cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11417241.v1
title: data_input1.xlsx

description: Data non real for rankspa<br>
DOI: 10.6084/m9.figshare.11417130
title: Histological and immunohistochemical characterization of the porcine ocular surface. Raw data.xlsx

description: <b>Raw data from porcine ocular surface goblet cell density, conjunctival associated limphoid tissue and corneal thickness</b><br>
DOI: 10.6084/m9.figshare.11417241.v2
title: data_input1.xlsx

description: Data non real for rankspa<br>
DOI: 10.6084/m9.figshare.11417082
title: Mining zebrafish microbiota reveals key community-level resistance against fish pathogen infection

description: Metagenomic dataset of zetabrafish microbiota.These data can be analysed with shaman.pasteur.fr
DOI: 10.6084/m9.figshare.11417130.v1
title: Histological and immunohistochemical characterization of the porcine ocular surface. Raw data.xlsx

description: <b>Raw data from porcine ocular surface goblet cell density, conjunctival associated limphoid tissue and corneal thickness</b><br>
DOI: 10.6084/m9.figshare.11417082.v2
title: Mining zebrafish microbiota reveals key community-level resistance against fish pathogen infection

description: Metagenomic dataset of zetabrafish microbiota.These data can be analysed with shaman.pasteur.fr
DOI: 10.6084/m9.figshare.11417070
title: Unmet Care Needs of Children with ADHD

description: To improve our understanding of receiving treatment in specialized mental health care, we studied unmet care needs of children with ADHD. Because care needs may vary depending on the intensity of care we included patients who had been referred to an outpatient mental healthcare setting, or to a setting providing youth Assertive Community Treatment (youth-ACT). This comparison enabled us to judge the influence of severity of psychiatric and psychosocial problems on unmet care need. Further, since parents are involved differently in younger versus older children, we investigated unmet care needs in two age groups: primary school children and adolescents.
DOI: 10.6084/m9.figshare.11417082.v1
title: Mining zebrafish microbiota reveals key community-level resistance against fish pathogen infection

description: Metagenomic dataset of zetabrafish microbiota.These data can be analysed with shaman.pasteur.fr
DOI: 10.6084/m9.figshare.11416998
title: manuscript2018MetaFinalSupMaterial_HOL.pdf

description: This is the supplementary material of the article : A new cut-based genetic algorithm for graph partitioning applied to cell formation. It contains some theoretic extensions and the examples' inputs. <br>
DOI: 10.6084/m9.figshare.11416998.v1
title: manuscript2018MetaFinalSupMaterial_HOL.pdf

description: This is the supplementary material of the article : A new cut-based genetic algorithm for graph partitioning applied to cell formation. It contains some theoretic extensions and the examples' inputs. <br>
DOI: 10.6084/m9.figshare.11416974
title: Extended theoretical analysis of crystallisation kinetics being studied by in situ XRD

description: Theoretical simulations were used to study the consequences of simplifying the replacement of the step-wise in situ X-ray diffraction (XRD) temperature programme by simple linear heating (at corresponding effective heating rate) during the kinetic calculations based on the multivariate kinetic analysis. The simulations were performed for a large variety of step-wise non-isothermal in situ XRD temperature programmes, covering most practically used combinations of the temperature step magnitude Δ<i>T</i>, rate of heating, and duration of the isothermal hold Δ<i>t</i>. To achieve the universal interpretation of the obtained results, the behaviour of the majority of crystallisation processes with commonly encountered kinetic profiles was explored: simulations were performed for single-process transformations with highly negative, symmetric and highly positive asymmetries; complex multi-process reactions with different degrees of sub-process overlaps and variable activation energy were analysed. It was found that the asymmetry and shape of the crystallisation peaks do not significantly influence the level of distortion of kinetic parameters. The main factors that increase the errors of in situ XRD kinetic evaluations are high Δ<i>t</i>, high Δ<i>T</i> and high activation energy (with the latter two being most important). Findings were discussed for the accuracy of the corresponding kinetic predictions. Generalisation of the present conclusions towards their universal utilisation for optimisation of in situ XRD experiments was suggested.
DOI: 10.6084/m9.figshare.11416968
title: Supplementary Table S8

