| 1. |
- Abaasa, A, et al.
(författare)
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Use of propensity score matching to create counterfactual group to assess potential HIV prevention interventions
- 2021
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Ingår i: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 11:1, s. 7017-
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Tidskriftsartikel (refereegranskat)abstract
- The design of HIV prevention trials in the context of effective HIV preventive methods is a challenge. Alternate designs, including using non-randomised ‘observational control arms’ have been proposed. We used HIV simulated vaccine efficacy trials (SiVETs) to show pitfalls that may arise from using such observational controls and suggest how to conduct the analysis in the face of the pitfalls. Two SiVETs were nested within previously established observational cohorts of fisherfolk (FF) and female sex workers (FSW) in Uganda. SiVET participants received a licensed Hepatitis B vaccine in a schedule (0, 1 and 6 months) similar to that for a possible HIV vaccine efficacy trial. All participants received HIV counselling and testing every quarter for one year to assess HIV incidence rate ratio (IRR) between SiVET and non-SiVET (observational data). Propensity scores, conditional on baseline characteristics were calculated for SiVET participation and matched between SiVET and non-SiVET in the period before and during the SiVET study. We compared IRR before and after propensity score matching (PSM). In total, 3989 participants were enrolled into observational cohorts prior to SiVET, (1575 FF prior to Jul 2012 and 2414 FSW prior to Aug 2014). SiVET enrolled 572 participants (Jul 2012 to Apr 2014 in FF and Aug 2014 to Apr 2017 in FSW), with 953 non-SiVET participants observed in the SiVET concurrent period and 2928 from the pre-SiVET period (before Jul 2012 in FF or before Apr 2014 in FSW). Imbalances in baseline characteristics were observed between SiVET and non-SiVET participants in both periods before PSM. Similarly, HIV incidence was lower in SiVET than non-SiVET; SiVET-concurrent period, IRR = 0.59, 95% CI 0.31–0.68, p = 0.033 and pre-SiVET period, IRR = 0.77, 95% CI 0.43–1.29, p = 0.161. After PSM, participants baseline characteristics were comparable and there were minimal differences in HIV incidence between SiVET and non-SiVET participants. The process of screening for eligibility for efficacy trial selects participants with baseline characteristics different from the source population, confounding any observed differences in HIV incidence. Propensity score matching can be a useful tool to adjust the imbalance in the measured participants’ baseline characteristics creating a counterfactual group to estimate the effect of interventions on HIV incidence.
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| 2. |
- Abdallah, Clement Kamil, et al.
(författare)
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Assessing the quality of water used for vegetable irrigation in Tamale Metropolis, Ghana
- 2021
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- This paper assesses water quality that is used for vegetable irrigation in Tamale Metropolis, Ghana. A mixed-method of research design was employed in this study to collect and analyze the data based on survey instruments. The paper found that Escherichia coli (E. coli) that is usually used as an indicator of water contamination and heavy metals exist in all taken water samples. The mean concentrations of nutrients such as ammonia, nitrate, nitrite and phosphate were recorded as 0.022 mg/l to 5.98 mg/l for ammonia, 1.06 mg/l to 7.52 mg/l for nitrate, 0.031 mg/l to 0.056 mg/l for nitrate and 0.037 mg/l to 0.069 mg/l for phosphate. E. coli and Total Coliforms levels for Sanghani, Kamina and Waterworks from the laboratory analysis were recorded as 3.2x10(3) CFU 100 m/l and 5.5x10(2) CFU 100 m/l, 4.0x10(3) CFU 100 m/l and 1x10(2) CFU 100 m/l, and 2.1x10(3) CFU 100 m/l and 4.6x10(2) CFU 100 m/l respectively. To conclude, based on the measured parameters, water used for irrigation in the Tamale Metropolitan is polluted and may cause potential health risks. Therefore, farmers, traders and consumers need to apply further safety measures to make the vegetables safe.
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| 3. |
- Abdullah Nasir, Ahmad, et al.
