cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6809798
title: Classification-based mapping of trees in commercial orchards and natural forests

description: Hyperspectral remote sensing (RS) and images of various spatial resolution open new vistas for classification and mapping trees. These approaches would improve plant classification in a complex population of forest trees of diverse species, genera, and families, as well as monitoring commercial orchards. In this work, we used new RS indices for cellulose, lignin, wax, chlorophyll, carotenoid, and anthocyanin for plant species classification in natural forests and commercial orchards. For proof of concept, the indices were applied to the classification and mapping of various horticultural crop orchards, where error due to the spatial mixing of different trees is minimal. The classification accuracy of the maps varied between 65 and 82%. This wide range was a result of the following factors: The RS index used, the season, and the spatial resolution of the hyperspectral images. The classification quality was highest when the full set of RS indices was used. The effect of the wax index on accuracy was significant. Furthermore, seasonality played an important role in the classification; the target species were better resolved in spring than in the summer. The higher spatial resolution of the images does not necessarily yield better classification and mapping results; it appeared to be case-specific and greatly depended on the species/crop and the unique environment.
DOI: 10.6084/m9.figshare.6809819.v3
title: DATABASE Avoidable workload of care for patients living with HIV infection in Abidjan, Côte d'Ivoire: a cross-sectional study

description: Database from "Avoidable workload of care for patients living with HIV infection in Abidjan, Côte d'Ivoire: a cross-sectional study"
DOI: 10.6084/m9.figshare.6809798.v1
title: Classification-based mapping of trees in commercial orchards and natural forests

description: Hyperspectral remote sensing (RS) and images of various spatial resolution open new vistas for classification and mapping trees. These approaches would improve plant classification in a complex population of forest trees of diverse species, genera, and families, as well as monitoring commercial orchards. In this work, we used new RS indices for cellulose, lignin, wax, chlorophyll, carotenoid, and anthocyanin for plant species classification in natural forests and commercial orchards. For proof of concept, the indices were applied to the classification and mapping of various horticultural crop orchards, where error due to the spatial mixing of different trees is minimal. The classification accuracy of the maps varied between 65 and 82%. This wide range was a result of the following factors: The RS index used, the season, and the spatial resolution of the hyperspectral images. The classification quality was highest when the full set of RS indices was used. The effect of the wax index on accuracy was significant. Furthermore, seasonality played an important role in the classification; the target species were better resolved in spring than in the summer. The higher spatial resolution of the images does not necessarily yield better classification and mapping results; it appeared to be case-specific and greatly depended on the species/crop and the unique environment.
DOI: 10.6084/m9.figshare.6809819.v2
title: DATABASE Avoidable workload of care for patients living with HIV infection in Abidjan, Côte d'Ivoire: a cross-sectional study

description: Database from "Avoidable workload of care for patients living with HIV infection in Abidjan, Côte d'Ivoire: a cross-sectional study"
DOI: 10.6084/m9.figshare.6809792
title: A novel <i>Atg5</i>-shRNA mouse model enables temporal control of Autophagy <i>in vivo</i>

description: Macroautophagy/autophagy is an evolutionarily conserved catabolic pathway whose modulation has been linked to diverse disease states, including age-associated disorders. Conventional and conditional whole-body knockout mouse models of key autophagy genes display perinatal death and lethal neurotoxicity, respectively, limiting their applications for <i>in vivo</i> studies. Here, we have developed an inducible shRNA mouse model targeting <i>Atg5</i>, allowing us to dynamically inhibit autophagy <i>in vivo</i>, termed ATG5i mice. The lack of brain-associated shRNA expression in this model circumvents the lethal phenotypes associated with complete autophagy knockouts. We show that ATG5i mice recapitulate many of the previously described phenotypes of tissue-specific knockouts. While restoration of autophagy in the liver rescues hepatomegaly and other pathologies associated with autophagy deficiency, this coincides with the development of hepatic fibrosis. These results highlight the need to consider the potential side effects of systemic anti-autophagy therapies.
DOI: 10.6084/m9.figshare.6809792.v2
title: A novel <i>Atg5</i>-shRNA mouse model enables temporal control of Autophagy <i>in vivo</i>

