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On Integrating Population-Based Metaheuristics with Cooperative Parallelism

On Integrating Population-Based Metaheuristics with Cooperative Parallelism

For harder problems, approximation methods are more ap- propriate. These methods aim at finding a solution of “good” quality (possibly sub-optimal) in a reasonable amount of time. Metaheuristics have proven to be the most efficient approxima- tion methods to address this class of problems. Metaheuristics are high-level procedures using choices (i.e., heuristics) to limit the part of the search space which actually gets visited, in order to make problems tractable. Metaheuristics can be clas- sified in two main categories: single-solution and population- based methods. Single-solution metaheuristics maintain, mod- ify and stepwise improve on a single candidate solution (also called a configuration). Examples of single-solutions methods include: Simulated Annealing [1], Local Search [2], Tabu Search [3], Variable Neighborhood Search [4], Adaptive Search [5], Extremal Optimization [6]. . . On the other hand, population-based methods, modify and improve a population, i.e. sets of candidate solutions. These methods include: Genetic Algorithms [7], Ant Colony Optimization [8], Particle Swarm Optimization [9]. . . Metaheuristics generally implement two main search strategies: intensification and diversification, also called exploitation and exploration [10]. Intensification guides the solver to deeply explore a promising part of the search space. In contrast, diversification aims at extending the search onto different parts of the search space [11]. In order to obtain the best performance, a metaheuristic should provide a useful balance between intensification and diversification. By design, some heuristics are better at intensifying the search while others are so at diversifying it. More generally, each metaheuristic has it own strengths and weaknesses, which may greatly vary according to the problem or even instance being solved.
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Metabolic profiles among COPD and controls in the CanCOLD population-based cohort

Metabolic profiles among COPD and controls in the CanCOLD population-based cohort

only 30% of individuals with COPD in this sub-study were previously diagnosed with the dis- ease, another similitude with other population-based cohorts [ 52 ], providing further reassur- ance regarding how representative the present cohort is of the general population. That said, despite all the care devoted to building a cohort of individuals representative of the general population, some biases may still be present. For example, the most fragile or diseased subjects would probably be less inclined to participate in a clinical study. Third, focusing on a represen- tative and occidental population of COPD, our findings do not necessarily apply to individuals with severe COPD or to those exhibiting particular phenotypes (inflammatory, underweight or obese, with preponderant vascular comorbidities). Finally, physical activity, an important confounder for cardiovascular risk, was not included in the analysis; also, sleep apnea, another potential contributor, was underdiagnosed by far in this cohort when considering the reported prevalence.
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Comprehensive population-based genome sequencing provides insight into hematopoietic regulatory mechanisms

Comprehensive population-based genome sequencing provides insight into hematopoietic regulatory mechanisms

Our study also demonstrated the benefits of using high-cov- erage WGS in a population-based biobank. Comprehensive ascertainment of genetic variation allowed us to identify the association near CEBPA, which would have been missed had we imputed to sparser reference panels, such as HapMap. Fur- thermore, the high-coverage WGS allowed us to comprehen- sively capture variation that might be missed by lower coverage sequencing approaches (such as longer indels and variants in low-complexity regions), giving us confidence that the true causal variant has been identified at each locus, an important pre- requisite for fine-mapping. Moreover, by performing our study in a population-based biobank, we were also able to link genetic data with EMRs to greatly increase sample sizes in a resource- efficient manner, providing support for similar programs such as the Precision Medicine Initiative (73). Together, our study dem- onstrates how key genetic and biological insights can be gained from comprehensive genetic studies in population-based biobanks. Materials and Methods
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Predictors of respiratory sickness absence: an international population-based study.

Predictors of respiratory sickness absence: an international population-based study.

