cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5951623.v1
title: Supplementary Material for: The Regulator Gene <b><i>rnc</i></b> Is Closely Involved in Biofilm Formation in <b><i>Streptococcus mutans</i></b>

description: <i>Streptococcus mutans</i> is an important factor in the etiology and pathogenesis of dental caries, largely owing to its ability to form a stable biofilm. Previous animal studies have indicated that <i>rnc</i> could decrease the amount of sulcal caries, and that the downregulation of cariogenicity might be due to its capacity to disrupt biofilm formation. However, the biofunctions by which <i>rnc</i> is involved in biofilm formation remain to be elucidated. In this study, we further investigate the role of <i>rnc</i> based on the study of mature biofilm. Scanning electron microscopy and the crystal violet assay were used to detect the biofilm forming ability. The production and distribution of exopolysaccharides within biofilm was analyzed by exopolysaccharide staining. Gel permeation chromatography was used to perform molecular weight assessment. Its adhesion force was measured by atomic force microscopy. The expression of biofilm formation-associated genes was analyzed at the mRNA level by qPCR. Here, we found that <i>rnc</i> could occur and function in biofilm formation by assembling well-structured, exopolysaccharide-encased, stable biofilms in <i>S. mutans</i>. The weakened biofilm forming ability of <i>rnc</i>-deficient strains was associated with the reduction of exopolysaccharide production and bacterial adhesion. Over all, these data illustrate an interesting situation in which an unappreciated regulatory gene acquired for virulence, <i>rnc</i>, most likely has been coopted as a potential regulator of biofilm formation in <i>S. mutans</i>. Further characterization of <i>rnc</i> may lead to the identification of a possible pathogenic biofilm-specific treatment for dental caries.
DOI: 10.6084/m9.figshare.5951611
title: Strengthening the reporting of empirical simulation studies: Introducing the STRESS guidelines

description: This study develops a standardised checklist approach to improve the reporting of discrete-event simulation, system dynamics and agent-based simulation models within the field of Operational Research and Management Science. Incomplete or ambiguous reporting means that many simulation studies are not reproducible, leaving other modellers with an incomplete picture of what has been done and unable to judge the reliability of the results. Crucially, unclear reporting makes it difficult to reproduce or reuse findings. In this paper, we review the evidence on the quality of model reporting and consolidate previous work. We derive general good practice principles and three 20-item checklists aimed at Strengthening The Reporting of Empirical Simulation Studies (STRESS): STRESS-DES, STRESS-ABS and STRESS-SD for discrete-event simulation, agent-based simulation and system dynamics, respectively. Given the variety of simulation projects, we provide usage and troubleshooting advice to cover a wide range of situations.
DOI: 10.6084/m9.figshare.5951611.v2
title: Strengthening the reporting of empirical simulation studies: Introducing the STRESS guidelines

description: This study develops a standardised checklist approach to improve the reporting of discrete-event simulation, system dynamics and agent-based simulation models within the field of Operational Research and Management Science. Incomplete or ambiguous reporting means that many simulation studies are not reproducible, leaving other modellers with an incomplete picture of what has been done and unable to judge the reliability of the results. Crucially, unclear reporting makes it difficult to reproduce or reuse findings. In this paper, we review the evidence on the quality of model reporting and consolidate previous work. We derive general good practice principles and three 20-item checklists aimed at Strengthening The Reporting of Empirical Simulation Studies (STRESS): STRESS-DES, STRESS-ABS and STRESS-SD for discrete-event simulation, agent-based simulation and system dynamics, respectively. Given the variety of simulation projects, we provide usage and troubleshooting advice to cover a wide range of situations.
DOI: 10.6084/m9.figshare.5951608
title: Supplementary Material for: Changes in the Proteomic Profile of Acquired Enamel Pellicles as a Function of Their Time of Formation and Hydrochloric Acid Exposure

