Under pressure: comparing in situ and boat tagging methods using time-to-event analyses

Abstract Background With the increase in telemetry studies over the past decade, improving understanding of how different tagging methods influence the probability of presence in a receiver array is important in maximizing the resulting data. Disappearance from the array may be due to mortality from surgery complications, tag loss, predation, or emigration. Internally tagging fish on a boat can cause barotrauma injuries, increased stress from prolonged handling times, or predation after fish have been released back into the water. Conducting in situ internal acoustic tagging at depth of capture removes barotrauma stresses and simplifies the release method, which may improve fish survival and decrease risk of disappearance from the array. In this study, we used 8 years of acoustic tagging data to determine if the tagging method (in situ versus on the boat) influenced the likelihood of a fish being detected 4 and 6 days after the tagging event. Results At 6 days after tagging, Kaplan–Meier survival curves revealed that the probability of presence for fish tagged on the boat was 66% compared to 90% for fish tagged in situ. Tagging method was the only variable to significantly affect probability of presence based on Cox proportional hazards models, with fish tagged in situ ~ 75% less likely to disappear from the array compared to fish tagged on the boat at both 4 and 6 days after tagging. Examining tagging methods separately, handling time only marginally influenced probability of presence of boat-tagged fish and no variables had a significant effect on probability of presence of in situ tagged fish. Conclusions In this study, tagging method was the only variable to significantly affect the probability of presence for internally tagged fish. Other factors had little to no influence, but correlation of variables limited what factors could be included in the models. Implanting internal acoustic tags in situ is not a practical method for every species and for every environment, but given the increased probability of presence demonstrated here, we strongly suggest it be considered where applicable.

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Under Pressure: Comparing Fish Survivorship Between in Situ and Boat Tagging Methods Using Internal Acoustic Tags

10.21203/rs.3.rs-56006/v1 ◽

2020 ◽

Author(s):

Jessica A. Keller ◽

Danielle Morley ◽

Jennifer Herbig ◽

Paul Barbera ◽

Michael W. Feeley ◽

...

Keyword(s):

Survival Probability ◽

Proportional Hazards ◽

Handling Time ◽

Practical Method ◽

Cox Proportional Hazards ◽

Cox Proportional Hazards Models ◽

Acoustic Tags ◽

Tagging Methods ◽

Acoustic Tagging

Abstract Background: With the increase in telemetry studies over the past decade, improving understanding of how different tagging methods influence fish survivorship is critical. By examining the effects of tagging methods, we can maximize the information gained from telemetry studies. Mortality resulting from internally tagging fish on a boat may be due to barotrauma injuries, increased stress from prolonged handling times, or predation after fish have been released back into the water. Conducting in situ internal acoustic tagging at depth of capture completely removes barotrauma stresses and simplifies the release method, which may improve fish survival. In this study, we used 8 years of acoustic tagging data to determine if the tagging method (in situ versus on the boat) influenced fish survivorship and evaluated the role of other tagging variables.Results: At 6 days after tagging, Kaplan–Meier survival curves revealed that the survival probability of fish tagged on the boat was 66% while survival probability of fish tagged in situ was 90%. Tagging method was the only variable to significantly affect survival probability based on Cox proportional hazards models, with fish tagged in situ ~75% less likely to have an “event” (mortality, tag loss, or emigration) compared to fish tagged on the boat at both 4 and 6 days after tagging. Examining tagging methods separately, handling time only marginally influenced survival probability of boat-tagged fish and no variables had a significant effect on survival of in situ tagged fish. Conclusions: In this study, tagging method was the only variable to significantly affect survival of internally tagged fish. Implanting internal acoustic tags in situ is not a practical method for every species and for every environment, but given the increased fish survivorship demonstrated here, we strongly suggest it be considered as the preferred tagging methodology where applicable.

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Under pressure: Comparing in situ and boat tagging methods using time-to-event analyses

10.21203/rs.3.rs-56006/v2 ◽

2021 ◽

Author(s):

Jessica A. Keller ◽

Danielle Morley ◽

Jennifer Herbig ◽

Paul Barbera ◽

Michael W. Feeley ◽

...

