31 results on '"Rasmussen TS"'
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2. Timing of nitrogen application to macadamias. 2. Storage carbohydrates
- Author
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Stephenson, RA, Rasmussen, TS, and Gallagher, EC
- Abstract
Samples of wood and bark were taken monthly from macadamia (Macadamia integrifolia Maiden and Betche) tree trunks and analysed for total 'fermentable' carbohydrates. Carbohydrates (%, w/w) were high during autumn-winter and declined to low levels in summer when oil was accumulating in kernels. Reproductive growth appeared to draw heavily on carbohydrate reserves. Vegetative growth, on the other hand, was not generally reflected in lower carbohydrate levels in tree trunks. Application of nitrogen (N) during summer resulted in higher carbohydrate levels than when applied in autumn or winter. Despite these differences, there was no apparent accumulation of carbohydrates in the months directly following application of N. The low N status of control trees was not reflected in low concentrations of storage carbohydrates. Wood tissues had a higher concentration of carbohydrates than bark, perhaps reflecting the sampling procedures used. Further work to quantify the contribution of storage carbohydrates and current photosynthesis to yield is justified.
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- 1989
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3. Impact of Manufacturing Process and Compounding on Properties and Quality of Follow-On GLP-1 Polypeptide Drugs.
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Hach M, Engelund DK, Mysling S, Mogensen JE, Schelde O, Haselmann KF, Lamberth K, Vilhelmsen TK, Malmstrøm J, Højlys-Larsen KB, Rasmussen TS, Borch-Jensen J, Mortensen RW, Jensen TMT, Kesting JR, Catarig AM, Asgreen DJ, Christensen L, and Staby A
- Subjects
- Hypoglycemic Agents chemistry, Hypoglycemic Agents administration & dosage, Humans, Drug Contamination prevention & control, Drug Stability, Administration, Oral, Liraglutide chemistry, Glucagon-Like Peptides chemistry, Glucagon-Like Peptides administration & dosage, Drug Compounding methods, Glucagon-Like Peptide 1 chemistry
- Abstract
Purpose: The prevalence of follow-on and compounded products of glucagon-like peptide-1 analogs is increasing. We assessed glucagon-like peptide-1 analogs semaglutide and liraglutide for purity, potential immunogenicity, and expected stability, by comparing a representative selection of commercially available follow-on drug substances (DSs) and drug products (DPs) with their corresponding originators., Methods: Tests included several chromatography methods coupled with ultraviolet and mass spectrometry detectors, inductively coupled plasma optical emission spectroscopy, inductively coupled plasma mass spectrometry, nuclear magnetic resonance, dissolution analyses, in silico peptide/major histocompatibility complex II-binding prediction, and fibrillation assays., Results: Overall, 16 injectable semaglutide, 8 oral semaglutide, and 2 injectable liraglutide follow-on products were analyzed alongside originator products. Compared with originator, follow-on injectable semaglutide DSs and DPs had new impurities and impurity patterns, including high molecular weight proteins, trace metals, anions, counterions, and residual solvents. Analyses showed that several commercialized follow-on oral semaglutide DPs had a markedly lower quantity of semaglutide than the label claim, while dissolution tests indicated different semaglutide and sodium N-(8-[2-hydroxybenzoyl] amino)caprylate (SNAC) release profiles, which may reduce bioavailability. Neoepitopes were identified in DS and DP semaglutide follow-ons, indicating potential immunogenicity. Fibrillation assays showed increased fibrillation tendency and reduced physical stability in liraglutide follow-on DP samples compared with originator., Conclusion: This study highlights that differences in the manufacturing processes of follow-on semaglutide and liraglutide (vs those used for originators) can result in several changes to the DSs and DPs. The impact of these changes on efficacy and safety outcomes remains unknown and should be investigated by clinical studies., (© 2024. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)
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- 2024
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4. Reproducible chemostat cultures to minimize eukaryotic viruses from fecal transplant material.
- Author
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Adamberg S, Rasmussen TS, Larsen SB, Mao X, Nielsen DS, and Adamberg K
- Abstract
Recent studies indicate an important role of bacteriophages for successful fecal microbiota transplantation (FMT). However, wider clinical applications of FMT are hampered by to donor variability and concerns of infection risks by bacteria and human viruses. To overcome these challenges, mouse cecal and human fecal material were propagated in a chemostat fermentation setup supporting multiplication of bacteria, and phages, while propagation of eukaryotic viruses will be prevented in the absence of eukaryotic host cells. The results showed decrease of the median relative abundance of viral contigs of classified eukaryotic viruses below 0.01%. The corresponding virome profiles showed dilution rate dependency, a reproducibility between biological replicates, and maintained high diversity regarding both the human and mouse inocula. This proof-of-concept cultivation approach may constitute the first step of developing novel therapeutic tools with high reproducibility and with low risk of infection from the donor material to target gut-related diseases., Competing Interests: The authors declare no competing interests., (© 2024 The Author(s).)
