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1.	Kauppila, Joonas H, et al. (författare) Gastrectomy compared to oesophagectomy for Siewert II and III gastro-oesophageal junctional cancer in relation to resection margins, lymphadenectomy and survival 2017 Ingår i: Scientific Reports. - Stockholm : Karolinska Institutet, Dept of Molecular Medicine and Surgery. - 2045-2322. Tidskriftsartikel (refereegranskat)abstract It is unclear whether gastrectomy or oesophagectomy offer better outcomes for gastro-oesophageal junction (GOJ) cancer. A total of 240 patients undergoing total gastrectomy (n = 85) or oesophagectomy (n = 155) for Siewert II-III GOJ adenocarcinoma were identified from a Swedish prospective population-based nationwide cohort. The surgical approaches were compared in relation to non-radical resection margins (main outcome) using multivariable logistic regression, providing odds ratios (ORs) and 95% confidence intervals (CIs), mean number of removed lymph nodes with standard deviation (SD) using ANCOVA, assessing mean differences and 95% CIs, and 5-year mortality using Cox regression estimating hazard ratios (HRs) and 95% CIs. The models were adjusted for age, sex, comorbidity, tumour stage, and surgeon volume. The non-radical resection rate was 15% for gastrectomy and 14% for oesophagectomy, and the adjusted OR was 1.61 (95% CI 0.68-3.83). The mean number of lymph nodes removed was 14.2 (SD +/- 9.6) for gastrectomy and 14.2 (SD +/- 10.4) for oesophagectomy, with adjusted mean difference of 2.4 (95% CI-0.2-5.0). The 5-year mortality was 76% following gastrectomy and 75% following oesophagectomy, with adjusted HR = 1.07 (95% CI 0.78-1.47). Gastrectomy and oesophagectomy for Siewert II or III GOJ cancer seem comparable regarding tumour-free resection margins, lymph nodes removal, and 5-year survival.
2.	Kauppila, Joonas H, et al. (författare) Neoadjuvant therapy in relation to lymphadenectomy and resection margins during surgery for oesophageal cancer 2018 Ingår i: Scientific Reports. - Stockholm : Karolinska Institutet, Dept of Molecular Medicine and Surgery. - 2045-2322. Tidskriftsartikel (refereegranskat)abstract It is unclear whether gastrectomy or oesophagectomy offer better outcomes for gastro-oesophageal junction (GOJ) cancer. A total of 240 patients undergoing total gastrectomy (n = 85) or oesophagectomy (n = 155) for Siewert II-III GOJ adenocarcinoma were identified from a Swedish prospective population-based nationwide cohort. The surgical approaches were compared in relation to non-radical resection margins (main outcome) using multivariable logistic regression, providing odds ratios (ORs) and 95% confidence intervals (CIs), mean number of removed lymph nodes with standard deviation (SD) using ANCOVA, assessing mean differences and 95% CIs, and 5-year mortality using Cox regression estimating hazard ratios (HRs) and 95% CIs. The models were adjusted for age, sex, comorbidity, tumour stage, and surgeon volume. The non-radical resection rate was 15% for gastrectomy and 14% for oesophagectomy, and the adjusted OR was 1.61 (95% CI 0.68-3.83). The mean number of lymph nodes removed was 14.2 (SD +/- 9.6) for gastrectomy and 14.2 (SD +/- 10.4) for oesophagectomy, with adjusted mean difference of 2.4 (95% CI-0.2-5.0). The 5-year mortality was 76% following gastrectomy and 75% following oesophagectomy, with adjusted HR = 1.07 (95% CI 0.78-1.47). Gastrectomy and oesophagectomy for Siewert II or III GOJ cancer seem comparable regarding tumour-free resection margins, lymph nodes removal, and 5-year survival.
3.	Lundqvist, Mikael, et al. (författare) Reduced variability of bursting activity during working memory 2022 Ingår i: Scientific Reports. - Stockholm : Karolinska Institutet, Dept of Clinical Neuroscience. - 2045-2322. Tidskriftsartikel (refereegranskat)abstract Working memories have long been thought to be maintained by persistent spiking. However, mounting evidence from multiple-electrode recording (and single-trial analyses) shows that the underlying spiking is better characterized by intermittent bursts of activity. A counterargument suggested this intermittent activity is at odds with observations that spike-time variability reduces during task performance. However, this counterargument rests on assumptions, such as randomness in the timing of the bursts, which may not be correct. Thus, we analyzed spiking and LFPs from monkeys' prefrontal cortex (PFC) to determine if task-related reductions in variability can co-exist with intermittent spiking. We found that it does because both spiking and associated gamma bursts were task-modulated, not random. In fact, the task-related reduction in spike variability could largely be explained by a related reduction in gamma burst variability. Our results provide further support for the intermittent activity models of working memory as well as novel mechanistic insights into how spike variability is reduced during cognitive tasks.