Keyword(s):

Survival Probability ◽

Proportional Hazards ◽

Handling Time ◽

Practical Method ◽

Cox Proportional Hazards ◽

Tag Loss ◽

Cox Proportional Hazards Models ◽

Tagging Methods ◽

Acoustic Tagging

Abstract Background With the increase in telemetry studies over the past decade, improving understanding of how different tagging methods influence fish survivorship is critical. By examining the effects of tagging methods, we can maximize the information gained from telemetry studies. Mortality resulting from internally tagging fish on a boat may be due to barotrauma injuries, increased stress from prolonged handling times, or predation after fish have been released back into the water. Conducting in situ internal acoustic tagging at depth of capture completely removes barotrauma stresses and simplifies the release method, which may improve fish survival. In this study, we used 8 years of acoustic tagging data to determine if the tagging method ( in situ versus on the boat) influenced fish survivorship and evaluated the role of other tagging variables. Results At 6 days after tagging, Kaplan–Meier survival curves revealed that the survival probability of fish tagged on the boat was 66% while survival probability of fish tagged in situ was 90%. Tagging method was the only variable to significantly affect survival probability based on Cox proportional hazards models, with fish tagged in situ ~75% less likely to have an “event” (mortality, tag loss, or emigration) compared to fish tagged on the boat at both 4 and 6 days after tagging. Examining tagging methods separately, handling time only marginally influenced survival probability of boat-tagged fish and no variables had a significant effect on survival of in situ tagged fish. Conclusions In this study, tagging method was the only variable to significantly affect survival of internally tagged fish. Implanting internal acoustic tags in situ is not a practical method for every species and for every environment, but given the increased fish survivorship demonstrated here, we strongly suggest it be considered as the preferred tagging methodology where applicable.

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Use of postmenopausal hormone therapies and risk of histology- and hormone receptor-defined breast cancer: results from a 15-year prospective analysis of NIH-AARP cohort

Breast Cancer Research ◽

10.1186/s13058-020-01365-9 ◽

2020 ◽

Vol 22 (1) ◽

Author(s):

Shao-Ming Wang ◽

Ruth M. Pfeiffer ◽

Gretchen L. Gierach ◽

Roni T. Falk

Keyword(s):

Breast Cancer ◽

Hormone Receptor ◽

Proportional Hazards ◽

Cox Proportional Hazards ◽

Cox Proportional Hazards Models ◽

Estrogen Plus Progestin ◽

Continued Use ◽

Progestin Therapy

Abstract Background Menopausal hormone therapy (MHT) increases breast cancer (BC) risk, but cohort studies largely consider use only at enrollment. Evidence is limited on how changes in MHT use alter the magnitude of risk, and whether risk varies between invasive and in situ cancer, by histology or by hormone receptor status. Methods We investigated the roles of estrogen-alone therapy (ET) and estrogen plus progestin therapy (EPT) on BC risk overall, by histology and estrogen receptor (ER) and progesterone receptor (PR) status, and on incidence of in situ disease, in the NIH-AARP cohort. Participants included 118,760 postmenopausal women (50–71 years), of whom 63.5% (n = 75,398) provided MHT use information at baseline in 1996 and in a follow-up survey in 2004, subsequent to the dissemination in 2002 of the Women’s Health Initiative trial safety concerns regarding EPT. ET analyses included 50,476 women with hysterectomy (31,439 with follow-up data); EPT analyses included 68,284 women with intact uteri (43,959 with follow-up data). Adjusted hazard ratios (HRs) were estimated using Cox proportional hazards models using age as the time metric with follow-up through 2011. Results Eight thousand three hundred thirty-three incident BC cases were accrued, 2479 in women with follow-up data. BC risk was not elevated in current ET users at baseline (HR = 1.05, 95% confidence interval [CI] CI = 0.95–1.16) but was higher in women continuing use through 2004 (HR = 1.35, 95% CI = 1.04–1.75). Ever EPT use at baseline was associated with elevated BC risk overall (HR = 1.54 (1.44–1.64), with a doubling in risk for women with 10 or more years of use, for in situ disease, and across subtypes defined by histology and ER/PR status (all p < 0.004). Risk persisted in women who continued EPT through 2004 (HR = 1.80, 95% CI = 1.39–2.32). In contrast, no association was seen in women who discontinued EPT before 2004 (HR = 1.14, 95% CI = 0.99–1.30). Conclusions ET use was not associated with BC risk in this cohort, although excess risk was suggested in women who continued use through 2004. EPT use was linked to elevated in situ and invasive BC risk, and elevated risk across invasive BC histologic and hormone receptor-defined subtypes, with the highest risk for women who continued use through the 2004 follow-up survey.