description: Macroautophagy/autophagy is an evolutionarily conserved catabolic pathway whose modulation has been linked to diverse disease states, including age-associated disorders. Conventional and conditional whole-body knockout mouse models of key autophagy genes display perinatal death and lethal neurotoxicity, respectively, limiting their applications for <i>in vivo</i> studies. Here, we have developed an inducible shRNA mouse model targeting <i>Atg5</i>, allowing us to dynamically inhibit autophagy <i>in vivo</i>, termed ATG5i mice. The lack of brain-associated shRNA expression in this model circumvents the lethal phenotypes associated with complete autophagy knockouts. We show that ATG5i mice recapitulate many of the previously described phenotypes of tissue-specific knockouts. While restoration of autophagy in the liver rescues hepatomegaly and other pathologies associated with autophagy deficiency, this coincides with the development of hepatic fibrosis. These results highlight the need to consider the potential side effects of systemic anti-autophagy therapies.
DOI: 10.6084/m9.figshare.6809792.v1
title: A novel <i>Atg5</i>-shRNA mouse model enables temporal control of Autophagy <i>in vivo</i>

description: Macroautophagy/autophagy is an evolutionarily conserved catabolic pathway whose modulation has been linked to diverse disease states, including age-associated disorders. Conventional and conditional whole-body knockout mouse models of key autophagy genes display perinatal death and lethal neurotoxicity, respectively, limiting their applications for <i>in vivo</i> studies. Here, we have developed an inducible shRNA mouse model targeting <i>Atg5</i>, allowing us to dynamically inhibit autophagy <i>in vivo</i>, termed ATG5i mice. The lack of brain-associated shRNA expression in this model circumvents the lethal phenotypes associated with complete autophagy knockouts. We show that ATG5i mice recapitulate many of the previously described phenotypes of tissue-specific knockouts. While restoration of autophagy in the liver rescues hepatomegaly and other pathologies associated with autophagy deficiency, this coincides with the development of hepatic fibrosis. These results highlight the need to consider the potential side effects of systemic anti-autophagy therapies.
DOI: 10.6084/m9.figshare.6809714
title: YFAS and BFD Data

description: This data set contains measures of body fat distribution, physical activity, caloric intake, gender, age and symptoms of food addiction for men and women of a general population from Newfoundland and Labrador. <br>
DOI: 10.6084/m9.figshare.6809714.v1
title: YFAS and BFD Data

description: This data set contains measures of body fat distribution, physical activity, caloric intake, gender, age and symptoms of food addiction for men and women of a general population from Newfoundland and Labrador. <br>
DOI: 10.6084/m9.figshare.6809717.v1
title: Vitamin D metabolites and type 2 diabetes supplemental file

description: Supplemental Files
DOI: 10.6084/m9.figshare.6809708.v1
title: FIGURE 7. (b).xlsx

description: the relationship between the damage degree and the times
DOI: 10.6084/m9.figshare.6809705.v1
title: FIGURE 7. (a).xlsx

description: the relationship between the damage degree and the times
DOI: 10.6084/m9.figshare.6809699.v1
title: FIGURE 6. (b).xlsx

description: the curves of the force-displacement
DOI: 10.6084/m9.figshare.6809693.v1
title: FIGURE 5. (a).xlsx

description: the time course curves of the displacement
DOI: 10.6084/m9.figshare.6809687.v1
title: FIGURE 4. (b).xlsx

description: the time course curves of the impact force under single impact
DOI: 10.6084/m9.figshare.6809690.v2
title: FIGURE 5. (b).xlsx

description: the time course curves of the displacement
DOI: 10.6084/m9.figshare.6809684
title: Supplementary Material for: Partially Hydrolyzed Whey Infant Formula: Literature Review on Effects on Growth and the Risk of Developing Atopic Dermatitis in Infants from the General Population

description: Limited evidence is available regarding the effect of partially hydrolyzed whey-based formula (pHF-W) on growth and atopic dermatitis (AD) risk reduction in infants within the general infant population, and without a familial history of allergy as an inclusion or exclusion criterion. We reviewed the current evidence available from studies using pHF-W in the general population and summarized the data on safety (growth) and efficacy outcomes (reduction of AD), comparing the studies side by side. A total of 8 clinical trials were identified from the literature search, 7 of which used the same pHF-W. Six out of 8 studies indicated a reduction of atopic manifestations using a specific pHF-W versus cow’s milk formula (CMF) in the first years of life. Data were summarized and compared side by side for growth (3 studies) and efficacy (5 studies). In these diverse general populations, the results on growth and AD were consistent with the previous findings reported on infants with a family history of allergy, but numerous limitations to these studies were identified. This literature review confirms that pHF-W supports normal growth in infants, and suggests that the risk of AD may be reduced in not-fully breastfed infants from the general population when supplemented with a specific pHF-W when compared to CMF during the first 4–6 months of life. Further studies are warranted to confirm these results.
DOI: 10.6084/m9.figshare.6809684.v1
title: Supplementary Material for: Partially Hydrolyzed Whey Infant Formula: Literature Review on Effects on Growth and the Risk of Developing Atopic Dermatitis in Infants from the General Population

