cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12527921.v1
title: WATNEEDS CODE

description: WATNEEDS code
DOI: 10.6084/m9.figshare.12527828.v1
title: Read me

description: Read me file
DOI: 10.6084/m9.figshare.12527219
title: Metadata record for: CU-BEMS, smart building electricity consumption and indoor environmental sensor datasets

description: This dataset contains key characteristics about the data described in the Data Descriptor CU-BEMS, smart building electricity consumption and indoor environmental sensor datasets. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format <br> <br> <br>
DOI: 10.6084/m9.figshare.12526973
title: Supplementary Material for: Single-Center Noninferiority Randomized Trial on the Efficacy and Safety of Low- and High-Dose Rush Oral Milk Immunotherapy for Severe Milk Allergy

description: <b><i>Introduction:</i></b> Oral immunotherapy (OIT) has been reported to be effective but associated with a risk of severe symptoms. Thus, an OIT method with decreased risk is required. <b><i>Objectives:</i></b> We aimed to evaluate the efficacy and safety of low- and high-dose OIT regimens in children with severe milk allergy. <b><i>Methods:</i></b> Overall, 33 participants (median age, 9 years; median final dose of the milk oral food challenge [OFC], 2 mL) were included. The participants were randomly assigned to groups that received either a low (20 mL; <i>n</i> = 19) or high (100 mL; <i>n</i> = 14) maintenance target dose of OIT. The dose was gradually increased to the target dose in the rush escalation phase and was then maintained daily at home. The primary endpoint was the final OFC dose at 6 months of OIT. Adverse events during OIT were evaluated. <b><i>Results:</i></b> The final OFC dose after OIT was significantly higher than that before OIT in both groups (low-dose, <i>p</i> = 0.000; high-dose, <i>p</i> = 0.006), but there was no significant difference in the final OFC dose between the 2 groups (<i>p</i> = 0.767). In the maintenance phase, the high-dose group had significantly more severe symptoms than did the low-dose group (0.5%, 11/2,355 total intake events vs. 0.1%, 4/3,230 total intake events; <i>p</i> = 0.018). <b><i>Conclusions:</i></b> An equally increased dose effect was observed for maintenance OIT doses of 20 and 100 mL in children with severe milk allergy. The risk of severe symptoms in the maintenance phase was lower in the low-dose group. A low-dose OIT regimen is recommended for severe milk allergy.
DOI: 10.6084/m9.figshare.12527381.v1
title: Pogostemon monticola T.C.Hsu, S.W.Chung & S.H.Liu, sp. nov.

description: Pogostemon monticola T.C.Hsu, S.W.Chung & S.H.Liu, sp. nov.
DOI: 10.6084/m9.figshare.12526631
title: Supplementary Material for: Comparison of Clinicopathological Features of Biliary Neuroendocrine Carcinoma with Adenocarcinoma

description: <b><i>Objective:</i></b> This study aimed to demonstrate the clinical features and postoperative outcomes of extrahepatic bile duct (EHBD) neuroendocrine carcinoma (NEC) and compared with those of adenocarcinoma. <b><i>Methods:</i></b> We retrospectively analyzed patients with EHBD cancer operated in our institution between 1995 and 2015. <b><i>Results:</i></b> Of 475 patients, 468 had adenocarcinoma, while 7 had NEC/mixed adenoneuroendocrine carcinoma (MANEC) in this study. There were no notable preoperative and pathological features in patients with NEC/MANEC. However, patients with NEC/MANEC had a higher recurrence rate (51.8 vs. 100%, <i>p</i> = 0.016), poorer relapse-free survival (RFS) time (the median RFS time: 35 vs. 12 months, <i>p</i> = 0.006), and poorer overall survival (OS) time (the median OS time: 60 vs. 19 months, <i>p</i> = 0.078) than those with adenocarcinoma. Furthermore, patients with NEC/MANEC had higher rates of liver metastasis (11.9 vs. 85.7%, <i>p</i> &lt; 0.001) than those with adenocarcinoma. In multivariable regression analysis, pathological type with NEC/MANEC was a risk factor for poorer RFS (<i>p</i> = 0.022, hazard ratio: 6.09). <b><i>Conclusions:</i></b> Patients with NEC/MANEC have high malignant potential and poor outcomes. It is necessary to develop an effective approach and postoperative adjuvant treatment for patients with NEC/MANEC.
DOI: 10.6084/m9.figshare.12526640
title: garlic chloroplast genome

description: garlic chloroplast genome
DOI: 10.6084/m9.figshare.12526571
title: CBM-Istudy2predata