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- 2024
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5. Overcoming donor variability and risks associated with fecal microbiota transplants through bacteriophage-mediated treatments.
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Rasmussen TS, Mao X, Forster S, Larsen SB, Von Münchow A, Tranæs KD, Brunse A, Larsen F, Mejia JLC, Adamberg S, Hansen AK, Adamberg K, Hansen CHF, and Nielsen DS
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- Animals, Mice, Disease Models, Animal, Humans, Mice, Inbred C57BL, Female, Fecal Microbiota Transplantation methods, Bacteriophages physiology, Bacteriophages isolation & purification, Clostridium Infections therapy, Clostridium Infections microbiology, Gastrointestinal Microbiome, Feces microbiology, Feces virology, Clostridioides difficile
- Abstract
Background: Fecal microbiota transplantation (FMT) and fecal virome transplantation (FVT, sterile filtrated donor feces) have been effective in treating recurrent Clostridioides difficile infections, possibly through bacteriophage-mediated modulation of the gut microbiome. However, challenges like donor variability, costly screening, coupled with concerns over pathogen transfer (incl. eukaryotic viruses) with FMT or FVT hinder their wider clinical application in treating less acute diseases., Methods: To overcome these challenges, we developed methods to broaden FVT's clinical application while maintaining efficacy and increasing safety. Specifically, we employed the following approaches: (1) chemostat-fermentation to reproduce the bacteriophage FVT donor component and remove eukaryotic viruses (FVT-ChP), (2) solvent-detergent treatment to inactivate enveloped viruses (FVT-SDT), and (3) pyronin-Y treatment to inhibit RNA virus replication (FVT-PyT). We assessed the efficacy of these processed FVTs in a C. difficile infection mouse model and compared them with untreated FVT (FVT-UnT), FMT, and saline., Results: FVT-SDT, FVT-UnT, and FVT-ChP reduced the incidence of mice reaching the humane endpoint (0/8, 2/7, and 3/8, respectively) compared to FMT, FVT-PyT, and saline (5/8, 7/8, and 5/7, respectively) and significantly reduced the load of colonizing C. difficile cells and associated toxin A/B levels. There was a potential elimination of C. difficile colonization, with seven out of eight mice treated with FVT-SDT testing negative with qPCR. In contrast, all other treatments exhibited the continued presence of C. difficile. Moreover, the results were supported by changes in the gut microbiome profiles, cecal cytokine levels, and histopathological findings. Assessment of viral engraftment following FMT/FVT treatment and host-phage correlations analysis suggested that transfer of phages likely were an important contributing factor associated with treatment efficacy., Conclusions: This proof-of-concept study shows that specific modifications of FVT hold promise in addressing challenges related to donor variability and infection risks. Two strategies lead to treatments significantly limiting C. difficile colonization in mice, with solvent/detergent treatment and chemostat propagation of donor phages emerging as promising approaches. Video Abstract., (© 2024. The Author(s).)
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- 2024
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6. Two weeks of acarbose treatment shows no effect on gut microbiome composition in patients with type 2 diabetes: a randomised, placebo-controlled, double-blind, crossover study.
- Author
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Dalsgaard NB, Gasbjerg LS, Hansen LS, Nielsen DS, Rasmussen TS, and Knop FK
- Abstract
Aim: The alpha-glucosidase inhibitor acarbose is approved for the treatment of type 2 diabetes (T2D). It acts in the lumen of the gut by reducing intestinal hydrolysis and absorption of ingested carbohydrates. This reduces postprandial blood glucose concentration and increases the content of carbohydrates in the distal parts of the intestine potentially influencing gut microbiome (GM) composition and possibly impacting the gut microbiome (GM) dysbiosis associated with T2D. Here, we investigated the effect of acarbose on GM composition in patients with T2D., Methods: Faecal samples were collected in a previously conducted randomised, placebo-controlled, double-blind, crossover study in which 15 individuals with metformin-treated T2D (age 57-85 years, HbA1c 40-74 mmol/mol, BMI 23.6-34.6 kg/m2) were subjected to two 14-day treatment periods with acarbose and placebo, respectively, separated by a 6-week wash-out period. Faecal samples were collected before and by the end of each treatment period. The GM profiles were evaluated by 16S rRNA gene amplicon sequencing., Results: The GM profiles after the treatment periods with acarbose or placebo remained unaffected (P > 0.7) when compared with the GM profiles before treatment. This applied to the analysis of within-sample diversity (α-diversity) and between-sample bacterial composition diversity (β-diversity). Additionally, no dominant bacterial species differentiated the treatment groups, and only minor increases in the relative abundances of Klebsiella spp. and Escherichia coli (P < 0.05) were observed after acarbose treatment., Conclusion: In patients with metformin-treated T2D, 14 days of treatment with acarbose showed only minor effects on GM as seen in increased relative abundances of Klebsiella spp. and Escherichia coli.
