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| 2. |
- Sushko, Iurii, et al.
(författare)
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Applicability Domains for Classification Problems : Benchmarking of Distance to Models for Ames Mutagenicity Set.
- 2010
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Ingår i: Journal of chemical information and modeling. - : American Chemical Society (ACS). - 1549-9596 .- 1549-960X. ; 50:12, s. 2094-2111
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Tidskriftsartikel (refereegranskat)abstract
- The estimation of accuracy and applicability of QSAR and QSPR models for biological and physicochemical properties represents a critical problem. The developed parameter of "distance to model" (DM) is defined as a metric of similarity between the training and test set compounds that have been subjected to QSAR/QSPR modeling. In our previous work, we demonstrated the utility and optimal performance of DM metrics that have been based on the standard deviation within an ensemble of QSAR models. The current study applies such analysis to 30 QSAR models for the Ames mutagenicity data set that were previously reported within the 2009 QSAR challenge. We demonstrate that the DMs based on an ensemble (consensus) model provide systematically better performance than other DMs. The presented approach identifies 30-60% of compounds having an accuracy of prediction similar to the interlaboratory accuracy of the Ames test, which is estimated to be 90%. Thus, the in silico predictions can be used to halve the cost of experimental measurements by providing a similar prediction accuracy. The developed model has been made publicly available at http://ochem.eu/models/1 .
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| 3. |
- Bahadoer, Renu R., et al.
(författare)
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One-year excess mortality and treatment in surgically treated patients with colorectal cancer : A EURECCA European comparison
- 2021
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Ingår i: European Journal of Surgical Oncology. - : Elsevier. - 0748-7983 .- 1532-2157. ; 47:7, s. 1651-1660
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Tidskriftsartikel (refereegranskat)abstract
- Background: Mortality in the first postoperative year represents an accurate reflection of the perioperative risk after colorectal cancer surgery. This research compares one-year mortality after surgery divided into three age-categories (18-64, 65-74, ≥75 years), focusing on time trends and comparing treatment strategies.Material: Population-based data of all patients diagnosed and treated surgically for stage I-III primary colorectal cancer from 2007 to 2016, were collected from Belgium, the Netherlands, Norway, and Sweden. Stratified for age-category and stage, treatment was evaluated, and 30-day, one-year and one-year excess mortality were calculated for colon and rectal cancer separately. Results were evaluated over two-year time periods.Results: Data of 206,024 patients were analysed. Postoperative 30-day and one-year mortality reduced significantly over time in all countries and age-categories. Within the oldest age category, in 2015–2016, one-year excess mortality varied from 9% in Belgium to 4% in Sweden for colon cancer and, from 9% in Belgium to 3% in the other countries for rectal cancer. With increasing age, patients were less likely to receive additional therapy besides surgery. In Belgium, colon cancer patients were more often treated with adjuvant chemotherapy (p < 0.001). For neoadjuvant treatment of rectal cancer, patients in Belgium and Norway were mostly treated with chemoradiotherapy. In the Netherlands and Sweden, radiotherapy alone was preferred (p < 0.001).Conclusions: Despite improvement over time in all countries and age-categories, substantial variation exists in one-year postoperative mortality. Differences in one-year excess postoperative mortality could be due to differences in treatment strategies, highlighting the consequences of under- and over-treatment on cancer survival.
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| 4. |
- Bahadoer, Renu R., et al.
(författare)
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The survival gap between young and older patients after surgical resection for colorectal cancer remains largely based on early mortality : A EURECCA comparison of four European countries
- 2022
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Ingår i: Journal of Geriatric Oncology. - : Elsevier. - 1879-4068 .- 1879-4076. ; 13:6, s. 803-812
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Tidskriftsartikel (refereegranskat)abstract
- Background: A decade ago, it was demonstrated that the difference in survival between older patients and younger patients with colorectal cancer (CRC) was mainly due to mortality in the first postoperative year. Over the last few years, improvements - especially in perioperative care - have increased survival. The current research investigates whether a survival gap between younger and older patients with CRC still exists on a national level in four European countries.Methods: Population-based data from Belgium, the Netherlands, Norway, and Sweden were collected from patients that underwent surgical resection for primary stage I-III CRC between 2007 and 2016. Relative survival and conditional relative survival (CS), with the condition of surviving the first postoperative year, were calculated for colon and rectal cancer separately, stratified for country and age category (<65, 65–75, ≥75 years). In addition, relative excess risk of death (RER) was estimated, and one-year excess mortality was calculated.Results: Data of 206,024 patients were analyzed. In general, compared to patients <65 years, patients ≥75 years had a worse survival during the first year after surgery, which was most pronounced in Belgium (RER colon cancer 2.5 [95% confidence interval (CI) 2.3–2.8] and RER rectal cancer 2.6 [95% CI 2.3–2.9]). After surviving the first year, CS was mostly not statistically different between patients <65 years and patients ≥75 years with stage I-II, with the exception of stage II colon cancer in Belgium. However, CS remained worse in the largest part of the patients ≥75 years with stage III colon or rectal cancer (except for rectal cancer in Norway).Conclusions: Although differences exist between the countries, the survival gap between young and older patients is based mainly on early mortality and remains only for stage III disease after surviving the first year.
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| 5. |
- Demichev, Vadim, et al.