(författare)
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Netrin-1 functions as a suppressor of bone morphogenetic protein (BMP) signaling
- 2021
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Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Netrin-1 is a secreted protein that is well known for its involvement in axonal guidance during embryonic development and as an enhancer of cancer cell metastasis. Despite extensive efforts, the molecular mechanisms behind many of the physiological functions of netrin-1 have remained elusive. Here, we show that netrin-1 functions as a suppressor of bone morphogenetic protein (BMP) signaling in various cellular systems, including a mutually inhibitory interaction with the BMP-promoting function of leucine-rich repeats and immunoglobulin-like domains (LRIG) proteins. The BMP inhibitory function of netrin-1 in mouse embryonic fibroblasts was dependent on the netrin receptor neogenin, with the expression level regulated by both netrin-1 and LRIG proteins. Our results reveal a previously unrecognized function of netrin-1 that may help to explain several of the developmental, physiological, and cancer-promoting functions of netrins at the signal transduction level.
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| 4. |
- Abend, M., et al.
(författare)
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Inter-laboratory comparison of gene expression biodosimetry for protracted radiation exposures as part of the RENEB and EURADOS WG10 2019 exercise
- 2021
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Large-scale radiation emergency scenarios involving protracted low dose rate radiation exposure (e.g. a hidden radioactive source in a train) necessitate the development of high throughput methods for providing rapid individual dose estimates. During the RENEB (Running the European Network of Biodosimetry) 2019 exercise, four EDTA-blood samples were exposed to an Iridium-192 source (1.36 TBq, Tech-Ops 880 Sentinal) at varying distances and geometries. This resulted in protracted doses ranging between 0.2 and 2.4 Gy using dose rates of 1.5-40 mGy/min and exposure times of 1 or 2.5 h. Blood samples were exposed in thermo bottles that maintained temperatures between 39 and 27.7 degrees C. After exposure, EDTA-blood samples were transferred into PAXGene tubes to preserve RNA. RNA was isolated in one laboratory and aliquots of four blinded RNA were sent to another five teams for dose estimation based on gene expression changes. Using an X-ray machine, samples for two calibration curves (first: constant dose rate of 8.3 mGy/min and 0.5-8 h varying exposure times; second: varying dose rates of 0.5-8.3 mGy/min and 4 h exposure time) were generated for distribution. Assays were run in each laboratory according to locally established protocols using either a microarray platform (one team) or quantitative real-time PCR (qRT-PCR, five teams). The qRT-PCR measurements were highly reproducible with coefficient of variation below 15% in >= 75% of measurements resulting in reported dose estimates ranging between 0 and 0.5 Gy in all samples and in all laboratories. Up to twofold reductions in RNA copy numbers per degree Celsius relative to 37 degrees C were observed. However, when irradiating independent samples equivalent to the blinded samples but increasing the combined exposure and incubation time to 4 h at 37 degrees C, expected gene expression changes corresponding to the absorbed doses were observed. Clearly, time and an optimal temperature of 37 degrees C must be allowed for the biological response to manifest as gene expression changes prior to running the gene expression assay. In conclusion, dose reconstructions based on gene expression measurements are highly reproducible across different techniques, protocols and laboratories. Even a radiation dose of 0.25 Gy protracted over 4 h (1 mGy/min) can be identified. These results demonstrate the importance of the incubation conditions and time span between radiation exposure and measurements of gene expression changes when using this method in a field exercise or real emergency situation.
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| 5. |
- Abreu, Ilka, et al.
(författare)
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A metabolomic study of Gomphrena agrestis in Brazilian Cerrado suggests drought-adaptive strategies on metabolism
- 2021
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- Drought is the main factor that limits the distribution and productivity of plant species. In the Brazilian Cerrado, the vegetation is adapted to a seasonal climate with long- and short-term periods of drought. To analyze the metabolic strategies under such conditions, a metabolomic approach was used to characterize Gomphrena agrestis Mart. (Amaranthaceae) a native species that grows under natural conditions, in a rock-field area. Roots and leaves material from native specimens were sampled along different seasons of the year and LC-MS and GC-MS analyzed for multiple chemical constituents. The datasets derived from the different measurements were combined and evaluated using multivariate analysis. Principal component analysis was used to obtain an overview of the samples and identify outliers. Later, the data was analyzed with orthogonal projection to latent structures discriminant analysis to obtain valid models that could explain the metabolite variations in the different seasons. Two hundred and eighty metabolites were annotated, generating a unique database to characterize metabolic strategies used to cope with the effects of drought. The accumulation of fructans in the thickened roots is consistent with the storage of carbons during the rainy season to support the energy demand during a long period of drought. The accumulation of Abscisic acid, sugars and sugar alcohols, phenolics, and pigment in the leaves suggests physiological adaptations. To cope with long-term drought, the data suggests that tissue water status and storage of reserves are important to support plant survival and regrowth. However, during short-term drought, osmoregulation and oxidative protection seems to be essential, probably to support the maintenance of active photosynthesis.