4.	Mer, Arvind Singh, et al. (författare) Study design requirements for RNA sequencing-based breast cancer diagnostics 2016 Ingår i: Scientific Reports. - Stockholm : Karolinska Institutet, Dept of Medical Epidemiology and Biostatistics. - 2045-2322. Tidskriftsartikel (refereegranskat)abstract Sequencing-based molecular characterization of tumors provides information required for individualized cancer treatment. There are well-defined molecular subtypes of breast cancer that provide improved prognostication compared to routine biomarkers. However, molecular subtyping is not yet implemented in routine breast cancer care. Clinical translation is dependent on subtype prediction models providing high sensitivity and specificity. In this study we evaluate sample size and RNA-sequencing read requirements for breast cancer subtyping to facilitate rational design of translational studies. We applied subsampling to ascertain the effect of training sample size and the number of RNA sequencing reads on classification accuracy of molecular subtype and routine biomarker prediction models (unsupervised and supervised). Subtype classification accuracy improved with increasing sample size up to N = 750 (accuracy = 0.93), although with a modest improvement beyond N = 350 (accuracy = 0.92). Prediction of routine biomarkers achieved accuracy of 0.94 (ER) and 0.92 (Her2) at N = 200. Subtype classification improved with RNA-sequencing library size up to 5 million reads. Development of molecular subtyping models for cancer diagnostics requires well-designed studies. Sample size and the number of RNA sequencing reads directly influence accuracy of molecular subtyping. Results in this study provide key information for rational design of translational studies aiming to bring sequencing-based diagnostics to the clinic.
5.	Rantalainen, Mattias, et al. (författare) Sequencing-based breast cancer diagnostics as an alternative to routine biomarkers 2016 Ingår i: Scientific Reports. - Stockholm : Karolinska Institutet, Dept of Medical Epidemiology and Biostatistics. - 2045-2322. Tidskriftsartikel (refereegranskat)abstract Sequencing-based breast cancer diagnostics have the potential to replace routine biomarkers and provide molecular characterization that enable personalized precision medicine. Here we investigate the concordance between sequencing-based and routine diagnostic biomarkers and to what extent tumor sequencing contributes clinically actionable information. We applied DNA- and RNA-sequencing to characterize tumors from 307 breast cancer patients with replication in up to 739 patients. We developed models to predict status of routine biomarkers (ER, HER2,Ki-67, histological grade) from sequencing data. Non-routine biomarkers, including mutations in BRCA1, BRCA2 and ERBB2(HER2), and additional clinically actionable somatic alterations were also investigated. Concordance with routine diagnostic biomarkers was high for ER status (AUC = 0.95;AUC(replication) = 0.97) and HER2 status (AUC = 0.97;AUC(replication) = 0.92). The transcriptomic grade model enabled classification of histological grade 1 and histological grade 3 tumors with high accuracy (AUC = 0.98;AUC(replication) = 0.94). Clinically actionable mutations in BRCA1, BRCA2 and ERBB2(HER2) were detected in 5.5% of patients, while 53% had genomic alterations matching ongoing or concluded breast cancer studies. Sequencing-based molecular profiling can be applied as an alternative to histopathology to determine ER and HER2 status, in addition to providing improved tumor grading and clinically actionable mutations and molecular subtypes. Our results suggest that sequencing-based breast cancer diagnostics in a near future can replace routine biomarkers
6.	Aaltonen, S, et al. (författare) Leisure-Time Physical Activity and Academic Performance: Cross-Lagged Associations from Adolescence to Young Adulthood 2016 Ingår i: Scientific reports. - 2045-2322. ; 6, s. 39215- Tidskriftsartikel (refereegranskat)
7.	Abaasa, A, et al. (författare) Use of propensity score matching to create counterfactual group to assess potential HIV prevention interventions 2021 Ingår i: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 11:1, s. 7017- 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.
