| 41. |
- Adamczyk, Barbara, 1985, et al.
(författare)
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Sample handling of gastric tissue and O-glycan alterations in paired gastric cancer and non-tumorigenic tissues
- 2018
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 8
-
Tidskriftsartikel (refereegranskat)abstract
- Sample collection, handling and storage are the most critical steps for ensuring the highest preservation of specimens. Pre-analytical variability can influence the results as protein signatures alter rapidly after tissue excision or during long-term storage. Hence, we evaluated current state-of-the-art biobank preservation methods from a glycomics perspective and analyzed O-glycan alterations occurring in the gastric cancer tissues. Paired tumor and adjacent normal tissue samples were obtained from six patients undergoing gastric cancer surgery. Collected samples (n = 24) were either snap-frozen or heat stabilized and then homogenized. Glycans were released from extracted glycoproteins and analyzed by LC-MS/MS. In total, the relative abundance of 83 O-glycans and 17 derived structural features were used for comparison. There was no statistically significant difference found in variables between snap frozen and heat-stabilized samples, which indicated the two preservation methods were comparable. The data also showed significant changes between normal and cancerous tissue. In addition to a shift from high sialylation in the cancer area towards blood group ABO in the normal area, we also detected that the LacdiNAc epitope (N, N'-diacetyllactosamine) was significantly decreased in cancer samples. The O-glycan alterations that are presented here may provide predictive power for the detection and prognosis of gastric cancer.
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| 42. |
- Adamik, Peter, et al.
(författare)
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Barrier crossing in small avian migrants : individual tracking reveals prolonged nocturnal flights into the day as a common migratory strategy
- 2016
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 6
-
Tidskriftsartikel (refereegranskat)abstract
- Over decades it has been unclear how individual migratory songbirds cross large ecological barriers such as seas or deserts. By deploying light-level geolocators on four songbird species weighing only about 12 g, we found that these otherwise mainly nocturnal migrants seem to regularly extend their nocturnal flights into the day when crossing the Sahara Desert and the Mediterranean Sea. The proportion of the proposed diurnally flying birds gradually declined over the day with similar landing patterns in autumn and spring. The prolonged flights were slightly more frequent in spring than in autumn, suggesting tighter migratory schedules when returning to breeding sites. Often we found several patterns for barrier crossing for the same individual in autumn compared to the spring journey. As only a small proportion of the birds flew strictly during the night and even some individuals might have flown non-stop, we suggest that prolonged endurance flights are not an exception even in small migratory species. We emphasise an individual’s ability to perform both diurnal and nocturnal migration when facing the challenge of crossing a large ecological barrier to successfully complete a migratory journey.
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| 43. |
- Adams, A, et al.
(författare)
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Formal Definitions of Unbounded Evolution and Innovation Reveal Universal Mechanisms for Open-Ended Evolution in Dynamical Systems
- 2017
-
Ingår i: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 7:1, s. 997-
-
Tidskriftsartikel (refereegranskat)abstract
- Open-ended evolution (OEE) is relevant to a variety of biological, artificial and technological systems, but has been challenging to reproduce in silico. Most theoretical efforts focus on key aspects of open-ended evolution as it appears in biology. We recast the problem as a more general one in dynamical systems theory, providing simple criteria for open-ended evolution based on two hallmark features: unbounded evolution and innovation. We define unbounded evolution as patterns that are non-repeating within the expected Poincare recurrence time of an isolated system, and innovation as trajectories not observed in isolated systems. As a case study, we implement novel variants of cellular automata (CA) where the update rules are allowed to vary with time in three alternative ways. Each is capable of generating conditions for open-ended evolution, but vary in their ability to do so. We find that state-dependent dynamics, regarded as a hallmark of life, statistically out-performs other candidate mechanisms, and is the only mechanism to produce open-ended evolution in a scalable manner, essential to the notion of ongoing evolution. This analysis suggests a new framework for unifying mechanisms for generating OEE with features distinctive to life and its artifacts, with broad applicability to biological and artificial systems.
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| 44. |
- Adav, Sunil S., et al.
(författare)
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Studies on the Proteome of Human Hair - Identification of Histones and Deamidated Keratins
- 2018
-
Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 8:1
-
Tidskriftsartikel (refereegranskat)abstract
- Human hair is laminar-fibrous tissue and an evolutionarily old keratinization product of follicle trichocytes. Studies on the hair proteome can give new insights into hair function and lead to the development of novel biomarkers for hair in health and disease. Human hair proteins were extracted by detergent and detergent-free techniques. We adopted a shotgun proteomics approach, which demonstrated a large extractability and variety of hair proteins after detergent extraction. We found an enrichment of keratin, keratin-associated proteins (KAPs), and intermediate filament proteins, which were part of protein networks associated with response to stress, innate immunity, epidermis development, and the hair cycle. Our analysis also revealed a significant deamidation of keratin type I and II, and KAPs. The hair shafts were found to contain several types of histones, which are well known to exert antimicrobial activity. Analysis of the hair proteome, particularly its composition, protein abundances, deamidated hair proteins, and modification sites, may offer a novel approach to explore potential biomarkers of hair health quality, hair diseases, and aging.