The present study is an analysis of data from the European Community Respiratory Health Survey (ECRHS) II, a follow-up study cohort derived from a population-based, multinational survey of adults aged 20-44 years at original recruitment at 26 study centers in 11 European and two non-European countries. The study designs of ECRHS II and its baseline counterpart, ECRHS I, have been previously described in detail [ European Respiratory Health Survey II Steering Committee 2002; Bedada et al., 2007; Burney et al., 1994]. In brief summary, the baseline study was performed in two stages, with each participant completing a screening questionnaire, and a randomly selected 20% subgroup of these respondents being invited for more extensive interviews and clinical testing [Burney et al., 1994]. In addition to this random subset of the screening questionnaire group, participants who reported respiratory symptoms at the screening stage and who were not already selected at random for the first group were considered eligible for participation in a “symptom-enriched” sub-group that was also invited to complete a supplemental questionnaire and participate in a clinical examination. Thus, a key feature of the ECHRS I is that symptomatic individuals could have been included in the extensive interview/clinical examination portion of the study either by random selection or because of their symptoms. The 20% random group was used to draw inferences about general population rates of symptoms and outcomes; the symptom-enriched group to provide the power to analyze associations with specific respiratory outcomes. All participants who underwent supplemental interviews and examinations (both the random 20% subgroup and the symptom enriched sub-group) were eligible for re-contact for inclusion eight years later in the ECRHS II follow-up, in which 65% of the baseline subjects ultimately participated [Bedada et al., 2007].
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Depression and socio-economic status: an 8-year longitudinal population-based study

Depression and socio-economic status: an 8-year longitudinal population-based study

D EPRESSION AND SOCIO - ECONOMIC STATUS : AN 8- YEAR LONGITUDINAL POPULATION - BASED STUDY V. Lorant 1 , C. Croux 2 , S. Weich 3 , D. Deliège 1 , J. Mackenbach 4 , M. Ansseau 5 1 Université Catholique de Louvain, Public Health School, Brussels, Belgium; 2 KU Leuven, Department of Applied Economics, Leuven, Belgium;

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Meta learning for population-based algorithms in black-box optimization

Meta learning for population-based algorithms in black-box optimization

according to the relative evaluation of the observed values. Many applications lead to different proposed search mechanisms in this field over the past years. In addition to their parallel computing power, the benefits we get by working with population-based optimizers are that different solutions can contribute jointly in order to explore different promising regions of the objective function, which can be more effective than single-solution based search for many cases. They also have shown competitive results in many complex optimization problems (e.g., training deep neural networks for machine learning tasks). Therefore, we believe that population-based algorithms possess the adaptability required to generate effective and robust general optimizers.
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Under-treatment of elderly patients with ovarian cancer: a population based study

Under-treatment of elderly patients with ovarian cancer: a population based study

Statistical analysis The chi square or Fisher’s exact test were used, as appropriate, to compare cancer characteristics accord- ing to age. Univariate and multivariate analysis using logistic regression were used to identify the associ- ation between treatment (Surgery and Chemotherapy: yes/No) and age, adjusted for other factors such as stage, grade, histological research, treatment location, and area of residence. Multivariate logistic regression was used to analyze the treatment pattern (surgery alone, surgery followed by chemotherapy, chemother- apy alone or neo-adjuvant chemotherapy, vs. no treat- ment) according to age. The Kappa test was used to assess agreement between the treatment administered and the treatment recommended by current guide- lines. Overall survival was estimated according the Kaplan-Meier method. Net survival (survival if the cause of death under consideration was the only cause of death) is now recommended as a substitute for relative survival methods in current use, to evalu- ate population-based cancer survival [17, 18]. We es- timated net survival using the non-parametric Pohar Perme estimator [19], which is based on the mortality rate of the general population and provides unbiased estimates of net survival. Overall survival curves were compared using the log rank test. All tests were two- sided and a p-value <0.05 was considered statistically significant. A Cox regression model was used to esti- mate hazard ratios for overall mortality, with adjust- ment for age and other confounding factors including grade and stage. We verified the conditions of appli- cation of the model by testing the proportionality of risks. All statistical analyses were performed with the R software package. Net survival analysis was
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Unhealthy behaviours and risk of visual impairment: The CONSTANCES population-based cohort