description: People with high anxiety tend to interpret ambiguous cues negatively, regardless of whether the cues are negative or positive. Cognitive bias modification for interpretation (CBM-I) may reduce such biases. However, CBM-I sessions for social anxiety in previous studies were held either only once or twice a week in the laboratory and did not test the Japanese population. In this study, we developed a Japanese version of CBM-I. The current study investigated the effects of a short, intensive program using two types of the Japanese version of CBM-I procedures. In Study 1, 74 participants were randomly placed into either a one-week program with online sessions of text-based scenarios training or a control condition. In Study 2, 120 participants were randomized into one-week online sessions of text-based scenarios training (four times) and picture-word cue training (three times) or a control condition. In both Study 1 and 2, participants in the control condition completed the same positive interpretation task after a one-week standby. In Study 1, individuals in the positive condition demonstrated significant improvements in depressive symptoms from pre-intervention to post-intervention compared to those in the control condition. Improvements in depressive symptoms and interpretation bias at a one-month follow-up were significant. In Study 2, in the positive condition, there was a significant reduction in negative affect compared to the control condition. In addition, there were greater reductions in negative affect, social evaluative fear, and negative interpretation bias at a one-month follow-up, irrespective of condition. Results suggest that text-based CBM-I affects depressive symptom and interpretation bias, text, and picture-based CBM-I especially affects these emotional characteristics. Depending on the assessment and treatment policy for patients, we might concurrently use two approaches, one with text stimuli when stimulating depressive symptoms and interpretations, and the other with picture stimuli when stimulating emotions.
DOI: 10.6084/m9.figshare.12526571.v1
title: CBM-Istudy2predata

description: People with high anxiety tend to interpret ambiguous cues negatively, regardless of whether the cues are negative or positive. Cognitive bias modification for interpretation (CBM-I) may reduce such biases. However, CBM-I sessions for social anxiety in previous studies were held either only once or twice a week in the laboratory and did not test the Japanese population. In this study, we developed a Japanese version of CBM-I. The current study investigated the effects of a short, intensive program using two types of the Japanese version of CBM-I procedures. In Study 1, 74 participants were randomly placed into either a one-week program with online sessions of text-based scenarios training or a control condition. In Study 2, 120 participants were randomized into one-week online sessions of text-based scenarios training (four times) and picture-word cue training (three times) or a control condition. In both Study 1 and 2, participants in the control condition completed the same positive interpretation task after a one-week standby. In Study 1, individuals in the positive condition demonstrated significant improvements in depressive symptoms from pre-intervention to post-intervention compared to those in the control condition. Improvements in depressive symptoms and interpretation bias at a one-month follow-up were significant. In Study 2, in the positive condition, there was a significant reduction in negative affect compared to the control condition. In addition, there were greater reductions in negative affect, social evaluative fear, and negative interpretation bias at a one-month follow-up, irrespective of condition. Results suggest that text-based CBM-I affects depressive symptom and interpretation bias, text, and picture-based CBM-I especially affects these emotional characteristics. Depending on the assessment and treatment policy for patients, we might concurrently use two approaches, one with text stimuli when stimulating depressive symptoms and interpretations, and the other with picture stimuli when stimulating emotions.
DOI: 10.6084/m9.figshare.12526640.v1
title: garlic chloroplast genome

description: garlic chloroplast genome
DOI: 10.6084/m9.figshare.12526535
title: Supplementary Material for: Impact of Kidney Disease on Peripheral Arterial Interventions: A Systematic Review and Meta-Analysis

description: <b><i>Background:</i></b> There are limited data on outcomes of patients undergoing peripheral arterial disease (PAD) interventions who have comorbid CKD/ESRD versus those who do not have such comorbid condition. We performed a systematic review and meta-analysis to analyze outcomes in this patient population. <b><i>Methods:</i></b> Five databases were searched for studies comparing outcomes of lower extremity PAD interventions for claudication and critical limb ischemia (CLI) in patients with CKD/ESRD versus non-CKD/non-ESRD from January 2000 to June 2019. <b><i>Results:</i></b> Our study included 16 observational studies with 44,138 patients. Mean follow-up was 48.9 ± 27.4 months. Major amputation was higher with CKD/ESRD compared with non-CKD/non-ESRD (odds ratio [OR 1.97] [95% confidence interval [CI] 1.39–2.80], <i>p</i> = 0.001). Higher major amputations with CKD/ESRD versus non-CKD/non-ESRD were only observed when indication for procedure was CLI (OR 2.27 [95% CI 1.53–3.36], <i>p</i> &lt; 0.0001) but were similar for claudication (OR 1.15 [95% CI 0.53–2.49], <i>p</i> = 0.72). The risk of early mortality was high with CKD/ESRD patients undergoing PAD interventions compared with non-CKD/non-ESRD (OR 2.55 [95% CI 1.65–3.96], <i>p</i> &lt; 0.0001), which when stratified based on indication, remained higher with CLI (OR 3.14 [95% CI 1.80–5.48], <i>p</i> &lt; 0.0001) but was similar with claudication (OR 1.83 [95% CI 0.90–3.72], <i>p</i> = 0.1). Funnel plot of included studies showed moderate bias. <b><i>Conclusions:</i></b> Patients undergoing lower extremity PAD interventions for CLI who also have comorbid CKD/ESRD have an increased risk of experiencing major amputations and early mortality. Randomized trials to understand outcomes of PAD interventions in this at-risk population are essential.
DOI: 10.6084/m9.figshare.12526529
title: JVASP-25784 to JVASP-28212

