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  • 2020-2024
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  • Canadian Institutes of Health Resea...

  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/

    Additional file7: Table S18. DNAmeQTL analysis for the loci significantly associated with DNAme-based XCI status calls. See additional files. These loci were independently tested as DNAmeQTLs in females and males, with some columns color coded based on sex (pink female, light blue male). There are also columns with the median and mean DNAme value at the gene’s island for samples with the reference or alternate allele at that loci; these columns are color coded based on whether the allele is in the range to escape from XCI (DNAme<0.01, blue) or in the range to be subject to XCI (DNAme>0.15, orange). There are mean and median columns for both males and females, but only the female columns are color coded based on XCI status. There are boxes around the genes with female median values with one allele in the range to escape XCI and the other allele in the range to be subject to XCI.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ figsharearrow_drop_down
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    Dataset . 2022
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    Dataset . 2022
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ figsharearrow_drop_down
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    Authors: Mealey, Nicole E.; O���Sullivan, Dylan E.; Peters, Cheryl E.; Heng, Daniel Y. C.; +1 Authors

    Additional file 6: Table S1. Comparison of COSMIC mutational signature contributions to non-seminomatous (n = 56) and seminomatous (n = 44) testicular tumors. Entries are number (proportion) of cases with a signature present above a threshold of 6% in each histologic group. P-values were calculated adjusting for age of onset * indicates statistical significance at a 0.05 level.

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    Dataset . 2021
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    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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    Dataset . 2021
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ figsharearrow_drop_down
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      Dataset . 2021
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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      Dataset . 2021
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    Authors: Akhabir, Loubna; Stringer, Randa; Desai, Dipika; Mandhane, Piush J; +6 Authors

    Additional file 6. Meta-analysis association of Gestational age with methylation in CHILD and START. Results of meta-analysis association analysis of Gestational age in CHILD and START with methylation in sites identified in the literature.

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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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    Authors: Faheem, Muhammad; Deneault, Eric; Alexandrova, Roumiana; Rodrigues, Deivid C.; +12 Authors

    Additional file 1. Supplementary tables.

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    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ figsharearrow_drop_down
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Visser, Pieter Jelle; Reus, Lianne M.; Gobom, Johan; Jansen, Iris; +25 Authors

    Additional file 1: Data S1. Participant characteristics. S1a: Characteristics of individuals with CSF Aβ1-42 and tau measurements available; S1b: Characteristics of individuals with CSF proteomic data. Data S2. Protein annotation and statistics of group comparisons of protein levels. Data S3a. Full list of GO biological processes associated with proteins that differ according to group and clinical stage. Data S3b. SynGO enriched synaptic cellular components and biological processes that differ according to group. Data S4a. Estimated marginal means of AD GWAS-based polygenic risk scores in controls, AD individuals with increased t-tau and AD individuals with normal t-tau. Data S4b. Top 1000 SNPS from GWAS on AD individuals with increased t-tau and normal t-tau in pooled ADNI and EMIF-AD MBD cohorts. Data S4c. Difference in MAGMA gene score between AD individuals with increased t-tau and normal t-tau based on t-tau GWAS in pooled ADNI and EMIF-AD MBD cohorts. Data S4d. Difference in GO biological process MAGMA geneset score between AD individuals with increased t-tau and normal t-tau based on t-tau GWAS in pooled ADNI and EMIF-AD MBD cohorts. Data S5a. Correlation between genetic risk score and CSF protein level in individuals with abnormal Aβ1-42. Data S5b. Association of the number of GMNC rs9877502-A risk alleles and number of APOE-e4 alleles with CSF protein concentrations in a linear model in individuals with AD. Data S5c. GO-BP processes enriched for proteins that have a positive or negative association with the number of rs9877502-A risk alleles in an additive model. Data S6. Annual change in imaging measures.

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    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
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    Many roles of human platelets in health and disease are linked to their ability to transport and secrete a variety of small molecules and proteins carried in dense (δ-) and α-granules. Determination of granule number and content is important for diagnosis of platelet disorders and for studies of platelet structure, function, and development. We have optimized methods for detection and localization of platelet proteins via antibody and lectin staining, imaging via structured illumination laser fluorescence microscopy (SIM), and three-dimension (3D) image analysis. The methods were validated via comparison with published studies based on electron microscopy and high-resolution fluorescence microscopy. The α-granule cargo proteins thrombospondin-1 (TSP1), osteonectin (SPARC), fibrinogen (FGN), and Von Willebrand factor (VWF) were localized within the granule lumen, as was the proteoglycan serglycin (SRGN). Colocalization analysis indicates that staining with fluorescently labeled wheat germ agglutinin (WGA) allows detection of α-granules as effectively as immunostaining for cargo proteins, with the advantage of not requiring antibodies. RAB27B was observed to be concentrated at dense granules, allowing them to be counted via visual scoring and object analysis. We present a workflow for counting dense and α-granules via object analysis of 3D SIM images of platelets stained for RAB27B and with WGA. Abbreviation: SIM: structured illumination microscopy; WGA: wheat germ agglutinin; FGN: fibrinogen; TSP1: thrombospondin 1; ER: endoplasmic reticulum Platelets support blood clotting, wound healing, and other essential processes. These functions rely on the ability of platelets to transport and release small molecules like serotonin carried in dense granules and a wide range of proteins carried in alpha granules. Several conditions have been linked to abnormalities in one or more of platelet granule number, content, structure, and function. These conditions can be difficult to diagnose because platelet granules are so small they cannot be consistently resolved by conventional light microscopy, while higher power electron microscopy is not widely accessible. The goal of this study was to develop a method for counting and examining platelet dense and alpha granules without the need of electron microscopy. Key to this was the discovery that alpha granules can be reliably stained with the plant lectin wheat germ agglutinin, which has the advantages of being a smaller and less expensive molecule than the antibodies commonly used to detect alpha granule cargo proteins. We also establish that dense granules can be detected with high specificity via antibody staining of the membrane-associated protein RAB27B. We used structured illumination laser fluorescence microscopy to obtain high-resolution images of stained platelets. These were assembled into 3D renders using image analysis software, which was used to validate a protocol for rapidly counting granules within individual platelets. Our method supports the relatively rapid, accurate, and cost-effective assessment of platelet granules. We have already shown that it can confirm dense granule deficiency, and we anticipate that this approach will also prove useful in diagnosing and studying alpha granule abnormalities.