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| 6. |
- Abzhandadze, Tamar, 1980, et al.
(författare)
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Barriers to cognitive screening in acute stroke units
- 2021
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Cognitive impairment is common after stroke. However, not all patients with stroke undergo cognitive screening, despite recommendations. The aim of this retrospective, explorative study was to examine the barriers to cognitive screening in acute stroke units. Data were retrieved from two Swedish Stroke registries. The outcome variable was cognitive screening during the stay at acute stroke units. Forty-three candidate explanatory variables were considered for analysis, encompassing sociodemographic factors and stroke-related outcomes during the stay at acute stroke units. The Least Absolute Shrinkage and Selection Operator and decision-tree methods were used. Of the 1120 patients (56% male, mean age: 72 years, 50% with mild stroke), 44% did not undergo cognitive screening. Walking 10 m post-stroke was the most important attribute for decisions regarding cognitive screening. The classification accuracy, sensitivity, and specificity of the model were 70% (95% CI 63-75%), 71% (63-78%), and 67% (55-77%), respectively. Patient-related parameters that influenced cognitive screening with a valid and reliable screening instrument in acute stroke units included new stroke during the hospitalisation, aphasia at admission, mobility problems, impaired verbal output skills, and planned discharge to another care facility. The barriers to cognitive screening were both patient- and organisation-related, suggesting the need for patient-tailored cognitive screening tools as well as the implementation and systematic adherence to guidelines.
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| 7. |
- Afzali, Maryam, et al.
(författare)
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Computing the orientational-average of diffusion-weighted MRI signals : a comparison of different techniques
- 2021
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Ingår i: Scientific Reports. - : Nature Research. - 2045-2322. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Numerous applications in diffusion MRI involve computing the orientationally-averaged diffusion-weighted signal. Most approaches implicitly assume, for a given b-value, that the gradient sampling vectors are uniformly distributed on a sphere (or shell), computing the orientationally-averaged signal through simple arithmetic averaging. One challenge with this approach is that not all acquisition schemes have gradient sampling vectors distributed over perfect spheres. To ameliorate this challenge, alternative averaging methods include: weighted signal averaging; spherical harmonic representation of the signal in each shell; and using Mean Apparent Propagator MRI (MAP-MRI) to derive a three-dimensional signal representation and estimate its isotropic part. Here, these different methods are simulated and compared under different signal-to-noise (SNR) realizations. With sufficiently dense sampling points (61 orientations per shell), and isotropically-distributed sampling vectors, all averaging methods give comparable results, (MAP-MRI-based estimates give slightly higher accuracy, albeit with slightly elevated bias as b-value increases). As the SNR and number of data points per shell are reduced, MAP-MRI-based approaches give significantly higher accuracy compared with the other methods. We also apply these approaches to in vivo data where the results are broadly consistent with our simulations. A statistical analysis of the simulated data shows that the orientationally-averaged signals at each b-value are largely Gaussian distributed.
