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Article: Xenomake: a pipeline for processing and sorting xenograft reads from spatial transcriptomic experiments.

Strope, Benjamin S / Pendleton, Katherine E / Bowie, William Z / Echeverria, Gloria V / Zhu, Qian

bioRxiv : the preprint server for biology

2023

Abstract: Xenograft models are attractive models that mimic human tumor biology and permit one to perturb the tumor microenvironment and study its drug response. Spatially resolved transcriptomics (SRT) provide a powerful way to study the organization of xenograft ...

Abstract	Xenograft models are attractive models that mimic human tumor biology and permit one to perturb the tumor microenvironment and study its drug response. Spatially resolved transcriptomics (SRT) provide a powerful way to study the organization of xenograft models, but currently there is a lack of specialized pipeline for processing xenograft reads originated from SRT experiments. Xenomake is a standalone pipeline for the automated handling of spatial xenograft reads. Xenomake handles read processing, alignment, xenograft read sorting, quantification, and connects well with downstream spatial analysis packages. We additionally show that Xenomake can correctly assign organism specific reads, reduce sparsity of data by increasing gene counts, while maintaining biological relevance for studies.
Language	English
Publishing date	2023-09-05
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.09.04.556109
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Book ; Conference proceedings: Chlamydial infections

Bowie, William R.

proceedings of the Seventh International Symposium on Human Chlamydial Infections, Harrison Hot Springs, British Columbia, Canada, 24 - 29 June 1990

1990

Event/congress	International Symposium on Human Chlamydial Infections (7, 1990, HarrisonHotSpringsBritishColumbia)
Author's details	ed. by William R. Bowie
Keywords	Chlamydia Infections / congresses ; Chlamydienkrankheit
Subject	Chlamydia ; Chlamydieninfektionskrankheit ; Chlamydieninfektion ; Chlamydiose
Size	XXI, 602 S. : Ill., graph. Darst.
Publisher	Cambridge Univ. Pr
Publishing place	Cambridge u.a.
Publishing country	Great Britain
Document type	Book ; Conference proceedings
HBZ-ID	HT003648666
ISBN	0-521-39082-6 ; 978-0-521-39082-8
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Article: Opinion du comité N

Smith, Graeme N / Moore, Kieran M / Hatchette, Todd F / Nicholson, Jennifer / Bowie, William / Langley, Joanne M

Journal of obstetrics and gynaecology Canada : JOGC = Journal d'obstetrique et gynecologie du Canada : JOGC

2020 Volume 42, Issue 5, Page(s) 654–664

Language	French
Publishing date	2020-05-15
Publishing country	Netherlands
Document type	Practice Guideline
ZDB-ID	2171082-X
ISSN	1701-2163
ISSN	1701-2163
DOI	10.1016/j.jogc.2020.02.110
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Zs.A 6445: Show issues

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Article: Committee Opinion No. 399: Management of Tick Bites and Lyme Disease During Pregnancy.

Smith, Graeme N / Moore, Kieran M / Hatchette, Todd F / Nicholson, Jennifer / Bowie, William / Langley, Joanne M

Journal of obstetrics and gynaecology Canada : JOGC = Journal d'obstetrique et gynecologie du Canada : JOGC

2020 Volume 42, Issue 5, Page(s) 644–653

Abstract: Objective: Lyme disease is an emerging infection in Canada caused by the bacterium belonging to the Borrelia burgdorferi sensu lato species complex, which is transmitted via the bite of an infected blacklegged tick. Populations of blacklegged ticks ... ...