description: <b><i>Objective:</i></b> Changes in the protein profile of acquired enamel pellicles (AEP) formed in vivo over different time periods were evaluated after the application of hydrochloric acid (HCl). <b><i>Methods:</i></b> Nine subjects were submitted to dental prophylaxis with pumice. After 3 or 120 min, the teeth were isolated with cotton rolls and 50 μL of 0.1 M HCl (pH 1.0), 0.01 M HCl (pH 2.0), or deionized water were applied on the buccal surface of the teeth for 10 s. The AEP was then collected using an electrode filter paper presoaked in 3% citric acid. After protein extraction, the samples were submitted to reverse-phase liquid chromatography coupled to mass spectrometry (nano LC-ESI-MS/MS). Label-free quantification was performed (Protein Lynx Global Service software). <b><i>Results:</i></b> A total of 180 proteins were successfully identified in the AEP samples. The number of identified proteins increased with the time of pellicle formation. Only 4 proteins were present in all the groups (isoforms of IgA, serum albumin,<i></i> and statherin). The greatest number of proteins identified uniquely in one of the groups was obtained for the groups treated with HCl after 2 h of pellicle formation (approx. 50 proteins). <b><i>Conclusion:</i></b> Proteins resistant to removal by HCl, such as serum albumin<i></i> and statherin, were identified even in the short-term AEP. In addition, 120-min pellicles present many proteins that are resistant to removal by HCl. This suggests an increase in protection against intrinsic acids with the time of pellicle formation, which should be evaluated in future studies.
DOI: 10.6084/m9.figshare.5951608.v1
title: Supplementary Material for: Changes in the Proteomic Profile of Acquired Enamel Pellicles as a Function of Their Time of Formation and Hydrochloric Acid Exposure

description: <b><i>Objective:</i></b> Changes in the protein profile of acquired enamel pellicles (AEP) formed in vivo over different time periods were evaluated after the application of hydrochloric acid (HCl). <b><i>Methods:</i></b> Nine subjects were submitted to dental prophylaxis with pumice. After 3 or 120 min, the teeth were isolated with cotton rolls and 50 μL of 0.1 M HCl (pH 1.0), 0.01 M HCl (pH 2.0), or deionized water were applied on the buccal surface of the teeth for 10 s. The AEP was then collected using an electrode filter paper presoaked in 3% citric acid. After protein extraction, the samples were submitted to reverse-phase liquid chromatography coupled to mass spectrometry (nano LC-ESI-MS/MS). Label-free quantification was performed (Protein Lynx Global Service software). <b><i>Results:</i></b> A total of 180 proteins were successfully identified in the AEP samples. The number of identified proteins increased with the time of pellicle formation. Only 4 proteins were present in all the groups (isoforms of IgA, serum albumin,<i></i> and statherin). The greatest number of proteins identified uniquely in one of the groups was obtained for the groups treated with HCl after 2 h of pellicle formation (approx. 50 proteins). <b><i>Conclusion:</i></b> Proteins resistant to removal by HCl, such as serum albumin<i></i> and statherin, were identified even in the short-term AEP. In addition, 120-min pellicles present many proteins that are resistant to removal by HCl. This suggests an increase in protection against intrinsic acids with the time of pellicle formation, which should be evaluated in future studies.
DOI: 10.6084/m9.figshare.5951566
title: Supplementary Material for: International Consensus Statement on Screening, Diagnosis and Treatment of Substance Use Disorder Patients with Comorbid Attention Deficit/Hyperactivity Disorder

description: Adult attention deficit/hyperactivity disorder (ADHD) often co-occurs with substance use disorders (SUD) and is associated with early onset and more severe development of SUD and with reduced treatment effectiveness. Screening tools allow for a good recognition of possible ADHD in adults with SUD and should be used routinely, followed by an ADHD diagnostic process initiated as soon as possible. Simultaneous and integrated treatment of ADHD and SUD, using a combination of pharmaco- and psychotherapy, is recommended. Long-acting methylphenidate, extended-release amphetamines, and atomoxetine with up-titration to higher dosages may be considered in patients unresponsive to standard doses. This paper includes evidence- and consensus-based recommendations developed to provide guidance in the screening, diagnosis and treatment of patients with ADHD-SUD comorbidity.
DOI: 10.6084/m9.figshare.5951563
title: normalized fMRI data

