The Experts below are selected from a list of 33645 Experts worldwide ranked by ideXlab platform
Daniel G Macarthur - One of the best experts on this subject based on the ideXlab platform.
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a synthetic diploid benchmark for accurate variant calling evaluation
Nature Methods, 2018Co-Authors: Jonathan M Bloom, Yossi Farjoun, Mark Fleharty, Laura D Gauthier, Benjamin M Neale, Daniel G MacarthurAbstract:Existing benchmark datasets for use in evaluating variant-calling accuracy are constructed from a consensus of known short-variant callers, and they are thus Biased toward easy regions that are accessible by these algorithms. We derived a new benchmark dataset from the de novo PacBio assemblies of two fully homozygous human cell lines, which provides a relatively more accurate and less Biased Estimate of small-variant-calling error rates in a realistic context.
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new synthetic diploid benchmark for accurate variant calling evaluation
bioRxiv, 2017Co-Authors: Jonathan M Bloom, Yossi Farjoun, Mark Fleharty, Laura D Gauthier, Benjamin M Neale, Daniel G MacarthurAbstract:Constructed from the consensus of multiple variant callers based on short-read data, existing benchmark datasets for evaluating variant calling accuracy are Biased toward easy regions accessible by known algorithms. We derived a new benchmark dataset from the de novo PacBio assemblies of two human cell lines that are homozygous across the whole genome. This benchmark provides a more accurate and less Biased Estimate of the error rate of small variant calls in a realistic context.
Ari Laor - One of the best experts on this subject based on the ideXlab platform.
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what controls the c iv line profile in active galactic nuclei
Monthly Notices of the Royal Astronomical Society, 2005Co-Authors: Alexei Baskin, Ari LaorAbstract:The high-ionization lines in active galactic nuclei (AGN), such as C IV, tend to be blueshifted with respect to the lower-ionization lines, such as Hβ, and often show a strong blue excess asymmetry not seen in the low-ionization lines. There is accumulating evidence that the Hβ profile is dominated by gravity, and thus provides a useful Estimate of the black hole mass in AGN. The shift and asymmetry commonly seen in C IV suggest that non-gravitational effects, such as obscuration and radiation pressure, may affect the line profile. We explore the relation between the Hβ and C IV profiles using the ultraviolet (UV) spectra available for 81 of the 87 z ≤ 0.5 PG quasars in the Boroson & Green sample. We find the following. (1) Narrow C IV lines (full width at half-maximum, FWHM 4000 km s -1 . This argues against the view that C IV generally originates closer to the centre, compared with Hβ. (3) C IV appears to provide a significantly less accurate, and possibly Biased Estimate of the black hole mass in AGN, compared with Hβ. (4) All objects where C IV is strongly blueshifted and asymmetric have a high L/L○ Edd , but the reverse is not true. This suggests that a high L/L Edd is a necessary but not sufficient condition for generating a blueshifted asymmetric C iv emission. (5) We also find indications for dust reddening and scattering in 'normal' AGN. In particular, PG quasars with a redder optical-UV continuum slope show weaker C iv emission, stronger C IV absorption and a higher optical continuum polarization.
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what controls the c iv line profile in active galactic nuclei
arXiv: Astrophysics, 2004Co-Authors: Alexei Baskin, Ari LaorAbstract:The high ionization lines in active galactic nuclei (AGN), such as C IV, tend to be blueshifted with respect to the lower ionization lines, such as H beta, and often show a strong blue excess asymmetry not seen in the low ionization lines. There is accumulating evidence that the H beta profile is dominated by gravity, and thus provides a useful Estimate of the black hole mass in AGN. The shift and asymmetry commonly seen in C IV suggest that non gravitational effects, such as obscuration and radiation pressure, may affect the line profile. We explore the relation between the H beta and C IV profiles using UV spectra available for 81 of the 87 z 4000 km/s. This argues against the view that C IV generally originates closer to the center, compared to H beta. (3) C IV appears to provide a significantly less accurate, and possibly Biased Estimate of the black hole mass in AGN, compared with H beta. (4) All objects where C IV is strongly blueshifted and asymmetric have a high L/L_Edd, but the reverse is not true. This suggests that a high L/L_Edd is a necessary but not sufficient condition for generating a blueshifted asymmetric C IV emission. (5) We also find indications for dust reddening and scattering in `normal' AGN. In particular, PG quasars with a redder optical-UV continuum slope show weaker C IV emission, stronger C IV absorption, and a higher optical continuum polarization.