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| 45. |
- Adeboye, Peter, 1982, et al.
(författare)
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ALD5, PAD1, ATF1 and ATF2 facilitate the catabolism of coniferyl aldehyde, ferulic acid and p-coumaric acid in Saccharomyces cerevisiae
- 2017
-
Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322 .- 2045-2322. ; 7
-
Tidskriftsartikel (refereegranskat)abstract
- The ability of Saccharomyces cerevisiae to catabolize phenolic compounds remains to be fully elucidated. Conversion of coniferyl aldehyde, ferulic acid and p-coumaric acid by S. cerevisiae under aerobic conditions was previously reported. A conversion pathway was also proposed. In the present study, possible enzymes involved in the reported conversion were investigated. Aldehyde dehydrogenase Ald5, phenylacrylic acid decarboxylase Pad1, and alcohol acetyltransferases Atf1 and Atf2, were hypothesised to be involved. Corresponding genes for the four enzymes were overexpressed in a S. cerevisiae strain named APT_1. The ability of APT_1 to tolerate and convert the three phenolic compounds was tested. APT_1 was also compared to strains B_CALD heterologously expressing coniferyl aldehyde dehydrogenase from Pseudomonas, and an ald5 Delta strain, all previously reported. APT_1 exhibited the fastest conversion of coniferyl aldehyde, ferulic acid and p-coumaric acid. Using the intermediates and conversion products of each compound, the catabolic route of coniferyl aldehyde, ferulic acid and p-coumaric acid in S. cerevisiae was studied in greater detail.
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| 46. |
- Adegboye, Oluwatayomi Rereloluwa, et al.
(författare)
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Chaotic opposition learning with mirror reflection and worst individual disturbance grey wolf optimizer for continuous global numerical optimization
- 2024
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Ingår i: Scientific Reports. - : NATURE PORTFOLIO. - 2045-2322. ; 14:1
-
Tidskriftsartikel (refereegranskat)abstract
- The effective meta-heuristic technique known as the grey wolf optimizer (GWO) has shown its proficiency. However, due to its reliance on the alpha wolf for guiding the position updates of search agents, the risk of being trapped in a local optimal solution is notable. Furthermore, during stagnation, the convergence of other search wolves towards this alpha wolf results in a lack of diversity within the population. Hence, this research introduces an enhanced version of the GWO algorithm designed to tackle numerical optimization challenges. The enhanced GWO incorporates innovative approaches such as Chaotic Opposition Learning (COL), Mirror Reflection Strategy (MRS), and Worst Individual Disturbance (WID), and it's called CMWGWO. MRS, in particular, empowers certain wolves to extend their exploration range, thus enhancing the global search capability. By employing COL, diversification is intensified, leading to reduced solution stagnation, improved search precision, and an overall boost in accuracy. The integration of WID fosters more effective information exchange between the least and most successful wolves, facilitating a successful exit from local optima and significantly enhancing exploration potential. To validate the superiority of CMWGWO, a comprehensive evaluation is conducted. A wide array of 23 benchmark functions, spanning dimensions from 30 to 500, ten CEC19 functions, and three engineering problems are used for experimentation. The empirical findings vividly demonstrate that CMWGWO surpasses the original GWO in terms of convergence accuracy and robust optimization capabilities.
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| 47. |
- Adel Fahmideh, Maral, et al.
(författare)
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A Weighted Genetic Risk Score of Adult Glioma Susceptibility Loci Associated with Pediatric Brain Tumor Risk.
- 2019
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Ingår i: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 9:1
-
Tidskriftsartikel (refereegranskat)abstract
- Genetic risk score (GRS) is used to demonstrate the genetic variants contributing to the polygenic architecture of complex diseases. By using a GRS, we have investigated the additive impact of the known adult glioma susceptibility loci on the pediatric brain tumor (PBT) risk and assessed the proportion of PBT heritability attributable to these susceptibility loci. A GRS was generated for PBTs based on the alleles and associated effect sizes derived from a previously published genome-wide association study on adult glioma. The GRS was calculated in CEFALO, a population-based case-control study of brain tumors in children and adolescents including saliva DNA of 245 cases and 489 controls. The unconditional logistic regression model was used to investigate the association between standardized GRS and risk of PBTs. To measure the variance explained by the effect of GRS, Nagelkerke pseudo-R2 was calculated. The GRS for adult brain tumors was associated with an increased risk of PBTs (OR 1.25 [95% CI 1.06-1.49], p=0.009) and 0.3% of the variance in PBTs could be explained by the effect of GRS on the liability scale. This study provides evidence that heritable risks of PBTs are in-part attributable to some common genetic variants associated with adult glioma.
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| 48. |
- Ademar, Karin, et al.