description: fMRI data to reproduce the analyses of our manuscript.<br>
DOI: 10.6084/m9.figshare.5951530
title: MOESM7 of TREE2FASTA: a flexible Perl script for batch extraction of FASTA sequences from exploratory phylogenetic trees

description: Additional file 7. Example FASTA file for the nested example shown in Fig.Â 1.
DOI: 10.6084/m9.figshare.5951530.v1
title: MOESM7 of TREE2FASTA: a flexible Perl script for batch extraction of FASTA sequences from exploratory phylogenetic trees

description: Additional file 7. Example FASTA file for the nested example shown in Fig.Â 1.
DOI: 10.6084/m9.figshare.5951524
title: Additional file 5: of Crossed beaks in a local Swiss chicken breed

description: Genotypes and diplotypes of Appenzeller Barthuhn and two other Swiss Chicken breeds. Genotypes of 12 variants and their diplotypes in LOC426217 of Appenzeller Barthuhn, Appenzeller Spitzhaubenhuhn and Schweizerhuhn. (XLSX 30Â kb)
DOI: 10.6084/m9.figshare.5951524.v1
title: Additional file 5: of Crossed beaks in a local Swiss chicken breed

description: Genotypes and diplotypes of Appenzeller Barthuhn and two other Swiss Chicken breeds. Genotypes of 12 variants and their diplotypes in LOC426217 of Appenzeller Barthuhn, Appenzeller Spitzhaubenhuhn and Schweizerhuhn. (XLSX 30Â kb)
DOI: 10.6084/m9.figshare.5951521
title: Additional file 9: of AKT1 restricts the invasive capacity of head and neck carcinoma cells harboring a constitutively active PI3 kinase activity

description: Electrical data used to generate the figures. The ECIS measurements of resistance in MΩ at a frequency of 4000 Hz were normalized to the first measurement and plotted in the Graphpad Prism software to generate the traces shown in Figs. 3a-c and 4a. The quantification data were obtained by measuring the mean resistance increase during the cell attachment phase (from 4 to 8 h after cell spreading). (XLSX 140 kb)
DOI: 10.6084/m9.figshare.5951521.v1
title: Additional file 9: of AKT1 restricts the invasive capacity of head and neck carcinoma cells harboring a constitutively active PI3 kinase activity

description: Electrical data used to generate the figures. The ECIS measurements of resistance in MΩ at a frequency of 4000 Hz were normalized to the first measurement and plotted in the Graphpad Prism software to generate the traces shown in Figs. 3a-c and 4a. The quantification data were obtained by measuring the mean resistance increase during the cell attachment phase (from 4 to 8 h after cell spreading). (XLSX 140 kb)
DOI: 10.6084/m9.figshare.5951515
title: MOESM6 of TREE2FASTA: a flexible Perl script for batch extraction of FASTA sequences from exploratory phylogenetic trees

description: Additional file 6. Example tree file for the nested example shown in Fig.Â 1.
DOI: 10.6084/m9.figshare.5951515.v1
title: MOESM6 of TREE2FASTA: a flexible Perl script for batch extraction of FASTA sequences from exploratory phylogenetic trees

description: Additional file 6. Example tree file for the nested example shown in Fig.Â 1.
DOI: 10.6084/m9.figshare.5951509
title: Additional file 8: of AKT1 restricts the invasive capacity of head and neck carcinoma cells harboring a constitutively active PI3 kinase activity

description: Detroit562 cells untreated or treated with MK-2206 or Rapamycin electrical resistance measurements. Raw output file of the ECIS measurement of resistance in MΩ at a frequency of 4000 Hz. (XLS 213 kb)
DOI: 10.6084/m9.figshare.5951509.v1
title: Additional file 8: of AKT1 restricts the invasive capacity of head and neck carcinoma cells harboring a constitutively active PI3 kinase activity

