| 1. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 2. |
- Santangelo, James S., et al.
(författare)
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Global urban environmental change drives adaptation in white clover
- 2022
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 375
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Tidskriftsartikel (refereegranskat)abstract
- Urbanization transforms environments in ways that alter biological evolution. We examined whether urban environmental change drives parallel evolution by sampling 110,019 white clover plants from 6169 populations in 160 cities globally. Plants were assayed for a Mendelian antiherbivore defense that also affects tolerance to abiotic stressors. Urban-rural gradients were associated with the evolution of clines in defense in 47% of cities throughout the world. Variation in the strength of clines was explained by environmental changes in drought stress and vegetation cover that varied among cities. Sequencing 2074 genomes from 26 cities revealed that the evolution of urban-rural dines was best explained by adaptive evolution, but the degree of parallel adaptation varied among cities. Our results demonstrate that urbanization leads to adaptation at a global scale.
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| 3. |
- Brandão, Andreia, et al.
(författare)
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The CHEK2 Variant C.349A>G Is Associated with Prostate Cancer Risk and Carriers Share a Common Ancestor
- 2020
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Ingår i: Cancers. - : MDPI AG. - 2072-6694. ; 12:11
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Tidskriftsartikel (refereegranskat)abstract
- The identification of recurrent founder variants in cancer predisposing genes may have important implications for implementing cost-effective targeted genetic screening strategies. In this study, we evaluated the prevalence and relative risk of the CHEK2 recurrent variant c.349A>G in a series of 462 Portuguese patients with early-onset and/or familial/hereditary prostate cancer (PrCa), as well as in the large multicentre PRACTICAL case-control study comprising 55,162 prostate cancer cases and 36,147 controls. Additionally, we investigated the potential shared ancestry of the carriers by performing identity-by-descent, haplotype and age estimation analyses using high-density SNP data from 70 variant carriers belonging to 11 different populations included in the PRACTICAL consortium. The CHEK2 missense variant c.349A>G was found significantly associated with an increased risk for PrCa (OR 1.9; 95% CI: 1.1-3.2). A shared haplotype flanking the variant in all carriers was identified, strongly suggesting a common founder of European origin. Additionally, using two independent statistical algorithms, implemented by DMLE+2.3 and ESTIAGE, we were able to estimate the age of the variant between 2300 and 3125 years. By extending the haplotype analysis to 14 additional carrier families, a shared core haplotype was revealed among all carriers matching the conserved region previously identified in the high-density SNP analysis. These findings are consistent with CHEK2 c.349A>G being a founder variant associated with increased PrCa risk, suggesting its potential usefulness for cost-effective targeted genetic screening in PrCa families.
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| 4. |
- Carvalho, Sérgio A., et al.
(författare)
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Efficacy of an ACT and Compassion-Based eHealth Program for Self-Management of Chronic Pain (iACTwithPain) : Study Protocol for a Randomized Controlled Trial
- 2021
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Ingår i: Frontiers in Psychology. - : Frontiers Media S.A.. - 1664-1078. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- Background: Chronic pain (CP) has serious medical and social consequences and leads to economic burden that threatens the sustainability of healthcare services. Thus, optimized management of pain tools to support CP patients in adjusting to their condition and improving their quality of life is timely. Although acceptance and commitment therapy (ACT) is considered an evidence-based psychological approach for CP, evidence for the efficacy of online-delivered ACT for CP is still scarce. At the same time, studies suggest that self-compassion mediates the change in disability and psychopathological symptoms in ACT interventions for CP, although self-compassion is not a specific target in ACT. Thus, an explicit focus on self-compassion might increase the efficacy of ACT interventions for CP, although this hypothesis has not been tested. This study aims to develop an eHealth ACT and compassion-based self-management intervention for CP, the iACTwithPain, and to compare its efficacy in improving health outcomes to a similar ACT-only intervention and a medical TAU group.Methods: The eHealth platform that will host the interventions will be developed using a flat design identity and will be interactive. The iACTwithPain intervention will comprise eight weekly self-management sessions and will be developed taking into consideration the psychological flexibility model applied to CP, with the addition of explicit compassion-based components. To analyze whether the iACTwithPain intervention will present superiority in improving CP's impact and related health markers over the two other conditions, this study will follow an RCT design with three arms. CP patients will be recruited through direct contact with patient associations and healthcare services and a national press release in Portugal. Outcome measurement will be conducted at baseline, post-intervention and at 3- and 6-month follow-ups. The interventions' acceptability will also be assessed.Discussion: The iACTwithPain intervention is expected to improve CP patients' psychosocial functioning, quality of life, and empowerment, by promoting adaptive disease management and regulation of pain-related internal experiences. Results will contribute to a better understanding on the pertinence of adding compassion elements to ACT for CP and to reach an optimized intervention for CP.
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| 5. |
- Conti, David, V, et al.