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A semi-supervised approach for rapidly creating clinical biomarker phenotypes in the UK Biobank using different primary care EHR and clinical terminology systems

JAMIA Open ◽

10.1093/jamiaopen/ooaa047 ◽

2020 ◽

Author(s):

Spiros Denaxas ◽

Anoop D Shah ◽

Bilal A Mateen ◽

Valerie Kuan ◽

Jennifer K Quint ◽

...

Keyword(s):

Primary Care ◽

Proportional Hazards ◽

Biomarker Discovery ◽

Data Extraction ◽

Cox Proportional Hazards ◽

Research Quality ◽

Uk Biobank ◽

Expert Review ◽

Cox Proportional Hazards Models ◽

The Uk

Abstract Objectives The UK Biobank (UKB) is making primary care electronic health records (EHRs) for 500 000 participants available for COVID-19-related research. Data are extracted from four sources, recorded using five clinical terminologies and stored in different schemas. The aims of our research were to: (a) develop a semi-supervised approach for bootstrapping EHR phenotyping algorithms in UKB EHR, and (b) to evaluate our approach by implementing and evaluating phenotypes for 31 common biomarkers. Materials and Methods We describe an algorithmic approach to phenotyping biomarkers in primary care EHR involving (a) bootstrapping definitions using existing phenotypes, (b) excluding generic, rare, or semantically distant terms, (c) forward-mapping terminology terms, (d) expert review, and (e) data extraction. We evaluated the phenotypes by assessing the ability to reproduce known epidemiological associations with all-cause mortality using Cox proportional hazards models. Results We created and evaluated phenotyping algorithms for 31 biomarkers many of which are directly related to COVID-19 complications, for example diabetes, cardiovascular disease, respiratory disease. Our algorithm identified 1651 Read v2 and Clinical Terms Version 3 terms and automatically excluded 1228 terms. Clinical review excluded 103 terms and included 44 terms, resulting in 364 terms for data extraction (sensitivity 0.89, specificity 0.92). We extracted 38 190 682 events and identified 220 978 participants with at least one biomarker measured. Discussion and conclusion Bootstrapping phenotyping algorithms from similar EHR can potentially address pre-existing methodological concerns that undermine the outputs of biomarker discovery pipelines and provide research-quality phenotyping algorithms.

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Changes in Metabolic Syndrome Status and Breast Cancer Risk: A Nationwide Cohort Study

Cancers ◽

10.3390/cancers13051177 ◽

2021 ◽

Vol 13 (5) ◽

pp. 1177

Author(s):

In Young Choi ◽

Sohyun Chun ◽

Dong Wook Shin ◽

Kyungdo Han ◽

Keun Hye Jeon ◽

...

