cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5562460.v1
title: Dataset for: Recurrence-associated gene signature optimizes recurrence free survival prediction of colorectal cancer

description: High throughput gene expression profiling has showed great promise in providing insight into molecular mechanisms. Metastasis-related mRNAs may potentially enrich genes with the ability to predict cancer recurrence，therefore we attempted to build a recurrence-associated gene signature to improve prognostic prediction of colorectal cancer (CRC). We identified 2848 differentially expressed mRNAs by analyzing CRC tissues with or without metastasis. For the selection of prognostic genes, a LASSO Cox regression model was employed. Using this method, a 13-mRNA signature was identified and then validated in two independent Gene Expression Omnibus (GEO) cohorts. This classifier could successfully discriminate the high-risk patients in discovery cohort (HR = 5.27, 95%CI= 2.30-12.08, P &lt; 0.0001). Analysis in two independent cohorts yielded consistent results (GSE14333: HR=4.55, 95%CI=2.18 – 9.508, P&lt;0.0001) (GSE33113: HR=3.26, 95%CI=2.16 – 9.16, P=0.0176). Further analysis revealed that the prognostic value of this signature was independent of tumor stage, postoperative chemotherapy and somatic mutation. Receiver operating characteristic (ROC) analysis showed that the area under receiver operating characteristic curve (AUC) of this signature was 0.8861 and 0.8157 in the discovery and validation cohort, respectively. A nomogram was constructed for clinicians, which did well in the calibration plots. Furthermore, this 13-mRNA signature outperformed other known gene signatures, including oncotypeDX colon cancer assay. Single-sample gene-set enrichment analysis (ssGSEA) revealed that a group of pathways related to drug resistance, cancer metastasis and stemness were significantly enriched in the high-risk patients. In conclusion, this 13-mRNA signature may be a useful tool for prognostic evaluation and will facilitate personalized management of CRC patients.
DOI: 10.6084/m9.figshare.5562433.v1
title: A decision support system to investigate dynamic last-mile distribution facilitating cargo-bikes

description: This work presents a decision support system to facilitate efficient urban last-mile distribution. Orders are collected and delivered by a fleet of both conventional vehicles owned by a logistics provider and cargo-bikes operated by freelancers. Additionally, micro-hubs are operated to perform transshipments between multiple vehicles. To investigate the corresponding problem setting, an agent-based simulation is developed, which uses dynamic optimisation procedures to generate and select vehicle routes and transshipment points. Experiments motivated by dynamic real-world urban restaurant delivery services investigate the impact of cargo-bikes, urban consolidation and guaranteed delivery times. Potentials are discussed and implications for successful implementations are provided. Results highlight the importance of having a sufficient number of active cargo-bikes available and benefits of incorporating consolidation strategies to guarantee timely deliveries.
DOI: 10.6084/m9.figshare.5562430
title: Supplementary Material for: Risk Factors and Outcomes of Emergency Room Visits in Intestinal Behçet’s Disease

description: <b><i>Background/Aims:</i></b> Intestinal Behçet’s disease (BD) is a chronic recurring intestinal vasculitic disorder that can lead to emergency room (ER) visits. We aimed to investigate the independent risk factors associated with intestinal BD-related ER visits. <b><i>Methods:</i></b> We retrospectively reviewed 606 patients with intestinal BD registered at the Inflammatory Bowel Disease Clinic of Severance Hospital, Seoul, Korea. <b><i>Results:</i></b> One hundred eighty-five patients (30.5%) visited the ER at least once (total visits, 510). In multivariate analysis, lower socioeconomic status (hazard ratio [HR] 1.884), higher comorbidity index (HR 1.548), corticosteroid use (HR 1.459), higher C-reactive protein (CRP; HR 1.375), and higher disease activity index for intestinal BD (DAIBD) score (HR 1.013) were independent risk factors. However, older age (HR 0.982), disease duration (HR 0.850), opioid use (HR 0.528), and higher hemoglobin level (HR 0.944) were significantly associated with decreased ER visits. <b><i>Conclusions:</i></b> The ER attendance rate of patients with intestinal BD was 30.5%. Lower socioeconomic status, higher comorbidity index, corticosteroid use, higher CRP, and higher DAIBD score were positively associated with ER visits. Older age, disease duration, opioid use, and higher hemoglobin level were significantly associated with decreased ER visits.
DOI: 10.6084/m9.figshare.5562430.v1
title: Supplementary Material for: Risk Factors and Outcomes of Emergency Room Visits in Intestinal Behçet’s Disease