description: Limited evidence is available regarding the effect of partially hydrolyzed whey-based formula (pHF-W) on growth and atopic dermatitis (AD) risk reduction in infants within the general infant population, and without a familial history of allergy as an inclusion or exclusion criterion. We reviewed the current evidence available from studies using pHF-W in the general population and summarized the data on safety (growth) and efficacy outcomes (reduction of AD), comparing the studies side by side. A total of 8 clinical trials were identified from the literature search, 7 of which used the same pHF-W. Six out of 8 studies indicated a reduction of atopic manifestations using a specific pHF-W versus cow’s milk formula (CMF) in the first years of life. Data were summarized and compared side by side for growth (3 studies) and efficacy (5 studies). In these diverse general populations, the results on growth and AD were consistent with the previous findings reported on infants with a family history of allergy, but numerous limitations to these studies were identified. This literature review confirms that pHF-W supports normal growth in infants, and suggests that the risk of AD may be reduced in not-fully breastfed infants from the general population when supplemented with a specific pHF-W when compared to CMF during the first 4–6 months of life. Further studies are warranted to confirm these results.
DOI: 10.6084/m9.figshare.6809657
title: Dataset S2. Nucleotide Alignments and Phylogenetic Trees of primate, rodent and bat GPC5

description: PRANK alignments of orthologous nucleotide sequences of GPC5 from primates, rodents and bats, retrieved from public databases. Corresponding accession numbers are found in the manuscript Table S1. Phylogenies were built using PhyML (more details in Methods).<br>
DOI: 10.6084/m9.figshare.6809663
title: Dataset S3. Eutherian NTCP and GPC5 codon alignments

description: Eutherian NTCP and GPC5 codon alignments. See Methods in the manuscript Jacquet et al. for details.<br>
DOI: 10.6084/m9.figshare.6809624
title: Supplementary Material for: Central Precocious Puberty Caused by a Heterozygous Deletion in the <b><i>MKRN3</i></b> Promoter Region

description: <b><i>Context:</i></b> Loss-of-function mutations in the coding region of <i>MKRN3</i>, a maternally imprinted gene at chromosome 15q11.2, are a common cause of familial central precocious puberty (CPP). Whether <i>MKRN3</i> alterations in regulatory regions can cause CPP has not been explored to date. We aimed to investigate potential pathogenic variants in the promoter region of <i>MKRN3</i> in patients with idiopathic CPP. <b><i>Patients/Methods:</i></b> A cohort of 110 patients with idiopathic CPP was studied. Family history of precocious sexual development was present in 25%. Mutations in the coding region of <i>MKRN3</i> were excluded in all patients. Genomic DNA was extracted from peripheral blood leukocytes, and 1,100 nucleotides (nt) of the 5′-regulatory region of <i>MKRN3</i> were amplified and sequenced. Luciferase assays were performed in GT1–7 cells transiently transfected with plasmids containing mutated and wild-type <i>MKRN3</i> promoter. <b><i>Results:</i></b> We identified a rare heterozygous 4-nt deletion (c.-150_-147delTCAG; –38 to –41 nt upstream to the transcription start site) in the proximal promoter region of <i>MKRN3</i> in a girl with CPP. In silico analysis predicted that this deletion would lead to the loss of a binding site for a downstream res­ponsive element antagonist modulator (DREAM), a potential transcription factor for <i>MKRN3</i> and <i>GNRH1</i> expression. Luciferase assays<i></i> demonstrated a significant reduction of <i>MKRN3</i> promoter activity in transfected cells with a c.-150_- 147delTCAG construct plasmid in both homozygous and heterozygous states when compared with cells transfected with the corresponding wild-type <i>MKRN3</i> promoter region. <b><i>Conclusion:</i></b> A rare genetic alteration in the regulatory region of <i>MKRN3</i> causes CPP.
DOI: 10.6084/m9.figshare.6809618
title: Dataset S1. Nucleotide Alignments of primate, rodent and bat NTCP

description: PRANK alignments of orthologous nucleotide sequences of NTCP from 27 primate (1,047 bp), 18 rodent (1,029 bp) and 21 bat (1,005 bp) species retrieved from public databases and newly sequenced in this study. Corresponding Accession Numbers are found in the Manuscript Table S1.
DOI: 10.6084/m9.figshare.6809624.v1
title: Supplementary Material for: Central Precocious Puberty Caused by a Heterozygous Deletion in the <b><i>MKRN3</i></b> Promoter Region