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- 2024
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7. Transfer of modified gut viromes improves symptoms associated with metabolic syndrome in obese male mice.
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Mao X, Larsen SB, Zachariassen LSF, Brunse A, Adamberg S, Mejia JLC, Larsen F, Adamberg K, Nielsen DS, Hansen AK, Hansen CHF, and Rasmussen TS
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- Animals, Male, Mice, Dysbiosis therapy, Feces virology, Feces microbiology, Bacteriophages physiology, Blood Glucose metabolism, Disease Models, Animal, Liver pathology, Liver metabolism, Adipose Tissue, Metabolic Syndrome therapy, Obesity therapy, Gastrointestinal Microbiome, Mice, Inbred C57BL, Fecal Microbiota Transplantation, Diet, High-Fat adverse effects, Virome, Mice, Obese
- Abstract
Metabolic syndrome encompasses amongst other conditions like obesity and type-2 diabetes and is associated with gut microbiome (GM) dysbiosis. Fecal microbiota transplantation (FMT) has been explored to treat metabolic syndrome by restoring the GM; however, concerns on accidentally transferring pathogenic microbes remain. As a safer alternative, fecal virome transplantation (FVT, sterile-filtrated feces) has the advantage over FMT in that mainly bacteriophages are transferred. FVT from lean male donors have shown promise in alleviating the metabolic effects of high-fat diet in a preclinical mouse study. However, FVT still carries the risk of eukaryotic viral infections. To address this, recently developed methods are applied for removing or inactivating eukaryotic viruses in the viral component of FVT. Modified FVTs are compared with unmodified FVT and saline in a diet-induced obesity model on male C57BL/6 N mice. Contrasted with obese control, mice administered a modified FVT (nearly depleted for eukaryotic viruses) exhibits enhanced blood glucose clearance but not weight loss. The unmodified FVT improves liver pathology and reduces the proportions of immune cells in the adipose tissue with a non-uniform response. GM analysis suggests that bacteriophage-mediated GM modulation influences outcomes. Optimizing these approaches could lead to the development of safe bacteriophage-based therapies targeting metabolic syndrome through GM restoration., (© 2024. The Author(s).)
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- 2024
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8. Choice of Ultrafilter Affects Recovery Rate of Bacteriophages.
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Larsen F, Offersen SM, Li VR, Deng L, Nielsen DS, and Rasmussen TS
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- Animals, Bacteriophage phi X 174, Mammals, Bacteriophages, Viruses, Caudovirales, Microbiota
- Abstract
Studies into the viral fraction of complex microbial communities, like in the mammalian gut, have recently garnered much interest. Yet there is still no standardized protocol for extracting viruses from such samples, and the protocols that exist employ procedures that skew the viral community of the sample one way or another. The first step of the extraction pipeline often consists of the basic filtering of macromolecules and bacteria, yet even this affects the viruses in a strain-specific manner. In this study, we investigate a protocol for viral extraction based on ultrafiltration and how the choice of ultrafilter might influence the extracted viral community. Clinical samples (feces, vaginal swabs, and tracheal suction samples) were spiked with a mock community of known phages (T4, c2, Φ6, Φ29, Φx174, and Φ2972), filtered, and quantified using spot and plaque assays to estimate the loss in recovery. The enveloped Φ6 phage is especially severely affected by the choice of filter, but also tailed phages such as T4 and c2 have a reduced infectivity after ultrafiltration. We conclude that the pore size of ultrafilters may affect the recovery of phages in a strain- and sample-dependent manner, suggesting the need for greater thought when selecting filters for virus extraction.
- Published
- 2023
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9. CRISPR-Cas provides limited phage immunity to a prevalent gut bacterium in gnotobiotic mice.
