cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9928868
title: Supplementary Material for: Real-World Outcomes of Rivaroxaban Treatment in Patients with Both Nonvalvular Atrial Fibrillation and a History of Ischemic Stroke/Transient Ischemic Attack

description: <b><i>Introduction:</i></b> Prior stroke is a risk factor for stroke and bleeding during anticoagulation in patients with atrial fibrillation (AF). Although rivaroxaban is widely prescribed to reduce their risk of stroke in patients with nonvalvular AF (NVAF), the real-world evidence on rivaroxaban treatment is limited. We aimed to examine the outcomes of rivaroxaban treatment in NVAF patients with prior ischemic stroke/transient ischemic attack (TIA) by using the data of the Xarelto Post-Authorization Safety and Effectiveness Study in Japanese ­Patients with AF, a prospective, single-arm, observational study. <b><i>Methods:</i></b> The clinical outcomes of 9,578 patients who completed the 1-year follow-up were evaluated. Safety and effectiveness outcomes were compared between patients with and without prior ischemic stroke/TIA. <b><i>Results:</i></b> Among the patients, 2,153 (22.5%) had prior ischemic stroke/TIA. They were significantly older and had lower body weight, lower creatinine clearance, higher CHADS<sub>2</sub>, CHA<sub>2</sub>DS<sub>2</sub>-VASc, and modified HAS-BLED scores as compared to those without prior ischemic stroke/TIA. Any bleeding (9.1 vs. 7.2 events per 100 patient-years), major bleeding (2.3 vs. 1.6 events per 100 patient-years), and stroke/non-central nervous system systemic embolism/myocardial infarction (3.4 vs. 1.3 events per 100 patient-years) were more frequent in patients with prior ischemic stroke/TIA. Stepwise regression analysis suggested that body weight of ≤50 kg and diabetes mellitus were predictive of major bleeding in patients with prior ischemic stroke/TIA. <b><i>Conclusions:</i></b> Safety and effectiveness event rates were higher in patients with prior ischemic stroke/TIA than those without. This might be explained by differences in several risk profiles including age, body weight, renal function, and risk scores such as CHADS<sub>2</sub> between the groups. Clinicaltrials.gov: NCT01582737.
DOI: 10.6084/m9.figshare.9928769
title: Test images

description: Test images for the paper titled "Joint Image Compression and Encryption Based on Sparse Bayesian Learning and Bit-level 3D Arnold Cat Maps"
DOI: 10.6084/m9.figshare.9928790
title: Supplementary Material for: Effectiveness and Safety of Double-Blind, Placebo-Controlled, Low-Dose Oral Immunotherapy with Low Allergen Egg-Containing Cookies for Severe Hen’s Egg Allergy: A Single-Center Analysis

description: <b><i>Introduction:</i></b> The usefulness of low-dose oral immunotherapy (OIT) for the treatment of egg allergy has been unclear. <b><i>Objective:</i></b> To evaluate the efficacy and safety of OIT with low allergen cookies (LACs) containing a low dose of hen’s egg. <b><i>Method:</i></b> Thirty-three patients with severe hen’s egg allergy were randomly administered either OIT with LACs (<i>n</i> = 21) or placebo (<i>n</i> = 12). Two patients in the LACs group withdrew before completing OIT. The primary endpoint was the number of good responders (G-R), patients with negative results in the oral food challenge (OFC) with a final dose of 2 g hard-boiled egg whites after 4 months of OIT, in each group. Total OFC Aichi score for anaphylaxis/cumulative protein dose (TS/Pro) as the marker of severity of food allergy was also compared. Adverse events during OIT were evaluated using patients’ diaries. <b><i>Results:</i></b> The proportion of G-R in the LACs group was higher than in the placebo group (7/19 [37%] vs. 1/12 [8%], χ<sup>2</sup> test; <i>p</i> = 0.077). The TS/Pro after OIT in the LACs group was lower than in the placebo group (median score, 44.2 vs. 104.1, <i>p</i> = 0.059; Mann-Whitney U test). The threshold and TS/Pro before and after OIT significantly improved in the LACs group (<i>p</i> = 0.015,<i> p</i> = 0.027, respectively; Wilcoxon signed-rank test). There were 99 recorded incidences of symptoms of 1,938 intake events in the LACs group during OIT. Of these, 90 were mild; no severe symptoms occurred. <b><i>Conclusions:</i></b> OIT with LACs potentially increases the OFC threshold and decreases allergy severity and is a relatively safe treatment modality.
DOI: 10.6084/m9.figshare.9928796
title: Supplementary Material for: Validation of the ILD-GAP Model and a Local Nomogram in a Singaporean Cohort