(författare)
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A time-resolved proteomic and prognostic map of COVID-19
- 2021
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Ingår i: Cell Systems. - : Elsevier BV. - 2405-4712 .- 2405-4720. ; 12:8, s. 780-794.e7
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Tidskriftsartikel (refereegranskat)abstract
- COVID-19 is highly variable in its clinical presentation, ranging from asymptomatic infection to severe organ damage and death. We characterized the time-dependent progression of the disease in 139 COVID-19 inpatients by measuring 86 accredited diagnostic parameters, such as blood cell counts and enzyme activities, as well as untargeted plasma proteomes at 687 sampling points. We report an initial spike in a systemic inflammatory response, which is gradually alleviated and followed by a protein signature indicative of tissue repair, metabolic reconstitution, and immunomodulation. We identify prognostic marker signatures for devising risk-adapted treatment strategies and use machine learning to classify therapeutic needs. We show that the machine learning models based on the proteome are transferable to an independent cohort. Our study presents a map linking routinely used clinical diagnostic parameters to plasma proteomes and their dynamics in an infectious disease.
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| 6. |
- Felix, Janine F, et al.
(författare)
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Genome-wide association analysis identifies three new susceptibility loci for childhood body mass index.
- 2016
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Ingår i: Human molecular genetics. - : Oxford University Press (OUP). - 1460-2083 .- 0964-6906. ; 25:2, s. 389-403
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Tidskriftsartikel (refereegranskat)abstract
- A large number of genetic loci are associated with adult body mass index. However, the genetics of childhood body mass index are largely unknown. We performed a meta-analysis of genome-wide association studies of childhood body mass index, using sex- and age-adjusted standard deviation scores. We included 35 668 children from 20 studies in the discovery phase and 11 873 children from 13 studies in the replication phase. In total, 15 loci reached genome-wide significance (P-value < 5 × 10(-8)) in the joint discovery and replication analysis, of which 12 are previously identified loci in or close to ADCY3, GNPDA2, TMEM18, SEC16B, FAIM2, FTO, TFAP2B, TNNI3K, MC4R, GPR61, LMX1B and OLFM4 associated with adult body mass index or childhood obesity. We identified three novel loci: rs13253111 near ELP3, rs8092503 near RAB27B and rs13387838 near ADAM23. Per additional risk allele, body mass index increased 0.04 Standard Deviation Score (SDS) [Standard Error (SE) 0.007], 0.05 SDS (SE 0.008) and 0.14 SDS (SE 0.025), for rs13253111, rs8092503 and rs13387838, respectively. A genetic risk score combining all 15 SNPs showed that each additional average risk allele was associated with a 0.073 SDS (SE 0.011, P-value = 3.12 × 10(-10)) increase in childhood body mass index in a population of 1955 children. This risk score explained 2% of the variance in childhood body mass index. This study highlights the shared genetic background between childhood and adult body mass index and adds three novel loci. These loci likely represent age-related differences in strength of the associations with body mass index.
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| 7. |
- Gut, Urs, et al.
(författare)
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No systematic effects of sampling direction on climate-growth relationships in a large-scale, multi-species tree-ring data set
- 2019
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Ingår i: Dendrochronologia. - : Elsevier BV. - 1125-7865 .- 1612-0051. ; 57
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Tidskriftsartikel (refereegranskat)abstract
- Ring-width series are important for diverse fields of research such as the study of past climate, forest ecology, forest genetics, and the determination of origin (dendro-provenancing) or dating of archaeological objects. Recent research suggests diverging climate-growth relationships in tree-rings due to the cardinal direction of extracting the tree cores (i.e. direction-specific effect). This presents an understudied source of bias that potentially affects many data sets in tree-ring research. In this study, we investigated possible direction-specific growth variability based on an international (10 countries), multi-species (8 species) tree-ring width network encompassing 22 sites. To estimate the effect of direction-specific growth variability on climate-growth relationships, we applied a combination of three methods: An analysis of signal strength differences, a Principal Component Gradient Analysis and a test on the direction-specific differences in correlations between indexed ring-widths series and climate variables. We found no evidence for systematic direction-specific effects on tree radial growth variability in high-pass filtered ring-width series. In addition, direction-specific growth showed only marginal effects on climate-growth correlations. These findings therefore indicate that there is no consistent bias caused by coring direction in data sets used for diverse dendrochronological applications on relatively mesic sites within forests in flat terrain, as were studied here. However, in extremely dry, warm or cold environments, or on steep slopes, and for different life-forms such as shrubs, further research is advisable.
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| 8. |
- Vogelezang, Suzanne, et al.
(författare)
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Novel loci for childhood body mass index and shared heritability with adult cardiometabolic traits.
- 2020
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Ingår i: PLoS genetics. - : Public Library of Science (PLoS). - 1553-7404. ; 16:10
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Tidskriftsartikel (refereegranskat)abstract
- The genetic background of childhood body mass index (BMI), and the extent to which the well-known associations of childhood BMI with adult diseases are explained by shared genetic factors, are largely unknown. We performed a genome-wide association study meta-analysis of BMI in 61,111 children aged between 2 and 10 years. Twenty-five independent loci reached genome-wide significance in the combined discovery and replication analyses. Two of these, located near NEDD4L and SLC45A3, have not previously been reported in relation to either childhood or adult BMI. Positive genetic correlations of childhood BMI with birth weight and adult BMI, waist-to-hip ratio, diastolic blood pressure and type 2 diabetes were detected (Rg ranging from 0.11 to 0.76, P-values <0.002). A negative genetic correlation of childhood BMI with age at menarche was observed. Our results suggest that the biological processes underlying childhood BMI largely, but not completely, overlap with those underlying adult BMI. The well-known observational associations of BMI in childhood with cardio-metabolic diseases in adulthood may reflect partial genetic overlap, but in light of previous evidence, it is also likely that they are explained through phenotypic continuity of BMI from childhood into adulthood.
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