- Author
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Rasmussen TS, Koefoed AK, Deng L, Muhammed MK, Rousseau GM, Kot W, Sprotte S, Neve H, Franz CMAP, Hansen AK, Vogensen FK, Moineau S, and Nielsen DS
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- Animals, Mice, CRISPR-Cas Systems, Bacteria genetics, Base Sequence, Plasmids, Bacteriophages genetics
- Abstract
Many bacteria and archaea harbor the adaptive CRISPR-Cas system, which stores small nucleotide fragments from previous invasions of nucleic acids via viruses or plasmids. This molecular archive blocks further invaders carrying identical or similar nucleotide sequences. However, few of these systems have been confirmed experimentally to be active in gut bacteria. Here, we demonstrate experimentally that the type I-C CRISPR-Cas system of the prevalent gut bacterium Eggerthella lenta can specifically target and cleave foreign DNA in vitro by using a plasmid transformation assay. We also show that the CRISPR-Cas system acquires new immunities (spacers) from the genome of a virulent E. lenta phage using traditional phage assays in vitro but also in vivo using gnotobiotic (GB) mice. Both high phage titer and an increased number of spacer acquisition events were observed when E. lenta was exposed to a low multiplicity of infection in vitro, and three phage genes were found to contain protospacer hotspots. Fewer new spacer acquisitions were detected in vivo than in vitro. Longitudinal analysis of phage-bacteria interactions showed sustained coexistence in the gut of GB mice, with phage abundance being approximately one log higher than the bacteria. Our findings show that while the type I-C CRISPR-Cas system is active in vitro and in vivo, a highly virulent phage in vitro was still able to co-exist with its bacterial host in vivo. Taken altogether, our results suggest that the CRISPR-Cas defense system of E. lenta provides only partial immunity in the gut., (© 2023. The Author(s), under exclusive licence to International Society for Microbial Ecology.)
- Published
- 2023
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10. Fecal virome transfer improves proliferation of commensal gut Akkermansia muciniphila and unexpectedly enhances the fertility rate in laboratory mice.
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Rasmussen TS, Mentzel CMJ, Danielsen MR, Jakobsen RR, Zachariassen LSF, Castro Mejia JL, Brunse A, Hansen LH, Hansen CHF, Hansen AK, and Nielsen DS
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- Pregnancy, Male, Humans, Female, Mice, Animals, Infant, Virome, Birth Rate, Mice, Inbred C57BL, Verrucomicrobia, Feces, Cell Proliferation, Gastrointestinal Microbiome
- Abstract
Probiotics are intended to improve gastrointestinal health when consumed. However, the probiotics marketed today only colonize the densely populated gut to a limited extent. Bacteriophages comprise the majority of viruses in the human gut virome and there are strong indications that they play important roles in shaping the gut microbiome. Here, we investigate the use of fecal virome transplantation (FVT, sterile filtrated feces) as a mean to alter the gut microbiome composition to lead the way for persistent colonization of two types of probiotics: Lacticaseibacillus rhamnosus GG (LGG) representing a well-established probiotic and Akkermansia muciniphila (AKM) representing a putative next-generation probiotic. Male and female C57BL/6NTac mice were cohoused in pairs from 4 weeks of age and received the following treatment by oral gavage at week 5 and 6: AKM+FVT, LGG+FVT, probiotic sham (Pro-sham)+FVT, LGG+Saline, AKM+Saline, and control (Pro-sham+Saline). The FVT donor material originated from mice with high relative abundance of A. muciniphila . All animals were terminated at age 9 weeks. The FVT treatment did not increase the relative abundance of the administered LGG or AKM in the recipient mice. Instead FVT significantly ( p < 0.05) increased the abundance of naturally occurring A. muciniphila compared to the control. This highlights the potential of propagating the existing commensal "probiotics" that have already permanently colonized the gut. Being co-housed male and female, a fraction of the female mice became pregnant. Unexpectedly, the FVT treated mice were found to have a significantly ( p < 0.05) higher fertility rate independent of probiotic administration. These preliminary observations urge for follow-up studies investigating interactions between the gut microbiome and fertility.
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- 2023
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11. Morphological and Genetic Characterization of Eggerthella lenta Bacteriophage PMBT5.