description: JARVIS-DFT input/output files
DOI: 10.6084/m9.figshare.12526526
title: JVASP-24907 to JVASP-25872

description: JARVIS-DFT input/output files
DOI: 10.6084/m9.figshare.12526256
title: JVASP-21949 to JVASP-22977

description: JARVIS-DFT input/output files
DOI: 10.6084/m9.figshare.12526259
title: JVASP-22979 to JVASP-24905

description: JARVIS-DFT input/output files
DOI: 10.6084/m9.figshare.12526247
title: Estimated and real vertebral lengths collated by testing group

description: Matching columns of real and estimated vertebral lengths, broken down by group for importing as a dataframe into R.
DOI: 10.6084/m9.figshare.12526241
title: FANTOM

description: Alternative splicing annotation of FANTOM
DOI: 10.6084/m9.figshare.12526247.v1
title: Estimated and real vertebral lengths collated by testing group

description: Matching columns of real and estimated vertebral lengths, broken down by group for importing as a dataframe into R.
DOI: 10.6084/m9.figshare.12526238
title: Tomographic PWV of the three Super Typhoon Events in Hong Kong

description: Tomographic PWV in five layers for the three Super Typhoon Events in Hong Kong
DOI: 10.6084/m9.figshare.12526223
title: AJPRenal1000SupplTable1.docx

description: How to re-sequence your data
DOI: 10.6084/m9.figshare.12526241.v1
title: FANTOM

description: Alternative splicing annotation of FANTOM
DOI: 10.6084/m9.figshare.12526217
title: Fractional order modeling and analysis of a variable structure hybrid energy storage system for EVs

description: ruslts of simulation experiments and the simulation data.<br>
DOI: 10.6084/m9.figshare.12526223.v1
title: AJPRenal1000SupplTable1.docx

description: How to re-sequence your data
DOI: 10.6084/m9.figshare.12526241.v2
title: FANTOM

description: Alternative splicing annotation of FANTOM
DOI: 10.6084/m9.figshare.12526217.v2
title: Fractional order modeling and analysis of a variable structure hybrid energy storage system for EVs

description: ruslts of simulation experiments and the simulation data.<br>
DOI: 10.6084/m9.figshare.12526217.v1
title: Fractional order modeling and analysis of a variable structure hybrid energy storage system for EVs

description: ruslts of simulation experiments and the simulation data.<br>
DOI: 10.6084/m9.figshare.12526241.v3
title: FANTOM

description: Alternative splicing annotation of FANTOM
DOI: 10.6084/m9.figshare.12525938
title: Gene database of Corynebacterium glutamicum ATCC 13032

description: An important biotechnology host, <i>Corynebacterium glutamicum</i> has seen significant research attention over the years. But, what endears this rod-shaped, Gram-positive microorganism to biotechnologists is its robust metabolic repertoire that could be shaped into a microbial cell factory for producing a variety of value-added products through metabolic engineering. This work describes the gene database of <i>C. glutamicum</i> ATCC 13032 obtained through parsing the annotated genome sequence file of the bacterium from Genbank. Comprising gene name, gene function descriptor and gene sequence for every gene in the genome of this biotechnology workhorse, the resource should find use in a variety of settings in applied and fundamental microbiology research seeking to expand the types of products synthesized by this microorganism through genetic engineering and metabolic engineering.
DOI: 10.6084/m9.figshare.12525965
title: Anti-Infection Essential Medicines_Database_21June20.xlsx