(författare)
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Acamprosate reduces ethanol intake in the rat by a combined action of different drug components
- 2023
-
Ingår i: Scientific Reports. - 2045-2322. ; 13:1
-
Tidskriftsartikel (refereegranskat)abstract
- Alcohol misuse accounts for a sizeable proportion of the global burden of disease, and Campral (R) (acamprosate; calcium-bis-(N-acetylhomotaurinate)) is widely used as relapse prevention therapy. The mechanism underlying its effect has in some studies been attributed to the calcium moiety and not to the N-acetylhomotaurine part of the compound. We recently suggested that the dopamine elevating effect of acamprosate is mediated both by N-acetylhomotaurine and calcium in a glycine receptor dependent manner. Here we aimed to explore, by means of in vivo microdialysis, if our previous study using local administration was functionally relevant and if systemic administration of the sodium salt of N-acetylhomotaurine (sodium acamprosate; 200 mg/kg, i.p.) enhanced the effects of calcium chloride (CaCl2; 73.5 mg/kg, i.p.) on nucleus accumbens (nAc) dopamine and/or taurine levels in male Wistar rats. In addition, we investigated the impact of regular acamprosate and the combination of CaCl(2 )and N-acetylhomotaurine on the alcohol deprivation effect (ADE). Finally, we assessed if N-acetylhomotaurine potentiates the ethanol-intake reducing effect of CaCl(2 )in a two-bottle choice voluntary ethanol consumption model followed by an ADE paradigm. Systemic administration of regular acamprosate, sodium acamprosate and CaCl(2 )all trended to increase nAc dopamine whereas the combination of CaCl(2)and sodium acamprosate produced a significant increase. Sodium acamprosate elevated extracellular taurine levels without additional effects of CaCl2. Ethanol intake was significantly reduced by systemic administration of CaCl(2 )without additional effects of the combination of CaCl(2 )and sodium acamprosate. Both acamprosate and CaCl(2 )combined with sodium acamprosate blocked the ADE following acute treatment. The data presented suggest that CaCl(2 )and N-acetylhomotaurine act in concert on a neurochemical level, but calcium appears to have the predominant effect on ethanol intake.
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| 49. |
- Afacan, B, et al.
(författare)
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Salivary secretory leukocyte protease inhibitor levels in patients with stage 3 grade C periodontitis: a comparative cross-sectional study
- 2022
-
Ingår i: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 12:1, s. 21267-
-
Tidskriftsartikel (refereegranskat)abstract
- Secretory leukocyte protease inhibitor (SLPI) is an anti-protease that protects mucosal tissue integrity owing to its anti-microbial and immunomodulatory properties. This study aimed to investigate SLPI levels in periodontal diseases, and analyze the potential correlation with clinical periodontal parameters. Whole saliva samples were obtained from healthy (n = 24), gingivitis (n = 24) and patients with stage 3 grade C periodontitis (n = 24). SLPI was measured by ELISA and normalized by total protein. Receiver operating characteristics (ROC) curve was used for estimating the area under the curve (AUC). The normalized SLPI levels were significantly reduced in periodontitis compared with gingivitis (4.84-fold) or health (1.83-fold) and negatively correlated with periodontal parameters. The ROC curves showed a good predictor value of the SLPI for differentiation of periodontitis versus health or gingivitis (AUC ≥ 0.80). This study demonstrates that the levels of SLPI are high in periodontal health, further elevated in gingivitis, but eventually decreased in severe periodontitis beyond the former two states. This observation may have broader implications in the context of inflammatory diseases affecting the oral mucosa, as it shows that the bacterial burden is disturbing the homeostatic balances of anti-microbial and anti-protease factors in the oral cavity.
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| 50. |
- Afacan, B, et al.
(författare)
-
Salivary secretory leukocyte protease inhibitor levels in patients with stage 3 grade C periodontitis: a comparative cross-sectional study
- 2022
-
Ingår i: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 12:1, s. 21267-
-
Tidskriftsartikel (refereegranskat)abstract
- Secretory leukocyte protease inhibitor (SLPI) is an anti-protease that protects mucosal tissue integrity owing to its anti-microbial and immunomodulatory properties. This study aimed to investigate SLPI levels in periodontal diseases, and analyze the potential correlation with clinical periodontal parameters. Whole saliva samples were obtained from healthy (n = 24), gingivitis (n = 24) and patients with stage 3 grade C periodontitis (n = 24). SLPI was measured by ELISA and normalized by total protein. Receiver operating characteristics (ROC) curve was used for estimating the area under the curve (AUC). The normalized SLPI levels were significantly reduced in periodontitis compared with gingivitis (4.84-fold) or health (1.83-fold) and negatively correlated with periodontal parameters. The ROC curves showed a good predictor value of the SLPI for differentiation of periodontitis versus health or gingivitis (AUC ≥ 0.80). This study demonstrates that the levels of SLPI are high in periodontal health, further elevated in gingivitis, but eventually decreased in severe periodontitis beyond the former two states. This observation may have broader implications in the context of inflammatory diseases affecting the oral mucosa, as it shows that the bacterial burden is disturbing the homeostatic balances of anti-microbial and anti-protease factors in the oral cavity.
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