *.pg=pigs, *po=poultry<br><br>World2kliv: Raw model numbers corrected at country level so that national totals match official FAO totals for 2000.<br>Worldtotcor: Raw model numbers corrected at subnational polygon level so that polygon totals match input polygon densities for 2000.<br>More recent versions at http://www.fao.org/livestock-systems/global-distributions/en/<br>
DOI: 10.6084/m9.figshare.12826724
title: 期刊要求上传数据.rar

description: the effect of personal control on bribery
DOI: 10.6084/m9.figshare.12826535
title: Corophiid filter mesh size - intraspecific variation

description: ID: identifier of individualssample_no: sample identifiers as in Table 1species: CC - Chelicorophium curvispinum CR - Chelicorophium robustum CS - Chelicorophium sowinskyilength: standard body length in mmgender: F - female, M - male, J - juvenilefilter_size: filter mesh size in μm<br>
DOI: 10.6084/m9.figshare.12826535.v1
title: Corophiid filter mesh size - intraspecific variation

description: ID: identifier of individualssample_no: sample identifiers as in Table 1species: CC - Chelicorophium curvispinum CR - Chelicorophium robustum CS - Chelicorophium sowinskyilength: standard body length in mmgender: F - female, M - male, J - juvenilefilter_size: filter mesh size in μm<br>
DOI: 10.6084/m9.figshare.12826493
title: Table S3. from Metagenomics of the modern and historical human oral microbiome with phylogenetic studies on <i>Streptococcus mutans</i> and <i>Streptococcus sobrinus</i>

description: SPARSE profiles Excel file
DOI: 10.6084/m9.figshare.12826493.v1
title: Table S3. from Metagenomics of the modern and historical human oral microbiome with phylogenetic studies on <i>Streptococcus mutans</i> and <i>Streptococcus sobrinus</i>

description: SPARSE profiles Excel file
DOI: 10.6084/m9.figshare.12826487
title: Table S5. from Metagenomics of the modern and historical human oral microbiome with phylogenetic studies on <i>Streptococcus mutans</i> and <i>Streptococcus sobrinus</i>

description: RefSeq Genomes Excel file
DOI: 10.6084/m9.figshare.12826487.v1
title: Table S5. from Metagenomics of the modern and historical human oral microbiome with phylogenetic studies on <i>Streptococcus mutans</i> and <i>Streptococcus sobrinus</i>

description: RefSeq Genomes Excel file
DOI: 10.6084/m9.figshare.12826514.v1
title: LA_NGCF.zip

description: Ťhe code and data of'"Location-Aware Neural Graph Collaborative Filtering"
DOI: 10.6084/m9.figshare.12826478
title: Table S6. from Metagenomics of the modern and historical human oral microbiome with phylogenetic studies on <i>Streptococcus mutans</i> and <i>Streptococcus sobrinus</i>

description: Pseudo-MAGs Excel file
DOI: 10.6084/m9.figshare.12826481
title: Table S1. from Metagenomics of the modern and historical human oral microbiome with phylogenetic studies on <i>Streptococcus mutans</i> and <i>Streptococcus sobrinus</i>

description: Metagenome metadata Excel file
DOI: 10.6084/m9.figshare.12826478.v1
title: Table S6. from Metagenomics of the modern and historical human oral microbiome with phylogenetic studies on <i>Streptococcus mutans</i> and <i>Streptococcus sobrinus</i>

description: Pseudo-MAGs Excel file
DOI: 10.6084/m9.figshare.12826481.v1
title: Table S1. from Metagenomics of the modern and historical human oral microbiome with phylogenetic studies on <i>Streptococcus mutans</i> and <i>Streptococcus sobrinus</i>

description: Metagenome metadata Excel file