description: <b><i>Context:</i></b> Loss-of-function mutations in the coding region of <i>MKRN3</i>, a maternally imprinted gene at chromosome 15q11.2, are a common cause of familial central precocious puberty (CPP). Whether <i>MKRN3</i> alterations in regulatory regions can cause CPP has not been explored to date. We aimed to investigate potential pathogenic variants in the promoter region of <i>MKRN3</i> in patients with idiopathic CPP. <b><i>Patients/Methods:</i></b> A cohort of 110 patients with idiopathic CPP was studied. Family history of precocious sexual development was present in 25%. Mutations in the coding region of <i>MKRN3</i> were excluded in all patients. Genomic DNA was extracted from peripheral blood leukocytes, and 1,100 nucleotides (nt) of the 5′-regulatory region of <i>MKRN3</i> were amplified and sequenced. Luciferase assays were performed in GT1–7 cells transiently transfected with plasmids containing mutated and wild-type <i>MKRN3</i> promoter. <b><i>Results:</i></b> We identified a rare heterozygous 4-nt deletion (c.-150_-147delTCAG; –38 to –41 nt upstream to the transcription start site) in the proximal promoter region of <i>MKRN3</i> in a girl with CPP. In silico analysis predicted that this deletion would lead to the loss of a binding site for a downstream res­ponsive element antagonist modulator (DREAM), a potential transcription factor for <i>MKRN3</i> and <i>GNRH1</i> expression. Luciferase assays<i></i> demonstrated a significant reduction of <i>MKRN3</i> promoter activity in transfected cells with a c.-150_- 147delTCAG construct plasmid in both homozygous and heterozygous states when compared with cells transfected with the corresponding wild-type <i>MKRN3</i> promoter region. <b><i>Conclusion:</i></b> A rare genetic alteration in the regulatory region of <i>MKRN3</i> causes CPP.
DOI: 10.6084/m9.figshare.6809537
title: Data S1 from Both stiff and compliant: morphological and biomechanical adaptations of stick insect antenna for tactile exploration

description: Raw data from mechanical tests.
DOI: 10.6084/m9.figshare.6809537.v1
title: Data S1 from Both stiff and compliant: morphological and biomechanical adaptations of stick insect antenna for tactile exploration

description: Raw data from mechanical tests.
DOI: 10.6084/m9.figshare.6809492
title: Table S4

description: <b>Table S4.</b> Summary of linkage disequilibrium analysis. Where more markers were closed together LD was computed only for one of them, in the table these markers are evidenced by the bold character. Position 1-2 means the physical coordinates of the SNP on the genome. S1-S2 means the site number of the SNP in the window of 60 SNPs used to compute LD. St1-St2 are the alternative nucleotides present at the Site1 or Site 2. Dist_bp is the distance between Position 1 and 2. Genic: if T (true) means that the position in linkage is inside a gene otherwise is reported the distance to the closest gene. For each position in linkage is reported the Accession number, the protein encoded and the conserved domains, where present, of each gene.
DOI: 10.6084/m9.figshare.6809492.v1
title: Table S4

description: <b>Table S4.</b> Summary of linkage disequilibrium analysis. Where more markers were closed together LD was computed only for one of them, in the table these markers are evidenced by the bold character. Position 1-2 means the physical coordinates of the SNP on the genome. S1-S2 means the site number of the SNP in the window of 60 SNPs used to compute LD. St1-St2 are the alternative nucleotides present at the Site1 or Site 2. Dist_bp is the distance between Position 1 and 2. Genic: if T (true) means that the position in linkage is inside a gene otherwise is reported the distance to the closest gene. For each position in linkage is reported the Accession number, the protein encoded and the conserved domains, where present, of each gene.
DOI: 10.6084/m9.figshare.6809471
title: Table S3

description: <b>Table S3. </b>Genes containing or near SNPs significantly associated with seedling response to <i>Fusarium</i> infection. Markers are identified by the progressive number reported in Table 3. For each marker, the genomic position (pos_AGP3), the surrounding or adjacent gene, the type and the conserved domain of the encoded protein (where available) and the amino acid variation caused by the SNP are reported.
DOI: 10.6084/m9.figshare.6809471.v1
title: Table S3