description: <b><i>Background:</i></b> The ILD-GAP model was developed and validated in a Western cohort to predict 1-, 2- and 3-year mortality in chronic interstitial lung disease (ILD). <b><i>Objectives:</i></b> We aimed to validate the ILD-GAP model and identify predictors of mortality to derive a nomogram to predict mortality in our local Asian population. <b><i>Methods:</i></b> Characteristics of patients on follow-up in a tertiary ILD referral center were retrospectively reviewed. <b><i>Results:</i></b> There were 181 patients and 48 mortalities. 29.8% had idiopathic pulmonary fibrosis, 2.8% unclassifiable ILD, 33.1% connective tissue disease-associated interstitial lung disease (CTD-ILD), 28.7% idiopathic nonspecific interstitial pneumonia and 5.5% chronic hypersensitivity pneumonitis. Univariable analysis showed that a higher ILD-GAP index, unclassified ILD, males, older age, higher pulmonary artery systolic pressure, lower forced vital capacity percent predicted and carbon monoxide diffusion capacity (DLCO) correlated with increased mortality, and CTD had lower mortality. Multivariable analysis utilizing Akaike’s information criterion stopping rule showed males and a lower DLCO predicted increased mortality, while CTD predicted lower mortality. These were used to generate a nomogram which predicted overall mortality better (C index 0.817, adequacy index 99.5%) than ILD-GAP (C index 0.777, adequacy index 60.7%) and provided superior estimates based on likelihood ratio testing. Calibration plots showed the nomogram predicted 1-year mortality better, whilst the ILD-GAP model predicted 2- and 3-year mortality closer to actual mortality rates but underpredicted 1-year mortality. <b><i>Conclusion:</i></b> The nomogram performed better than ILD-GAP in predicting overall mortality and 1-year mortality. Both demonstrated good performance in predicting mortality risk.
DOI: 10.6084/m9.figshare.9928796.v1
title: Supplementary Material for: Validation of the ILD-GAP Model and a Local Nomogram in a Singaporean Cohort

description: <b><i>Background:</i></b> The ILD-GAP model was developed and validated in a Western cohort to predict 1-, 2- and 3-year mortality in chronic interstitial lung disease (ILD). <b><i>Objectives:</i></b> We aimed to validate the ILD-GAP model and identify predictors of mortality to derive a nomogram to predict mortality in our local Asian population. <b><i>Methods:</i></b> Characteristics of patients on follow-up in a tertiary ILD referral center were retrospectively reviewed. <b><i>Results:</i></b> There were 181 patients and 48 mortalities. 29.8% had idiopathic pulmonary fibrosis, 2.8% unclassifiable ILD, 33.1% connective tissue disease-associated interstitial lung disease (CTD-ILD), 28.7% idiopathic nonspecific interstitial pneumonia and 5.5% chronic hypersensitivity pneumonitis. Univariable analysis showed that a higher ILD-GAP index, unclassified ILD, males, older age, higher pulmonary artery systolic pressure, lower forced vital capacity percent predicted and carbon monoxide diffusion capacity (DLCO) correlated with increased mortality, and CTD had lower mortality. Multivariable analysis utilizing Akaike’s information criterion stopping rule showed males and a lower DLCO predicted increased mortality, while CTD predicted lower mortality. These were used to generate a nomogram which predicted overall mortality better (C index 0.817, adequacy index 99.5%) than ILD-GAP (C index 0.777, adequacy index 60.7%) and provided superior estimates based on likelihood ratio testing. Calibration plots showed the nomogram predicted 1-year mortality better, whilst the ILD-GAP model predicted 2- and 3-year mortality closer to actual mortality rates but underpredicted 1-year mortality. <b><i>Conclusion:</i></b> The nomogram performed better than ILD-GAP in predicting overall mortality and 1-year mortality. Both demonstrated good performance in predicting mortality risk.
DOI: 10.6084/m9.figshare.9928547
title: ANA Revised.rar

description: 92 coarse speckled, 18 fine speckled, 27 nucleolar and 29 peripheral
DOI: 10.6084/m9.figshare.9928541
title: Onimaru_et_al_Supplementary_Data