Abstract	Objective: Lyme disease is an emerging infection in Canada caused by the bacterium belonging to the Borrelia burgdorferi sensu lato species complex, which is transmitted via the bite of an infected blacklegged tick. Populations of blacklegged ticks continue to expand and are now established in different regions in Canada. It usually takes more than 24 hours of tick attachment to transfer B. burgdorferi to a human. The diagnosis of early localized Lyme disease is made by clinical assessment, as laboratory tests are not reliable at this stage. Most patients with early localized Lyme disease will present with a skin lesion (i.e., erythema migrans) expanding from the tick bite site and/or non-specific "influenza-like" symptoms (e.g., arthralgia, myalgia, and fever). Signs and symptoms may occur from between 3 and 30 days following the tick bite. The care of pregnant patients with a tick bite or suspected Lyme disease should be managed similarly to non-pregnant adults, including the consideration of antibiotics for prophylaxis and treatment. The primary objective of this committee opinion is to inform practitioners about Lyme disease and provide an approach to managing the care of pregnant women who may have been infected via a blacklegged tick bite. Intended users: Health care providers who care for pregnant women or women of reproductive age. Target population: Women of reproductive age. Evidence: In November 2018, Medline, EMBASE, PubMed, and CENTRAL databases were searched for 2 main categories: (1) Lyme disease and (2) other tick-borne diseases. Because the main focus was Lyme disease, and considering the limited number of the articles, no further filters were applied for publication time or type of study. For other tick-borne diseases, the results were restricted to a publication date within the last 10 years (2008-2018). The search terms were developed using MeSH terms and keywords including Lyme Disease, Pregnancy, Pregnant Women, Pregnancy Complications, Ehrlichiosis, Anaplasmosis, Rocky Mountain Spotted Fever, Babesiosis, Tularemia, Powassan Virus, Encephalitis Viruses, Tick-Borne, Tick-Borne Diseases, Colorado Tick Fever, Q Fever, Relapsing Fever, and Southern Tick-Associated Rash Illness. All articles on Lyme disease and other tick-borne diseases with a target population of pregnant women were included; other groups and populations were excluded. Validation methods: The content and recommendations of this committee opinion were drafted and agreed upon by the authors. The Board of Directors of the Society of Obstetricians and Gynaecologists of Canada approved the final draft for publication.
MeSH term(s)	Adult ; Animals ; Anti-Bacterial Agents/therapeutic use ; Canada ; Female ; Humans ; Lyme Disease/diagnosis ; Lyme Disease/drug therapy ; Lyme Disease/prevention & control ; Pregnancy ; Pregnancy Complications/therapy ; Tick Bites/prevention & control ; Tick Bites/therapy ; Tick-Borne Diseases/diagnosis ; Tick-Borne Diseases/prevention & control ; Ticks
Chemical Substances	Anti-Bacterial Agents
Language	English
Publishing date	2020-05-15
Publishing country	Netherlands
Document type	Journal Article ; Practice Guideline
ZDB-ID	2171082-X
ISSN	1701-2163
ISSN	1701-2163
DOI	10.1016/j.jogc.2020.01.001
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Article: Guidelines for the management of lyme disease : the controversy and the quandary.

Bowie, William R

Drugs

2007 Volume 67, Issue 18, Page(s) 2661–2666

MeSH term(s)	Anti-Infective Agents/adverse effects ; Anti-Infective Agents/therapeutic use ; Clinical Trials as Topic ; Evidence-Based Medicine ; Humans ; Lyme Disease/diagnosis ; Lyme Disease/drug therapy ; Lyme Disease/epidemiology ; North America/epidemiology ; Physician-Patient Relations ; Practice Guidelines as Topic
Chemical Substances	Anti-Infective Agents
Language	English
Publishing date	2007-12-07
Publishing country	New Zealand
Document type	Journal Article
ZDB-ID	120316-2
ISSN	1179-1950 ; 0012-6667
ISSN (online)	1179-1950
ISSN	0012-6667
DOI	10.2165/00003495-200767180-00002
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Article ; Online: Lyme disease: How reliable are serologic results?

Gregson, Dan / Evans, G / Patrick, David / Bowie, William

CMAJ : Canadian Medical Association journal = journal de l'Association medicale canadienne

2015 Volume 187, Issue 16, Page(s) 1193–1194

MeSH term(s)	Clinical Laboratory Services/standards ; Humans ; Lyme Disease/diagnosis ; Male ; Private Sector/standards
Language	English
Publishing date	2015-08-31
Publishing country	Canada
Document type	Journal Article ; Comment
ZDB-ID	215506-0
ISSN	1488-2329 ; 0008-4409 ; 0820-3946
ISSN (online)	1488-2329
ISSN	0008-4409 ; 0820-3946
DOI	10.1503/cmaj.150874
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Article ; Online: Influenza surveillance case definitions miss a substantial proportion of older adults hospitalized with laboratory-confirmed influenza: A report from the Canadian Immunization Research Network (CIRN) Serious Outcomes Surveillance (SOS) Network.