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| 8. |
- Agren, R
(författare)
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Worldwide antipsychotic drug search intensities: pharmacoepidemological estimations based on Google Trends data
- 2021
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Ingår i: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 11:1, s. 13136-
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Tidskriftsartikel (refereegranskat)abstract
- Prescription patterns of antipsychotic drugs (APDs) are typically sourced from country-specific data. In this study, a digital pharmacoepidemiological approach was used to investigate APD preferences globally. Publicly available data on worldwide web search intensities in Google for 19 typical and 22 atypical APDs were temporally and spatially normalized and correlated with reported prescription data. The results demonstrated an increasing global preference for atypical over typical APDs since 2007, with quetiapine, olanzapine, risperidone, and aripiprazole showing the largest search intensities in 2020. Cross-sectional analysis of 122 countries in 2020 showed pronounced differences in atypical/typical APD preferences that correlated with gross domestic product per capita. In conclusion, the investigation provides temporal and spatial assessments of global APD preferences and shows a trend towards atypical APDs, although with a relative preference for typical APDs in low-income countries. Similar data-sourcing methodologies allow for prospective studies of other prescription drugs.
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| 9. |
- Ahlinder, Jon, et al.
(författare)
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Life stage-specific inbreeding depression in long-lived Pinaceae species depends on population connectivity
- 2021
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Ingår i: Scientific Reports. - : Springer Nature. - 2045-2322. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Inbreeding depression (ID) is a fundamental selective pressure that shapes mating systems and population genetic structures in plants. Although it has been shown that ID varies over the life stages of shorter-lived plants, less is known about how the fitness effects of inbreeding vary across life stages in long-lived species. We conducted a literature survey in the Pinaceae, a tree family known to harbour some of the highest mutational loads ever reported. Using a meta-regression model, we investigated distributions of inbreeding depression over life stages, adjusting for effects of inbreeding levels and the genetic differentiation of populations within species. The final dataset contained 147 estimates of ID across life stages from 41 studies. 44 Fst estimates were collected from 40 peer-reviewed studies for the 18 species to aid genetic differentiation modelling. Partitioning species into fragmented and well-connected groups using Fst resulted in the best way (i.e. trade-off between high goodness-of-fit of the model to the data and reduced model complexity) to incorporate genetic connectivity in the meta-regression analysis. Inclusion of a life stage term and its interaction with the inbreeding coefficient (F) dramatically increased model precision. We observed that the correlation between ID and F was significant at the earliest life stage. Although partitioning of species populations into fragmented and well-connected groups explained little of the between-study heterogeneity, the inclusion of an interaction between life stage and population differentiation revealed that populations with fragmented distributions suffered lower inbreeding depression at early embryonic stages than species with well-connected populations. There was no evidence for increased ID in late life stages in well-connected populations, although ID tended to increase across life stages in the fragmented group. These findings suggest that life stage data should be included in inbreeding depression studies and that inbreeding needs to be managed over life stages in commercial populations of long-lived plants.
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| 10. |
- Ahmad, A, et al.
(författare)
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High-throughput spatial sensitive quantitative phase microscopy using low spatial and high temporal coherent illumination
- 2021
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Ingår i: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 11:1, s. 15850-
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Tidskriftsartikel (refereegranskat)abstract
- High space-bandwidth product with high spatial phase sensitivity is indispensable for a single-shot quantitative phase microscopy (QPM) system. It opens avenue for widespread applications of QPM in the field of biomedical imaging. Temporally low coherence light sources are implemented to achieve high spatial phase sensitivity in QPM at the cost of either reduced temporal resolution or smaller field of view (FOV). In addition, such light sources have low photon degeneracy. On the contrary, high temporal coherence light sources like lasers are capable of exploiting the full FOV of the QPM systems at the expense of less spatial phase sensitivity. In the present work, we demonstrated that use of narrowband partially spatially coherent light source also called pseudo-thermal light source (PTLS) in QPM overcomes the limitations of conventional light sources. The performance of PTLS is compared with conventional light sources in terms of space bandwidth product, phase sensitivity and optical imaging quality. The capabilities of PTLS are demonstrated on both amplitude (USAF resolution chart) and phase (thin optical waveguide, height ~ 8 nm) objects. The spatial phase sensitivity of QPM using PTLS is measured to be equivalent to that for white light source and supports the FOV (18 times more) equivalent to that of laser light source. The high-speed capabilities of PTLS based QPM is demonstrated by imaging live sperm cells that is limited by the camera speed and large FOV is demonstrated by imaging histopathology human placenta tissue samples. Minimal invasive, high-throughput, spatially sensitive and single-shot QPM based on PTLS will enable wider penetration of QPM in life sciences and clinical applications.
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