description: This folder contains Supplementary data forTitle: “Developmental hourglass and heterochronic shifts in fin and limb development”Authors: Koh Onimaru*1,2, Kaori Tatsumi1, Chiharu Tanegashima1, Mitsutaka Kadota1, Osamu Nishimura1, Shigehiro Kuraku*1Affiliations:1. Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan2. Laboratory for Bioinformatics Research, RIKEN BDR, 1-2 Hirosawa, Wako city, Saitama, 351-0198, Japan*Corresponding authors. Email: koh.onimaru@riken.jp, shigehiro.kuraku@riken.jpdoi: https://doi.org/10.1101/2020.01.10.901173<br><br>===file descriptions===<br>Onimaru_et_al_Supplementary_data_amino_acid_seqs_based_on_gene_model.fa.gz: Amino acid sequences of the genes in the bamboo shark genome<br>Onimaru_et_al_Supplementary_data_ATAC_seq_GO_analysis.zip: the source data of Supplementary file 12 (GO analysis of clusterd ATAC-seq peaks). c1 to c8 correspond to Figure 5A. <br>Onimaru_et_al_Supplementary_data_ATAC_seq_motifs.zip: the source data of Figure 5A and Figure 5-figure supplement 2 and 3.<br>Onimaru_et_al_supplementary_data_ATAC_seq_peaks_by_clusters.sip: peak regions sorted by the clusters in Figure 5A.<br>Onimaru_et_al_Supplementary_data_bamboo_shark_genome.fa.gz: a bambooshark genome assembly used in this paper. This assembly is equal to https://transcriptome.riken.jp/squalomix/resources/01.GCA_003427335.1_Cpunctatum_v1.0_genomic.rn.fna.gz except that scaffold ids are named scaffold_XXXXX in this file.<br>Onimaru_et_al_Supplementary_data_bamboo_shark_transcriptome_assembly.fa.gz: a bamboo shark transcriptomic assembly used in this paper.Onimaru_et_al_Supplementary_data_bamboo_shark_transcriptome_assembly_amino_acid_seq.fa.gz: amino acid sequences of the above transcriptome.<br><br>Onimaru_et_al_Supplementary_data_gene_model_with_orthology_annotation.gff3.gz: a gff3 file based on orthology annoation in this paper. This file is prepared to visualize ATAC-seq peak data and RNA-seq data on the bambooshark genome provided in this folder.<br>
DOI: 10.6084/m9.figshare.9928529
title: ANA Origin.rar

description: 167 coarse speckled, 20 fine speckled, 38 nucleolar and 35 peripheral
DOI: 10.6084/m9.figshare.9928526
title: Preferences for digital noise reduction and microphone mode settings in hearing-impaired listeners with low and high tolerances for background noise

description: <b>Objective:</b> To examine whether people with low and high acceptable noise levels (ANLs) have different preferences for aggressiveness of noise reduction (NR) and microphone mode, and whether they get different noise tolerance benefit with these two features. <b>Design:</b> Participants completed laboratory tests of unaided ANL and aided modified ANLs (with speech fixed at two levels) and preferences (at two SNRs) while listening to four levels of NR, three microphone modes and four combinations of NR/directionality. <b>Study sample:</b> Twenty adults with hearing loss; 10 with low ANLs and 10 with high ANLs. <b>Results:</b> Seven individuals with low ANLs and 10 individuals with high ANLs preferred the maximum NR setting; the remaining three individuals with low ANLs had inconsistent preference for NR. Eight people in each ANL group preferred the maximum directional setting (broadband (BB) directionality), the remaining two people in each group had inconsistent preferences for microphone mode. <b>Conclusions:</b> Because most participants preferred the maximum NR and directionality settings, ANLs could not be used to differentially prescribe these hearing aid settings.
DOI: 10.6084/m9.figshare.9928541.v1
title: Onimaru_et_al_Supplementary_Data

description: Supplementary Data S1-S7.Data S1: amino acid sequences of the brown-banded bamboo shark predicted by Augustus.Data S2: transcript contigs of the brown-banded bamboo shark assembled by Trinity.<br>Data S3: protein-coding contigs of the brown-banded bamboo shark assembled by Transdecoder.<br>Data S4: a gff3 file of the bamboo shark genome with gene symbols.<br>Data S5: orthology annotation of a bamboo shark transcriptome from data S3.<br>Data S6: orthology annotation of bamboo shark genes predicted by Augustus from data S1.<br>Data S7: PCA loadings in Fig. 3.<br>
DOI: 10.6084/m9.figshare.9928526.v1
title: Preferences for digital noise reduction and microphone mode settings in hearing-impaired listeners with low and high tolerances for background noise