8.	Abadpour, Shadab, et al. (författare) Glial cell-line derived neurotrophic factor protects human islets from nutrient deprivation and endoplasmic reticulum stress induced apoptosis 2017 Ingår i: Scientific Reports. - : NATURE PUBLISHING GROUP. - 2045-2322. ; 7 Tidskriftsartikel (refereegranskat)abstract One of the key limitations to successful human islet transplantation is loss of islets due to stress responses pre- and post-transplantation. Nutrient deprivation and ER stress have been identified as important mechanisms leading to apoptosis. Glial Cell-line Derived Neurotrophic Factor (GDNF) has recently been found to promote islet survival after isolation. However, whether GDNF could rescue human islets from nutrient deprivation and ER stress-mediated apoptosis is unknown. Herein, by mimicking those conditions in vitro, we have shown that GDNF significantly improved glucose stimulated insulin secretion, reduced apoptosis and proinsulin: insulin ratio in nutrient deprived human islets. Furthermore, GDNF alleviated thapsigargin-induced ER stress evidenced by reduced expressions of IRE1 alpha and BiP and consequently apoptosis. Importantly, this was associated with an increase in phosphorylation of PI3K/AKT and GSK3B signaling pathway. Transplantation of ER stressed human islets pre- treated with GDNF under kidney capsule of diabetic mice resulted in reduced expressions of IRE1 alpha and BiP in human islet grafts with improved grafts function shown by higher levels of human C-peptide post-transplantation. We suggest that GDNF has protective and anti-apoptotic effects on nutrient deprived and ER stress activated human islets and could play a significant role in rescuing human islets from stress responses.
9.	Abah, SE, et al. (författare) Low plasma haptoglobin is a risk factor for life-threatening childhood severe malarial anemia and not an exclusive consequence of hemolysis 2018 Ingår i: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 8:1, s. 17527- Tidskriftsartikel (refereegranskat)abstract Severe Malarial Anemia (SMA), a life-threatening childhood Plasmodium falciparum malaria syndrome requiring urgent blood transfusion, exhibits inflammatory and hemolytic pathology. Differentiating between hypo-haptoglobinemia due to hemolysis or that of genetic origin is key to understand SMA pathogenesis. We hypothesized that while malaria-induced hypo-haptoglobinemia should reverse at recovery, that of genetic etiology should not. We carried-out a case-control study of children living under hyper-endemic holoendemic malaria burden in the sub-Saharan metropolis of Ibadan, Nigeria. We show that hypo-haptoglobinemia is a risk factor for childhood SMA and not solely due to intravascular hemolysis from underlying schizogony. In children presenting with SMA, hypo-haptoglobinemia remains through convalescence to recovery suggesting a genetic cause. We identified a haptoglobin gene variant, rs12162087 (g.-1203G > A, frequency = 0.67), to be associated with plasma haptoglobin levels (p = 8.5 × 10−6). The Homo-Var:(AA) is associated with high plasma haptoglobin while the reference Homo-Ref:(GG) is associated with hypo-haptoglobinemia (p = 2.3 × 10−6). The variant is associated with SMA, with the most support for a risk effect for Homo-Ref genotype. Our insights on regulatory haptoglobin genotypes and hypo-haptoglobinemia suggest that haptoglobin screening could be part of risk-assessment algorithms to prevent rapid disease progression towards SMA in regions with no-access to urgent blood transfusion where SMA accounts for high childhood mortality rates.
10.	Abate Waktola, Ebba Abate, et al. (författare) Polymorphisms in CARD8 and NLRP3 are associated with extrapulmonary TB and poor clinical outcome in active TB in Ethiopia 2019 Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 9 Tidskriftsartikel (refereegranskat)abstract Innate immunity is a first line defense against Mycobacterium tuberculosis infection where inflammasome activation and secretion of the pro-inflammatory cytokine IL-1beta, plays a major role. Thus, genetic polymorphisms in innate immunity-related genes such as CARD8 and NLRP3 may contribute to the understanding of why most exposed individuals do not develop infection. Our aim was to investigate the association between polymorphisms in CARD8 and NLRP3 and active tuberculosis (TB) as well as their relationship to treatment outcome in a high-endemic setting for TB. Polymorphisms in CARD8 (C10X) and NLRP3 (Q705K) were analysed in 1190 TB patients and 1990 healthy donors (HD). There was a significant association between homozygotes in the CARD8 polymorphism and extrapulmonary TB (EPTB), which was not the case for pulmonary TB or HDs. Among TB-patients, there was an association between poor treatment outcome and the NLRP3 (Q705K) polymorphism. Our study shows that inflammasome polymorphisms are associated with EPTB and poor clinical outcome in active TB in Ethiopia. The practical implications and determining causal relationships on a mechanistic level needs further study.