description: <b>Table S3. </b>Genes containing or near SNPs significantly associated with seedling response to <i>Fusarium</i> infection. Markers are identified by the progressive number reported in Table 3. For each marker, the genomic position (pos_AGP3), the surrounding or adjacent gene, the type and the conserved domain of the encoded protein (where available) and the amino acid variation caused by the SNP are reported.
DOI: 10.6084/m9.figshare.6809438
title: Supplementary Material for: Effects of Selenium in the Microcirculation of Fructose-Fed Hamsters

description: <b><i>Background and Aims:</i></b> Fructose intake is directly related to vascular dysfunction and it is a risk factor for the development of metabolic and cardiovascular diseases, such as obesity, diabetes, and hypertension. Selenium, a component of antioxidant enzymes, improves hyperglycemia and vascular function in diabetic animals. The aim of this study was to evaluate the effects of dietary selenium supplementation on microcirculatory and metabolic parameters of fructose-fed hamsters. <b><i>Methods and Results:</i></b> Male hamsters (<i>Mesocricetus auratus</i>) had their drinking water substituted or not by 10% fructose solution for 60 days, during which their microcirculatory function was evaluated in the cheek pouch preparation. Blood glucose and serum insulin levels were also tested. Microcirculatory responses to acetylcholine (an endothelium-dependent vasodilator) and to sodium nitroprusside (SNP, an endothelium-independent vasodilator), and macromolecular permeability increase induced by a 30-min ischemia/reperfusion (I/R) procedure, showed that endothelium-dependent and independent vasodilatation was significantly increased in animals that had high selenium supplementation, in both the control and fructose-fed groups. Selenium supplementation protected against plasma leakage induced by I/R in all control and fructose-fed groups. <b><i>Conclusion:</i></b> Our results indicate that dietary selenium supplementation reduces microvascular dysfunction by increasing endothelial-dependent and independent dilatation and reducing macromolecular permeability increase in fructose-fed animals.
DOI: 10.6084/m9.figshare.6809459
title: Table S2

description: <b>Table S2.</b> SNP identification (Marker) and progressive number (N°), allelic variants (SNP), lines carrying each allelic variant (OBS), additive effect and significance values for the association between the SNP and the phenotype (P-value and RMIP) and proportion of the phenotypic variance explained by the SNP (R<sup>2</sup>).
DOI: 10.6084/m9.figshare.6809318
title: Kiatmetha_Raw Data 3&4

description: <b>Figure 3D</b>: Agarose gel electrophoresis of the encapsidated EGFP-plasmid DNA into the VLP interior showing a major DNA band at 3.1 kbp (lane 4). An additional minor band at 6.2 kbp (lane 3; arrowheads) of unloaded plasmid was also noted. <br> <br> <b>Figure 4A</b>: Agarose gel electrophoresis of EGFP gene (600 bp product) present in the shrimp muscle, gill and hepatopancreas.<br><b>Figure 4B</b>: Confocal microscopy of shrimp tissues injected with EGFP-IHHNV-VLPs (green), and stained with anti-GFP (red). The bottom-most row represents control where the shrimp are injected with unloaded IHHNV-VLPs.<br><b>Figure 4C</b>: Western blot showing anti-GFP reactivity in the EGFP-IHHNV-VLPs injected shrimp's tissues.
DOI: 10.6084/m9.figshare.6809309
title: Stencila - Day 2 Introduction to R

description: This is the file for the 2nd Day / 2 part of the Introduction to R workshop
DOI: 10.6084/m9.figshare.6809309.v2
title: Stencila - Day 2 Introduction to R

description: This is the file for the 2nd Day / 2 part of the Introduction to R workshop
DOI: 10.6084/m9.figshare.6809270
title: Kiatmetha_Raw Data

description: <b>Figure 1A:</b> Agarose gel electrophoresis showing the expression of IHHNV capsid ORF at 990 bp upon transforming vectors into various transformed <i>E. coli</i>, S1-S4.<br><b> Figure 1B:</b> SDS-PAGE protein profiling of a highly purified IHHNV capsid protein at 37.5 kDa (arrowhead) through a Nikel affinity chromatography.<br><b>Figure 2A:</b> Physical stability tests of IHHNV-VLPs against long term storage at 4ºC, from 1 day storsge up to 30 days. <br><b></b><i></i><sub></sub><sup></sup><b></b><i></i><sub></sub><sup></sup><b></b><i></i><sub></sub><sup></sup><br><b></b><i></i><sub></sub><sup></sup><b></b><i></i><sub></sub><sup></sup><br><b></b><i></i><sub></sub><sup></sup><b></b><i></i><sub></sub><sup></sup><br><br>