Keyword(s):

Breast Cancer ◽

Metabolic Syndrome ◽

Proportional Hazards ◽

Screening Program ◽

Cox Proportional Hazards ◽

Cox Proportional Hazards Models ◽

Hazard Ratios ◽

Increased Risk ◽

Health Screening Program ◽

Design And Methods

Objective: To our knowledge, no studies have yet looked at how the risk of developing breast cancer (BC) varies with changes in metabolic syndrome (MetS) status. This study aimed to investigate the association between changes in MetS and subsequent BC occurrence. Research Design and Methods: We enrolled 930,055 postmenopausal women aged 40–74 years who participated in a biennial National Health Screening Program in 2009–2010 and 2011–2012. Participants were categorized into four groups according to change in MetS status during the two-year interval screening: sustained non-MetS, transition to MetS, transition to non-MetS, and sustained MetS. We calculated multivariable-adjusted hazard ratios (aHRs) and 95% confidence intervals (CIs) for BC incidence using the Cox proportional hazards models. Results: At baseline, MetS was associated with a significantly increased risk of BC (aHR 1.11, 95% CI 1.06–1.17) and so were all of its components. The risk of BC increased as the number of the components increased (aHR 1.46, 95% CI 1.26–1.61 for women with all five components). Compared to the sustained non-MetS group, the aHR (95% CI) for BC was 1.11 (1.04–1.19) in the transition to MetS group, 1.05 (0.96–1.14) in the transition to non-MetS group, and 1.18 (1.12–1.25) in the sustained MetS group. Conclusions: Significantly increased BC risk was observed in the sustained MetS and transition to MetS groups. These findings are clinically meaningful in that efforts to recover from MetS may lead to reduced risk of BC.

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Pre-diagnosis neutrophil-to-lymphocyte ratio and mortality in individuals who develop lung cancer

Cancer Causes & Control ◽

10.1007/s10552-021-01469-3 ◽

2021 ◽

Author(s):

Laurie Grieshober ◽

Stefan Graw ◽

Matt J. Barnett ◽

Gary E. Goodman ◽

Chu Chen ◽

...

Keyword(s):

Lung Cancer ◽

Proportional Hazards ◽

Smoking Status ◽

Cox Proportional Hazards ◽

Neutrophil To Lymphocyte Ratio ◽

Blood Draw ◽

Lymphocyte Ratio ◽

Cox Proportional Hazards Models ◽

Inflammatory Profile ◽

Heavy Smokers

Abstract Purpose The neutrophil-to-lymphocyte ratio (NLR) is a marker of systemic inflammation that has been reported to be associated with survival after chronic disease diagnoses, including lung cancer. We hypothesized that the inflammatory profile reflected by pre-diagnosis NLR, rather than the well-studied pre-treatment NLR at diagnosis, may be associated with increased mortality after lung cancer is diagnosed in high-risk heavy smokers. Methods We examined associations between pre-diagnosis methylation-derived NLR (mdNLR) and lung cancer-specific and all-cause mortality in 279 non-small lung cancer (NSCLC) and 81 small cell lung cancer (SCLC) cases from the β-Carotene and Retinol Efficacy Trial (CARET). Cox proportional hazards models were adjusted for age, sex, smoking status, pack years, and time between blood draw and diagnosis, and stratified by stage of disease. Models were run separately by histotype. Results Among SCLC cases, those with pre-diagnosis mdNLR in the highest quartile had 2.5-fold increased mortality compared to those in the lowest quartile. For each unit increase in pre-diagnosis mdNLR, we observed 22–23% increased mortality (SCLC-specific hazard ratio [HR] = 1.23, 95% confidence interval [CI]: 1.02, 1.48; all-cause HR = 1.22, 95% CI 1.01, 1.46). SCLC associations were strongest for current smokers at blood draw (Interaction Ps = 0.03). Increasing mdNLR was not associated with mortality among NSCLC overall, nor within adenocarcinoma (N = 148) or squamous cell carcinoma (N = 115) case groups. Conclusion Our findings suggest that increased mdNLR, representing a systemic inflammatory profile on average 4.5 years before a SCLC diagnosis, may be associated with mortality in heavy smokers who go on to develop SCLC but not NSCLC.