11.	Abbaszad Rafi, Abdolrahim, et al. (författare) A facile route for concurrent fabrication and surface selective functionalization of cellulose nanofibers by lactic acid mediated catalysis 2023 Ingår i: Scientific Reports. - : Springer Nature. - 2045-2322 .- 2045-2322. ; 13:1 Tidskriftsartikel (refereegranskat)abstract Celulose nanofibers are lightweight, recycable, biodegradable, and renewable. Hence, there is a great interest of using them instead of fossil-based components in new materials and biocomposites. In this study, we disclose an environmentally benign (green) one-step reaction approach to fabricate lactic acid ester functionalized cellulose nanofibrils from wood-derived pulp fibers in high yields. This was accomplished by converting wood-derived pulp fibers to nanofibrillated “cellulose lactate” under mild conditions using lactic acid as both the reaction media and catalyst. Thus, in parallel to the cellulose nanofibril production, concurrent lactic acid-catalyzed esterification of lactic acid to the cellulose nanofibers surface occured. The direct lactic acid esterification, which is a surface selective functionalization and reversible (de-attaching the ester groups by cleavage of the ester bonds), of the cellulose nanofibrils was confirmed by low numbers of degree of substitution, and FT-IR analyses. Thus, autocatalytic esterification and cellulose hydrolysis occurred without the need of metal based or a harsh mineral acid catalysts, which has disadvantages such as acid corrosiveness and high recovery cost of acid. Moreover, adding a mineral acid as a co-catalyst significantly decreased the yield of the nanocellulose. The lactic acid media is successfully recycled in multiple reaction cycles producing the corresponding nanocellulose fibers in high yields. The disclosed green cellulose nanofibril production route is industrial relevant and gives direct access to nanocellulose for use in variety of applications such as sustainable filaments, composites, packaging and strengthening of recycled fibers.
12.	Abbaszad Rafi, Abdolrahim, et al. (författare) Copper nanoparticles on controlled pore glass (CPG) as highly efficient heterogeneous catalysts for “click reactions” 2020 Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 10:1 Tidskriftsartikel (refereegranskat)abstract We herein report that supported copper nanoparticles (CuNPs) on commercially available controlled pore glass (CPG), which exhibit high mechanical, thermal and chemical stability as compared to other silica-based materials, serve as a useful heterogeneous catalyst system for 1,3-dipolar cycloadditions (“click” reactions) between terminal alkynes and organic azides under green chemistry conditions. The supported CuNPs-CPG catalyst exhibited a broad substrate scope and gave the corresponding triazole products in high yields. The CuNPs-CPG catalyst exhibit recyclability and could be reuced multiple times without contaminating the products with Cu.
13.	Abbey-Lee, Robin, et al. (författare) Experimental manipulation of monoamine levels alters personality in crickets 2018 Ingår i: Scientific Reports. - : NATURE PUBLISHING GROUP. - 2045-2322. ; 8 Tidskriftsartikel (refereegranskat)abstract Animal personality has been described in a range of species with ecological and evolutionary consequences. Factors shaping and maintaining variation in personality are not fully understood, but monoaminergic systems are consistently linked to personality variation. We experimentally explored how personality was influenced by alterations in two key monoamine systems: dopamine and serotonin. This was done using ropinirole and fluoxetine, two common human pharmaceuticals. Using the Mediterranean field cricket (Gryllus bimaculatus), we focused on the personality traits activity, exploration, and aggression, with confirmed repeatability in our study. Dopamine manipulations explained little variation in the personality traits investigated, while serotonin manipulation reduced both activity and aggression. Due to limited previous research, we created a dose-response curve for ropinirole, ranging from concentrations measured in surface waters to human therapeutic doses. No ropinirole dose level strongly influenced cricket personality, suggesting our results did not come from a dose mismatch. Our results indicate that the serotonergic system explains more variation in personality than manipulations of the dopaminergic system. Additionally, they suggest that monoamine systems differ across taxa, and confirm the importance of the mode of action of pharmaceuticals in determining their effects on behaviour.