description: This database provides information on anti-infection essential medicines approved for use in the USA. It includes information on active ingredients, applicant holders, market status, dosage forms, FDA approval dates, generic versions of the medicines approved and more.Data was extracted from the FDA Orange book, as part of the Breaking Good citizen science project - E$$ENTIAL MEDICINE$. https://www.breakinggoodproject.com/essentialmedicines
DOI: 10.6084/m9.figshare.12525929
title: JVASP-20993 to JVASP-21948

description: JARVIS-DFT input/output files
DOI: 10.6084/m9.figshare.12526241.v4
title: FANTOM

description: Alternative splicing annotation of FANTOM
DOI: 10.6084/m9.figshare.12525926
title: JVASP-20286 to JVASP-20992

description: JARVIS-DFT input/output files
DOI: 10.6084/m9.figshare.12525872
title: Vertebral length database

description: Spreadsheet of measurements of anteroposterior centrum length, in mm.
DOI: 10.6084/m9.figshare.12526241.v6
title: FANTOM

description: Alternative splicing annotation of FANTOM
DOI: 10.6084/m9.figshare.12525872.v1
title: Vertebral length database

description: Spreadsheet of measurements of anteroposterior centrum length, in mm.
DOI: 10.6084/m9.figshare.12526241.v5
title: FANTOM

description: Alternative splicing annotation of FANTOM
DOI: 10.6084/m9.figshare.12525548
title: Landsat-L1-20171010-ONAQ-scene

description: This landsat scene is an example used in the sagebrush-ecosystem-modeling github workflow for NEON's Onaqui Mountains (ONAQ) site.<br><br><em>Landsat-8 image courtesy of the U.S. Geological Survey</em>
DOI: 10.6084/m9.figshare.12525563
title: JVASP-19668 to JVASP-20285

description: JARVIS-DFT input/output files
DOI: 10.6084/m9.figshare.12525563.v1
title: JVASP-19668 to JVASP-20285

description: JARVIS-DFT input/output files
DOI: 10.6084/m9.figshare.12525548.v1
title: Landsat-L1-038_032-201710-ONAQ-scene

description: This landsat scene is an example used in the sagebrush-ecosystem-modeling github workflow for NEON's Onaqui Mountains (ONAQ) site.<br><br><em>Landsat-8 image courtesy of the U.S. Geological Survey</em>
DOI: 10.6084/m9.figshare.12525524
title: Source Data.xlsx

description: Source data for essential figures in the main text and Supplementary Information of the paper "Ambient methane functionalization initiated by electrochemical oxidaiton of a vanadium (V)-oxo dimer".<br>
DOI: 10.6084/m9.figshare.12525548.v3
title: Landsat-L1-20171010-ONAQ-scene

description: This landsat scene is an example used in the sagebrush-ecosystem-modeling github workflow for NEON's Onaqui Mountains (ONAQ) site.<br><br><em>Landsat-8 image courtesy of the U.S. Geological Survey</em>
DOI: 10.26180/5eeff97d604f1
title: The ontogeny of sea turtle hatchling swimming performance

description: Dataset for research published in the Biological Journal of the Linnean Society (2020). Includes hatchling morphology and swimming performance measurements taken at 0, 4, 12 and 24 weeks of age.
DOI: 10.6084/m9.figshare.12525548.v2
title: Landsat-L1-038_032-20171010-ONAQ-scene

description: This landsat scene is an example used in the sagebrush-ecosystem-modeling github workflow for NEON's Onaqui Mountains (ONAQ) site.<br><br><em>Landsat-8 image courtesy of the U.S. Geological Survey</em>
DOI: 10.6084/m9.figshare.12525449
title: KMCG6 metagenome replicate A and B

description: We reported a microbial consortium with efficient keratinolytic capacity obtained by selective enrichment from a soil sample. To identify the genetic processes involved in the keratinolytic activity and the synergy among community members, shotgun metagenomic sequencing was preformed.
DOI: 10.6084/m9.figshare.12525467
title: Landsat-L1-20170921-CPER-scene

description: This landsat scene is an example used in the sagebrush-ecosystem-modeling github workflow for NEON's Central Plains Experimental Range (CPER) site.<br><br><em>Landsat-8 image courtesy of the U.S. Geological Survey</em>
DOI: 10.6084/m9.figshare.12525401
title: Data PIP5K2A.xls

description: dataset for study
DOI: 10.6084/m9.figshare.12525449.v2
title: KMCG6 metagenome replicate A and B

description: We reported a microbial consortium with efficient keratinolytic capacity obtained by selective enrichment from a soil sample. To identify the genetic processes involved in the keratinolytic activity and the synergy among community members, shotgun metagenomic sequencing was preformed.
DOI: 10.6084/m9.figshare.12525467.v2
title: Landsat-L1-20170921-CPER-scene