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Association Between Informant-Reported Sleep Disturbance and Incident Dementia: An Analysis of the National Alzheimer’s Coordinating Center Uniform Data Set

Journal of Applied Gerontology ◽

10.1177/0733464820967202 ◽

2020 ◽

pp. 073346482096720

Author(s):

Woojung Lee ◽

Shelly L. Gray ◽

Douglas Barthold ◽

Donovan T. Maust ◽

Zachary A. Marcum

Keyword(s):

Older Adults ◽

Sleep Disturbance ◽

Proportional Hazards ◽

Cox Proportional Hazards ◽

Cognitive Screening ◽

Cognitive Level ◽

Data Set ◽

Cox Proportional Hazards Models ◽

Incident Dementia ◽

Normal Cognition

Informants’ reports can be useful in screening patients for future risk of dementia. We aimed to determine whether informant-reported sleep disturbance is associated with incident dementia, whether this association varies by baseline cognitive level and whether the severity of informant-reported sleep disturbance is associated with incident dementia among those with sleep disturbance. A longitudinal retrospective cohort study was conducted using the uniform data set collected by the National Alzheimer’s Coordinating Center. Older adults without dementia at baseline living with informants were included in analysis. Cox proportional hazards models showed that participants with an informant-reported sleep disturbance were more likely to develop dementia, although this association may be specific for older adults with normal cognition. In addition, older adults with more severe sleep disturbance had a higher risk of incident dementia than those with mild sleep disturbance. Informant-reported information on sleep quality may be useful for prompting cognitive screening.

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Patterns of Care and Outcomes of Primary Adenoid Cystic Carcinoma of the Trachea

Annals of Otology Rhinology & Laryngology ◽

10.1177/00034894211008101 ◽

2021 ◽

pp. 000348942110081

Author(s):

Sara Behbahani ◽

Gregory L. Barinsky ◽

David Wassef ◽

Boris Paskhover ◽

Rachel Kaye

Keyword(s):

Radiation Therapy ◽

Adenoid Cystic Carcinoma ◽

Surgical Resection ◽

Proportional Hazards ◽

Invasive Disease ◽

Cox Proportional Hazards ◽

Tumor Diameter ◽

Adenoid Cystic ◽

Cox Proportional Hazards Models ◽

Age Of Diagnosis

Objective: Primary tracheal malignancies are relatively rare cancers, representing 0.1% to 0.4% of all malignancies. Adenoid cystic carcinoma (ACC) is the second most common histology of primary tracheal malignancy, after squamous cell carcinoma. This study aims to analyze demographic characteristics and potential influencing factors on survival of tracheal ACC (TACC). Methods: This was a retrospective cohort study utilizing the National Cancer Database (NCDB). The NCDB was queried for all cases of TACC diagnosed from 2004 to 2016 (n = 394). Kaplan-Meier (KM) and Cox proportional-hazards models were used to determine clinicopathological and treatment factors associated with survival outcomes. Results: Median age of diagnosis was 56 (IQR: 44.75-66.00). Females were affected slightly more than males (53.8% vs 46.2%). The most prevalent tumor diameter range was 20 to 39 mm (34.8%) followed by greater than 40 mm in diameter (17.8%). Median overall survival (OS) was 9.72 years with a 5- and 10-year OS of 70% and 47.5%, respectively. Localized disease was not associated with a survival benefit over invasive disease ( P = .388). The most common intervention was surgery combined with radiation therapy (RT) at 46.2%, followed by surgery alone (16.8%), and standalone RT (8.9%). When adjusting for confounders, surgical resection was independently associated with improved OS (HR 0.461, 95% CI 0.225-0.946). Tumor size greater than 40 mm was independently associated with worse OS (HR 2.808; 95% CI 1.096-7.194). Conclusion: Our data suggests that surgical resection, possibly in conjunction with radiation therapy, is associated with improved survival, and tumor larger than 40 mm are associated with worse survival.

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Total and cause-specific mortality in patients with personality disorders: the association between comorbid severe mental illness and substance use disorders

Social Psychiatry and Psychiatric Epidemiology ◽

10.1007/s00127-021-02055-3 ◽

2021 ◽

Author(s):

Anne Høye ◽

Bjarne K. Jacobsen ◽

Jørgen G. Bramness ◽

Ragnar Nesvåg ◽

Ted Reichborn-Kjennerud ◽

...