Andrew, Melissa K / McElhaney, Janet E / McGeer, Allison A / Hatchette, Todd F / Leblanc, Jason / Webster, Duncan / Bowie, William / Poirier, Andre / Nichols, Michaela K / McNeil, Shelly A

Infection control and hospital epidemiology

2020 Volume 41, Issue 5, Page(s) 499–504

Abstract: Objective: Older adults often have atypical presentation of illness and are particularly vulnerable to influenza and its sequelae, making the validity of influenza case definitions particularly relevant. We sought to assess the performance of influenza- ... ...

Abstract	Objective: Older adults often have atypical presentation of illness and are particularly vulnerable to influenza and its sequelae, making the validity of influenza case definitions particularly relevant. We sought to assess the performance of influenza-like illness (ILI) and severe acute respiratory illness (SARI) criteria in hospitalized older adults. Design: Prospective cohort study. Setting: The Serious Outcomes Surveillance Network of the Canadian Immunization Research Network undertakes active surveillance for influenza among hospitalized adults. Methods: Data were pooled from 3 influenza seasons: 2011/12, 2012/13, and 2013/14. The ILI and SARI criteria were defined clinically, and influenza was laboratory confirmed. Frailty was measured using a validated frailty index. Results: Of 11,379 adult inpatients (7,254 aged ≥65 years), 4,942 (2,948 aged ≥65 years) had laboratory-confirmed influenza. Their median age was 72 years (interquartile range [IQR], 58-82) and 52.6% were women. The sensitivity of ILI criteria was 51.1% (95% confidence interval [CI], 49.6-52.6) for younger adults versus 44.6% (95% CI, 43.6-45.8) for older adults. SARI criteria were met by 64.1% (95% CI, 62.7-65.6) of younger adults versus 57.1% (95% CI, 55.9-58.2) of older adults with laboratory-confirmed influenza. Patients with influenza who were prefrail or frail were less likely to meet ILI and SARI case definitions. Conclusions: A substantial proportion of older adults, particularly those who are frail, are missed by standard ILI and SARI case definitions. Surveillance using these case definitions is biased toward identifying younger cases, and does not capture the true burden of influenza. Because of the substantial fraction of cases missed, surveillance definitions should not be used to guide diagnosis and clinical management of influenza.
MeSH term(s)	Aged ; Aged, 80 and over ; Bias ; Canada/epidemiology ; Female ; Frail Elderly ; Hospitalization ; Humans ; Immunization ; Influenza, Human/diagnosis ; Influenza, Human/epidemiology ; Laboratories, Hospital ; Male ; Prospective Studies ; Research ; Sensitivity and Specificity ; Sentinel Surveillance
Language	English
Publishing date	2020-03-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	639378-0
ISSN	1559-6834 ; 0195-9417 ; 0899-823X
ISSN (online)	1559-6834
ISSN	0195-9417 ; 0899-823X
DOI	10.1017/ice.2020.22
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Article ; Online: Persistent Functional Decline Following Hospitalization with Influenza or Acute Respiratory Illness.

Andrew, Melissa K / MacDonald, Sarah / Godin, Judith / McElhaney, Janet E / LeBlanc, Jason / Hatchette, Todd F / Bowie, William / Katz, Kevin / McGeer, Allison / Semret, Makeda / McNeil, Shelly A

Journal of the American Geriatrics Society

2020 Volume 69, Issue 3, Page(s) 696–703

Abstract: Background/objectives: Influenza is associated with significant morbidity and mortality, particularly for older adults. Persistent functional decline following hospitalization has important impacts on older adults' wellbeing and independence, but has ... ...