14.	Abd El-Daim, Islam Ahmed Moustafa, et al. (författare) Bacillus velezensis 5113 Induced Metabolic and Molecular Reprogramming during Abiotic Stress Tolerance in Wheat 2019 Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 9 Tidskriftsartikel (refereegranskat)abstract Abiotic stresses are main limiting factors for agricultural production around the world. Plant growth promoting rhizobacteria (PGPR) have been shown to improve abiotic stress tolerance in several plants. However, the molecular and physiological changes connected with PGPR priming of stress management are poorly understood. The present investigation aimed to explore major metabolic and molecular changes connected with the ability of Bacillus velezensis 5113 to mediate abiotic stress tolerance in wheat. Seedlings treated with Bacillus were exposed to heat, cold/freezing or drought stress. Bacillus improved wheat survival in all stress conditions. SPAD readings showed higher chlorophyll content in 5113-treated stressed seedlings. Metabolite profiling using NMR and ESI-MS provided evidences for metabolic reprograming in 5113-treated seedlings and showed that several common stress metabolites were significantly accumulated in stressed wheat. Two-dimensional gel electrophoresis of wheat leaves resolved more than 300 proteins of which several were differentially expressed between different treatments and that cold stress had a stronger impact on the protein pattern compared to heat and drought. Peptides maps or sequences were used for database searches which identified several homologs. The present study suggests that 5113 treatment provides systemic effects that involve metabolic and regulatory functions supporting both growth and stress management.
15.	Abdalla Elsayed, Maram E.A., et al. (författare) Incidence of Intraocular Lens Exchange after Cataract Surgery 2019 Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 9:1 Tidskriftsartikel (refereegranskat)abstract Intraocular lens (IOL) exchange after cataract surgery is unusual but may be associated with suboptimal visual outcome. The incidence of IOL exchange has not been consistently estimated. Such information is invaluable when counseling patients prior to cataract surgery. We examined the incidence of, and indications and risk factors for, IOL exchange after cataract surgery. We also assessed visual outcome of eyes that had an IOL exchange. A cohort design was used to estimate the incidence of IOL exchange and a case-control design to identify factors associated with it. All phacoemulsification surgeries with IOL (n = 17415 eyes) during 2010-2017 and those that had a subsequent IOL removal or replacement during the same time period were identified (n = 34 eyes). The incidence of IOL exchange was 2 per 1000 surgeries (95% confidence interval [CI] 1 to 3) over 8 years. Eyes that underwent subsequent IOL removal or replacement were compared with eyes that had cataract surgery only (n = 47) across demographic and clinical characteristics. In a binary logistic regression analysis, two factors were significantly associated with IOL exchange/removal: an adverse event during cataract surgery (adjusted odds ratio [aOR] 19.45; 95% CI 4.89-77.30, P < 0.001) and a pre-existing ocular comorbidity (aOR 10.70; 95% CI 1.69-67.63, P = 0.021). The effect of gender was marginally significant (P = 0.077). Eyes that underwent IOL exchange or explantation were nearly two and a half times more likely to have a final best-corrected visual acuity of <20/60 compared to those that had cataract surgery alone (adjusted RR 2.60 95% CI, 1.13-6.02; P = 0.025).
16.	Abdalla, Hassan, et al. (författare) Effective Temperature and Universal Conductivity Scaling in Organic Semiconductors 2015 Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 5 Tidskriftsartikel (refereegranskat)abstract We investigate the scalability of the temperature-and electric field-dependence of the conductivity of disordered organic semiconductors to universal curves by two different but commonly employed methods; by so-called universal scaling and by using the effective temperature concept. Experimentally both scaling methods were found to be equally applicable to the out-of-plane charge transport in PEDOT: PSS thin films of various compositions. Both methods are shown to be equivalent in terms of functional dependence and to have identical limiting behavior. The experimentally observed scaling behavior can be reproduced by a numerical nearest-neighbor hopping model, accounting for the Coulomb interaction, the high charge carrier concentration and the energetic disorder. The underlying physics can be captured in a simple empirical model, describing the effective temperature of the charge carrier distribution as the outcome of a heat balance between Joule heating and (effective) temperature-dependent energy loss to the lattice.
17.	Abdallah, Clement Kamil, et al. (författare) Assessing the quality of water used for vegetable irrigation in Tamale Metropolis, Ghana 2021 Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 11 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.