Ruth Gilbert - One of the best experts on this subject based on the ideXlab platform.
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linkage evaluation and analysis of national electronic healthcare data application to providing enhanced blood stream infection surveillance in paediatric intensive care
PLOS ONE, 2013Co-Authors: Katie Harron, Harvey Goldstein, Angie Wade, Berit Mullerpebody, Roger Parslow, Ruth GilbertAbstract:Linkage of risk-factor data for blood-stream infection (BSI) in paediatric intensive care (PICU) with bacteraemia surveillance data to monitor risk-adjusted infection rates in PICU is complicated by a lack of unique identifiers and under-ascertainment in the national surveillance system. We linked, evaluated and performed preliminary analyses on these data to provide a practical guide on the steps required to handle linkage of such complex data sources. Data on PICU admissions in England and Wales for 2003-2010 were extracted from the Paediatric Intensive Care Audit Network. Records of all positive isolates from blood cultures taken for children <16 years and captured by the national voluntary laboratory surveillance system for 2003-2010 were extracted from the Public Health England database, LabBase2. "Gold-standard" datasets with unique identifiers were obtained directly from three laboratories, containing microbiology reports that were eligible for submission to LabBase2 (defined as "clinically significant" by laboratory microbiologists). Reports in the gold-standard datasets were compared to those in LabBase2 to Estimate ascertainment in LabBase2. Linkage evaluated by comparing results from two classification methods (highest-weight classification of match weights and prior-informed imputation using match probabilities) with linked records in the gold-standard data. BSI rate was Estimated as the proportion of admissions associated with at least one BSI. Reporting gaps were identified in 548/2596 lab-months of LabBase2. Ascertainment of clinically significant BSI in the remaining months was approximately 80-95%. Prior-informed imputation provided the least Biased Estimate of BSI rate (5.8% of admissions). Adjusting for ascertainment, the Estimated BSI rate was 6.1-7.3%. Linkage of PICU admission data with national BSI surveillance provides the opportunity for enhanced surveillance but analyses based on these data need to take account of biases due to ascertainment and linkage error. This study provides a generalisable guide for linkage, evaluation and analysis of complex electronic healthcare data.
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linkage evaluation and analysis of national electronic healthcare data application to providing enhanced blood stream infection surveillance in paediatric intensive care
PLOS ONE, 2013Co-Authors: Katie Harron, Harvey Goldstein, Angie Wade, Berit Mullerpebody, Roger Parslow, Ruth GilbertAbstract:Background Linkage of risk-factor data for blood-stream infection (BSI) in paediatric intensive care (PICU) with bacteraemia surveillance data to monitor risk-adjusted infection rates in PICU is complicated by a lack of unique identifiers and under-ascertainment in the national surveillance system. We linked, evaluated and performed preliminary analyses on these data to provide a practical guide on the steps required to handle linkage of such complex data sources. Methods Data on PICU admissions in England and Wales for 2003-2010 were extracted from the Paediatric Intensive Care Audit Network. Records of all positive isolates from blood cultures taken for children <16 years and captured by the national voluntary laboratory surveillance system for 2003-2010 were extracted from the Public Health England database, LabBase2. “Gold-standard” datasets with unique identifiers were obtained directly from three laboratories, containing microbiology reports that were eligible for submission to LabBase2 (defined as “clinically significant” by laboratory microbiologists). Reports in the gold-standard datasets were compared to those in LabBase2 to Estimate ascertainment in LabBase2. Linkage evaluated by comparing results from two classification methods (highest-weight classification of match weights and prior-informed imputation using match probabilities) with linked records in the gold-standard data. BSI rate was Estimated as the proportion of admissions associated with at least one BSI. Results Reporting gaps were identified in 548/2596 lab-months of LabBase2. Ascertainment of clinically significant BSI in the remaining months was approximately 80-95%. Prior-informed imputation provided the least Biased Estimate of BSI rate (5.8% of admissions). Adjusting for ascertainment, the Estimated BSI rate was 6.1-7.3%. Conclusion Linkage of PICU admission data with national BSI surveillance provides the opportunity for enhanced surveillance but analyses based on these data need to take account of biases due to ascertainment and linkage error. This study provides a generalisable guide for linkage, evaluation and analysis of complex electronic healthcare data.