Unhealthy behaviours and risk of visual impairment: The CONSTANCES population-based cohort

Bénédicte M. J. Merle 1 , Gwendoline Moreau 1 , Anna Ozguler 2 , Bernard Srour 1 , Audrey Cougnard-Grégoire 1 , Marcel Goldberg 3 , Marie Zins 3 & Cécile Delcourt 1 Unhealthy behaviours are linked to a higher risk of eye diseases, but their combined effect on visual function is unknown. We aimed to examine the individual and combined associations of diet, physical activity, smoking and alcohol consumption with visual impairment among French adults. 38 903 participants aged 18–73 years from the CONSTANCES nationwide cohort (2012–2016) with visual acuity measured and who completed, lifestyle, medical and food frequency questionnaires were included. Visual impairment was defined as a presenting visual acuity <20/40 in the better eye. After full multivariate adjustment, the odds for visual impairment increased with decreasing diet quality (p for trend = 0.04), decreasing physical activity (p for trend = 0.02) and increasing smoking pack-years (p for trend = 0.03), whereas no statistically significant association with alcohol consumption was found. Combination of several unhealthy behaviours was associated with increasing odds for visual impairment (p for trend = 0.0002), with a fully-adjusted odds ratio of 1.81 (95% CI 1.18 to 2.79) for participants reporting 2 unhealthy behaviours and 2.92 (95% CI 1.60 to 5.32) for those reporting 3 unhealthy behaviours. An unhealthy lifestyle including low/intermediate diet quality, low physical activity and heavy smoking was associated with visual impairment in this large population-based study.
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Anaphylaxis in pregnancy: a population-based multinational European study

Anaphylaxis in pregnancy: a population-based multinational European study

11 Senior Researcher, Research Laboratory for Human Reproduction, Universite Libre de Bruxelles, Brussels, Belgium 12 Midwife and Research Co-ordinator, Perinatal Epidemiology Center (CEpiP), Brussels, Belgium Summary Anaphylaxis in pregnancy is a rare but severe complication for both mother and infant. Population-based data on anaphylaxis in pregnancy are lacking from mainland European countries. This multinational study presents the incidence, causative agents, management and maternal and infant outcomes of anaphylaxis in pregnancy. This descriptive multinational study used a combination of retrospective (Finnish medical registries) and prospective population-based studies (UK, France, Belgium and the Netherlands) to identify cases of anaphylaxis. Sixty-five cases were identified among 4,446,120 maternities (1.5 per 100,000 maternities; 95%CI 1.1–1.9). The incidence did not vary between countries. Approximately three-quarters of reactions occurred at the time of delivery. The most common causes were antibiotics in 27 women (43%), and anaesthetic agents in 11 women (17%; including neuromuscular blocking drugs, 7), which varied between countries. Anaphylaxis had very poor outcomes for one in seven mothers and one in seven babies; the maternal case fatality rate was 3.2% (95%CI 0.4 –11.0) and the neonatal encephalopathy rate was 14.3% (95%CI 4.8–30.3). Across Europe, anaphylaxis related to pregnancy is rare despite having a multitude of causative agents and different antibiotic prophylaxis protocols.
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Descriptive and Intuitive Population-Based Cardiac Motion Analysis via Sparsity Constrained Tensor Decomposition

Descriptive and Intuitive Population-Based Cardiac Motion Analysis via Sparsity Constrained Tensor Decomposition

