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- Romagnoni, A, et al.
(författare)
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Comparative performances of machine learning methods for classifying Crohn Disease patients using genome-wide genotyping data
- 2019
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Ingår i: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 9:1, s. 10351-
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Tidskriftsartikel (refereegranskat)abstract
- Crohn Disease (CD) is a complex genetic disorder for which more than 140 genes have been identified using genome wide association studies (GWAS). However, the genetic architecture of the trait remains largely unknown. The recent development of machine learning (ML) approaches incited us to apply them to classify healthy and diseased people according to their genomic information. The Immunochip dataset containing 18,227 CD patients and 34,050 healthy controls enrolled and genotyped by the international Inflammatory Bowel Disease genetic consortium (IIBDGC) has been re-analyzed using a set of ML methods: penalized logistic regression (LR), gradient boosted trees (GBT) and artificial neural networks (NN). The main score used to compare the methods was the Area Under the ROC Curve (AUC) statistics. The impact of quality control (QC), imputing and coding methods on LR results showed that QC methods and imputation of missing genotypes may artificially increase the scores. At the opposite, neither the patient/control ratio nor marker preselection or coding strategies significantly affected the results. LR methods, including Lasso, Ridge and ElasticNet provided similar results with a maximum AUC of 0.80. GBT methods like XGBoost, LightGBM and CatBoost, together with dense NN with one or more hidden layers, provided similar AUC values, suggesting limited epistatic effects in the genetic architecture of the trait. ML methods detected near all the genetic variants previously identified by GWAS among the best predictors plus additional predictors with lower effects. The robustness and complementarity of the different methods are also studied. Compared to LR, non-linear models such as GBT or NN may provide robust complementary approaches to identify and classify genetic markers.
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- Crous, P. W., et al.
(författare)
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Fungal Planet description sheets : 951-1041
- 2019
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Ingår i: Persoonia. - : RIJKSHERBARIUM. - 0031-5850 .- 1878-9080. ; 43, s. 223-425
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Tidskriftsartikel (refereegranskat)abstract
- Novel species of fungi described in this study include those from various countries as follows: Antarctica,Apenidiella antarctica from permafrost, Cladosporium fildesense from an unidentified marine sponge. Argentina,Geastrum wrightii on humus in mixed forest. Australia, Golovinomyces glandulariae on Glandularia aristigera,Neoanungitea eucalyptorum on leaves of Eucalyptus grandis, Teratosphaeria corymbiicola on leaves of Corymbiaficifolia, Xylaria eucalypti on leaves of Eucalyptus radiata. Brazil, Bovista psammophila on soil, Fusarium awaxy onrotten stalks of Zea mays, Geastrum lanuginosum on leaf litter covered soil, Hermetothecium mikaniae-micranthae(incl. Hermetothecium gen. nov.) on Mikania micrantha, Penicillium reconvexovelosoi in soil, Stagonosporopsis vannacciifrom pod of Glycine max. British Virgin Isles, Lactifluus guanensis on soil. Canada, Sorocybe oblongisporaon resin of Picea rubens. Chile, Colletotrichum roseum on leaves of Lapageria rosea. China, Setophoma cavernafrom carbonatite in Karst cave. Colombia, Lareunionomyces eucalypticola on leaves of Eucalyptus grandis. CostaRica, Psathyrella pivae on wood. Cyprus, Clavulina iris on calcareous substrate. France, Chromosera ambiguaand Clavulina iris var. occidentalis on soil. French West Indies, Helminthosphaeria hispidissima