(författare)
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Trans-ancestry genome-wide association meta-analysis of prostate cancer identifies new susceptibility loci and informs genetic risk prediction
- 2021
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Ingår i: Nature Genetics. - : Springer Nature. - 1061-4036 .- 1546-1718. ; 53:1, s. 65-75
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Tidskriftsartikel (refereegranskat)abstract
- Prostate cancer is a highly heritable disease with large disparities in incidence rates across ancestry populations. We conducted a multiancestry meta-analysis of prostate cancer genome-wide association studies (107,247 cases and 127,006 controls) and identified 86 new genetic risk variants independently associated with prostate cancer risk, bringing the total to 269 known risk variants. The top genetic risk score (GRS) decile was associated with odds ratios that ranged from 5.06 (95% confidence interval (CI), 4.84-5.29) for men of European ancestry to 3.74 (95% CI, 3.36-4.17) for men of African ancestry. Men of African ancestry were estimated to have a mean GRS that was 2.18-times higher (95% CI, 2.14-2.22), and men of East Asian ancestry 0.73-times lower (95% CI, 0.71-0.76), than men of European ancestry. These findings support the role of germline variation contributing to population differences in prostate cancer risk, with the GRS offering an approach for personalized risk prediction. A meta-analysis of genome-wide association studies across different populations highlights new risk loci and provides a genetic risk score that can stratify prostate cancer risk across ancestries.
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| 6. |
- Cooper, Declan L.M., et al.
(författare)
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Consistent patterns of common species across tropical tree communities
- 2024
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Ingår i: Nature. - 0028-0836 .- 1476-4687. ; 625:7996, s. 728-734
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Tidskriftsartikel (refereegranskat)abstract
- Trees structure the Earth’s most biodiverse ecosystem, tropical forests. The vast number of tree species presents a formidable challenge to understanding these forests, including their response to environmental change, as very little is known about most tropical tree species. A focus on the common species may circumvent this challenge. Here we investigate abundance patterns of common tree species using inventory data on 1,003,805 trees with trunk diameters of at least 10 cm across 1,568 locations 1–6 in closed-canopy, structurally intact old-growth tropical forests in Africa, Amazonia and Southeast Asia. We estimate that 2.2%, 2.2% and 2.3% of species comprise 50% of the tropical trees in these regions, respectively. Extrapolating across all closed-canopy tropical forests, we estimate that just 1,053 species comprise half of Earth’s 800 billion tropical trees with trunk diameters of at least 10 cm. Despite differing biogeographic, climatic and anthropogenic histories 7, we find notably consistent patterns of common species and species abundance distributions across the continents. This suggests that fundamental mechanisms of tree community assembly may apply to all tropical forests. Resampling analyses show that the most common species are likely to belong to a manageable list of known species, enabling targeted efforts to understand their ecology. Although they do not detract from the importance of rare species, our results open new opportunities to understand the world’s most diverse forests, including modelling their response to environmental change, by focusing on the common species that constitute the majority of their trees.
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| 7. |
- Couto Bazame, Helizani, et al.
(författare)
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Mapping coffee yield with computer vision
- 2022
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Ingår i: Precision Agriculture. - : Springer Science and Business Media LLC. - 1385-2256 .- 1573-1618. ; 23:6, s. 2372-2387
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Tidskriftsartikel (refereegranskat)abstract
- Yield maps guide investigations into the causes of spatial and temporal variations in crop yields. The objective of this work was to implement an algorithm based on computer vision to quantify the number of coffee fruits and to build yield maps. Data were collected in two areas of a commercial Arabica coffee (Coffea arabica) plantation. The images of the coffee fruits were taken from 90 videos acquired during the harvest. The You Only Look Once version 4 (YOLOv4) model was used for the detection and counting of coffee fruits. Geographic coordinates were registered at the same time the videos were recorded and associated with video frames. The number of coffee fruit detections for each frame was converted into yield considering the average distance covered by the harvester and the distance between coffee rows of 4 m. The yield maps were interpolated from the video frames’ respective geographic coordinates. The YOLOv4 model had a mean average precision of 83.5%. The yield map estimated from the detections obtained by the computer vision model was able to explain 81% of the variance of the reference yield map. The main contributions of the proposed methodology are its low implementation cost and the independence of specific brands of coffee harvesters for the implementation of the image capture structure. Another advantage of this methodology is the possibility of saving raw data from the entire harvest. Thus, its user can pursue further improvements for the model in the future and validate its performance under different scenarios.
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| 8. |
- Daelman, Bo, et al.