description: <b><i>Background/Aims:</i></b> Intestinal Behçet’s disease (BD) is a chronic recurring intestinal vasculitic disorder that can lead to emergency room (ER) visits. We aimed to investigate the independent risk factors associated with intestinal BD-related ER visits. <b><i>Methods:</i></b> We retrospectively reviewed 606 patients with intestinal BD registered at the Inflammatory Bowel Disease Clinic of Severance Hospital, Seoul, Korea. <b><i>Results:</i></b> One hundred eighty-five patients (30.5%) visited the ER at least once (total visits, 510). In multivariate analysis, lower socioeconomic status (hazard ratio [HR] 1.884), higher comorbidity index (HR 1.548), corticosteroid use (HR 1.459), higher C-reactive protein (CRP; HR 1.375), and higher disease activity index for intestinal BD (DAIBD) score (HR 1.013) were independent risk factors. However, older age (HR 0.982), disease duration (HR 0.850), opioid use (HR 0.528), and higher hemoglobin level (HR 0.944) were significantly associated with decreased ER visits. <b><i>Conclusions:</i></b> The ER attendance rate of patients with intestinal BD was 30.5%. Lower socioeconomic status, higher comorbidity index, corticosteroid use, higher CRP, and higher DAIBD score were positively associated with ER visits. Older age, disease duration, opioid use, and higher hemoglobin level were significantly associated with decreased ER visits.
DOI: 10.6084/m9.figshare.5562406
title: The accuracy of neck circumference for assessing overweight and obesity: a systematic review and meta-analysis

description: <b>Context:</b> Neck circumference (NC) has been suggested as an alternative measure to screen for excess body weight. <b>Objective:</b> The aim of this study was to demonstrate the accuracy of neck circumference (NC) as a measure for assessing overweight and obesity in both sexes in different age groups. <b>Methods:</b> Detailed individual search strategies were developed for each of the following bibliographic databases: Cochrane, LILACS, PubMed/MEDLINE, Science Direct, Scopus and Web of Science. The QUADAS-2 checklist was used to assess the methodology of the studies included. <b>Results:</b> Thirty-eight assessments were performed in 11 articles according to age, sex and weight status. Using sensitivity and specificity, 27 assessments (71.0%) considered NC an accurate measure to diagnose overweight and obesity. The best sensitivity and specificity were found for the age &gt;19 years (82.0%, 82.0%), female (80.0%, 73.0%), and obese (80.0%, 85.0%) categories. <b>Conclusion:</b> NC is an accurate tool for assessing overweight and obesity in males and females of different age groups and could be used to screen for excess body weight in routine medical practice or epidemiological studies. It is also believed that more studies will permit the creation of a reference dataset of NC cut-off values for world populations.
DOI: 10.6084/m9.figshare.5562406.v1
title: The accuracy of neck circumference for assessing overweight and obesity: a systematic review and meta-analysis

description: <b>Context:</b> Neck circumference (NC) has been suggested as an alternative measure to screen for excess body weight. <b>Objective:</b> The aim of this study was to demonstrate the accuracy of neck circumference (NC) as a measure for assessing overweight and obesity in both sexes in different age groups. <b>Methods:</b> Detailed individual search strategies were developed for each of the following bibliographic databases: Cochrane, LILACS, PubMed/MEDLINE, Science Direct, Scopus and Web of Science. The QUADAS-2 checklist was used to assess the methodology of the studies included. <b>Results:</b> Thirty-eight assessments were performed in 11 articles according to age, sex and weight status. Using sensitivity and specificity, 27 assessments (71.0%) considered NC an accurate measure to diagnose overweight and obesity. The best sensitivity and specificity were found for the age &gt;19 years (82.0%, 82.0%), female (80.0%, 73.0%), and obese (80.0%, 85.0%) categories. <b>Conclusion:</b> NC is an accurate tool for assessing overweight and obesity in males and females of different age groups and could be used to screen for excess body weight in routine medical practice or epidemiological studies. It is also believed that more studies will permit the creation of a reference dataset of NC cut-off values for world populations.
DOI: 10.6084/m9.figshare.5562298
title: Vital signs of 15 Volunteers

description: Vital signs such as blood pressure and heart rate were recorded before and after sauna<br>
DOI: 10.6084/m9.figshare.5562166
title: TraRECo: Assembled data