Given that a set of motion parameters is typically high dimensional (due to the need to account for the spatial and temporal factors), model reduction can be useful to reduce the dimensionality of the data while retaining a small number of latent variables that describe the data. Tensor decomposition is one such technique that has been widely studied in the last years for a wide range of applications (see [6] for a review of tensor decomposition methods). PCA of dis- placement field has already been proposed for population-based cardiac motion analysis in [4], and singular value decomposition (SVD) of stacked Polyaffine motion parameters was proposed in [7]. A difficulty with these methods is in in- terpreting the results since both PCA and SVD are unconstrained and can thus result in factor matrices with a large number of mode combinations required for each subject.
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High quality standards for a large-scale prospective population-based observational cohort: Constances

High quality standards for a large-scale prospective population-based observational cohort: Constances

The authors wish to thank the INSERM-Versailles Saint Quentin en Yvelines University “Population-based Epidemiological Cohorts Unit” (Cohortes épidémiologiques en population) which designed and manages the Constances Cohort Study. They also thank the National Health Insurance Fund ( “Caisse nationale d’assurance maladie des travailleurs salaries”, CNAMTS) and its Health Screening Centres ( “Centres d’examens de santé”), responsible for collecting a large part of the data, as well as the National Retirement Fund (Caisse nationale d ’assurance vieillesse), ClinSearch, Asqualab and Eurocell, responsible for the data quality control.
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Fatigue and physical activity in cancer survivors: A cross‐sectional population‐based study

Fatigue and physical activity in cancer survivors: A cross‐sectional population‐based study

Methods: Using the national populationbased French cross‐sectional study Vie après le cancer 2, we included 1984 patients with early breast (61.1%), prostate (21.5%), and colorectal (17.4%) cancer. Severe fatigue at 2 years postdiagnosis was defined by a score ≥40 in the European Organization for Research and Treatment of Cancer quality of life questionnaire (EORTC QLQ C30) fatigue subscale. PA was defined as (a) self‐reported PA before diagnosis (active/inactive) and (b) change in PA since diagnosis (increased/maintained exposure vs decreased exposure/remain- ing inactive). Multivariate regression examined associations of severe fatigue with PA, adjusting for baseline clinical and treatment variables.
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Population-based meta-heuristic for active modules identification

Population-based meta-heuristic for active modules identification

6 CONCLUSION In this article, we have proposed a new method, AMI-NSGAII, to identify important subgraphs in weighted-nodes graphs. This study addresses a biological need to identify one or more sets of genes interacting together that may be related to a given phenotype. In the context of biological applications, the weighted-nodes graphs are constructed by enriching genes in a protein-protein interaction network with weights representing their activity. Our approach of active module identification relies on a population-based meta- heuristic that differs from existing methods in three important points: i) the use of a relaxed notion of connectedness that we call d-connectedness, ii) the use of a new crossover operator that combines d-connected sub-graphs according to the d value, iii) the consideration, when evaluating potential solutions, of the weight of the nodes but also of the essentiality of the nodes measured by taking into account the influence on their neighbors.
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Socioeconomic environment and cancer incidence: a French population-based study in Normandy.

Socioeconomic environment and cancer incidence: a French population-based study in Normandy.

Extrapolation of the PAFs needs further investigations in order to ascertain their variability due to gradient in relative risks, or to distribution across social quintiles. Errors in interpretation can appear, as highlighted in the article by Rockhill, et al. [16] with the use of the PAF. Firstly, Rockhill et al. point out many errors possible when analyzing multiple risk factors which is not the case of our study. The second point is the overuse of the word “explain” in the interpretation of the PAF. Rather than explain, it measures the extent of the phenomenon of deprivation on cancer incidence. The PAF should be considered as the population resultant of the overall ex- cess of cases in deprived compared with privileged people. The socioeconomic environment is not a causal factor of cancer in the biological sense of the term. However, since much of the proximal risk factor is more prevalent in the deprived, the socioeconomic environ- ment can be considered as the "cause of the cause", a distal determinant, pathways from deprivation to health including different types of mediators such as behav- ioral, community, social, educational, work-related, cul- tural and political factors [28]. Such quantification of social disparities at a community level points to the need to jointly take actions in a universal approach and also in approaches targeting deprived people, rather than global population actions only that fail to reduce social gradients because they generally benefit the more affluent. The PAF makes it possible to estimate the col- lective gain that could be obtained by public actions aiming to reduce the social gradient of incidence by measuring the extent of the population for which it is necessary to lead effective cancer prevention.
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The effect of physical activity on asthma incidence over 10 years: population-based study

