Contribution of causal factors to disease burden: how to interpret attributable fractions

What proportion of the risk in a given population is attributable to a risk factor? The population attributable fraction (PAF) answers this question. “Attributable to” is understood as “due to”, which makes PAFs closely related to the concept of potential impact or potential benefits of reducing the exposure. The PAF is a tool at the border between science and decision making. PAFs are estimated based on strong assumptions and the calculations are data intensive, making them vulnerable to gaps in knowledge and data. Current misconceptions include summing up PAFs to 100% or subtracting a PAF for a factor from 100% to deduce what proportion is left to be explained or prevented by other factors. This error is related to unrecognised multicausality or shared causal responsibility in disease aetiology. Attributable cases only capture cases in excess and should be regarded as a lower bound for aetiological cases, which cannot be estimated based on epidemiological data alone (exposure-induced cases). The population level might not be relevant to discuss prevention priorities based on PAFs, for instance when exposures concentrate in a subgroup of the population, as for occupational lung carcinogens and other workplace hazards. Alternative approaches have been proposed based on absolute rather than relative metrics, such as estimating potential gains in life expectancy that can be expected from a specific policy (prevention) or years of life lost due to a specific exposure that already happened (compensation).

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Enhancing the use of Object Based Contents Addressable Storage

Computing Trendz - The Journal of Emerging Trends in Information Technology ◽

10.21844/cttjetit.v6i1.6697 ◽

2016 ◽

Vol 6 (1) ◽

Author(s):

Simab Hasan Rizvi

Keyword(s):

File System ◽

Application Performance ◽

Shared Storage ◽

Data Intensive ◽

Network Bandwidth ◽

Storage Performance ◽

Efficient Management ◽

Object Based ◽

Data Volume ◽

Potential Benefits

In Today's age of Tetra Scale computing, the application has become more data intensive than ever. The increased data volume from applications, in now tackling larger and larger problems, and has fuelled the need for efficient management of this data. In this paper, a technique called Content Addressable Storage or CAS, for managing large volume of data is evaluated. This evaluation focuses on the benefits and demerits of using CAS it focuses, i) improved application performance via lockless and lightweight synchronization ofaccess to shared storage data, ii) improved cache performance, iii) increase in storage capacity and, iv) increase network bandwidth. The presented design of a CAS-Based file store significantly improves the storage performance that provides lightweight lock less user defined consistency semantics. As a result, this file system shows a 28% increase in read bandwidth and 13% increase in write bandwidth, over a popular file system in common use. In this paper the potential benefits of using CAS for a virtual machine are estimated. The study also explains mobility application for active use and public deployment.

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Novel Method to Evaluate Diagnostic Shifting After a Pediatric Antibiotic Stewardship Intervention

Infection Control and Hospital Epidemiology ◽

10.1017/ice.2020.937 ◽

2020 ◽

Vol 41 (S1) ◽

pp. s332-s333

Author(s):

Nora Fino ◽

Benjamin Haaland ◽

Karl Madaras-Kelly ◽

Katherine Fleming-Dutra ◽

Adam Hersh ◽

...

Keyword(s):