description: Values of LY transport (%) to the basolateral compartment of the Transwell system are expressed as mean ± SEM (n =6).
DOI: 10.6084/m9.figshare.11416974.v1
title: Extended theoretical analysis of crystallisation kinetics being studied by in situ XRD

description: Theoretical simulations were used to study the consequences of simplifying the replacement of the step-wise in situ X-ray diffraction (XRD) temperature programme by simple linear heating (at corresponding effective heating rate) during the kinetic calculations based on the multivariate kinetic analysis. The simulations were performed for a large variety of step-wise non-isothermal in situ XRD temperature programmes, covering most practically used combinations of the temperature step magnitude Δ<i>T</i>, rate of heating, and duration of the isothermal hold Δ<i>t</i>. To achieve the universal interpretation of the obtained results, the behaviour of the majority of crystallisation processes with commonly encountered kinetic profiles was explored: simulations were performed for single-process transformations with highly negative, symmetric and highly positive asymmetries; complex multi-process reactions with different degrees of sub-process overlaps and variable activation energy were analysed. It was found that the asymmetry and shape of the crystallisation peaks do not significantly influence the level of distortion of kinetic parameters. The main factors that increase the errors of in situ XRD kinetic evaluations are high Δ<i>t</i>, high Δ<i>T</i> and high activation energy (with the latter two being most important). Findings were discussed for the accuracy of the corresponding kinetic predictions. Generalisation of the present conclusions towards their universal utilisation for optimisation of in situ XRD experiments was suggested.
DOI: 10.6084/m9.figshare.11416968.v1
title: Supplementary Table S8

description: Values of LY transport (%) to the basolateral compartment of the Transwell system are expressed as mean ± SEM (n =6).
DOI: 10.6084/m9.figshare.11416902
title: Supplementary Table S6

description: Differences in TNF-α levels in the hepatic cells between different treatments and between high and low glucose conditions. There was no significant difference between treatments (<i>P&gt;0.05</i>) indicating no effect of any treatment on TNF-α levels. The differences between treatments are marked by lower-case letters and were assessed by one-way Anova test using Tukey’s method with significance at P&lt;0.05. Values represent the mean in % ± SEM; n ≥ 3.
DOI: 10.6084/m9.figshare.11416932
title: Supplementary Table S7

description: TEER values (Ohms) are expressed as mean ± SEM (n =6).
DOI: 10.6084/m9.figshare.11416899
title: Supplementary Material for: Linking Colony Size with Foraging Behavior and Brain Investment in Odorous Ants (Formicidae: Dolichoderinae)

description: Superorganisms represent a unique level of biological organization in which the phenotype of the reproductive unit, the colony, results from traits expressed at the level of individual workers. Because body size scaling has important consequences for cell diversity and system complexity in solitary organisms, colony size is a trait of particular interest in superorganism evolution. In some instances, division of labor and worker polymorphism scale with colony size, but in general little is known about how colony size drives differences in individual-level behavior or neural traits. Ants represent the greatest diversity of superorganisms and provide a manner of natural experiment to test trends in trait evolution across multiple instances of colony size expansion. In this study, we control for environmental differences and worker size polymorphism to test if colony size correlates with measures of foraging behavior and brain size in dolichoderine ants. We present data from 3 species ranked by colony size. Our results suggest colony size correlates with measures of exploratory behavior and brain investment, with small-colony ants showing higher exploratory drive and faster exploration rate than the larger colony species, and greater relative investment in the primary olfactory brain region, the antennal lobe, than the larger colony species.
DOI: 10.6084/m9.figshare.11416932.v1
title: Supplementary Table S7

description: TEER values (Ohms) are expressed as mean ± SEM (n =6).
DOI: 10.6084/m9.figshare.11416893
title: Supplementary Table S5