The effect of physical activity on asthma incidence over 10 years: population-based study

There was little association between the vigorous physical activity measures and asthma outcomes (table 1). No differences were observed in the sensitivity analyses, and no interactions were found with the potential effect modifiers investigated (results not shown). In this population of initially asthma-free middle-aged adults, we found little association between vigorous physical activity and the onset of asthma measures over a 10-year period. These results are consistent with some previous research investigating the effect of physical activity on asthma incidence [6, 7]. Of the two studies that found a beneficial effect of physical activity on asthma incidence, one appeared not to adjust for relevant confounders, such as age and smoking [4], and the other study used lighter physical activity as the exposure [5]. The lack of observable beneficial associations from physical activity in our study may be because of insufficient statistical power, that only less vigorous physical activity protects against asthma incidence, or that there is no benefit from physical activity in regard to asthma incidence.
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Incretin based drugs and risk of cholangiocarcinoma among patients with type 2 diabetes: population based cohort study

Incretin based drugs and risk of cholangiocarcinoma among patients with type 2 diabetes: population based cohort study

Exposure definition We used a time varying exposure definition, where we categorised each person day of follow-up into one of four mutually exclusive categories: use of DPP-4 inhibitors (alone or in combination with other antidiabetic drugs, excluding GLP-1 receptor agonists); use of GLP-1 receptor agonists (alone or in combination with other antidiabetic drugs, including previous use of DPP-4 inhibitors, as this is a common treatment strategy); use of other second or third line drugs (defined as initiation of treatment with either thiazolidinediones, prandial glucose regulators, acarbose, sodium-glucose cotransporter-2 inhibitors, insulin, or combination of oral antidiabetic drugs; or switch to or add-on of an antidiabetic drug, including insulin, after failure with metformin or sulfonylurea in monotherapy); and use of first line drugs (defined as use of metformin or sulfonylurea in monotherapy). Exposures were lagged by one year for latency purposes and to minimise reverse causality. As part of this exposure definition, we considered participants switching to or adding-on an incretin based drug to be exposed until the end of follow-up (analogous to an intention-to-treat approach; supplementary figure 1). To minimise potential confounding by indication, we compared use of incretin based drugs (second or third line drugs) 1 with use of other second or third line drugs.
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A population-based atlas of the human pyramidal tract in 410 healthy participants

A population-based atlas of the human pyramidal tract in 410 healthy participants

Abstract With the advances in diffusion MRI and tractography, numerous atlases of the human pyramidal tract (PyT) have been proposed but the inherent limitation of tractography to resolve crisscrossed bundles within the centrum semiovale have so far prevented the complete description of the most lateral PyT projections. Here, we combined a precise manual positioning of individual subcortical regions of interest along the descending pathway of the PyT with a new bundle-specific tractography algorithm. This later is based on anatomical priors to improve streamlines tracking in crossing areas. We then extracted both left and right PyT in a large cohort of 410 healthy participants and built a probabilistic atlas of the whole-fanning PyT with a complete description of its most cortico-lateral projections. Clinical applications are envisaged, the whole-fanning probabilistic PyT atlas being likely a better marker of corticospinal integrity metrics than those currently used within the frame of prediction of post-stroke motor recovery. The present probabilistic PyT, freely available, provides an interesting tool for clinical applications in order to locate specific PyT damage and its impact to the short and long-term motor recovery after stroke.
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A population-based atlas of the human pyramidal tract in 410 healthy participants

A population-based atlas of the human pyramidal tract in 410 healthy participants