description: Transcriptome data assembled using TraRECo, a de novo transcriptome assembler with read error correction, developed by S. Yoon. Also include data assembled with other benchmark assemblers, such as Trinity, Trans-ABySS, multi-k OASES, Bridger and BinPacker.<br>
DOI: 10.6084/m9.figshare.5562163
title: TraRECo Workshop for SRX062280 (SRR203276) - No read data

description: This is a workshop for TraRECo, a de novo transcriptome assembler with read error correction, developed by S. Yoon.The workshop include MATLAB scripts to implement the assembly and configuration file for the read data provided.Read data must be separately downloaded with accession code SRX062280.<br>Require MATLAB 2009 or later. A C-compiler that can be used for mex-setup. System memory at leat 8GB.
DOI: 10.6084/m9.figshare.5562157
title: TraRECo Workshop for SRR445718

description: This is a workshop for TraRECo, a de novo transcriptome assembler with read error correction, developed by S. Yoon.The workshop include MATLAB scripts to implement the assembly, read data to analyze and configuration file for the read data provided.<br>Require MATLAB 2009 or later. A C-compiler that can be used for mex-setup. System memory at leat 8GB.
DOI: 10.6084/m9.figshare.5562154
title: TraRECo Workshop for Simulated_read

description: This is a workshop for TraRECo, a de novo transcriptome assembler with read error correction, developed by S. Yoon.The workshop include MATLAB scripts to implement the assembly, read data to analyze and configuration file for the read data provided.<br>Require MATLAB 2009 or later. A C-compiler that can be used for mex-setup. System memory at leat 8GB.
DOI: 10.6084/m9.figshare.5562154.v1
title: TraRECo Workshop for Simulated_read

description: This is a workshop for TraRECo, a de novo transcriptome assembler with read error correction, developed by S. Yoon.The workshop include MATLAB scripts to implement the assembly, read data to analyze and configuration file for the read data provided.<br>Require MATLAB 2009 or later. A C-compiler that can be used for mex-setup. System memory at leat 8GB.
DOI: 10.6084/m9.figshare.5562157.v2
title: TraRECo Workshop for SRR445718

description: This is a workshop for TraRECo, a de novo transcriptome assembler with read error correction, developed by S. Yoon.The workshop include MATLAB scripts to implement the assembly, read data to analyze and configuration file for the read data provided.<br>Require MATLAB 2009 or later. A C-compiler that can be used for mex-setup. System memory at leat 8GB.
DOI: 10.6084/m9.figshare.5562163.v2
title: TraRECo Workshop for SRX062280 (SRR203276) - No read data

description: This is a workshop for TraRECo, a de novo transcriptome assembler with read error correction, developed by S. Yoon.The workshop include MATLAB scripts to implement the assembly and configuration file for the read data provided.Read data must be separately downloaded with accession code SRX062280.<br>Require MATLAB 2009 or later. A C-compiler that can be used for mex-setup. System memory at leat 8GB.
DOI: 10.6084/m9.figshare.5562157.v1
title: TraRECo Workshop for SRR445718

description: This is a workshop for TraRECo, a de novo transcriptome assembler with read error correction, developed by S. Yoon.The workshop include MATLAB scripts to implement the assembly, read data to analyze and configuration file for the read data provided.<br>Require MATLAB 2009 or later. A C-compiler that can be used for mex-setup. System memory at leat 8GB.
DOI: 10.6084/m9.figshare.5562007
title: Supplemental Tables 1-6

description: Supplemental Tables 1-6 for West et al., Genome Biology 2017.<br>
DOI: 10.6084/m9.figshare.5562007.v1
title: Supplemental Tables 1-6

description: Supplemental Tables 1-6 for West et al., Genome Biology 2017.<br>
DOI: 10.6084/m9.figshare.5561890
title: Data set_Cipro intercalation on NaFh.xlsx

description: The Excel file contains 8 sheets with all minimal data set.<br>
DOI: 10.6084/m9.figshare.5561890.v1
title: Data set_Cipro intercalation on NaFh.xlsx

description: The Excel file contains 8 sheets with all minimal data set.<br>
DOI: 10.4225/03/59fa71b5291c8
title: Janion Scheepers et al. Basal Resistance Enhances Warming Tolerance of Alien over Indigenous Species Across Latitude - Supporting Data