on dead wood.Guatemala, Talaromyces guatemalensis in soil. Malaysia, Neotracylla pini (incl. Tracyllales ord. nov. and Neotracyllagen. nov.) and Vermiculariopsiella pini on needles of Pinus tecunumanii. New Zealand, Neoconiothyriumviticola on stems of Vitis vinifera, Parafenestella pittospori on Pittosporum tenuifolium, Pilidium novae-zelandiaeon Phoenix sp. Pakistan, Russula quercus-floribundae on forest floor. Portugal, Trichoderma aestuarinum fromsaline water. Russia, Pluteus liliputianus on fallen branch of deciduous tree, Pluteus spurius on decaying deciduous wood or soil. South Africa, Alloconiothyrium encephalarti, Phyllosticta encephalarticola and Neothyrostromaencephalarti (incl. Neothyrostroma gen. nov.) on leaves of Encephalartos sp., Chalara eucalypticola on leaf spots ofEucalyptus grandis x urophylla, Clypeosphaeria oleae on leaves of Olea capensis, Cylindrocladiella postalofficiumon leaf litter of Sideroxylon inerme, Cylindromonium eugeniicola (incl. Cylindromonium gen. nov.) on leaf litter ofEugenia capensis, Cyphellophora goniomatis on leaves of Gonioma kamassi, Nothodactylaria nephrolepidis (incl.Nothodactylaria gen. nov. and Nothodactylariaceae fam. nov.) on leaves of Nephrolepis exaltata, Falcocladiumeucalypti and Gyrothrix eucalypti on leaves of Eucalyptus sp., Gyrothrix oleae on leaves of Olea capensis subsp.macrocarpa, Harzia metro-sideri on leaf litter of Metrosideros sp., Hippopotamyces phragmitis (incl. Hippopotamycesgen. nov.) on leaves of Phragmites australis, Lectera philenopterae on Philenoptera violacea, Leptosilliamayteni on leaves of Maytenus heterophylla, Lithohypha aloicola and Neoplatysporoides aloes on leaves of Aloesp., Millesimomyces rhoicissi (incl. Millesimomyces gen. nov.) on leaves of Rhoicissus digitata, Neodevriesiastrelitziicola on leaf litter of Strelitzia nicolai, Neokirramyces syzygii (incl. Neokirramyces gen. nov.) on leaf spots of Syzygium sp., Nothoramichloridium perseae (incl. Nothoramichloridium gen. nov. and Anungitiomycetaceae fam.nov.) on leaves of Persea americana, Paramycosphaerella watsoniae on leaf spots of Watsonia sp., Penicilliumcuddlyae from dog food, Podocarpomyces knysnanus (incl. Podocarpomyces gen. nov.) on leaves of Podocarpusfalcatus, Pseudocercospora heteropyxidicola on leaf spots of Heteropyxis natalensis, Pseudopenidiella podocarpi,Scolecobasidium podocarpi and Ceramothyrium podocarpicola on leaves of Podocarpus latifolius, Scolecobasidiumblechni on leaves of Blechnum capense, Stomiopeltis syzygii on leaves of Syzygium chordatum, Strelitziomycesknysnanus (incl. Strelitziomyces gen. nov.) on leaves of Strelitzia alba, Talaromyces clemensii from rotting wood ingoldmine, Verrucocladosporium visseri on Carpobrotus edulis. Spain, Boletopsis mediterraneensis on soil, Calycinacortegadensisi on a living twig of Castanea sativa, Emmonsiellopsis tuberculata in fluvial sediments, Mollisia cortegadensison dead attached twig of Quercus robur, Psathyrella ovispora on soil, Pseudobeltrania lauri on leaf litterof Laurus azorica, Terfezia dunensis in soil, Tuber lucentum in soil, Venturia submersa on submerged plant debris.Thailand, Cordyceps jakajanicola on cicada nymph, Cordyceps kuiburiensis on spider, Distoseptispora caricis onleaves of Carex sp., Ophiocordyceps khonkaenensis on cicada nymph. USA, Cytosporella juncicola and Davidiellomycesjuncicola on culms of Juncus effusus, Monochaetia massachusettsianum from air sample, Neohelicomycesmelaleucae and Periconia neobrittanica on leaves of Melaleuca styphelioides x lanceolata, Pseudocamarosporiumeucalypti on leaves of Eucalyptus sp., Pseudogymnoascus lindneri from sediment in a mine, Pseudogymnoascusturneri from sediment in a railroad tunnel, Pulchroboletus sclerotiorum on soil, Zygosporium pseudomasonii onleaf of Serenoa repens. Vietnam, Boletus candidissimus and Veloporphyrellus vulpinus on soil. Morphological andculture characteristics are supported by DNA barcodes.
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- Rusak, J. A., et al.