Abstract With the advances in diffusion MRI and tractography, numerous atlases of the human pyramidal tract (PyT) have been proposed but the inherent limitation of tractography to resolve crisscrossed bundles within the centrum semiovale have so far prevented the complete description of the most lateral PyT projections. Here, we combined a precise manual positioning of individual subcortical regions of interest along the descending pathway of the PyT with a new bundle-specific tractography algorithm. This later is based on anatomical priors to improve streamlines tracking in crossing areas. We then extracted both left and right PyT in a large cohort of 410 healthy participants and built a probabilistic atlas of the whole-fanning PyT with a complete description of its most cortico-lateral projections. Clinical applications are envisaged, the whole-fanning probabilistic PyT atlas being likely a better marker of corticospinal integrity metrics than those currently used within the frame of prediction of post-stroke motor recovery. The present probabilistic PyT, freely available, provides an interesting tool for clinical applications in order to locate specific PyT damage and its impact to the short and long-term motor recovery after stroke.
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Risk factors for ectopic pregnancy: a comprehensive analysis based on a large case-control, population-based study in France.

Risk factors for ectopic pregnancy: a comprehensive analysis based on a large case-control, population-based study in France.

In a previous study on another French population, we found an association between induced abortion and EP (55). We interpreted the association as the consequence of uterine injuries or infections following abortion because most, if not all, of the abortions in this previous study were surgical. This interpretation was not confirmed by the study presented here: the risk of EP was higher only for women who underwent medical abortions. However, the hypothesis that induced abortion leads to a higher risk of EP as a result of infection cannot be rejected. The association with medical abortion may be accounted for by the absence of systematic antibiotic prophylaxis in this group of women, whereas such prophylaxis is more routinely given in cases of surgical abortion.
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AZFc Deletions and Spermatogenic Failure: A Population-Based Survey of 20,000 Y Chromosomes

AZFc Deletions and Spermatogenic Failure: A Population-Based Survey of 20,000 Y Chromosomes

As suggested by the examples of the b2/b3 deletion in haplogroup N1 and the gr/gr deletion in haplogroup D2a, variation in deletion prevalence across populations might be due to a combination of two factors: (1) variation in deletion prevalence across Y chromosome haplogroups and (2) the enrichment for these haplogroups in particular populations. Therefore, we investigated whether deletion prevalence varies by haplogroup within the two largest population samples, those from Poland and the United States. Using seven Y chromosome SNPs, we assigned deleted chromosomes and a subsample of nondeleted chromosomes to one of nine Y chromosome haplogroups ( Table S5 ). 19 Figure 3 summarizes the findings and analysis. We excluded haplogroup N1, in which essentially all chromosomes have a b2/b3 deletion, to allow us to focus on other differences in deletion prevalence across haplogroups. We found, for example, that haplogroup R1a is significantly enriched among gr/gr-deleted chromo- somes in the Polish population and among b1/b3-deleted chromosomes in the United States population. In both the Polish and United States populations, non-N1 b2/ b3-deleted chromosomes, as compared to nondeleted chromosomes, show significant differences in haplogroup distribution ( Figure 3 and Table S6 provide statistical details). Thus, these populations include haplogroups (in addition to N1) that are enriched with the b2/b3 deletion. Of particular note is that two haplogroups—BC*xDEF and E—are enriched among b2/b3-deleted chromosomes in both Poland and the United States. The simplest explana- tion is that there exists in each of these haplogroups some yet-unidentified sub-branch that features the b2/b3 deletion—just as it is a universal feature of haplogroup N1. The current results, together with previous findings, allow us to estimate several population-genetic and epide- miological parameters for three AZFc-region deletions that cause or predispose to SSF: gr/gr, b1/b3, and b2/b4 (in decreasing order of prevalence in the general population). We will discuss them in order of their relative contribu- tions to SSF in the population: b2/b4, gr/gr, and b1/b3.
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