Harvey Goldstein - One of the best experts on this subject based on the ideXlab platform.
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linkage evaluation and analysis of national electronic healthcare data application to providing enhanced blood stream infection surveillance in paediatric intensive care
PLOS ONE, 2013Co-Authors: Katie Harron, Harvey Goldstein, Angie Wade, Berit Mullerpebody, Roger Parslow, Ruth GilbertAbstract:Linkage of risk-factor data for blood-stream infection (BSI) in paediatric intensive care (PICU) with bacteraemia surveillance data to monitor risk-adjusted infection rates in PICU is complicated by a lack of unique identifiers and under-ascertainment in the national surveillance system. We linked, evaluated and performed preliminary analyses on these data to provide a practical guide on the steps required to handle linkage of such complex data sources. Data on PICU admissions in England and Wales for 2003-2010 were extracted from the Paediatric Intensive Care Audit Network. Records of all positive isolates from blood cultures taken for children <16 years and captured by the national voluntary laboratory surveillance system for 2003-2010 were extracted from the Public Health England database, LabBase2. "Gold-standard" datasets with unique identifiers were obtained directly from three laboratories, containing microbiology reports that were eligible for submission to LabBase2 (defined as "clinically significant" by laboratory microbiologists). Reports in the gold-standard datasets were compared to those in LabBase2 to Estimate ascertainment in LabBase2. Linkage evaluated by comparing results from two classification methods (highest-weight classification of match weights and prior-informed imputation using match probabilities) with linked records in the gold-standard data. BSI rate was Estimated as the proportion of admissions associated with at least one BSI. Reporting gaps were identified in 548/2596 lab-months of LabBase2. Ascertainment of clinically significant BSI in the remaining months was approximately 80-95%. Prior-informed imputation provided the least Biased Estimate of BSI rate (5.8% of admissions). Adjusting for ascertainment, the Estimated BSI rate was 6.1-7.3%. Linkage of PICU admission data with national BSI surveillance provides the opportunity for enhanced surveillance but analyses based on these data need to take account of biases due to ascertainment and linkage error. This study provides a generalisable guide for linkage, evaluation and analysis of complex electronic healthcare data.
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linkage evaluation and analysis of national electronic healthcare data application to providing enhanced blood stream infection surveillance in paediatric intensive care
PLOS ONE, 2013Co-Authors: Katie Harron, Harvey Goldstein, Angie Wade, Berit Mullerpebody, Roger Parslow, Ruth GilbertAbstract:Background Linkage of risk-factor data for blood-stream infection (BSI) in paediatric intensive care (PICU) with bacteraemia surveillance data to monitor risk-adjusted infection rates in PICU is complicated by a lack of unique identifiers and under-ascertainment in the national surveillance system. We linked, evaluated and performed preliminary analyses on these data to provide a practical guide on the steps required to handle linkage of such complex data sources. Methods Data on PICU admissions in England and Wales for 2003-2010 were extracted from the Paediatric Intensive Care Audit Network. Records of all positive isolates from blood cultures taken for children <16 years and captured by the national voluntary laboratory surveillance system for 2003-2010 were extracted from the Public Health England database, LabBase2. “Gold-standard” datasets with unique identifiers were obtained directly from three laboratories, containing microbiology reports that were eligible for submission to LabBase2 (defined as “clinically significant” by laboratory microbiologists). Reports in the gold-standard datasets were compared to those in LabBase2 to Estimate ascertainment in LabBase2. Linkage evaluated by comparing results from two classification methods (highest-weight classification of match weights and prior-informed imputation using match probabilities) with linked records in the gold-standard data. BSI rate was Estimated as the proportion of admissions associated with at least one BSI. Results Reporting gaps were identified in 548/2596 lab-months of LabBase2. Ascertainment of clinically significant BSI in the remaining months was approximately 80-95%. Prior-informed imputation provided the least Biased Estimate of BSI rate (5.8% of admissions). Adjusting for ascertainment, the Estimated BSI rate was 6.1-7.3%. Conclusion Linkage of PICU admission data with national BSI surveillance provides the opportunity for enhanced surveillance but analyses based on these data need to take account of biases due to ascertainment and linkage error. This study provides a generalisable guide for linkage, evaluation and analysis of complex electronic healthcare data.
