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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: Lynch, Karlene H; Stothard, Paul; Dennis, Jonathan J;

    Abstract Background The Burkholderia cepacia complex (BCC) is comprised of at least seventeen Gram-negative species that cause infections in cystic fibrosis patients. Because BCC bacteria are broadly antibiotic resistant, phage therapy is currently being investigated as a possible alternative treatment for these infections. The purpose of our study was to sequence and characterize three novel BCC-specific phages: KS5 (vB_BceM-KS5 or vB_BmuZ-ATCC 17616), KS14 (vB_BceM-KS14) and KL3 (vB_BamM-KL3 or vB_BceZ-CEP511). Results KS5, KS14 and KL3 are myoviruses with the A1 morphotype. The genomes of these phages are between 32317 and 40555 base pairs in length and are predicted to encode between 44 and 52 proteins. These phages have over 50% of their proteins in common with enterobacteria phage P2 and so can be classified as members of the Peduovirinae subfamily and the "P2-like viruses" genus. The BCC phage proteins similar to those encoded by P2 are predominantly structural components involved in virion morphogenesis. As prophages, KS5 and KL3 integrate into an AMP nucleosidase gene and a threonine tRNA gene, respectively. Unlike other P2-like viruses, the KS14 prophage is maintained as a plasmid. The P2 E+E' translational frameshift site is conserved among these three phages and so they are predicted to use frameshifting for expression of two of their tail proteins. The lysBC genes of KS14 and KL3 are similar to those of P2, but in KS5 the organization of these genes suggests that they may have been acquired via horizontal transfer from a phage similar to λ. KS5 contains two sequence elements that are unique among these three phages: an ISBmu 2-like insertion sequence and a reverse transcriptase gene. KL3 encodes an EcoRII-C endonuclease/methylase pair and Vsr endonuclease that are predicted to function during the lytic cycle to cleave non-self DNA, protect the phage genome and repair methylation-induced mutations. Conclusions KS5, KS14 and KL3 are the first BCC-specific phages to be identified as P2-like. As KS14 has previously been shown to be active against Burkholderia cenocepacia in vivo, genomic characterization of these phages is a crucial first step in the development of these and similar phages for clinical use against the BCC.

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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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    Collection . 2021
    License: CC BY
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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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    Collection . 2021
    License: CC BY
    Data sources: Datacite
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      Collection . 2021
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      Collection . 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/
    Authors: Labelle, Jonathan Bourgon; Farand, Paul; Vincelette, Christian; Dumont, Myriam; +2 Authors

    Abstract Introduction Postoperative atrial fibrillation (POAF) is a frequent complication of cardiac surgery associated with important morbidity, mortality, and costs. To assess the effectiveness of preventive interventions, an important prerequisite is to have access to accurate measures of POAF incidence. The aim of this study was to develop and validate such a measure. Methods A validation study was conducted at two large Canadian university health centers. First, a random sample of 976 (10.4%) patients who had cardiac surgery at these sites between 2010 and 2016 was generated. Then, a reference standard assessment of their medical records was performed to determine their true POAF status on discharge (positive/negative). The accuracy of various algorithms combining diagnostic and procedure codes from: 1) the current hospitalization, and 2) hospitalizations up to 6 years before the current hospitalization was assessed in comparison with the reference standard. Overall and site-specific estimates of sensitivity, specificity, positive (PPV), and negative (NPV) predictive values were generated, along with their 95%CIs. Results Upon manual review, 324 (33.2%) patients were POAF-positive. Our best-performing algorithm combining data from both sites used a look-back window of 6 years to exclude patients previously known for AF. This algorithm achieved 70.4% sensitivity (95%CI: 65.1–75.3), 86.0% specificity (95%CI: 83.1–88.6), 71.5% PPV (95%CI: 66.2–76.4), and 85.4% NPV (95%CI: 82.5–88.0). However, significant site-specific differences in sensitivity and NPV were observed. Conclusion An algorithm based on administrative data can identify POAF patients with moderate accuracy. However, site-specific variations in coding practices have significant impact on accuracy.