Respiratory Infections ◽

Population Attributable Fraction ◽

Acute Otitis Media ◽

Population Level ◽

Estimating Equation ◽

Audit And Feedback ◽

Antibiotic Prescribing ◽

Post Intervention ◽

Intervention Effect ◽

Diagnostic Coding

Background: Audit-and-feedback interventions track clinician practice patterns for a targeted practice behavior. Audit and feedback of antibiotic prescribing data for acute respiratory infections (ARI) is an effective stewardship strategy that relies on administrative coding to identify eligible visits for audit. Diagnostic shifting is the misclassification of a patient’s diagnosis in response to audit and feedback and is a potential unintended consequence of audit and feedback. Objective: To develop a method to identify patterns consistent with diagnostic shifting including both positive shifting (improved diagnosis and documentation) and negative shifting (intentionally altering documentation of diagnosis to justify antibiotic prescribing), after implementation of an audit-and-feedback intervention to improve ARI management. Methods: We evaluated the intervention effect on diagnostic shifting within 12 University of Utah pediatric clinics (293 providers). Data included 66,827 ARI diagnoses: pneumonia, sinusitis, bronchitis, pharyngitis, upper respiratory infection (URI), acute otitis media (AOM), or serous otitis with effusion (OME). To determine whether rates of ARI diagnoses changed after the intervention, we developed logistic generalized estimating equation (GEE) models with robust sandwich standard error estimates to account for clinic-wise clustering. Outcomes included the change in each ARI diagnosis relative to the competing 6 diagnoses included in audit-and-feedback reports before and after intervention implementation. Models tested for a change in outcomes after the intervention (ie, diagnostic shift) after adjustment for month of diagnosis. For each diagnosis, we estimated the population attributable fraction (PAF) for antibiotic prescriptions due to combined shifts in diagnostic frequencies and prescription rates for each diagnosis. The PAF is the estimated fraction of antibiotic prescriptions that would have changed under a population-level intervention. Results: In month-adjusted analyses, diagnoses of pneumonia and OME decreased after the intervention: odds ratio (OR), 0.46 (95% CI, 0.31–0.68) and OR, 0.81 (95% CI, 0.67–0.99), respectively. In addition, URI diagnoses increased: OR, 1.05 (95% CI 1.00, 1.11). We did not detect changes in the diagnosis rates of sinusitis, AOM, bronchitis, and pharyngitis post intervention. The intervention effect on the PAF for antibiotics prescriptions was consistently positive but relatively small in magnitude. PAF was highest for URIs (PAF, 8.87%), followed by AOM (PAF, 3.56%) and sinusitis (PAF, 2.76%), and was lowest for pneumonia and bronchitis (PAF, 0.41% for both). Conclusions: Our analysis found minimal evidence overall of diagnostic shifting after a stewardship intervention using audit and feedback in these pediatric clinics. Small changes in diagnostic coding may reflect more appropriate diagnosis and coding, a positive effect of audit and feedback, rather than intentional negative diagnostic shift.Funding: NoneDisclosures: None

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Reddit Users’ Experiences of Suicidal Thoughts During the COVID-19 Pandemic: A Qualitative Analysis of r/Covid19_support Posts (Preprint)

10.2196/preprints.28891 ◽

2021 ◽

Author(s):

Allie Slemon ◽

Corey McAuliffe ◽

Trevor Goodyear ◽

Liza McGuinness ◽

Elizabeth Shaffer ◽

...

Keyword(s):

Mental Health ◽

Qualitative Research ◽

Social Media ◽

Coping Strategies ◽

Health Resources ◽

Population Level ◽

Epidemiological Data ◽

Qualitative Inquiry ◽

Search Term ◽

Suicidal Thoughts

BACKGROUND The COVID-19 pandemic is having considerable impacts on population-level mental health, with research illustrating an increased prevalence in suicidal thoughts due to pandemic stressors. While the drivers of suicidal thoughts amid the pandemic are poorly understood, qualitative research holds great potential for expanding upon projections from pre-pandemic work and contextualizing emerging epidemiological data. Despite calls for qualitative inquiry, there is a paucity of qualitative research examining experiences of suicidality related to COVID-19. The use of publicly available data from social media offers timely and pertinent information into ongoing pandemic-related mental health, including individual experiences of suicidal thoughts. OBJECTIVE The objective of this paper is to examine online posts that discuss suicidal thoughts within one Reddit community r/COVID19_support with the aim to identify contributing stressors and coping strategies related to the COVID-19 pandemic. METHODS This study draws on online posts from within the Reddit community r/COVID19_support that describe users’ suicidal thoughts during and related to the COVID-19 pandemic. Data were collected from creation of this subreddit on February 12, 2020 until December 31, 2020. Using the search term “suicide”, we used the NCapture add-on tool, hosted by NVivo, to conduct our investigation. A qualitative thematic analysis, as described by Braun and Clarke, was conducted to generate themes reflecting users’ experiences of suicidal thoughts. RESULTS A total of 83 posts from 57 users were included in the analysis. Reddit posts described a range of users’ lived experiences of suicidal thoughts related to the pandemic, including deterioration in mental health, complex emotions associated with suicidal thinking, and concern that suicidal thoughts may progress to action. Seven prominent and compounding stressors were identified as contributing to Reddit users’ suicidal thoughts, including social isolation, employment and finances, virus exposure and COVID-19 illness, uncertain timeline of the pandemic, news and social media, pre-existing mental health conditions, and lack of access to mental health resources. Some users described individual coping strategies used in attempt to manage suicidal thoughts, however these were recognized as insufficient for addressing the multilevel stressors of the pandemic. CONCLUSIONS Multiple and intersecting stressors have contributed to individuals’ experiences of suicidal thoughts in the context of the COVID-19 pandemic, requiring thoughtful and complex public health and policy responses. While ongoing challenges exist with self-disclosure of mental health challenges on social media, Reddit and other online platforms may a supportive space for users to share suicidal thoughts and discuss potential coping strategies.