(författare)
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Wind and trophic status explain within and among‐lake variability of algal biomass
- 2018
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Ingår i: Limnology and Oceanography Letters. - : John Wiley & Sons. - 2378-2242. ; 3:6, s. 409-418
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Tidskriftsartikel (refereegranskat)abstract
- Phytoplankton biomass and production regulates key aspects of freshwater ecosystems yet its variability and subsequent predictability is poorly understood. We estimated within‐lake variation in biomass using high‐frequency chlorophyll fluorescence data from 18 globally distributed lakes. We tested how variation in fluorescence at monthly, daily, and hourly scales was related to high‐frequency variability of wind, water temperature, and radiation within lakes as well as productivity and physical attributes among lakes. Within lakes, monthly variation dominated, but combined daily and hourly variation were equivalent to that expressed monthly. Among lakes, biomass variability increased with trophic status while, within‐lake biomass variation increased with increasing variability in wind speed. Our results highlight the benefits of high‐frequency chlorophyll monitoring and suggest that predicted changes associated with climate, as well as ongoing cultural eutrophication, are likely to substantially increase the temporal variability of algal biomass and thus the predictability of the services it provides.
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- Farzan, N, et al.
(författare)
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Rationale and design of the multiethnic Pharmacogenomics in Childhood Asthma consortium
- 2017
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Ingår i: Pharmacogenomics. - : Future Medicine Ltd. - 1744-8042 .- 1462-2416. ; 18:10, s. 931-943
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Tidskriftsartikel (refereegranskat)abstract
- Aim: International collaboration is needed to enable large-scale pharmacogenomics studies in childhood asthma. Here, we describe the design of the Pharmacogenomics in Childhood Asthma (PiCA) consortium. Materials & methods: Investigators of each study participating in PiCA provided data on the study characteristics by answering an online questionnaire. Results: A total of 21 studies, including 14,227 children/young persons (58% male), from 12 different countries are currently enrolled in the PiCA consortium. Fifty six percent of the patients are Caucasians. In total, 7619 were inhaled corticosteroid users. Among patients from 13 studies with available data on asthma exacerbations, a third reported exacerbations despite inhaled corticosteroid use. In the future pharmacogenomics studies within the consortium, the pharmacogenomics analyses will be performed separately in each center and the results will be meta-analyzed. Conclusion: PiCA is a valuable platform to perform pharmacogenetics studies within a multiethnic pediatric asthma population.
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| 13. |
- Fleming, E.J., et al.
(författare)
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Provenance of Triassic sandstones on the southwest Barents Shelf and the implication for sediment dispersal patterns in northwest Pangaea.
- 2016
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Ingår i: Marine and Petroleum Geology. - : Elsevier BV. - 0264-8172 .- 1873-4073. ; 78, s. 516-535
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Tidskriftsartikel (refereegranskat)abstract
- Thick Triassic siliciclastic units form major reservoir targets for hydrocarbon exploration on the Barents Shelf; however, poor reservoir quality, possibly associated with variation in provenance, remains a key risk factor in the area. In this study, sandstone dispersal patterns on the southwest Barents Shelf are investigated through petrographic and heavy mineral analysis, garnet and rutile geochemistry and zircon U-Pb geochronology. The results show that until the Early Norian Maximum Flooding Surface, two contrasting sand types were present: (i) a Caledonian Sand Type, characterised by a high compositional maturity, a heavy mineral assemblage dominated by garnet and low chrome-spinel:zircon (CZi) values, predominantly metapelitic rutiles and mostly Proterozoic and Archaean detrital zircon ages, interpreted to be sourced from the Caledonides, and (ii) a Uralian Sand Type, characterised by a low compositional maturity, high CZi values, predominantly metamafic rutiles and Carboniferous zircon ages, sourced from the Uralian Orogeny. In addition, disparity in detrital zircon ages of the Uralian Sand Type with contiguous strata on the northern Barents Shelf reveals the presence of a Northern Uraloid Sand Type, interpreted to have been sourced from Taimyr and Severnaya Zemlya. As such, a coincidental system is inferred which delivered sand to the Northern Barents Shelf in the late Carnian/early Norian. Following the Early Norian Maximum Flooding Surface, a significant provenance change occurs. In response to Late Triassic/Early Jurassic hinterland rejuvenation, supply from the Uralian Orogen ceased and the northern Scandinavian (Caledonian) source became dominant, extending northwards out on to the southwest Barents Shelf. The data reveal a link between reservoir quality and sand type and illustrate how provenance played an important role in the development of clastic reservoirs within the Triassic of the Barents Shelf.
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| 14. |
- Rosengren, Annika, 1951, et al.