(författare)
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Frailty and cognitive function in middle-aged and older adults with congenital heart disease
- 2024
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Ingår i: Journal of the American College of Cardiology. - : Elsevier. - 0735-1097 .- 1558-3597. ; 83:12, s. 1149-1159
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Tidskriftsartikel (refereegranskat)abstract
- Background: Life expectancy of patients with congenital heart disease (CHD) has increased rapidly, resulting in a growing and aging population. Recent studies have shown that older people with CHD have higher morbidity, health care use, and mortality. To maintain longevity and quality of life, understanding their evolving medical and psychosocial challenges is essential.Objectives: The authors describe the frailty and cognitive profile of middle-aged and older adults with CHD to identify predictor variables and to explore the relationship with hospital admissions and outpatient visits.Methods: Using a cross-sectional, multicentric design, we included 814 patients aged ≥40 years from 11 countries. Frailty phenotype was determined using the Fried method. Cognitive function was assessed by the Montreal Cognitive Assessment.Results: In this sample, 52.3% of patients were assessed as robust, 41.9% as prefrail, and 5.8% as frail; 38.8% had cognitive dysfunction. Multinomial regression showed that frailty was associated with older age, female sex, higher physiologic class, and comorbidities. Counterintuitively, patients with mild heart defects were more likely than those with complex lesions to be prefrail. Patients from middle-income countries displayed more prefrailty than those from higher-income countries. Logistic regression demonstrated that cognitive dysfunction was related to older age, comorbidities, and lower country-level income.Conclusions: Approximately one-half of included patients were (pre-)frail, and more than one-third experienced cognitive impairment. Frailty and cognitive dysfunction were identified in patients with mild CHD, indicating that these concerns extend beyond severe CHD. Assessing frailty and cognition routinely could offer valuable insights into this aging population.
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| 9. |
- Gomes-Ferreira, Pedro Henrique Silva, et al.
(författare)
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PTH 1-34-functionalized bioactive glass improves peri-implant bone repair in orchiectomized rats: Microscale and ultrastructural evaluation
- 2022
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Ingår i: Biomaterials Advances. - : Elsevier BV. - 2772-9508. ; 134
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Tidskriftsartikel (refereegranskat)abstract
- The objective of this work was to investigate the use of Biogran® functionalized with parathyroid hormone (PTH) 1–34 by sonochemistry for the local delivery of this anabolic agent to the implant site. The effects of Biogran® and topical administration of PTH 1–34 on peri-implant bone regeneration were evaluated from the microscale to ultrastructural levels in healthy (SHAM) and orchiectomized (ORQ). While some animals only received a titanium implant in their tibial metaphyses (CLOT group), in others the peri-implant defect was first filled with Biogran® either without or with PTH 1–34 functionalization (BG and BGPTH groups, respectively) prior to implant installation. Osseointegration was characterized from a biomechanical perspective by measuring the removal torque with the counter-torque technique. Micro-CT was used to evaluate the percentage of bone volume, trabecular thickness, number and separation, and bone-implant contact (BIC). Dynamics of new bone formation were assessed by measuring fluorochrome area, daily mineral apposition rate, and neoformed bone area using confocal laser microscopy. RT-PCR was performed to evaluate ALP and osteocalcin expression. The interface between newly formed bone and Biogran® was examined using scanning electron microscopy (SEM) and scanning transmission electron microscopy (STEM) at the micro-and nanoscale, respectively, while elemental analyses were completed in SEM with energy-dispersive X-ray spectroscopy (EDS). STEM imaging demonstrated the intimate attachment of bone to Biogran® (nanoscale level). Overall, the results suggest that the effectiveness of the topical administration of PTH 1–34 at the implant site seems enhanced in osteoporotic bone, promoting peri-implant bone regeneration to comparable levels in healthy conditions.
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| 10. |
- Guiomar, Raquel, et al.
(författare)
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Usability Study of the iACTwithPain Platform : An Online Acceptance and Commitment Therapy and Compassion-Based Intervention for Chronic Pain
- 2022
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Ingår i: Frontiers in Psychology. - : Frontiers Media S.A.. - 1664-1078. ; 13
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Tidskriftsartikel (refereegranskat)abstract
- Background: This pilot study aims to test the usability of the iACTwithPain platform, an online ACT-based intervention for people with chronic pain, to obtain information on which intervention and usability aspects need improvement and on expected retention rates.Methods: Seventy-three Portuguese women with chronic pain were invited to complete the first three sessions of the iACTwithPain intervention assess their quality, usefulness and the platform's usability. Twenty-one accepted the invitation. Additionally, eight healthcare professionals working with chronic medical conditions assessed the platform and the intervention from a practitioner's point of view.Results: This study presented a considerable attrition rate (71.43%) among chronic pain participants, with six completers. There were no significant differences in demographic or clinical variables between dropouts and completers except for completed education (participants who dropped out presented less education than completers). Reasons for dropout were related to difficult personal events occurring during the time of the intervention, lack of time, or having forgotten. There seemed to be an overall satisfaction with both the intervention, its contents and form of presentation of information, and the platform, concerning its design, appearance, and usability. Real image videos were preferred over animations or audio by chronic pain participants. Healthcare professionals emphasized the appealing and dynamic aspects of the animation format.Conclusion: This study informs the ongoing improvement of the iACTwithPain platform and provides valuable information on aspects researchers should consider while developing online psychological interventions for chronic pain. Further implications are discussed.
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