description: This landsat scene is an example used in the sagebrush-ecosystem-modeling github workflow for NEON's Central Plains Experimental Range (CPER) site.<br><br><em>Landsat-8 image courtesy of the U.S. Geological Survey</em>
DOI: 10.6084/m9.figshare.12525401.v2
title: Data PIP5K2A.xls

description: dataset for study
DOI: 10.6084/m9.figshare.12525449.v1
title: KMCG6 metagenome replicate A and B

description: We reported a microbial consortium with efficient keratinolytic capacity obtained by selective enrichment from a soil sample. To identify the genetic processes involved in the keratinolytic activity and the synergy among community members, shotgun metagenomic sequencing was preformed.
DOI: 10.6084/m9.figshare.12525467.v1
title: Landsat-L1-033_032-20170921-CPER-scene

description: This landsat scene is an example used in the sagebrush-ecosystem-modeling github workflow for NEON's Central Plains Experimental Range (CPER) site.<br><br><em>Landsat-8 image courtesy of the U.S. Geological Survey</em>
DOI: 10.6084/m9.figshare.12525401.v1
title: Data PIP5K2A.xls

description: dataset for study
DOI: 10.6084/m9.figshare.12524786
title: Signal conflict in mitochondrial genes of land plants

description: Using a codon-naive maximum likelihood (ML) and non-parametric bootstrap (BS) analysis of the data set used by Sousa et al. (<i>PeerJ </i><b>8: </b>e8995; 2020) in combination with consensus networks one can explore and visualise the character and gene support for the found Septaphyta clade.<br>As outlined in the related post, <i></i><i>Can we dig too deep?</i> (a copy is provided as PDF here), the inferred Septaphyta clade is probably a model-induced branching artefact ("short-branch culling") rejected by most genes and poorly supported by character splits in a few other genes. The earlier alternative, mosses as first-diverging lineage of land plants, likely represents a data/signal artefact related to the primitive sequence structure of their mitochondrial genes.Overall, the analysis shows that mitochondrial genes provide little signal to resolve any deep splits in surviving land plants. <br><br>The xlsx spread sheet file tabulates the support of competing splits per gene. All files to reproduce the analysis and check the results are included in the 7z-archive.<br><br>
DOI: 10.6084/m9.figshare.12525242
title: kraken2_human_and_phiX_db

description: kraken2_human_and_phiX_db<br>created on 19-June, as detailed here: https://hackmd.io/@cov-irt/kraken2-read-filtering
DOI: 10.6084/m9.figshare.12525365
title: syn-gtotree-example

description: syn-gtotree-example that goes with this page: https://astrobiomike.github.io/genomics/phylogenomics<br><br>
DOI: 10.6084/m9.figshare.12524393
title: GENCODE

description: Annotation of alternative splicing events in GENCODE
DOI: 10.6084/m9.figshare.12524786.v1
title: Signal conflict in mitochondrial genes of land plants

description: Using a codon-naive maximum likelihood (ML) and non-parametric bootstrap (BS) analysis of the data set used by Sousa et al. (<i>PeerJ </i><b>8: </b>e8995; 2020) in combination with consensus networks one can explore and visualise the character and gene support for the found Septaphyta clade.<br>As outlined in the related post, <i></i><i>Can we dig too deep?</i> (a copy is provided as PDF here), the inferred Septaphyta clade is probably a model-induced branching artefact ("short-branch culling") rejected by most genes and poorly supported by character splits in a few other genes. The earlier alternative, mosses as first-diverging lineage of land plants, likely represents a data/signal artefact related to the primitive sequence structure of their mitochondrial genes.Overall, the analysis shows that mitochondrial genes provide little signal to resolve any deep splits in surviving land plants. <br><br>The xlsx spread sheet file tabulates the support of competing splits per gene. All files to reproduce the analysis and check the results are included in the 7z-archive.<br><br>
DOI: 10.6084/m9.figshare.12525365.v2
title: syn-gtotree-example

description: syn-gtotree-example that goes with this page: https://astrobiomike.github.io/genomics/phylogenomics<br><br>
DOI: 10.6084/m9.figshare.12525365.v1
title: syn-gtotree-example

description: syn-gtotree-example that goes with this page: https://astrobiomike.github.io/genomics/phylogenomics<br><br>
DOI: 10.6084/m9.figshare.12524393.v1
title: GENCODE

description: Annotation of alternative splicing events in GENCODE