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Epidemiological trends in digestive cancers compared to trends in alcohol consumption. Facts from Romania: correlation or coincidence?

Medicine and Pharmacy Reports ◽

10.15386/cjmed-1067 ◽

2018 ◽

Vol 91 (4) ◽

pp. 376-386

Author(s):

Simona Valean ◽

Romeo Chira ◽

Dan Dumitrascu

Keyword(s):

Alcohol Consumption ◽

Population Level ◽

Epidemiological Data ◽

Epidemiological Studies ◽

Incidence Rates ◽

Human Populations ◽

Causative Relationship ◽

Consumption Data ◽

Digestive Cancers ◽

Epidemiological Trends

Cancer has emerged as the leading cause of death in human populations, according to recent estimations. Epidemiological studies emphasized the role of life style and of environmental factors in promoting the risk for digestive cancers. The contribution of alcohol was highly suspected. Even for digestive cancers with dominant infection etiology, like liver cancer and gastric cancer, the contribution of alcohol should be assessed. At population level there is therefore a need to compare trends in epidemiological data of gastrointestinal cancers and data on alcohol consumption, in order to extrapolate any causative relationship. The purpose of this review was to analyze the time trend of digestive cancers in Romania, in terms of mortality rates (between 1955-2012), and incidence rates (between 2008-2012), in males and females, and to analyze the alcohol consumption data, aiming to find out if there is any association.

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Abstract P299: Changes in Race-Sex Specific Population Attributable Fraction for Obesity-Related Diabetes, 2001-2016

Circulation ◽

10.1161/circ.141.suppl_1.p299 ◽

2020 ◽

Vol 141 (Suppl_1) ◽

Author(s):

Natalie Cameron ◽

Megan McCabe ◽

Lucia Petito ◽

Norrina B Allen ◽

Mercedes R Carnethon ◽

...

Keyword(s):

Population Attributable Fraction ◽

Population Level ◽

Attributable Fraction ◽

Incident Diabetes ◽

Obesity Prevalence ◽

Longitudinal Assessment ◽

Prevalence Of Obesity ◽

Race Ethnicity ◽

Nationally Representative ◽

Over Time

Introduction: Estimating effects of population-level increases in obesity on diabetes has important implications for public health policy. Therefore, we used the population attributable fraction (PAF) to quantify trends in the burden of obesity on incident diabetes in key sex and race/ethnicity subgroups over time. Hypothesis: PAFs for obesity attributable incident diabetes will be greatest for women, differ by race/ethnicity and increase over time. Methods: Using data from the Multi-Ethnic Study of Atherosclerosis (MESA), we estimated unadjusted and adjusted hazard ratios (HRs) of obesity on incident diabetes mellitus (DM). We included non-Hispanic White (NHW), non-Hispanic Black (NHB) and Hispanic-Mexican (MA) MESA participants with available data on body mass index and key covariates and without DM at baseline. Next, we estimated the prevalence of obesity in four pooled groups of NHANES survey cycles from 2001-2016 with similar characteristics to MESA participants (age 45-80 years, NHW, NHB, and MA without cardiovascular disease). Lastly, we combined estimates from MESA and NHANES to quantify unadjusted and adjusted PAFs (adjusted for age, income, education, physical activity and diet). Leveraging the objective longitudinal assessment of incident DM in MESA and a nationally representative sample of NHANES, we estimated broadly generalizable PAF estimates over time. Results: Of 3869 MESA participants, mean age was 61 (± 10) years with 47% men, 56% NHW, 31% NHB, and 13% MA. Incidence of DM was 11% with overall adjusted HR of 2.75 (95% CI 2.26, 3.34) for obesity. Prevalence of obesity increased from 34% (32, 37) in 2001-2004 to 41% (39, 44) in 2013-2016. Overall adjusted PAFs ranged from 0.23 to 0.52 over the study period (TABLE), with greatest estimates in NHW women. Conclusions: In conclusion, over time, the proportion of diabetes due to obesity has increased across multiple subgroups of the population, further highlighting the health burden of obesity in the population.

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Cardiovascular Health and Stroke in Older British Men

Stroke ◽

10.1161/strokeaha.120.030546 ◽

2020 ◽

Vol 51 (11) ◽

pp. 3286-3294

Author(s):

Ayesha Ahmed ◽

Snehal M. Pinto Pereira ◽

Lucy Lennon ◽

Olia Papacosta ◽

Peter Whincup ◽

...