description: Differences in IL-6 levels in the hepatic cells between different treatments and between high and low glucose conditions. There was no significant difference between treatments (<i>P&gt;0.05</i>) indicating no effect of any treatment on IL-6 levels. The differences between treatments are marked by lower-case letters and were assessed by one-way Anova test using Tukey’s method with significance at P&lt;0.05. Values represent the mean in % ± SEM; n ≥ 3.
DOI: 10.6084/m9.figshare.11416902.v1
title: Supplementary Table S6

description: Differences in TNF-α levels in the hepatic cells between different treatments and between high and low glucose conditions. There was no significant difference between treatments (<i>P&gt;0.05</i>) indicating no effect of any treatment on TNF-α levels. The differences between treatments are marked by lower-case letters and were assessed by one-way Anova test using Tukey’s method with significance at P&lt;0.05. Values represent the mean in % ± SEM; n ≥ 3.
DOI: 10.6084/m9.figshare.11416893.v1
title: Supplementary Table S5

description: Differences in IL-6 levels in the hepatic cells between different treatments and between high and low glucose conditions. There was no significant difference between treatments (<i>P&gt;0.05</i>) indicating no effect of any treatment on IL-6 levels. The differences between treatments are marked by lower-case letters and were assessed by one-way Anova test using Tukey’s method with significance at P&lt;0.05. Values represent the mean in % ± SEM; n ≥ 3.
DOI: 10.6084/m9.figshare.11416872
title: Proteome database of Pseudomonas putida KT2440

description: A member of the <i>Pseudomonas </i>family, <i>Pseudomonas putida</i> KT2440 is a Gram-negative bacterium possessing a relatively large genome. This implies that <i>P. putida</i> KT2440 should harbour many as-yet unknown metabolic pathways and regulatory mechanisms useful for biotechnology applications. Indeed, there has been an upsurge in research activities aiming to develop <i>P. putida</i> KT2440 as a microbial cell factory. But, more importantly, <i>P. putida </i>KT2440 primary role in biotech has been its use in various environmental remediation applications, particularly with respects to ameliorating soil and water pollution. Such remediation applications dovetail with the microbe’s inherent metabolic diversity in catabolizing a variety of toxic organic compounds recalcitrant to degradation by other common biotechnology strains. This work sought to provide some fundamental information of <i>P. putida</i> KT2440 through parsing its UniProt proteome using an in-house MATLAB software. In particular, a proteome database was built that comprises protein name, amino acid sequence, number of residues in proteins, molecular weight as well as nucleotide sequence of proteins. Such a global level proteome database should find use in informing presence/absence of particular metabolic pathways in the bacterium as well as enabling hitherto unknown signalling and regulatory effectors to be uncovered.<br><br>
DOI: 10.6084/m9.figshare.11416878
title: Supplementary Material for: Targeted Searches of the Electronic Health Record and Genomics Identify an Etiology in Three Patients with Short Stature and High IGF-I Levels

description: <b><i>Introduction:</i></b> Short stature is one of the most common reasons for referral to a pediatric endocrinologist and can result from many etiologies. However, many patients with short stature do not receive a definitive diagnosis. <b><i>Objective:</i></b> To ascertain whether integrating targeted bioinformatics searches of electronic health records (EHRs) combined with genomic studies could identify patients with previously undiagnosed rare genetic etiologies of short stature. We focused on a specific rare phenotypic subgroup: patients with short stature and elevated IGF-I levels. <b><i>Methods:</i></b> We performed a cross-sectional cohort study at three large academic pediatric healthcare networks. Eligible subjects included children with heights below –2 SD, IGF-I levels &gt;90th percentile, and no known etiology for short stature. We performed a search of the EHRs to identify eligible patients. Patients were then recruited for phenotyping followed by exome sequencing and in vitro assays of IGF1R function. <b><i>Results:</i></b> A total of 234 patients were identified by the bioinformatics algorithm with 39 deemed eligible after manual review (17%). Of those, 9 were successfully recruited. A genetic etiology was identified in 3 of the 9 patients including 2 novel variants in <i>IGF1R</i> and a de novo variant in <i>CHD2</i>. In vitro studies supported the pathogenicity of the <i>IGF1R</i> variants. <b><i>Conclusions:</i></b> This study provides proof of principle that patients with rare phenotypic subgroups can be identified based on discrete data elements in the EHRs. Although limitations exist to fully automating this approach, these searches may help find patients with previously unidentified rare genetic disorders.
DOI: 10.6084/m9.figshare.11416878.v1
title: Supplementary Material for: Targeted Searches of the Electronic Health Record and Genomics Identify an Etiology in Three Patients with Short Stature and High IGF-I Levels