description: Detroit562 cells untreated or treated with MK-2206 or Rapamycin electrical resistance measurements. Raw output file of the ECIS measurement of resistance in MΩ at a frequency of 4000 Hz. (XLS 213 kb)
DOI: 10.6084/m9.figshare.5951506
title: Additional file 4: of Crossed beaks in a local Swiss chicken breed

description: Table with all cases for phenotype description and genetic analyses. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.5951506.v1
title: Additional file 4: of Crossed beaks in a local Swiss chicken breed

description: Table with all cases for phenotype description and genetic analyses. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.5951491
title: Additional file 7: of AKT1 restricts the invasive capacity of head and neck carcinoma cells harboring a constitutively active PI3 kinase activity

description: Detroit562 cells untreated or treated with MK-2206 or Rapamycin electrical resistance measurements. Raw output file of the ECIS measurement of resistance in MΩ at a frequency of 4000 Hz. (XLS 227 kb)
DOI: 10.6084/m9.figshare.5951491.v1
title: Additional file 7: of AKT1 restricts the invasive capacity of head and neck carcinoma cells harboring a constitutively active PI3 kinase activity

description: Detroit562 cells untreated or treated with MK-2206 or Rapamycin electrical resistance measurements. Raw output file of the ECIS measurement of resistance in MΩ at a frequency of 4000 Hz. (XLS 227 kb)
DOI: 10.6084/m9.figshare.5951473
title: Additional file 6: of AKT1 restricts the invasive capacity of head and neck carcinoma cells harboring a constitutively active PI3 kinase activity

description: Detroit562 and CAL27 cells untreated or treated with MK-2206 electrical resistance measurements. Raw output file of the ECIS measurement of resistance in MΩ at a frequency of 4000 Hz. (XLS 1380 kb)
DOI: 10.6084/m9.figshare.5951473.v1
title: Additional file 6: of AKT1 restricts the invasive capacity of head and neck carcinoma cells harboring a constitutively active PI3 kinase activity

description: Detroit562 and CAL27 cells untreated or treated with MK-2206 electrical resistance measurements. Raw output file of the ECIS measurement of resistance in MΩ at a frequency of 4000 Hz. (XLS 1380 kb)
DOI: 10.6084/m9.figshare.5951467
title: Additional file 2: of Crossed beaks in a local Swiss chicken breed

description: Phenotype details of Appenzeller Barthuhn chickens with crossed beak and all cases used in the study. (XLSX 19Â kb)
DOI: 10.6084/m9.figshare.5951467.v1
title: Additional file 2: of Crossed beaks in a local Swiss chicken breed

description: Phenotype details of Appenzeller Barthuhn chickens with crossed beak and all cases used in the study. (XLSX 19Â kb)
DOI: 10.6084/m9.figshare.5951446
title: Additional file 5: of AKT1 restricts the invasive capacity of head and neck carcinoma cells harboring a constitutively active PI3 kinase activity

description: CAL33-shControl cells untreated or treated with MK-2206 and CAL33-shAKT1.1 and 1.2 cells electrical resistance measurements. Raw output file of the ECIS measurement of resistance in MΩ at a frequency of 4000 Hz. (XLS 86 kb)
DOI: 10.6084/m9.figshare.5951446.v1
title: Additional file 5: of AKT1 restricts the invasive capacity of head and neck carcinoma cells harboring a constitutively active PI3 kinase activity

description: CAL33-shControl cells untreated or treated with MK-2206 and CAL33-shAKT1.1 and 1.2 cells electrical resistance measurements. Raw output file of the ECIS measurement of resistance in MΩ at a frequency of 4000 Hz. (XLS 86 kb)
DOI: 10.6084/m9.figshare.5951422
title: Additional file 4: of AKT1 restricts the invasive capacity of head and neck carcinoma cells harboring a constitutively active PI3 kinase activity