18.	Abdollahi Sani, Negar, et al. (författare) Flexible lamination-fabricated ultra-high frequency diodes based on self-supporting semiconducting composite film of silicon micro-particles and nano-fibrillated cellulose 2016 Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 6 Tidskriftsartikel (refereegranskat)abstract Low cost and flexible devices such as wearable electronics, e-labels and distributed sensors will make the future "internet of things" viable. To power and communicate with such systems, high frequency rectifiers are crucial components. We present a simple method to manufacture flexible diodes, operating at GHz frequencies, based on self-adhesive composite films of silicon micro-particles (Si-ÎŒPs) and glycerol dispersed in nanofibrillated cellulose (NFC). NFC, Si-ÎŒPs and glycerol are mixed in a water suspension, forming a self-supporting nanocellulose-silicon composite film after drying. This film is cut and laminated between a flexible pre-patterned Al bottom electrode and a conductive Ni-coated carbon tape top contact. A Schottky junction is established between the Al electrode and the Si-ÎŒPs. The resulting flexible diodes show current levels on the order of mA for an area of 2 mm2, a current rectification ratio up to 4 Ã— 103 between 1 and 2 V bias and a cut-off frequency of 1.8 GHz. Energy harvesting experiments have been demonstrated using resistors as the load at 900 MHz and 1.8 GHz. The diode stack can be delaminated away from the Al electrode and then later on be transferred and reconfigured to another substrate. This provides us with reconfigurable GHz-operating diode circuits.
19.	Abdullah, Gamil M. S., et al. (författare) Boosting-based ensemble machine learning models for predicting unconfined compressive strength of geopolymer stabilized clayey soil 2024 Ingår i: Scientific Reports. - : Springer Nature. - 2045-2322. ; 14:1 Tidskriftsartikel (refereegranskat)abstract The present research employs new boosting-based ensemble machine learning models i.e., gradient boosting (GB) and adaptive boosting (AdaBoost) to predict the unconfined compressive strength (UCS) of geopolymer stabilized clayey soil. The GB and AdaBoost models were developed and validated using 270 clayey soil samples stabilized with geopolymer, with ground-granulated blast-furnace slag and fly ash as source materials and sodium hydroxide solution as alkali activator. The database was randomly divided into training (80%) and testing (20%) sets for model development and validation. Several performance metrics, including coefficient of determination (R2), mean absolute error (MAE), root mean square error (RMSE), and mean squared error (MSE), were utilized to assess the accuracy and reliability of the developed models. The statistical results of this research showed that the GB and AdaBoost are reliable models based on the obtained values of R2 (= 0.980, 0.975), MAE (= 0.585, 0.655), RMSE (= 0.969, 1.088), and MSE (= 0.940, 1.185) for the testing dataset, respectively compared to the widely used artificial neural network, random forest, extreme gradient boosting, multivariable regression, and multi-gen genetic programming based models. Furthermore, the sensitivity analysis result shows that ground-granulated blast-furnace slag content was the key parameter affecting the UCS.
20.	Abdullah Nasir, Ahmad, et al. (författare) Netrin-1 functions as a suppressor of bone morphogenetic protein (BMP) signaling 2021 Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 11:1 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.
21.	Abelein, A, et al. (författare) High-yield Production of Amyloid-β Peptide Enabled by a Customized Spider Silk Domain 2020 Ingår i: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 10:1, s. 235- Tidskriftsartikel (refereegranskat)abstract During storage in the silk gland, the N-terminal domain (NT) of spider silk proteins (spidroins) keeps the aggregation-prone repetitive region in solution at extreme concentrations. We observe that NTs from different spidroins have co-evolved with their respective repeat region, and now use an NT that is distantly related to previously used NTs, for efficient recombinant production of the amyloid-β peptide (Aβ) implicated in Alzheimer’s disease. A designed variant of NT from Nephila clavipes flagelliform spidroin, which in nature allows production and storage of β-hairpin repeat segments, gives exceptionally high yields of different human Aβ variants as a solubility tag. This tool enables efficient production of target peptides also in minimal medium and gives up to 10 times more isotope-labeled monomeric Aβ peptides per liter bacterial culture than previously reported.
22.	Abend, M., et al. (författare) Inter-laboratory comparison of gene expression biodosimetry for protracted radiation exposures as part of the RENEB and EURADOS WG10 2019 exercise 2021 Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 11:1 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.