Alexei Baskin - One of the best experts on this subject based on the ideXlab platform.
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what controls the c iv line profile in active galactic nuclei
Monthly Notices of the Royal Astronomical Society, 2005Co-Authors: Alexei Baskin, Ari LaorAbstract:The high-ionization lines in active galactic nuclei (AGN), such as C IV, tend to be blueshifted with respect to the lower-ionization lines, such as Hβ, and often show a strong blue excess asymmetry not seen in the low-ionization lines. There is accumulating evidence that the Hβ profile is dominated by gravity, and thus provides a useful Estimate of the black hole mass in AGN. The shift and asymmetry commonly seen in C IV suggest that non-gravitational effects, such as obscuration and radiation pressure, may affect the line profile. We explore the relation between the Hβ and C IV profiles using the ultraviolet (UV) spectra available for 81 of the 87 z ≤ 0.5 PG quasars in the Boroson & Green sample. We find the following. (1) Narrow C IV lines (full width at half-maximum, FWHM 4000 km s -1 . This argues against the view that C IV generally originates closer to the centre, compared with Hβ. (3) C IV appears to provide a significantly less accurate, and possibly Biased Estimate of the black hole mass in AGN, compared with Hβ. (4) All objects where C IV is strongly blueshifted and asymmetric have a high L/L○ Edd , but the reverse is not true. This suggests that a high L/L Edd is a necessary but not sufficient condition for generating a blueshifted asymmetric C iv emission. (5) We also find indications for dust reddening and scattering in 'normal' AGN. In particular, PG quasars with a redder optical-UV continuum slope show weaker C iv emission, stronger C IV absorption and a higher optical continuum polarization.
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what controls the c iv line profile in active galactic nuclei
arXiv: Astrophysics, 2004Co-Authors: Alexei Baskin, Ari LaorAbstract:The high ionization lines in active galactic nuclei (AGN), such as C IV, tend to be blueshifted with respect to the lower ionization lines, such as H beta, and often show a strong blue excess asymmetry not seen in the low ionization lines. There is accumulating evidence that the H beta profile is dominated by gravity, and thus provides a useful Estimate of the black hole mass in AGN. The shift and asymmetry commonly seen in C IV suggest that non gravitational effects, such as obscuration and radiation pressure, may affect the line profile. We explore the relation between the H beta and C IV profiles using UV spectra available for 81 of the 87 z 4000 km/s. This argues against the view that C IV generally originates closer to the center, compared to H beta. (3) C IV appears to provide a significantly less accurate, and possibly Biased Estimate of the black hole mass in AGN, compared with H beta. (4) All objects where C IV is strongly blueshifted and asymmetric have a high L/L_Edd, but the reverse is not true. This suggests that a high L/L_Edd is a necessary but not sufficient condition for generating a blueshifted asymmetric C IV emission. (5) We also find indications for dust reddening and scattering in `normal' AGN. In particular, PG quasars with a redder optical-UV continuum slope show weaker C IV emission, stronger C IV absorption, and a higher optical continuum polarization.