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Sprotte S, Rasmussen TS, Cho GS, Brinks E, Lametsch R, Neve H, Vogensen FK, Nielsen DS, and Franz CMAP
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- Actinobacteria, Agar, DNA, Viral chemistry, DNA, Viral genetics, Genome, Viral, Humans, Bacteriophages genetics, Siphoviridae genetics
- Abstract
Eggerthella lenta is a common member of the human gut microbiome. We here describe the isolation and characterization of a putative virulent bacteriophage having E. lenta as host. The double-layer agar method for isolating phages was adapted to anaerobic conditions for isolating bacteriophage PMBT5 from sewage on a strictly anaerobic E. lenta strain of intestinal origin. For this, anaerobically grown E. lenta cells were concentrated by centrifugation and used for a 24 h phage enrichment step. Subsequently, this suspension was added to anaerobically prepared top (soft) agar in Hungate tubes and further used in the double-layer agar method. Based on morphological characteristics observed by transmission electron microscopy, phage PMBT5 could be assigned to the Siphoviridae phage family. It showed an isometric head with a flexible, noncontractile tail and a distinct single 45 nm tail fiber under the baseplate. Genome sequencing and assembly resulted in one contig of 30,930 bp and a mol% GC content of 51.3, consisting of 44 predicted protein-encoding genes. Phage-related proteins could be largely identified based on their amino acid sequence, and a comparison with metagenomes in the human virome database showed that the phage genome exhibits similarity to two distantly related phages.
- Published
- 2022
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12. Theory of microscopic semiconductor lasers with external optical feedback.
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Rasmussen TS and Mork J
- Abstract
The properties of microscopic semiconductor lasers with external optical feedback are theoretically analysed. The size-dependence of the critical feedback level, at which the laser first becomes unstable, is clarified, showing how the dominant indicator of feedback stability is the gain of the laser, irrespective of size. The impact of increased spontaneous emission β-factors and over-damped operation is evaluated, exposing a diminished phase sensitivity of microscopic lasers, and a trade-off between modulation bandwidth and feedback stability is identified.
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- 2021
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13. Inter-vendor variance of enteric eukaryotic DNA viruses in specific pathogen free C57BL/6N mice.
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Rasmussen TS, Jakobsen RR, Castro-Mejía JL, Kot W, Thomsen AR, Vogensen FK, Nielsen DS, and Hansen AK
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- Animals, DNA Viruses genetics, Diet, High-Fat, Mice, Phenotype, Reproducibility of Results, Specific Pathogen-Free Organisms, DNA Viruses isolation & purification, Gastrointestinal Microbiome, Mice, Inbred C57BL virology
- Abstract
The laboratory mouse strain C57BL/6 is widely used as an animal model for various applications. It is becoming increasingly clear that the bacterial enteric community highly influences the phenotype. Eukaryotic viruses represent a sparsely investigated member of the enteric microbiome that might also affect the phenotype. We here investigated the presence of enteric eukaryotic DNA viruses (EDVs) in specific pathogen-free (SPF) C57BL/6N mice purchased from three vendors upon arrival and after being fed a low-fat diet (LFD) or high-fat diet (HFD). We detected genetic fragments of EDVs belonging to the viral families of Herpes-, Mimi-, Baculo- and Phycodnaviridae represented by two genera; Chlorovirus and Prasinovirus. The EDVs were detected in the mice upon arrival and persisted for 13 weeks. However, these signals of EDVs were only detected at notable levels in mice fed LFD from 2 out of 3 vendors, which suggested that the enteric composition of these EDVs were affected by both vendor (p < 0.003) and different dietary regimes (p < 0.013). This highlights the need of additional studies assessing the potential function of these EDVs that may influence the mouse phenotype and the reproducibility of animal studies using this C57BL/6N substrain., (Copyright © 2021 Elsevier Ltd. All rights reserved.)
- Published
- 2021
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14. Faecal virome transplantation decreases symptoms of type 2 diabetes and obesity in a murine model.