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    Collection . 2020
    License: CC BY
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    Collection . 2020
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      Collection . 2020
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      Collection . 2020
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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: Lalonde, Simon; Valérie-Anne Codina-Fauteux; Bellefon, Sébastian; Leblanc, Francis; +7 Authors

    Biological pathways that are enriched for transcription factors that bind within ATACseq peaks profiled in NT and TNFα treated teloHAEC. (XLSX 14 kb)

    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 . 2019
    License: CC BY
    Data sources: Datacite
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    Dataset . 2019
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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 . 2019
      License: CC BY
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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 . 2019
      License: CC BY
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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: McCarron, Tamara L.; Clement, Fiona; Jananee Rasiah; Moffat, Karen; +2 Authors

    Abstract Background Patient partners can be described as individuals who assume roles as active members on research teams, indicative of individuals with greater involvement, increased sharing of power, and increased responsibility than traditionally described by patient participants who are primarily studied. A gap still remains in the understanding of how to engage patients. The objective of this commentary is to describe the involvement of four patient partners who worked with researchers during a scoping review. Main body We describe approaches to meaningfully engage patient partners in conducting a scoping review. Patient partners were recruited through existing patient networks. Capacity development in the form of the training was provided to these four patient partners. Engagement strategies were co-designed with them to address potential barriers of involvement and acquiring the necessary skills for the successful completion of this scoping review. Conclusion Involving patients partners early in the project established the foundational relationship so patient partners could contribute to their fullest. We witnessed the success of working alongside patient partners as members of the research team with a clear and mutually agreed upon purpose of the engagement in health research activities and how this seemed to contribute to an effective and rewarding experience for both researcher and patient partner.

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    Collection . 2021
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    Collection . 2021
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      Collection . 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/
    Authors: Balaton, Bradley P.; Fornes, Oriol; Wyeth W. Wasserman; Brown, Carolyn J.;

    Abstract Background X-chromosome inactivation (XCI) in eutherian mammals is the epigenetic inactivation of one of the two X chromosomes in XX females in order to compensate for dosage differences with XY males. Not all genes are inactivated, and the proportion escaping from inactivation varies between human and mouse (the two species that have been extensively studied). Results We used DNA methylation to predict the XCI status of X-linked genes with CpG islands across 12 different species: human, chimp, bonobo, gorilla, orangutan, mouse, cow, sheep, goat, pig, horse and dog. We determined the XCI status of 342 CpG islands on average per species, with most species having 80–90% of genes subject to XCI. Mouse was an outlier, with a higher proportion of genes subject to XCI than found in other species. Sixteen genes were found to have discordant X-chromosome inactivation statuses across multiple species, with five of these showing primate-specific escape from XCI. These discordant genes tended to cluster together within the X chromosome, along with genes with similar patterns of escape from XCI. CTCF-binding, ATAC-seq signal and LTR repeats were enriched at genes escaping XCI when compared to genes subject to XCI; however, enrichment was only observed in three or four of the species tested. LINE and DNA repeats showed enrichment around subject genes, but again not in a consistent subset of species. Conclusions In this study, we determined XCI status across 12 species, showing mouse to be an outlier with few genes that escape inactivation. Inactivation status is largely conserved across species. The clustering of genes that change XCI status across species implicates a domain-level control. In contrast, the relatively consistent, but not universal correlation of inactivation status with enrichment of repetitive elements or CTCF binding at promoters demonstrates gene-based influences on inactivation state. This study broadens enrichment analysis of regulatory elements to species beyond human and mouse.

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    Collection . 2021
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    Authors: Stroo, Ingrid; Diba Emal; Butter, Loes; Teske, Gwen; +5 Authors

    Figure S1. The genotype of NOD1/2 DKO mice. Genomic DNA from mice was amplified by PCR with specific primers to detect the disrupted sequences on a 1% agarose gel with a 100Â bp marker. First 5 bands are the KO mice and the last bands are the WT mice in A and B. NÂ =â 5/3 per group. (TIFF 12868 kb)

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    Image . 2018
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    Authors: Dwarkanath, Pratibha; Muhihi, Alfa; Sudfeld, Christopher R.; Rani, Shobha; +16 Authors

    Abstract Background Hypertensive disorders of pregnancy are important causes of maternal morbidity and mortality, as well as preterm birth, the leading cause of death for children under 5 years globally. The World Health Organization currently recommends that pregnant women receive high-dose calcium supplementation (1500���2000 mg elemental calcium) for prevention of preeclampsia in populations with low dietary calcium intake. Trials of low-dose calcium supplementation (

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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: Bharambe, Harish; Raikamal Paul; Panwalkar, Pooja; Jalali, Rakesh; +15 Authors