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    Authors: Curtin, Kimberley D.; Thomson, Mathew; Nykiforuk, Candace I. J.;

    Additional file 1. An additional table is available describing the variables and regression results included in each binary logistic regression model created for each survey question separated by imputed and complete case datasets. The file name is “BLR-Additional Table 1-BMC.xlsx” and it titled “Logistic Regression Models”.

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    Authors: Mehdi, Ali; Cheishvili, David; Arakelian, Ani; Bismar, Tarek A.; +2 Authors

    Additional file 3: Supplementary Table 2. List of the primers used for pyrosequencing and amplicon sequencing (Illumina MiSeq system).

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    Additional file 7: Table S6. GEO and ENCODE FASTQ identification numbers per cell line for the data that were used to identify differential TF peaks.

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    Authors: Lowe, Darby J. E.; Sorkhou, Maryam; George, Tony P.;

    Background: The use of cannabis is highly prevalent during adolescence compared to the general adult population. In addition to the high comorbidity between cannabis use and anxiety disorders, early evidence suggests that cannabis may precede the development of anxiety. Moreover, adolescence represents a major developmental period for both neurobiological and psychological processes, placing these individuals at a heightened vulnerability to the influence of cannabis. Objectives: This systematic review and meta-analysis examined the prospective associations between adolescent cannabis use and subsequent anxiety outcomes (i.e. anxiety disorders and/or symptoms). Methods: Following PRISMA guidelines, a systematic review and meta-analysis were conducted encompassing data from articles published between database inception and September 2022. Results: Six longitudinal studies were identified for quantitative analysis, while twelve non-overlapping longitudinal studies were identified for qualitative review (total N = 18; 33380 subjects). Meta-analytical findings supported an association between adolescent cannabis use and the development of a subsequent anxiety disorder (Odds Ratio = 2.14, 95% CI: 1.37–3.36, p < .01). These findings were consistent with our qualitative synthesis where nine of the twelve longitudinal studies observed a significant relationship between adolescent cannabis use and exacerbation of anxiety symptoms later in life, irrespective of an anxiety disorder diagnosis. Discussion: In summary, the current evidence suggests a prospective association between adolescent cannabis use and later anxiety symptoms and disorders. These findings underscore the importance of refining research methodologies, considering sex-based differences and controlling for confounding factors, as well as implementing educational initiatives and developing clinical interventions to address the mental health risks associated with cannabis use among adolescents.

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    Additional file7: Table S18. DNAmeQTL analysis for the loci significantly associated with DNAme-based XCI status calls. See additional files. These loci were independently tested as DNAmeQTLs in females and males, with some columns color coded based on sex (pink female, light blue male). There are also columns with the median and mean DNAme value at the gene’s island for samples with the reference or alternate allele at that loci; these columns are color coded based on whether the allele is in the range to escape from XCI (DNAme<0.01, blue) or in the range to be subject to XCI (DNAme>0.15, orange). There are mean and median columns for both males and females, but only the female columns are color coded based on XCI status. There are boxes around the genes with female median values with one allele in the range to escape XCI and the other allele in the range to be subject to XCI.

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    Authors: Mealey, Nicole E.; O���Sullivan, Dylan E.; Peters, Cheryl E.; Heng, Daniel Y. C.; +1 Authors

    Additional file 6: Table S1. Comparison of COSMIC mutational signature contributions to non-seminomatous (n = 56) and seminomatous (n = 44) testicular tumors. Entries are number (proportion) of cases with a signature present above a threshold of 6% in each histologic group. P-values were calculated adjusting for age of onset * indicates statistical significance at a 0.05 level.

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    Authors: Akhabir, Loubna; Stringer, Randa; Desai, Dipika; Mandhane, Piush J; +6 Authors

    Additional file 6. Meta-analysis association of Gestational age with methylation in CHILD and START. Results of meta-analysis association analysis of Gestational age in CHILD and START with methylation in sites identified in the literature.

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      License: CC BY
      Data sources: Datacite
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      Dataset . 2022
      License: CC BY
      Data sources: Datacite
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    Authors: Faheem, Muhammad; Deneault, Eric; Alexandrova, Roumiana; Rodrigues, Deivid C.; +12 Authors

    Additional file 1. Supplementary tables.

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    Dataset . 2023
    License: CC BY
    Data sources: Datacite
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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    Dataset . 2023
    License: CC BY
    Data sources: Datacite
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    This Research product is the result of merged Research products in OpenAIRE.

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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ figsharearrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      figshare
      Dataset . 2023
      License: CC BY
      Data sources: Datacite
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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      Dataset . 2023
      License: CC BY
      Data sources: Datacite