description: <b>Objective:</b> To examine whether people with low and high acceptable noise levels (ANLs) have different preferences for aggressiveness of noise reduction (NR) and microphone mode, and whether they get different noise tolerance benefit with these two features. <b>Design:</b> Participants completed laboratory tests of unaided ANL and aided modified ANLs (with speech fixed at two levels) and preferences (at two SNRs) while listening to four levels of NR, three microphone modes and four combinations of NR/directionality. <b>Study sample:</b> Twenty adults with hearing loss; 10 with low ANLs and 10 with high ANLs. <b>Results:</b> Seven individuals with low ANLs and 10 individuals with high ANLs preferred the maximum NR setting; the remaining three individuals with low ANLs had inconsistent preference for NR. Eight people in each ANL group preferred the maximum directional setting (broadband (BB) directionality), the remaining two people in each group had inconsistent preferences for microphone mode. <b>Conclusions:</b> Because most participants preferred the maximum NR and directionality settings, ANLs could not be used to differentially prescribe these hearing aid settings.
DOI: 10.6084/m9.figshare.9928463
title: vegetation phenophases and related data

description: vegetation phenophases data and related data of 32 cities in the Northern Hemisphere and key code
DOI: 10.6084/m9.figshare.9928421
title: Velocity and quality factor of slow P wave in Berea sandstone

description: Velocities and quality factors of slow P wave in Biot theory and diffussive wave from storitivity equation<br>
DOI: 10.6084/m9.figshare.9928463.v1
title: vegetation phenophases and related data

description: vegetation phenophases data and related data of 32 cities in the Northern Hemisphere and key code
DOI: 10.6084/m9.figshare.9928421.v1
title: Velocity and quality factor of slow P wave in Berea sandstone

description: Velocities and quality factors of slow P wave in Biot theory and diffussive wave from storitivity equation<br>
DOI: 10.6084/m9.figshare.9927986
title: opt-SNE datasets

description: Data files referenced within the opt-SNE preprint (https://doi.org/10.1101/451690) are available for download belowFlow18parameter18 parameter fluorescent flow cytometry file from http://doi.wiley.com/10.1002/cyto.a.22983.flow18_annotated.fcs - an FCS file with all original channels. An extra channel is included that identifies cell types assigned by expert gating. The data are compensated and all fluorescent parameters scaled by the function asinh(x/150).flow18_for_optsne.csv - the data from above but converted to a CSV file that can be used as input to the open-source Multicore-opt-SNE package. Only channels used for opt-SNE analysis are included in the file. Note that the events are sorted by class ID, so if subsetting the file it is recommended to randomize the row order beforehand.tsne_results_flow18.csv - an example of opt-SNE results for the Flow18parameter dataset.Mass41parameter41 parameter mass cytometry dataset from https://doi.org/10.1126/science.1198704.mass41_annotated.fcs - an FCS file produced by concatenation of multiple files from the original dataset. An extra channel is included that identifies cell types assigned by expert gating. An additional extra channel identifies file of origin. All mass parameters are scaled by the function asinh(x/5).mass41_for_optsne.csv - the data from above but converted to a CSV file that can be used as input to the open-source Multicore-opt-SNE package. Only channels used for opt-SNE analysis are included in the file. Note that the events are sorted by class ID, so if subsetting the file it is recommended to randomize the row order beforehand.tsne_results_mass41.csv - an example of opt-SNE results for the Mass41parameter dataset.
DOI: 10.6084/m9.figshare.9927977
title: The perception of death in medical professionals and students

description: Abstract The psycho-emotional pressure generated with the death of a patient is one of the most difficult issues to be faced in medicine. This survey aims to analyze how physicians and medical students perceive the end of life. The study was characterized as a data survey, with a descriptive and quantitative approach. The data were organized into two categories for analysis: perception of death; and the influence of the medical experience in facing patient death. The results show that students feel unprepared to face this reality and that the professional experience is the main modifying factor of the doctors’ understanding of the death. It is concluded that thanatology and its unfoldings are part of an academic gap in medicine, and the confrontation of death is a painful issue for professionals. Aprovação CEP-Fadip CAAE 68401717.6.0000.8063
DOI: 10.6084/m9.figshare.9927980
title: ULTRASOUND-ASSISTED TRANSESTERIFICATION OF SOYBEAN OIL USING COMBI-LIPASE BIOCATALYSTS