description: Supporting data for Janion-Scheepers, C., Phillips L, Sgrò, C.M., Duffy, G.A., Hallas, R. & Chown, S.L. Basal resistance enhances warming tolerance of alien over indigenous species across latitude. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. doi:10.1073/pnas.1715598115
DOI: 10.6084/m9.figshare.5561872
title: Supporting Data for Fig. 2 & S1 of "In vitro and in vivo phasor analysis of stoichiometry and pharmacokinetics using near-infrared dyes"

description: This data is part of the manuscript "In vitro and in vivo phasor analysis of stoichiometry and pharmacokinetics using near-infrared dyes" by Sez-Jade Chen, Nattawut Sinsuebphon, Alena Rudkouskaya, Margarida Barroso, Xavier Intes and Xavier Michalet<br>
DOI: 10.6084/m9.figshare.5561881.v1
title: Resolving a phylogenetic hypothesis for parrots: implications from systematics to conservation

description: Advances in sequencing technology and phylogenetics have revolutionised avian biology by providing an evolutionary framework for studying natural groupings. In the parrots (Psittaciformes), DNA-based studies have led to a reclassification of clades, yet substantial gaps remain in the data gleaned from genetic information. Here we provide an overview of published genetic data of parrots, characterise sampling depth across the phylogeny, and evaluate support for existing systematic treatments. We inferred a concatenated tree with 307 species from a 30-gene supermatrix. We recovered well-supported relationships among recently proposed clades. Taxonomic groups were more stable towards the base of the tree and increased sampling will be required to clarify relationships at the tips, particularly below the generic level. Only a third of species have been sampled intraspecifically in population genetic or phylogeographic surveys. Intraspecific sampling has not been geographically or phylogenetically even across Psittaciformes, especially poor in the cockatoos, Southeast Asia, and parts of Australo-Papua. Threatened species are poorly sampled in the Neotropics. We highlight where effort should be focused to improve sampling based on geography and conservation status. In sum, phylogenetic relationships among the major parrot clades are robust, but relationships within and between genera and species provide opportunities for future investigations.
DOI: 10.6084/m9.figshare.5561890.v2
title: Data set_Cipro intercalation on NaFh.xlsx

description: The Excel file contains 8 sheets with all minimal data set.<br>
DOI: 10.6084/m9.figshare.5561872.v1
title: Supporting Data for Fig. 2 & S1 of "In vitro and in vivo phasor analysis of stoichiometry and pharmacokinetics using near-infrared dyes"

description: This data is part of the manuscript "In vitro and in vivo phasor analysis of stoichiometry and pharmacokinetics using near-infrared dyes" by Sez-Jade Chen, Nattawut Sinsuebphon, Alena Rudkouskaya, Margarida Barroso, Xavier Intes and Xavier Michalet<br>
DOI: 10.6084/m9.figshare.5561764
title: Developing Critical-Analytic Thinking as a Means of Reducing Belief in Conspiracy Theories

description: Data for the study "Developing Critical-Analytic Thinking as a Means of Reducing Belief in Conspiracy Theories"
DOI: 10.25373/ctsnet.5561749
title: Redo Valve-Sparing Ascending Aorta and Total Arch Replacement in a Young Patient With Loeys-Dietz Syndrome: A Challenging Procedure

description: The authors present a successful surgical treatment in a 14-year-old girl with Loeys-Dietz syndrome; a redo aortic arch and ascending aorta replacement with a valve-sparing operation was performed. Special considerations were taken, and a well-established surgical plan was designed to reduce risk and improve outcomes in this complex aortic redo operation. Learn more: https://www.ctsnet.org/article/redo-valve-sparing-ascending-aorta-and-total-arch-replacement-young-patient-loeys-dietz
DOI: 10.6084/m9.figshare.5561764.v1
title: Developing Critical-Analytic Thinking as a Means of Reducing Belief in Conspiracy Theories

description: Data for the study "Developing Critical-Analytic Thinking as a Means of Reducing Belief in Conspiracy Theories"
DOI: 10.25373/ctsnet.5561749.v1
title: Redo Valve-Sparing Ascending Aorta and Total Arch Replacement in a Young Patient With Loeys-Dietz Syndrome: A Challenging Procedure