description: CAL33-shControl cells untreated or treated with MK-2206 and CAL33-shAKT1.1 and 1.2 cells electrical resistance measurements. Raw output file of the ECIS measurement of resistance in MΩ at a frequency of 4000 Hz. (XLS 220 kb)
DOI: 10.6084/m9.figshare.5951422.v1
title: Additional file 4: of AKT1 restricts the invasive capacity of head and neck carcinoma cells harboring a constitutively active PI3 kinase activity

description: CAL33-shControl cells untreated or treated with MK-2206 and CAL33-shAKT1.1 and 1.2 cells electrical resistance measurements. Raw output file of the ECIS measurement of resistance in MΩ at a frequency of 4000 Hz. (XLS 220 kb)
DOI: 10.6084/m9.figshare.5951416
title: Additional file 2: of Analysis of MAPK and MAPKK gene families in wheat and related Triticeae species

description: Triticeae MPK and MKK accessions from Ensembl Plants. The table includes scaffold locations, intron numbers, molecular weight, isoelectric point and gene descriptions. (XLSX 54 kb)
DOI: 10.6084/m9.figshare.5951416.v1
title: Additional file 2: of Analysis of MAPK and MAPKK gene families in wheat and related Triticeae species

description: Triticeae MPK and MKK accessions from Ensembl Plants. The table includes scaffold locations, intron numbers, molecular weight, isoelectric point and gene descriptions. (XLSX 54 kb)
DOI: 10.6084/m9.figshare.5951404
title: Additional file 3: of AKT1 restricts the invasive capacity of head and neck carcinoma cells harboring a constitutively active PI3 kinase activity

description: CAL33-shControl cells untreated or treated with MK-2206 and CAL33-shAKT1.1 and 1.2 cells electrical resistance measurements. Raw output file of the ECIS measurement of resistance in MΩ at a frequency of 4000 Hz. (XLS 147 kb)
DOI: 10.6084/m9.figshare.5951404.v1
title: Additional file 3: of AKT1 restricts the invasive capacity of head and neck carcinoma cells harboring a constitutively active PI3 kinase activity

description: CAL33-shControl cells untreated or treated with MK-2206 and CAL33-shAKT1.1 and 1.2 cells electrical resistance measurements. Raw output file of the ECIS measurement of resistance in MΩ at a frequency of 4000 Hz. (XLS 147 kb)
DOI: 10.6084/m9.figshare.5951383
title: Additional file 2: of AKT1 restricts the invasive capacity of head and neck carcinoma cells harboring a constitutively active PI3 kinase activity

description: CAL33-shControl cells untreated or treated with Rapamycin and MK-2206 electrical resistance measurements. Raw output file of the ECIS measurement of resistance in MΩ at a frequency of 4000 Hz. (XLS 213 kb)
DOI: 10.6084/m9.figshare.5951383.v1
title: Additional file 2: of AKT1 restricts the invasive capacity of head and neck carcinoma cells harboring a constitutively active PI3 kinase activity

description: CAL33-shControl cells untreated or treated with Rapamycin and MK-2206 electrical resistance measurements. Raw output file of the ECIS measurement of resistance in MΩ at a frequency of 4000 Hz. (XLS 213 kb)
DOI: 10.6084/m9.figshare.5951368
title: Additional file 1: of AKT1 restricts the invasive capacity of head and neck carcinoma cells harboring a constitutively active PI3 kinase activity

description: CAL33-shControl cells treated with Erlotinib, Rapamycin and MK-2206 electrical resistance measurements. Raw output file of the ECIS measurement of resistance in MΩ at a frequency of 4000 Hz. (XLS 432 kb)
DOI: 10.6084/m9.figshare.5951368.v1
title: Additional file 1: of AKT1 restricts the invasive capacity of head and neck carcinoma cells harboring a constitutively active PI3 kinase activity