(författare)
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Socioeconomic status and risk of cardiovascular disease in 20 low-income, middle-income, and high-income countries: the Prospective Urban Rural Epidemiologic (PURE) study
- 2019
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Ingår i: Lancet Global Health. - : Elsevier BV. - 2214-109X. ; 7:6
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Tidskriftsartikel (refereegranskat)abstract
- Background Socioeconomic status is associated with differences in risk factors for cardiovascular disease incidence and outcomes, including mortality However, it is unclear whether the associations between cardiovascular disease and common measures of socioeconomic status-wealth and education-differ among high-income, middle-income, and low-income countries, and, if so, why these differences exist. We explored the association between education and household wealth and cardiovascular disease and mortality to assess which marker is the stronger predictor of outcomes, and examined whether any differences in cardiovascular disease by socioeconomic status parallel differences in risk factor levels or differences in management. Methods In this large-scale prospective cohort study, we recruited adults aged between 35 years and 70 years from 367 urban and 302 rural communities in 20 countries. We collected data on families and households in two questionnaires, and data on cardiovascular risk factors in a third questionnaire, which was supplemented with physical examination. We assessed socioeconomic status using education and a household wealth index. Education was categorised as no or primary school education only, secondary school education, or higher education, defined as completion of trade school, college, or university. Household wealth, calculated at the household level and with household data, was defined by an index on the basis of ownership of assets and housing characteristics. Primary outcomes were major cardiovascular disease (a composite of cardiovascular deaths, strokes, myocardial infarction, and heart failure), cardiovascular mortality, and all-cause mortality. Information on specific events was obtained from participants or their family. Findings Recruitment to the study began on Jan 12, 2001, with most participants enrolled between Jan 6, 2005, and Dec 4, 2014. 160 299 (87.9%) of 182 375 participants with baseline data had available follow-up event data and were eligible for inclusion. After exclusion of 6130 (3.8%) participants without complete baseline or follow-up data, 154 169 individuals remained for analysis, from five low-income, 11 middle-income, and four high-income countries. Participants were followed-up for a mean of 7.5 years. Major cardiovascular events were more common among those with low levels of education in all types of country studied, but much more so in low-income countries. After adjustment for wealth and other factors, the HR (low level of education vs high level of education) was 1.23 (95% CI 0.96-1.58) for high-income countries, 1.59 (1.42-1.78) in middle-income countries, and 2.23 (1.79-2.77) in low-income countries (p(interaction)<0 .0001). We observed similar results for all-cause mortality, with HRs of 1.50 (1.14-1.98) for high-income countries, 1.80 (1.58-2.06) in middle-income countries, and 2.76 (2.29-3.31) in low-income countries (p(interaction)<0. 0001). By contrast, we found no or weak associations between wealth and these two outcomes. Differences in outcomes between educational groups were not explained by differences in risk factors, which decreased as the level of education increased in high-income countries, but increased as the level of education increased in low-income countries (p(interaction)<0.0001). Medical care (eg, management of hypertension, diabetes, and secondary prevention) seemed to play an important part in adverse cardiovascular disease outcomes because such care is likely to be poorer in people with the lowest levels of education compared to those with higher levels of education in low-income countries; however, we observed less marked differences in care based on level of education in middle-income countries and no or minor differences in high-income countries. Interpretation Although people with a lower level of education in low-income and middle-income countries have higher incidence of and mortality from cardiovascular disease, they have better overall risk factor profiles. However, these individuals have markedly poorer health care. Policies to reduce health inequities globally must include strategies to overcome barriers to care, especially for those with lower levels of education. Copyright (C) 2019 The Author(s). Published by Elsevier Ltd.
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| 15. |
- Lagergren, J, et al.
(författare)
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Oesophageal cancer
- 2017
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Ingår i: Lancet (London, England). - 1474-547X. ; 390:10110, s. 2383-2396
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Tidskriftsartikel (refereegranskat)
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| 17. |
- Smyth, Joshua M., et al.