Keyword(s):

Physical Activity ◽

Older Adults ◽

Cardiovascular Health ◽

Population Attributable Fraction ◽

Cox Models ◽

Population Attributable Fractions ◽

Hazard Ratios ◽

Attributable Fractions ◽

Time Point

Background and Purpose: Research exploring the utility of cardiovascular health (CVH) and its Life’s Simple 7 (LS7) components (body mass index, blood pressure [BP], glucose, cholesterol, physical activity, smoking, and diet) for prevention of stroke in older adults is limited. In the British Regional Heart Study, we explored (1) prospective associations of LS7 metrics and composite CVH scores with, and their impact on, stroke in middle and older age; and (2) if change in CVH was associated with subsequent stroke. Methods: Men without cardiovascular disease were followed from baseline recruitment (1978–1980), and again from re-examination 20 years later, for stroke over a median period of 20 years and 16 years, respectively. LS7 were measured at each time point except baseline diet. Cox models estimated hazard ratios (95% CI) of stroke for (1) ideal and intermediate versus poor levels of LS7; (2) composite CVH scores; and (3) 4 CVH trajectory groups (low-low, low-high, high-low, high-high) derived by dichotomising CVH scores from each time point across the median value. Population attributable fractions measured impact of LS7. Results: At baseline (n=7274, mean age 50 years), healthier levels of BP, physical activity, and smoking were associated with reduced stroke risk. At 20-year follow-up (n=3798, mean age 69 years) only BP displayed an association. Hazard ratios for intermediate and ideal (versus poor) levels of BP 0.65 (0.52–0.81) and 0.40 (0.24–0.65) at baseline; and 0.84 (0.67–1.05) and 0.57 (0.36–0.90) at 20-year follow-up. With reference to low-low trajectory, the low-high trajectory was associated with 40% reduced risk, hazard ratio 0.60 (0.44–0.83). Associations of CVH scores weakened, and population attributable fractions of LS7 reduced, from middle to old age; population attributable fraction of nonideal BP from 53% to 39%. Conclusions: Except for BP, CVH is weakly associated with stroke at older ages. Prevention strategies for older adults should prioritize BP control but also enhance focus beyond traditional risk factors.

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On the complexity of haplotyping a microbial community

Bioinformatics ◽

10.1093/bioinformatics/btaa977 ◽

2020 ◽

Author(s):

Samuel M Nicholls ◽

Wayne Aubrey ◽

Kurt De Grave ◽

Leander Schietgat ◽

Christopher J Creevey ◽

...

Keyword(s):

Microbial Communities ◽

Community Sample ◽

Population Level ◽

Single Individual ◽

Metagenomic Sample ◽

Potential Benefits ◽

Software Implementations ◽

Occurrence Matrix ◽

Number Of Individuals ◽

Traversal Algorithm

Abstract Motivation Population-level genetic variation enables competitiveness and niche specialization in microbial communities. Despite the difficulty in culturing many microbes from an environment, we can still study these communities by isolating and sequencing DNA directly from an environment (metagenomics). Recovering the genomic sequences of all isoforms of a given gene across all organisms in a metagenomic sample would aid evolutionary and ecological insights into microbial ecosystems with potential benefits for medicine and biotechnology. A significant obstacle to this goal arises from the lack of a computationally tractable solution that can recover these sequences from sequenced read fragments. This poses a problem analogous to reconstructing the two sequences that make up the genome of a diploid organism (i.e. haplotypes), but for an unknown number of individuals and haplotypes. Results The problem of single individual haplotyping (SIH) was first formalised by Lancia et al. in 2001. Now, nearly two decades later, we discuss the complexity of “haplotyping” metagenomic samples, with a new formalisation of Lancia et al’s data structure that allows us to effectively extend the single individual haplotype problem to microbial communities. This work describes and formalizes the problem of recovering genes (and other genomic subsequences) from all individuals within a complex community sample, which we term the metagenomic individual haplotyping (MIH) problem. We also provide software implementations for a pairwise single nucleotide variant (SNV) co-occurrence matrix and greedy graph traversal algorithm. Availability and implementation Our reference implementation of the described pairwise SNV matrix (Hansel) and greedy haplotype path traversal algorithm (Gretel) are open source, MIT licensed and freely available online at github.com/samstudio8/hansel and github.com/samstudio8/gretel, respectively.