23.	Abolhalaj, Milad, et al. (författare) Profiling dendritic cell subsets in head and neck squamous cell tonsillar cancer and benign tonsils. 2018 Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 8:8030 Tidskriftsartikel (refereegranskat)abstract Dendritic cells (DCs) have a key role in orchestrating immune responses and are considered important targets for immunotherapy against cancer. In order to develop effective cancer vaccines, detailed knowledge of the micromilieu in cancer lesions is warranted. In this study, flow cytometry and human transcriptome arrays were used to characterize subsets of DCs in head and neck squamous cell tonsillar cancer and compare them to their counterparts in benign tonsils to evaluate subset-selective biomarkers associated with tonsillar cancer. We describe, for the first time, four subsets of DCs in tonsillar cancer: CD123+ plasmacytoid DCs (pDC), CD1c+, CD141+, and CD1c-CD141- myeloid DCs (mDC). An increased frequency of DCs and an elevated mDC/pDC ratio were shown in malignant compared to benign tonsillar tissue. The microarray data demonstrates characteristics specific for tonsil cancer DC subsets, including expression of immunosuppressive molecules and lower expression levels of genes involved in development of effector immune responses in DCs in malignant tonsillar tissue, compared to their counterparts in benign tonsillar tissue. Finally, we present target candidates selectively expressed by different DC subsets in malignant tonsils and confirm expression of CD206/MRC1 and CD207/Langerin on CD1c+ DCs at protein level. This study descibes DC characteristics in the context of head and neck cancer and add valuable steps towards future DC-based therapies against tonsillar cancer.
24.	Aboshady, Hadeer Moursy, et al. (författare) Immunoglobulins as Biomarkers for Gastrointestinal Nematodes Resistance in Small Ruminants: A systematic review 2020 Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 10 Forskningsöversikt (refereegranskat)abstract The rise of anthelmintic resistance worldwide has led to the development of alternative control strategies for gastrointestinal nematodes (GIN) infections, which are one of the main constraints on the health of grazing small ruminants. Presently, breeding schemes rely mainly on fecal egg count (FEC) measurements on infected animals which are time-consuming and requires expertise in parasitology. Identifying and understanding the role of immunoglobulins in the mechanisms of resistance could provide a more efficient and sustainable method of identifying nematode-resistant animals for selection. In this study we review the findings on immunoglobulin response to GIN in the literature published to date (june 2019) and discuss the potential to use immunoglobulins as biomarkers. The literature review revealed 41 studies which measured at least one immunoglobulin: 35 focused on lamb immune response (18 used non-naive lambs) and 7 on yearlings. In this review we propose a conceptual model summarizing the role of immunoglobulins in resistance to GIN. We highlight the need for more carefully designed and documented studies to allow comparisons across different populations on the immunoglobulin response to GIN infection.
25.	Abrahamsson, Annelie, 1966-, et al. (författare) Increased nutrient availability in dense breast tissue of postmenopausal women in vivo 2017 Ingår i: Scientific Reports. - : NATURE PUBLISHING GROUP. - 2045-2322. ; 7 Tidskriftsartikel (refereegranskat)abstract Metabolic reprogramming is a hallmark of cancer. Nutrient availability in the tissue microenvironment determines cellular events and may play a role in breast carcinogenesis. High mammographic density is an independent risk factor for breast cancer. Whether nutrient availability differs in normal breast tissues with various densities is unknown. Therefore we investigated whether breast tissues with various densities exhibited differences in nutrient availability. Healthy postmenopausal women from the regular mammographic screening program who had either predominantly fatty breast tissue (nondense), n = 18, or extremely dense breast tissue (dense), n = 20, were included. Microdialysis was performed for the in vivo sampling of amino acids (AAs), analyzed by ultra-high performance liquid chromatography with tandem mass spectroscopy, glucose, lactate and vascular endothelial growth factor (VEGF) in breast tissues and, as a control, in abdominal subcutaneous (s.c.) fat. We found that dense breast tissue exhibited significantly increased levels of 20 proteinogenic AAs and that 18 of these AAs correlated significantly with VEGF. No differences were found in the s.c. fat, except for one AA, suggesting tissue-specific alterations in the breast. Glucose and lactate were unaltered. Our findings provide novel insights into the biology of dense breast tissue that may be explored for breast cancer prevention strategies.

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