(författare)
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Everyday stress response targets in the science of behavior change
- 2018
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Ingår i: Behaviour Research and Therapy. - : Elsevier. - 0005-7967 .- 1873-622X. ; 101, s. 20-29
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Tidskriftsartikel (refereegranskat)abstract
- Stress is an established risk factor for negative health outcomes, and responses to everyday stress can interfere with health behaviors such as exercise and sleep. In accordance with the Science of Behavior Change (SOBC) program, we apply an experimental medicine approach to identifying stress response targets, developing stress response assays, intervening upon these targets, and testing intervention effectiveness. We evaluate an ecologically valid, within-person approach to measuring the deleterious effects of everyday stress on physical activity and sleep patterns, examining multiple stress response components (i.e., stress reactivity, stress recovery, and stress pile-up) as indexed by two key response indicators (negative affect and perseverative cognition). Our everyday stress response assay thus measures multiple malleable stress response targets that putatively shape daily health behaviors (physical activity and sleep). We hypothesize that larger reactivity, incomplete recovery, and more frequent stress responses (pile-up) will negatively impact health behavior enactment in daily life. We will identify stress-related reactivity, recovery, and response in the indicators using coordinated analyses across multiple naturalistic studies. These results are the basis for developing a new stress assay and replicating the initial findings in a new sample. This approach will advance our understanding of how specific aspects of everyday stress responses influence health behaviors, and can be used to develop and test an innovative ambulatory intervention for stress reduction in daily life to enhance health behaviors. (C) 2017 Elsevier Ltd. All rights reserved.
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| 18. |
- Yates, E. J., et al.
(författare)
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Out-of-hospital cardiac arrest termination of resuscitation with ongoing CPR : An observational study
- 2018
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Ingår i: Resuscitation. - : Elsevier BV. - 0300-9572. ; 130, s. 21-27
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Tidskriftsartikel (refereegranskat)abstract
- Introduction: Termination of resuscitation guidelines for out-of-hospital cardiac arrest can identify patients in whom continuing resuscitation has little chance of success. This study examined the outcomes of patients transferred to hospital with ongoing CPR. It assessed outcomes for those who would have met the universal prehospital termination of resuscitation criteria (no shocks administered, unwitnessed by emergency medical services, no return of spontaneous circulation). Methods: A retrospective cohort study of consecutive adult patients who were transported to hospital with ongoing CPR was conducted at three hospitals in the West Midlands, UK between September 2016 and November 2017. Patient characteristics, interventions and response to treatment (ROSC, survival to discharge) were identified. Results: 227 (median age 69 years, 67.8% male) patients were identified. 89 (39.2%) met the universal prehospital termination of resuscitation criteria. Seven (3.1%) were identified with a potentially reversible cause of cardiac arrest. After hospital arrival, patients received few specialist interventions that were not available in the prehospital setting. Most (n = 210, 92.5%) died in the emergency department. 17 were admitted (14 to intensive care), of which 3 (1.3%) survived to hospital discharge. There were no survivors (0%) in those who met the criteria for universal prehospital termination of resuscitation. Conclusion: Overall survival amongst patients transported to hospital with ongoing CPR was very poor. Application of the universal prehospital termination of resuscitation rule, in patients without obvious reversible causes of cardiac arrest, would have allowed resuscitation to have been discontinued at the scene for 39.2% of patients who did not survive.
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| 19. |
- Zawadzki, Matthew J., et al.
(författare)
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Understanding stress reports in daily life : a coordinated analysis of factors associated with the frequency of reporting stress
- 2019
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Ingår i: Journal of behavioral medicine. - : Springer. - 0160-7715 .- 1573-3521. ; 42:3, s. 545-560
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Tidskriftsartikel (refereegranskat)abstract
- Although stress is a common experience in everyday life, a clear understanding of how often an individual experiences and reports stress is lacking. Notably, there is little information regarding factors that may influence how frequently stress is reported, including which stress dimension is measured (i.e., stressorsdid an event happen, subjective stresshow stressed do you feel, conditional stresshow stressful a stressor was) and the temporal features of that assessment (i.e., time of day, day of study, weekday vs. weekend day). The purpose of the present study was to conduct a coordinated analysis of five independent ecological momentary assessment studies utilizing varied stress reporting dimensions and temporal features. Results indicated that, within days, stress was reported at different frequencies depending on the stress dimension. Stressors were reported on 15-32% of momentary reports made within a day; across days, the frequency ranged from 42 to 76% of days. Depending on the cutoff, subjective stress was reported more frequently ranging about 8-56% of all moments within days, and 40-90% of days. Likewise, conditional stress ranged from just 3% of moments to 22%, and 11-69% of days. For the temporal features, stress was reported more frequently on weekdays (compared to weekend days) and on days earlier in the study (relative to days later in the study); time of day was inconsistently related to stress reports. In sum, stress report frequency depends in part on how stress is assessed. As such, researchers may wish to measure stress in multiple ways and, in the case of subjective and conditional stress with multiple operational definitions, to thoroughly characterize the frequency of stress reporting.
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