description: Abstract We applied ultrasonic technology for the transesterification of soybean oil catalyzed by a mixture of lipases (combi-lipase: 75 % Novozym 435; 10 % Lipozyme TL-IM; and 15 % Lipozyme RM-IM), verifying the effects of ultrasonic amplitude, pulse conditions, the ethanol:oil molar ratio, enzyme concentration, and the influence of solvent (tert-butanol on the reaction. We also compared this system against ultrasound combined with mechanical stirring, and the efficiency of the combi-lipase, compared with the individual use of each lipase. The optimum conditions for the transesterification reaction were determined as enzyme concentration of 15 % (in relation to oil mass); ethanol:oil molar ratio of 3:1; ultrasonic amplitude of 30 %, duty cycle of 50 % and time pulse of 15 sec. The yields of conversion of ethyl esters with and without solvent were similar, indicating that the use of solvents during enzymatic transesterification reactions is not necessary when ultrasonic technology is applied to the system. The combination of mechanical stirring and ultrasound did not improve the yields of conversion compared to ultrasonic technology alone. The proposed combi-lipase produced higher yields of ethyl esters (75 %) than the individual lipases (55 %) in 5 h under ultrasonic-assisted batch reactions.
DOI: 10.6084/m9.figshare.9927977.v1
title: The perception of death in medical professionals and students

description: Abstract The psycho-emotional pressure generated with the death of a patient is one of the most difficult issues to be faced in medicine. This survey aims to analyze how physicians and medical students perceive the end of life. The study was characterized as a data survey, with a descriptive and quantitative approach. The data were organized into two categories for analysis: perception of death; and the influence of the medical experience in facing patient death. The results show that students feel unprepared to face this reality and that the professional experience is the main modifying factor of the doctors’ understanding of the death. It is concluded that thanatology and its unfoldings are part of an academic gap in medicine, and the confrontation of death is a painful issue for professionals. Aprovação CEP-Fadip CAAE 68401717.6.0000.8063
DOI: 10.6084/m9.figshare.9927971
title: Agricultural Productivity and Efficiency in the Portuguese Speaking African Countries (PALOP) and East-Timor

description: Abstract The Portuguese-Speaking African Countries (Palop) and East Timor are countries in the early stages of development with a strong presence of agricultural sector in their economies. The objective of this study is to investigate the agricultural productivity and efficiency of these countries. The Stochastic Frontier procedure was used to estimate the agricultural production frontier for Palop and East Timor, from which the Malmquist Total Factor Productivity Index (IPTF) was determined. In the Palop and East Timor, Total Agricultural Factor Productivity (TFP) is low against the technological availability in the sector worldwide. The dominance of small production makes efficiency the most important component of the sector’s performance in these countries.
DOI: 10.6084/m9.figshare.9927980.v1
title: ULTRASOUND-ASSISTED TRANSESTERIFICATION OF SOYBEAN OIL USING COMBI-LIPASE BIOCATALYSTS

description: Abstract We applied ultrasonic technology for the transesterification of soybean oil catalyzed by a mixture of lipases (combi-lipase: 75 % Novozym 435; 10 % Lipozyme TL-IM; and 15 % Lipozyme RM-IM), verifying the effects of ultrasonic amplitude, pulse conditions, the ethanol:oil molar ratio, enzyme concentration, and the influence of solvent (tert-butanol on the reaction. We also compared this system against ultrasound combined with mechanical stirring, and the efficiency of the combi-lipase, compared with the individual use of each lipase. The optimum conditions for the transesterification reaction were determined as enzyme concentration of 15 % (in relation to oil mass); ethanol:oil molar ratio of 3:1; ultrasonic amplitude of 30 %, duty cycle of 50 % and time pulse of 15 sec. The yields of conversion of ethyl esters with and without solvent were similar, indicating that the use of solvents during enzymatic transesterification reactions is not necessary when ultrasonic technology is applied to the system. The combination of mechanical stirring and ultrasound did not improve the yields of conversion compared to ultrasonic technology alone. The proposed combi-lipase produced higher yields of ethyl esters (75 %) than the individual lipases (55 %) in 5 h under ultrasonic-assisted batch reactions.
DOI: 10.6084/m9.figshare.9927968
title: ALKALINE PROTEASE PRODUCTION BY Bacillus licheniformis LBA 46 IN A BENCH REACTOR: EFFECT OF TEMPERATURE AND AGITATION

description: Abstract The production of protease from Bacillus licheniformis LBA 46 was studied in a 6 L reactor using the experimental design tool. The higher protease production was obtained in the exponential phase of growth reaching maximum activity (~3,000 U/mL) after 48 h of fermentation at 30 ºC and 300 rpm in a culture medium made of agroindustrial by-products. In the thermostability study, the semi-purified enzyme retained about 78% of the initial activity after 120 min at 50 ºC. The protease was purified 3.33 times by ammonium sulfate precipitation and DEAE-Sepharose column chromatography and had a molecular mass estimated at 40 kDa by SDS-PAGE. The purified protease showed optimum activity at 50 and 60 ºC, optimal activity in pH 8.5 and stability in the range between pH 5-10 after 24 h of incubation at 4 ºC, presenting more than 86% of the initial activity.