Abstract	Background/objectives: Influenza is associated with significant morbidity and mortality, particularly for older adults. Persistent functional decline following hospitalization has important impacts on older adults' wellbeing and independence, but has been under-studied in relation to influenza. We aimed to investigate persistent functional change in older adults admitted to hospital with influenza and other acute respiratory illness (ARI). Design: Protective observational cohort study. Setting: Canadian Immunization Research Network Serious Outcomes Surveillance Network 2011 to 2012 influenza season. Participants: A total of 925 patients aged 65 and older admitted to hospital with influenza and other ARI. Measurements: Influenza was laboratory-confirmed. Frailty was measured using a Frailty index (FI). Functional status was measured using the Barthel index (BI); moderate persistent functional decline was defined as a clinically meaningful loss of ≥10 to <20 points on the 100-point BI. Catastrophic disability (CD) was defined as a loss of ≥20 points, equivalent to full loss of independence in two basic activities of daily living. Results: Five hundred and nineteen (56.1%) were women; mean age was 79.4 (standard deviation=8.4) years. Three hundred and forty-six (37.4%) had laboratory-confirmed influenza. Influenza cases had lower baseline function (BI = 77.0 vs 86.9, P < .001) and higher frailty (FI = 0.23 vs 0.20, P < .001) than those with other ARI. A total of 8.4% died, 8.2% experienced persistent moderate functional decline, and 9.9% experienced CD. Higher baseline frailty was associated with increased odds of experiencing functional decline, CD, and death. The experience of functional decline and CD, and its association with frailty, was the same for influenza and other ARI. Conclusion: Functional loss in hospital is common among older adults; for some this functional loss is persistent and catastrophic. This highlights the importance of prevention and optimal management of acute declines in health, including influenza, to avoid hospitalization. In the case of influenza, for which vaccines exist, this raises the potential of vaccine preventable disability.
MeSH term(s)	Aged ; Aged, 80 and over ; Canada ; Disability Evaluation ; Female ; Frailty/epidemiology ; Hospitalization/statistics & numerical data ; Humans ; Influenza, Human/epidemiology ; Male ; Outcome Assessment, Health Care/statistics & numerical data ; Prospective Studies ; Respiratory Distress Syndrome/epidemiology
Language	English
Publishing date	2020-12-08
Publishing country	United States
Document type	Journal Article ; Multicenter Study ; Observational Study ; Research Support, Non-U.S. Gov't
ZDB-ID	80363-7
ISSN	1532-5415 ; 0002-8614
ISSN (online)	1532-5415
ISSN	0002-8614
DOI	10.1111/jgs.16950
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Article: Leveraging Influenza Virus Surveillance From 2012 to 2015 to Characterize the Burden of Respiratory Syncytial Virus Disease in Canadian Adults ≥50 Years of Age Hospitalized With Acute Respiratory Illness.

ElSherif, May / Andrew, Melissa K / Ye, Lingyun / Ambrose, Ardith / Boivin, Guy / Bowie, William / David, Marie-Pierre / Gruselle, Olivier / Halperin, Scott A / Hatchette, Todd F / Johnstone, Jennie / Katz, Kevin / Langley, Joanne M / Loeb, Mark / MacKinnon-Cameron, Donna / McCarthy, Anne / McElhaney, Janet E / McGeer, Allison / Poirier, Andre /

Pirçon, Jean-Yves / Powis, Jeff / Richardson, David / Semret, Makeda / Smith, Stephanie / Smyth, Daniel / Trottier, Sylvie / Valiquette, Louis / Webster, Duncan / McNeil, Shelly A / LeBlanc, Jason J

Open forum infectious diseases

2023 Volume 10, Issue 7, Page(s) ofad315

Abstract: Background: Respiratory syncytial virus (RSV) disease in older adults is undercharacterized. To help inform future immunization policies, this study aimed to describe the disease burden in Canadian adults aged ≥50 years hospitalized with RSV.: Methods! ...

Abstract	Background: Respiratory syncytial virus (RSV) disease in older adults is undercharacterized. To help inform future immunization policies, this study aimed to describe the disease burden in Canadian adults aged ≥50 years hospitalized with RSV. Methods: Using administrative data and nasopharyngeal swabs collected from active surveillance among adults aged ≥50 years hospitalized with an acute respiratory illness (ARI) during the 2012-2013, 2013-2014, and 2014-2015 influenza seasons, RSV was identified using a respiratory virus multiplex polymerase chain reaction test to describe the associated disease burden, incidence, and healthcare costs. Results: Of 7797 patients tested, 371 (4.8%) were RSV positive (2.2% RSV-A and 2.6% RSV-B). RSV prevalence varied by season from 4.2% to 6.2%. Respiratory virus coinfection was observed in 11.6% (43/371) of RSV cases, with influenza A being the most common. RSV hospitalization rates varied between seasons and increased with age, from 8-12 per 100 000 population in adults aged 50-59 years to 174-487 per 100 000 in adults aged ≥80 years. The median age of RSV cases was 74.9 years, 63.7% were female, and 98.1% of cases had ≥1 comorbidity. Among RSV cases, the mean length of hospital stay was 10.6 days, 13.7% were admitted to the intensive care unit, 6.4% required mechanical ventilation, and 6.1% died. The mean cost per RSV case was $13 602 (Canadian dollars) but varied by age and Canadian province. Conclusions: This study adds to the growing literature on adult RSV burden by showing considerable morbidity, mortality, and healthcare costs in hospitalized adults aged ≥50 years with ARIs such as influenza.
Language	English
Publishing date	2023-06-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	2757767-3
ISSN	2328-8957
ISSN	2328-8957
DOI	10.1093/ofid/ofad315
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Article ; Online: Vaccine Effectiveness of non-adjuvanted and adjuvanted trivalent inactivated influenza vaccines in the prevention of influenza-related hospitalization in older adults: A pooled analysis from the Serious Outcomes Surveillance (SOS) Network of the Canadian Immunization Research Network (CIRN).