description: <b><i>Introduction:</i></b> Short stature is one of the most common reasons for referral to a pediatric endocrinologist and can result from many etiologies. However, many patients with short stature do not receive a definitive diagnosis. <b><i>Objective:</i></b> To ascertain whether integrating targeted bioinformatics searches of electronic health records (EHRs) combined with genomic studies could identify patients with previously undiagnosed rare genetic etiologies of short stature. We focused on a specific rare phenotypic subgroup: patients with short stature and elevated IGF-I levels. <b><i>Methods:</i></b> We performed a cross-sectional cohort study at three large academic pediatric healthcare networks. Eligible subjects included children with heights below –2 SD, IGF-I levels &gt;90th percentile, and no known etiology for short stature. We performed a search of the EHRs to identify eligible patients. Patients were then recruited for phenotyping followed by exome sequencing and in vitro assays of IGF1R function. <b><i>Results:</i></b> A total of 234 patients were identified by the bioinformatics algorithm with 39 deemed eligible after manual review (17%). Of those, 9 were successfully recruited. A genetic etiology was identified in 3 of the 9 patients including 2 novel variants in <i>IGF1R</i> and a de novo variant in <i>CHD2</i>. In vitro studies supported the pathogenicity of the <i>IGF1R</i> variants. <b><i>Conclusions:</i></b> This study provides proof of principle that patients with rare phenotypic subgroups can be identified based on discrete data elements in the EHRs. Although limitations exist to fully automating this approach, these searches may help find patients with previously unidentified rare genetic disorders.
DOI: 10.6084/m9.figshare.11416869
title: Supplementary Table S4

description: Differences in IL-8 levels in the hepatic cells between different treatments and between high and low glucose conditions. The decrease in IL-8 when the supernatant from the PPC was added indicates the potential positive effect of PPC towards decreasing inflammatory markers in the case of high glucose. The differences between treatments are marked by lower-case letters and were assessed by one-way Anova test using Tukey’s method with significance at P&lt;0.05. Values represent the mean in % ± SEM; n=3.
DOI: 10.6084/m9.figshare.11416851
title: Supplementary Table S3

description: Differences in lipoprotein lipase (LPL) activity levels in the hepatic cells between different treatments and between high and low glucose conditions. The significant increase in LPL when the supernatant from the PPC was added indicates positive effect of PPC towards increasing LPL activity storange in the case of high glucose (P&lt;0.05). The differences between treatments are marked with lower case letters and were assessed by one-way Anova test using Tukey’s method with significance at P&lt;0.05. Values represent the mean in % ± SEM; n ≥ 3.
DOI: 10.6084/m9.figshare.11416869.v1
title: Supplementary Table S4

description: Differences in IL-8 levels in the hepatic cells between different treatments and between high and low glucose conditions. The decrease in IL-8 when the supernatant from the PPC was added indicates the potential positive effect of PPC towards decreasing inflammatory markers in the case of high glucose. The differences between treatments are marked by lower-case letters and were assessed by one-way Anova test using Tukey’s method with significance at P&lt;0.05. Values represent the mean in % ± SEM; n=3.
DOI: 10.6084/m9.figshare.11416851.v1
title: Supplementary Table S3

description: Differences in lipoprotein lipase (LPL) activity levels in the hepatic cells between different treatments and between high and low glucose conditions. The significant increase in LPL when the supernatant from the PPC was added indicates positive effect of PPC towards increasing LPL activity storange in the case of high glucose (P&lt;0.05). The differences between treatments are marked with lower case letters and were assessed by one-way Anova test using Tukey’s method with significance at P&lt;0.05. Values represent the mean in % ± SEM; n ≥ 3.
DOI: 10.6084/m9.figshare.11416815
title: Supplementary Table S2