description: CAL33-shControl cells treated with Erlotinib, Rapamycin and MK-2206 electrical resistance measurements. Raw output file of the ECIS measurement of resistance in MΩ at a frequency of 4000 Hz. (XLS 432 kb)
DOI: 10.6084/m9.figshare.5951356
title: Additional file 10: of Analysis of MAPK and MAPKK gene families in wheat and related Triticeae species

description: Summary of MAPK identifiers and complementary information obtained from eight studies. The table includes gene identifiers and complementary annotations for 8 published sets of MAPKs that were used for comparison in this work. (XLSX 53 kb)
DOI: 10.6084/m9.figshare.5951356.v1
title: Additional file 10: of Analysis of MAPK and MAPKK gene families in wheat and related Triticeae species

description: Summary of MAPK identifiers and complementary information obtained from eight studies. The table includes gene identifiers and complementary annotations for 8 published sets of MAPKs that were used for comparison in this work. (XLSX 53 kb)
DOI: 10.6084/m9.figshare.5951260
title: Additional file 7: of IntLIM: integration using linear models of metabolomics and gene expression data

description: Data S2. Breast Cancer Results. FDR Adjusted p-value 0.5. (XLSX 220 kb)
DOI: 10.6084/m9.figshare.5951260.v1
title: Additional file 7: of IntLIM: integration using linear models of metabolomics and gene expression data

description: Data S2. Breast Cancer Results. FDR Adjusted p-value 0.5. (XLSX 220 kb)
DOI: 10.6084/m9.figshare.5951212
title: Additional file 1: of Early life Triclosan exposure and child adiposity at 8Â Years of age: a prospective cohort study

description: Results of all secondary analysis and DAGs. (ZIP 160 kb)
DOI: 10.6084/m9.figshare.5951212.v1
title: Additional file 1: of Early life Triclosan exposure and child adiposity at 8Â Years of age: a prospective cohort study

description: Results of all secondary analysis and DAGs. (ZIP 160 kb)
DOI: 10.6084/m9.figshare.5951191
title: Additional file 4: of IntLIM: integration using linear models of metabolomics and gene expression data

description: Data S1. NCI-60 Results with FDR Adjusted p-value 0.50. (XLSX 104 kb)
DOI: 10.6084/m9.figshare.5951191.v1
title: Additional file 4: of IntLIM: integration using linear models of metabolomics and gene expression data

description: Data S1. NCI-60 Results with FDR Adjusted p-value 0.50. (XLSX 104 kb)
DOI: 10.6084/m9.figshare.5951143
title: Additional file 2: of Petri net-based prediction of therapeutic targets that recover abnormally phosphorylated proteins in muscle atrophy

description: Table S1. The 37 characterized therapeutic targets. Table S2. The enriched GO terms and KEGG pathways. Table S3. Hypergeometric test with gold standard from CTD. (XLSX 19Â kb)
DOI: 10.6084/m9.figshare.5951143.v1
title: Additional file 2: of Petri net-based prediction of therapeutic targets that recover abnormally phosphorylated proteins in muscle atrophy

description: Table S1. The 37 characterized therapeutic targets. Table S2. The enriched GO terms and KEGG pathways. Table S3. Hypergeometric test with gold standard from CTD. (XLSX 19Â kb)
DOI: 10.6084/m9.figshare.5951107
title: Additional file 1: of RNAseq analysis of bronchial epithelial cells to identify COPD-associated genes and SNPs

description: Tables S1, S2, S3, S4, S5 and S6. Table S1. This table provides: a) Gene-specific assay information including SNP sites, primer and internal standard sequences, b) Subject-specific demographic information, and c) assay- and subject-specific transcript abundance values (target gene molecules/106 ACTB molecules). Table S2. Population used for allele specific expression analysis: Summary demographic characteristics of the study population of allele specific expression (subject total n = 180). Table S3. Transcription factor-target inter-gene correlation in Control, COPD, or All subjects (p-value 0.95) and with p