Pott, Henrique / Andrew, Melissa K / Shaffelburg, Zachary / Nichols, Michaela K / Ye, Lingyun / ElSherif, May / Hatchette, Todd F / LeBlanc, Jason / Ambrose, Ardith / Boivin, Guy / Bowie, William / Johnstone, Jennie / Katz, Kevin / Lagacé-Wiens, Phillipe / Loeb, Mark / McCarthy, Anne / McGeer, Allison / Poirier, Andre / Powis, Jeff /

Richardson, David / Semret, Makeda / Smith, Stephanie / Smyth, Daniel / Stiver, Grant / Trottier, Sylvie / Valiquette, Louis / Webster, Duncan / McNeil, Shelly A

Vaccine

2023 Volume 41, Issue 42, Page(s) 6359–6365

Abstract: Background: Influenza vaccines prevent influenza-related morbidity and mortality; however, suboptimal vaccine effectiveness (VE) of non-adjuvanted trivalent inactivated influenza vaccine (naTIV) or quadrivalent formulations in older adults prompted the ... ...

Abstract	Background: Influenza vaccines prevent influenza-related morbidity and mortality; however, suboptimal vaccine effectiveness (VE) of non-adjuvanted trivalent inactivated influenza vaccine (naTIV) or quadrivalent formulations in older adults prompted the use of enhanced products such as adjuvanted TIV (aTIV). Here, the VE of aTIV is compared to naTIV for preventing influenza-associated hospitalization among older adults. Methods: A test-negative design study was used with pooled data from the 2012 to 2015 influenza seasons. An inverse probability of treatment (IPT)-weighted logistic regression estimated the Odds Ratio (OR) for laboratory-confirmed influenza-associated hospitalization. VE was calculated as (1-OR)100% with accompanying 95% confidence intervals (CI). Results:* Of 7,101 adults aged ≥ 65, 3,364 received naTIV and 526 received aTIV. The overall VE against influenza hospitalization was 45.9% (95% CI: 40.2%-51.1%) for naTIV and 53.5% (42.8%-62.3%) for aTIV. No statistically significant differences in VE were found between aTIV and naTIV by age group or influenza season, though a trend favoring aTIV over naTIV was noted. Frailty may have impacted VE in aTIV recipients compared to those receiving naTIV, according to an exploratory analysis; VE adjusted by frailty was 59.1% (49.6%-66.8%) for aTIV and 44.8% (39.1%-50.0%) for naTIV. The overall relative VE of aTIV to naTIV against laboratory-confirmed influenza hospital admission was 25% (OR 0.75; 0.61-0.92), demonstrating statistically significant benefit favoring aTIV. Conclusions: Adjusting for frailty, aTIV showed statistically significantly better protection than naTIV against influenza-associated hospitalizations in older adults. In future studies, it is important to consider frailty as a significant confounder of VE.
MeSH term(s)	Aged ; Humans ; Adjuvants, Immunologic ; Canada/epidemiology ; Frailty ; Hospitalization ; Immunization ; Influenza Vaccines/therapeutic use ; Influenza, Human/prevention & control ; Influenza, Human/epidemiology ; Seasons ; Vaccine Efficacy ; Vaccines, Inactivated ; Vaccines, Combined/therapeutic use
Chemical Substances	Adjuvants, Immunologic ; Influenza Vaccines ; Vaccines, Inactivated ; Vaccines, Combined
Language	English
Publishing date	2023-09-10
Publishing country	Netherlands
Document type	Journal Article ; Meta-Analysis ; Research Support, Non-U.S. Gov't
ZDB-ID	605674-x
ISSN	1873-2518 ; 0264-410X
ISSN (online)	1873-2518
ISSN	0264-410X
DOI	10.1016/j.vaccine.2023.08.070
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