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Deaths and years of life lost due to suboptimal breast-feeding among children in the developing world: a global ecological risk assessment

Public Health Nutrition ◽

10.1079/phn2005891 ◽

2006 ◽

Vol 9 (6) ◽

pp. 673-685 ◽

Cited By ~ 60

Author(s):

Jeremy A Lauer ◽

Ana Pilar Betrán ◽

Aluísio JD Barros ◽

Mercedes de Onís

Keyword(s):

Developing Countries ◽

Breast Feeding ◽

Respiratory Tract Infections ◽

Diarrhoeal Disease ◽

Infants And Children ◽

Years Of Life Lost ◽

Attributable Fractions ◽

Second Year ◽

Tract Infections ◽

Mother To Child

AbstractObjectiveWe estimate attributable fractions, deaths and years of life lost among infants and children ≤2 years of age due to suboptimal breast-feeding in developing countries.DesignWe compare actual practices to a minimum exposure pattern consisting of exclusive breast-feeding for infants ≤6 months of age and continued breast-feeding for older infants and children ≤2 years of age. For infants, we consider deaths due to diarrhoeal disease and lower respiratory tract infections, and deaths due to all causes are considered in the second year of life. Outcome measures are attributable fractions, deaths, years of life lost and offsetting deaths potentially caused by mother-to-child transmission of HIV through breast-feeding.SettingDeveloping countries.SubjectsInfants and children ≤2 years of age.ResultsAttributable fractions for deaths due to diarrhoeal disease and lower respiratory tract infections are 55% and 53%, respectively, for the first six months of infancy, 20% and 18% for the second six months, and are 20% for all-cause deaths in the second year of life. Globally, as many as 1.45 million lives (117 million years of life) are lost due to suboptimal breast-feeding in developing countries. Offsetting deaths caused by mother-to-child transmission of HIV through breast-feeding could be as high as 242 000 (18.8 million years of life lost) if relevant World Health Organization recommendations are not followed.ConclusionsThe size of the gap between current practice and recommendations is striking when one considers breast-feeding involves no out-of-pocket costs, that there exists universal consensus on best practices, and that implementing current international recommendations could potentially save 1.45 million children's lives each year.

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Epidemiology of incident chlamydia and gonorrhoea infections and population attributable fractions associated with living in the inner-core of Winnipeg, Canada

International Journal of STD & AIDS ◽

10.1177/0956462415614168 ◽

2016 ◽

Vol 28 (6) ◽

pp. 550-557 ◽

Cited By ~ 4

Author(s):

Souradet Y Shaw ◽

Deborah L Nowicki ◽

Erin Schillberg ◽

Christopher G Green ◽

Craig P Ross ◽

...

Keyword(s):

Inner Core ◽

Disease Risk ◽

Population Attributable Fraction ◽

Population Based ◽

Incidence Rates ◽

Age Group ◽

Complex Processes ◽

Population Attributable Fractions ◽

Attributable Fractions ◽

Health Significance

Population attributable fractions help to convey public health significance of differential disease risk for chlamydia and gonorrhoea. Geographical residence serves as a useful proxy for complex processes creating ill health. Using population-based data, Poisson regression models were used to examine factors associated with chlamydia and gonorrhoea incidence. Population attributable fractions due to residency in the Winnipeg Health Region’s inner-core were determined for chlamydia/gonorrhoea infections among 15–59-year olds (2005–2013), stratified by age group. For both chlamydia and gonorrhoea, it was found that the 15–24-year old age group had the highest incidence rates. There was also a stronger association between residency in the inner-core and incidence for gonorrhoea, compared to chlamydia. Overall, 24% (95% CI: 12–34%) of chlamydia infections were attributable to residency in the inner-core, compared to 46% (95% CI: 35–54%) for gonorrhoea ( p < .05). Within chlamydia/gonorrhoea, no statistically significant differences in population attributable fraction were observed by age group. The conclusion was that a concentration of efforts towards inner-core residents with gonorrhoea infections may result in a relatively larger decrease in incidence.

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Adult obesity complications: challenges and clinical impact

Therapeutic Advances in Endocrinology and Metabolism ◽

10.1177/2042018820934955 ◽

2020 ◽

Vol 11 ◽

pp. 204201882093495

Author(s):

Saleem Ansari ◽

Hasan Haboubi ◽

Nadim Haboubi

Keyword(s):

Population Level ◽

Epidemiological Data ◽

Healthcare Systems ◽

Clinical Impact ◽

Adult Obesity ◽

Individual Level ◽

National Healthcare ◽

Obesity Complications

The complications associated with adult obesity are overwhelming national healthcare systems. No country has yet implemented a successful population-level strategy to reverse the rising trends of obesity. This article presents epidemiological data on the complications of adult obesity and discusses some of the challenges associated with managing this disease at a population and individual level.

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