    Abstract Genome-wide expression profiling studies have identified four core molecular subgroups of medulloblastoma: WNT, SHH, Group 3 and Group 4. Molecular markers are necessary for accurate risk stratification in the non-WNT subgroups due to the underlying heterogeneity in genetic alterations and overall survival. MiR-204 expression was evaluated in molecularly classified 260 medulloblastomas from an Indian cohort and in 763 medulloblastomas from the MAGIC cohort, SickKids, Canada. Low expression of miR-204 in the Group 3 / Group 4 tumors identify a highly aggressive subset of tumors having poor overall survival, in the two independent cohorts of medulloblastomas. Downregulation of miR-204 expression correlates with poor survival within the Group 4 as well indicating it as a valuable risk-stratification marker in the subgroup. Restoration of miR-204 expression in multiple medulloblastoma cell lines was found to inhibit their anchorage-independent growth, invasion potential and tumorigenicity. IGF2R was identified as a novel target of miR-204. MiR-204 expression resulted in downregulation of both M6PR and IGF2R that transport lysosomal proteases from the Golgi apparatus to the lysosomes. Consistent with this finding, miR-204 expression resulted in reduction in the levels of the lysosomal proteases in medulloblastoma cells. MiR-204 expression also resulted in inhibition of autophagy that is known to be dependent on the lysosomal degradation pathway and LC3B, a known miR-204 target. Treatment with HDAC inhibitors resulted in upregulation of miR-204 expression in medulloblastoma cells, suggesting therapeutic role for these inhibitors in the treatment of medulloblastomas. In summary, miR-204 is not only a valuable risk stratification marker in the combined cohort of Group 3 / Group 4 medulloblastomas as well as in the Group 4 itself, that has paucity of good prognostication markers, but also has therapeutic potential as indicated by its tumor suppressive effect on medulloblastoma cells.

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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: Beck, Andrew; LeBlanc, John C.; Morissette, Kate; Hamel, Candyce; +21 Authors

    Abstract Background Major depressive disorder is common, debilitating, and affects feelings, thoughts, mood, and behaviors. Childhood and adolescence are critical periods for the development of depression and adolescence is marked by an increased incidence of mental health disorders. This protocol outlines the planned scope and methods for a systematic review update that will evaluate the benefits and harms of screening for depression in children and adolescents. Methods This review will update a previously published systematic review by Roseman and colleagues. Eligible studies are randomized controlled trials (RCTs) assessing formal screening in primary care to identify children or adolescents not already self-reporting symptoms of, diagnosed with, or treated for depression. If no or only a single RCT is available, we will consider controlled studies without random assignment. Studies of participants with characteristics associated with an elevated risk of depression will be analyzed separately. Outcomes of interest are symptoms of depression, classification of major depressive disorder based on a validated diagnostic interview, suicidality, health-related quality of life, social function, impact on lifestyle behavior (e.g., substance use, school performance, lost time at work, or school), false-positive results, overdiagnosis, overtreatment, labeling, and other harms such as those arising from treatment. We will search MEDLINE, Embase, PsycINFO, CINAHL, the Cochrane Library, and grey literature sources. Two reviewers will independently screen the titles and abstracts using the liberal accelerated method. Full-text screening will be performed independently by two reviewers using pre-specified eligibility criteria. Data extraction and risk of bias assessments will be performed independently by two reviewers. Pre-planned analyses, including subgroup and sensitivity analyses, are detailed within this protocol. Two independent reviewers will assess and finalize through consensus the certainty of evidence using the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach, and prepare GRADE evidence profiles and summary of findings tables for each outcome of interest. Discussion The systematic review will provide a current state of the evidence of benefits and harms of depression screening in children and adolescents. These findings will be used by the Canadian Task Force on Preventive Health Care to inform the development of recommendations on depression screening. Systematic review registration PROSPERO CRD42020150373

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

    Additional file 5: Figure S5. Mutational signatures extracted de novo with NMF and r = 20 using the package ���SomaticSignatures��� [28].

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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: Lynch, Karlene H; Stothard, Paul; Dennis, Jonathan J;