Keyword(s):

Mental Illness ◽

Substance Use ◽

Severe Mental Illness ◽

Personality Disorders ◽

Health Care Services ◽

Causes Of Death ◽

Proportional Hazards ◽

Young Female ◽

Cox Proportional Hazards ◽

Cox Proportional Hazards Models

Abstract Purpose To investigate the mortality in both in- and outpatients with personality disorders (PD), and to explore the association between mortality and comorbid substance use disorder (SUD) or severe mental illness (SMI). Methods All residents admitted to Norwegian in- and outpatient specialist health care services during 2009–2015 with a PD diagnosis were included. Standardized mortality ratios (SMRs) with 95% confidence intervals (CI) were estimated in patients with PD only and in patients with PD and comorbid SMI or SUD. Cox proportional hazards models were used to estimate adjusted hazard ratios (HRs) with 95% CIs in patients with PD and comorbid SMI or SUD compared to patients with PD only. Results Mortality was increased in both in- and outpatients with PD. The overall SMR was 3.8 (95% CI 3.6–4.0). The highest SMR was estimated for unnatural causes of death (11.0, 95% CI 10.0–12.0), but increased also for natural causes of death (2.2, 95% CI 2.0–2.5). Comorbidity was associated with higher SMRs, particularly due to poisoning and suicide. Patients with comorbid PD & SUD had almost four times higher all-cause mortality HR than patients with PD only; young women had the highest HR. Conclusion The SMR was high in both in- and outpatients with PD, and particularly high in patients with comorbid PD & SUD. Young female patients with PD & SUD were at highest risk. The higher mortality in patients with PD cannot, however, fully be accounted for by comorbidity.

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Added value of cardiovascular calcifications for prediction of recurrent cardiovascular events and cardiovascular interventions in patients with established cardiovascular disease

The International Journal of Cardiovascular Imaging ◽

10.1007/s10554-021-02164-9 ◽

2021 ◽

Author(s):

Cilie C. van ’t Klooster ◽

◽

Yolanda van der Graaf ◽

Hendrik M. Nathoe ◽

Michiel L. Bots ◽

...

Keyword(s):

Cardiovascular Disease ◽

Heart Valve ◽

Cardiovascular Events ◽

Proportional Hazards ◽

Cox Proportional Hazards ◽

Added Value ◽

Cvd Risk ◽

Major Cardiovascular Events ◽

Cox Proportional Hazards Models ◽

Cardiovascular Interventions

AbstractThe purpose is to investigate the added prognostic value of coronary artery calcium (CAC), thoracic aortic calcium (TAC), and heart valve calcium scores for prediction of a combined endpoint of recurrent major cardiovascular events and cardiovascular interventions (MACE +) in patients with established cardiovascular disease (CVD). In total, 567 patients with established CVD enrolled in a substudy of the UCC-SMART cohort, entailing cardiovascular CT imaging and calcium scoring, were studied. Five Cox proportional hazards models for prediction of 4-year risk of MACE + were developed; traditional CVD risk predictors only (model I), with addition of CAC (model II), TAC (model III), heart valve calcium (model IV), and all calcium scores (model V). Bootstrapping was performed to account for optimism. During a median follow-up of 3.43 years (IQR 2.28–4.74) 77 events occurred (MACE+). Calibration of predicted versus observed 4-year risk for model I without calcium scores was good, and the c-statistic was 0.65 (95%CI 0.59–0.72). Calibration for models II–V was similar to model I, and c-statistics were 0.67, 0.65, 0.65, and 0.68 for model II, III, IV, and V, respectively. NRIs showed improvement in risk classification by model II (NRI 15.24% (95%CI 0.59–29.39)) and model V (NRI 20.00% (95%CI 5.59–34.92)), but no improvement for models III and IV. In patients with established CVD, addition of the CAC score improved performance of a risk prediction model with classical risk factors for the prediction of the combined endpoint MACE+ . Addition of the TAC or heart valve score did not improve risk predictions.

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