description: Differences in glycogen storage in the hepatic cells between different treatments and between high and low glucose conditions. The significant increase in glycogen when the supernatant from the PPC was added indicates positive effect of PPC towards increasing glycogen storage in the case of high glucose (P&lt;0.05). The differences between treatments are marked with lower case letters and were assessed by one-way Anova test using Tukey’s method with significance at P&lt;0.05. Values represent the mean in % ± SEM; n ≥ 3
DOI: 10.6084/m9.figshare.11416824
title: Proteome database of Pseudomonas protegens Pf-5

description: Harbouring a large genome relative to bacterial standards, the Gram-negative bacterium, <i>Pseudomonas protegens</i> Pf-5 possess a versatile metabolism that enables it to colonize a variety of environments. More importantly, <i>P. protegens</i> Pf-5 has found applications in biotechnology such as its emerging role as a useful bacterium for leaching precious metals from electronic scrap materials. Biotechnology potential aside, <i>P. protegens</i> Pf-5 is fundamentally interesting given its large genome harbouring hitherto unknown metabolic and signalling pathways that may find use in biotechnology. This work sought to provide some fundamental information about <i>P. protegens</i> Pf-5 through constructing a proteome database of the organism at the global level. Parsed by an in-house MATLAB software, the database comprises protein name, amino acid sequence, number of residues, molecular weight and corresponding nucleotide sequence of the protein. The latter three features were calculated using MATLAB built-in functions. Overall, the proteome database of <i>P. protegens</i> Pf-5 should inform researchers of the ensemble of proteins detected in the species, which forms the foundation on which a variety of fundamental and applied microbiology studies could be tackled.<br><br>
DOI: 10.6084/m9.figshare.11416815.v1
title: Supplementary Table S2

description: Differences in glycogen storage in the hepatic cells between different treatments and between high and low glucose conditions. The significant increase in glycogen when the supernatant from the PPC was added indicates positive effect of PPC towards increasing glycogen storage in the case of high glucose (P&lt;0.05). The differences between treatments are marked with lower case letters and were assessed by one-way Anova test using Tukey’s method with significance at P&lt;0.05. Values represent the mean in % ± SEM; n ≥ 3
DOI: 10.6084/m9.figshare.11416824.v1
title: Proteome database of Pseudomonas protegens Pf-5

description: Harbouring a large genome relative to bacterial standards, the Gram-negative bacterium, <i>Pseudomonas protegens</i> Pf-5 possess a versatile metabolism that enables it to colonize a variety of environments. More importantly, <i>P. protegens</i> Pf-5 has found applications in biotechnology such as its emerging role as a useful bacterium for leaching precious metals from electronic scrap materials. Biotechnology potential aside, <i>P. protegens</i> Pf-5 is fundamentally interesting given its large genome harbouring hitherto unknown metabolic and signalling pathways that may find use in biotechnology. This work sought to provide some fundamental information about <i>P. protegens</i> Pf-5 through constructing a proteome database of the organism at the global level. Parsed by an in-house MATLAB software, the database comprises protein name, amino acid sequence, number of residues, molecular weight and corresponding nucleotide sequence of the protein. The latter three features were calculated using MATLAB built-in functions. Overall, the proteome database of <i>P. protegens</i> Pf-5 should inform researchers of the ensemble of proteins detected in the species, which forms the foundation on which a variety of fundamental and applied microbiology studies could be tackled.<br><br>
DOI: 10.6084/m9.figshare.11416800
title: Supplementary Material for: Lack of Evidence for the Effect of Oxytocin on Placebo Analgesia and Nocebo Hyperalgesia

description: Medicine
DOI: 10.6084/m9.figshare.11416800.v1
title: Supplementary Material for: Lack of Evidence for the Effect of Oxytocin on Placebo Analgesia and Nocebo Hyperalgesia

description: Medicine