    Abstract Background The Burkholderia cepacia complex (BCC) is comprised of at least seventeen Gram-negative species that cause infections in cystic fibrosis patients. Because BCC bacteria are broadly antibiotic resistant, phage therapy is currently being investigated as a possible alternative treatment for these infections. The purpose of our study was to sequence and characterize three novel BCC-specific phages: KS5 (vB_BceM-KS5 or vB_BmuZ-ATCC 17616), KS14 (vB_BceM-KS14) and KL3 (vB_BamM-KL3 or vB_BceZ-CEP511). Results KS5, KS14 and KL3 are myoviruses with the A1 morphotype. The genomes of these phages are between 32317 and 40555 base pairs in length and are predicted to encode between 44 and 52 proteins. These phages have over 50% of their proteins in common with enterobacteria phage P2 and so can be classified as members of the Peduovirinae subfamily and the "P2-like viruses" genus. The BCC phage proteins similar to those encoded by P2 are predominantly structural components involved in virion morphogenesis. As prophages, KS5 and KL3 integrate into an AMP nucleosidase gene and a threonine tRNA gene, respectively. Unlike other P2-like viruses, the KS14 prophage is maintained as a plasmid. The P2 E+E' translational frameshift site is conserved among these three phages and so they are predicted to use frameshifting for expression of two of their tail proteins. The lysBC genes of KS14 and KL3 are similar to those of P2, but in KS5 the organization of these genes suggests that they may have been acquired via horizontal transfer from a phage similar to λ. KS5 contains two sequence elements that are unique among these three phages: an ISBmu 2-like insertion sequence and a reverse transcriptase gene. KL3 encodes an EcoRII-C endonuclease/methylase pair and Vsr endonuclease that are predicted to function during the lytic cycle to cleave non-self DNA, protect the phage genome and repair methylation-induced mutations. Conclusions KS5, KS14 and KL3 are the first BCC-specific phages to be identified as P2-like. As KS14 has previously been shown to be active against Burkholderia cenocepacia in vivo, genomic characterization of these phages is a crucial first step in the development of these and similar phages for clinical use against the BCC.

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    Authors: Labelle, Jonathan Bourgon; Farand, Paul; Vincelette, Christian; Dumont, Myriam; +2 Authors

    Abstract Introduction Postoperative atrial fibrillation (POAF) is a frequent complication of cardiac surgery associated with important morbidity, mortality, and costs. To assess the effectiveness of preventive interventions, an important prerequisite is to have access to accurate measures of POAF incidence. The aim of this study was to develop and validate such a measure. Methods A validation study was conducted at two large Canadian university health centers. First, a random sample of 976 (10.4%) patients who had cardiac surgery at these sites between 2010 and 2016 was generated. Then, a reference standard assessment of their medical records was performed to determine their true POAF status on discharge (positive/negative). The accuracy of various algorithms combining diagnostic and procedure codes from: 1) the current hospitalization, and 2) hospitalizations up to 6 years before the current hospitalization was assessed in comparison with the reference standard. Overall and site-specific estimates of sensitivity, specificity, positive (PPV), and negative (NPV) predictive values were generated, along with their 95%CIs. Results Upon manual review, 324 (33.2%) patients were POAF-positive. Our best-performing algorithm combining data from both sites used a look-back window of 6 years to exclude patients previously known for AF. This algorithm achieved 70.4% sensitivity (95%CI: 65.1–75.3), 86.0% specificity (95%CI: 83.1–88.6), 71.5% PPV (95%CI: 66.2–76.4), and 85.4% NPV (95%CI: 82.5–88.0). However, significant site-specific differences in sensitivity and NPV were observed. Conclusion An algorithm based on administrative data can identify POAF patients with moderate accuracy. However, site-specific variations in coding practices have significant impact on accuracy.

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      Collection . 2020
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      Data sources: Datacite
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      Collection . 2020
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    Authors: Lalonde, Simon; Valérie-Anne Codina-Fauteux; Bellefon, Sébastian; Leblanc, Francis; +7 Authors

    Biological pathways that are enriched for transcription factors that bind within ATACseq peaks profiled in NT and TNFα treated teloHAEC. (XLSX 14 kb)

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    Dataset . 2019
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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 . 2019
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      Dataset . 2019
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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 . 2019
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    Authors: McCarron, Tamara L.; Clement, Fiona; Jananee Rasiah; Moffat, Karen; +2 Authors

    Abstract Background Patient partners can be described as individuals who assume roles as active members on research teams, indicative of individuals with greater involvement, increased sharing of power, and increased responsibility than traditionally described by patient participants who are primarily studied. A gap still remains in the understanding of how to engage patients. The objective of this commentary is to describe the involvement of four patient partners who worked with researchers during a scoping review. Main body We describe approaches to meaningfully engage patient partners in conducting a scoping review. Patient partners were recruited through existing patient networks. Capacity development in the form of the training was provided to these four patient partners. Engagement strategies were co-designed with them to address potential barriers of involvement and acquiring the necessary skills for the successful completion of this scoping review. Conclusion Involving patients partners early in the project established the foundational relationship so patient partners could contribute to their fullest. We witnessed the success of working alongside patient partners as members of the research team with a clear and mutually agreed upon purpose of the engagement in health research activities and how this seemed to contribute to an effective and rewarding experience for both researcher and patient partner.

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    Collection . 2021
    License: CC BY
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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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    Collection . 2021
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      Collection . 2021
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