description: The authors present a successful surgical treatment in a 14-year-old girl with Loeys-Dietz syndrome; a redo aortic arch and ascending aorta replacement with a valve-sparing operation was performed. Special considerations were taken, and a well-established surgical plan was designed to reduce risk and improve outcomes in this complex aortic redo operation. Learn more: https://www.ctsnet.org/article/redo-valve-sparing-ascending-aorta-and-total-arch-replacement-young-patient-loeys-dietz
DOI: 10.23641/asha.5561254
title: Intensive treatment for persisting rhotic distortions (Preston & Leece, 2017)

description: <b>Purpose:</b> The study explored changes in accuracy of American English rhotics as a result of an intensive 1-week therapy program for adolescents and young adults with residual speech sound errors that had not resolved with previous therapy.<b>Method: </b>Four case reports are presented of individuals aged 13, 17, 21, and 22 years with residual /ɹ/ distortions. Each participant attended a 1-week intensive program consisting of pretreatment assessments, 14 hr of therapy, and posttreatment assessment. Treatment sessions included structured motor-based practice, ultrasound visual feedback of the tongue, and auditory speech perception training. To assess generalization, untreated words and sentences with rhotics were recorded before and after therapy; these were rated by listeners who were blind to when the recordings were taken.<b>Results: </b>All participants showed measurable and statistically significant improvement in speech sound accuracy. Averaged across the 4 participants, rhotic accuracy at the word level improved from 35% to 83%. At the sentence level, rhotic accuracy increased from 11% pretreatment to 66% posttreatment in 1 week.<b>Conclusion: </b>The promise of an intensive treatment program that includes motor-based practice, biofeedback, and auditory perception training is illustrated by the case presentations in which substantial improvements in speech sound accuracy were observed.<b><br></b><b>Supplemental Material S1.</b> Video example of prepractice, the first phase of treatment, which involved eliciting 12 correct syllable-level targets. <br><b>Supplemental Material S2. </b>Sample video of structured chaining practice with ultrasound feedback.<b><br></b><b>Supplemental Material S3.</b> Sample video of structured chaining practice without ultrasound feedback.<br><b>Supplemental Material S4. </b>Samples of pretreatment and posttreatment generalization probes.<br> <b>Supplemental Material S5. </b>Sample datasheet with the feedback schedule and sample stimuli.<br> <b>Supplemental Material S6. </b>Generalization probe lists, which were used to track progress. <br>Preston, J. L., & Leece, M. C. (2017). Intensive treatment for persisting rhotic distortions: A case series. <i>American Journal of Speech-Language Pathology, 26, </i>1066–1079<i>.</i> https://doi.org/10.1044/2017_AJSLP-16-0232
DOI: 10.6084/m9.figshare.5559448
title: Subgroups Among Smokers in Preparation: A Cluster Analysis Using the I-Change Model

description: <i>Background:</i> Investigating potential sub-stages of change could provide important information that could be used to improve the tailoring of smoking cessation interventions to individual smokers' profiles. Smokers in the preparation stage may be most interesting, as they are most likely to participate in smoking cessation interventions. <i>Objective</i>: To examine whether Dutch adult smokers in the preparation stage of change, i.e. motivated to quit smoking within one month, can be organized into subgroups. <i>Methods</i>: Data from 753 smokers who participated in an effectiveness trial of a web-based, computer-tailored smoking cessation programme were subjected to secondary analysis. Cluster analyses were based on respondents' baseline responses to items on pros and cons of quitting and quitting self-efficacy. Chi-squared tests and ANOVA were used to compare the baseline characteristics of the resulting clusters. Logistic and multinomial regression were used for longitudinal comparisons of clusters with respect to smoking abstinence and stage transition at six-week and six-month follow-ups. <i>Results</i>: Four clusters were identified; Classic, Unprepared, Progressing and Disengaged Preparers. Cross-sectional and longitudinal analyses validated these clusters: they differed with respect to the clustering variables, gender, cigarette dependence and educational level. Disengaged Preparers were less likely than Progressing Preparers to report smoking abstinence at six months (OR = 0.28; <i>p</i> &lt; .05). <i>Conclusions</i>: These results suggest that smoking cessation interventions tailored to the preparation stage of change, i.e. the set of cognitions usually present in preparers, are only appropriate for the subgroup we defined as Classic Preparers. The other clusters might need different interventions as they display different cognition sets.
DOI: 10.6084/m9.figshare.5561236
title: Antenna coupling information

description: Measured results related to antenna coupling
DOI: 10.6084/m9.figshare.5561236.v1
title: Antenna coupling information

description: Measured results related to antenna coupling