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Rasmussen TS, Mentzel CMJ, Kot W, Castro-Mejía JL, Zuffa S, Swann JR, Hansen LH, Vogensen FK, Hansen AK, and Nielsen DS
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- Animals, Blood Glucose analysis, Diabetes Mellitus, Experimental therapy, Diet, High-Fat, Disease Models, Animal, Gastrointestinal Microbiome, Gene Expression, Insulin-Like Growth Factor Binding Protein 2 genetics, Insulin-Like Growth Factor Binding Protein 2 metabolism, Klotho Proteins, Membrane Proteins genetics, Membrane Proteins metabolism, Metabolome, Mice, Inbred C57BL, Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha genetics, Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha metabolism, Proof of Concept Study, Proto-Oncogene Proteins c-myc genetics, Proto-Oncogene Proteins c-myc metabolism, Receptors, G-Protein-Coupled genetics, Receptors, G-Protein-Coupled metabolism, Receptors, Leptin genetics, Receptors, Leptin metabolism, Suppressor of Cytokine Signaling 3 Protein genetics, Suppressor of Cytokine Signaling 3 Protein metabolism, Weight Gain, Diabetes Mellitus, Type 2 therapy, Fecal Microbiota Transplantation, Obesity therapy, Virome
- Abstract
Objective: Development of obesity and type 2 diabetes (T2D) are associated with gut microbiota (GM) changes. The gut viral community is predominated by bacteriophages (phages), which are viruses that attack bacteria in a host-specific manner. The antagonistic behaviour of phages has the potential to alter the GM. As a proof-of-concept, we demonstrate the efficacy of faecal virome transplantation (FVT) from lean donors for shifting the phenotype of obese mice into closer resemblance of lean mice., Design: The FVT consisted of viromes with distinct profiles extracted from the caecal content of mice from different vendors that were fed a low-fat (LF) diet for 14 weeks. Male C57BL/6NTac mice were divided into five groups: LF (as diet control), high-fat (HF) diet, HF+ampicillin (Amp), HF+Amp+FVT and HF+FVT. At weeks 6 and 7 of the study, the HF+FVT and HF+Amp+FVT mice were treated with FVT by oral gavage. The Amp groups were treated with Amp 24 hours prior to first FVT treatment., Results: Six weeks after first FVT, the HF+FVT mice showed a significant decrease in weight gain compared with the HF group. Further, glucose tolerance was comparable between the LF and HF+FVT mice, while the other HF groups all had impaired glucose tolerance. These observations were supported by significant shifts in GM composition, blood plasma metabolome and expression levels of genes associated with obesity and T2D development., Conclusions: Transfer of caecal viral communities from mice with a lean phenotype into mice with an obese phenotype led to reduced weight gain and normalised blood glucose parameters relative to lean mice. We hypothesise that this effect is mediated via FVT-induced GM changes., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2020. No commercial re-use. See rights and permissions. Published by BMJ.)
- Published
- 2020
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15. Theory of slow-light semiconductor optical amplifiers.
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Saldutti M, Rasmussen TS, Gioannini M, and Mørk J
- Abstract
We have developed an efficient framework for analyzing the reflection and transmission properties of semiconductor photonic crystal optical amplifiers. Specifically, we have investigated the use of slow light to enhance the gain of short integrated amplifiers. We find that the expected enhancement in transmission is limited by distributed feedback induced by the material gain itself. Such back-scattering is further enhanced by the refractive index variation associated with the linewidth enhancement factor. The inclusion of this effect reveals that for a given material gain, devices with smaller linewidth enhancement factor may offer better performance.
- Published
- 2020
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16. [Bakteriofager - de hjælpsomme vira].
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Rasmussen TS and Nielsen DS
- Subjects
- Bacterial Proteins, Humans, Phage Therapy
- Published
- 2020
17. All-optical non-linear activation function for neuromorphic photonic computing using semiconductor Fano lasers.
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Rasmussen TS, Yu Y, and Mork J
- Abstract
We predict that semiconductor Fano lasers can be used to realize an all-optical non-linear activation function for neuromorphic photonic computing. By exploiting optical control of a Fano mirror, the laser can generate optical pulses with low threshold energy, gigahertz repetition rates, and orders of magnitude suppression between the on- and off-states. Analytical estimates of the switching threshold energy, extinction ratio, and refractory period agree well with numerical results.
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- 2020
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18. Bacteriophage-mediated manipulation of the gut microbiome - promises and presents limitations.
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Rasmussen TS, Koefoed AK, Jakobsen RR, Deng L, Castro-Mejía JL, Brunse A, Neve H, Vogensen FK, and Nielsen DS
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- Diabetes Mellitus, Type 2 therapy, Fecal Microbiota Transplantation standards, Humans, Obesity therapy, Virome, Bacteriophages physiology, Fecal Microbiota Transplantation trends, Gastrointestinal Microbiome
- Abstract
Gut microbiome (GM) composition and function are linked to human health and disease, and routes for manipulating the GM have become an area of intense research. Due to its high treatment efficacy, the use of fecal microbiota transplantation (FMT) is generally accepted as a promising experimental treatment for patients suffering from GM imbalances (dysbiosis), e.g. caused by recurrent Clostridioides difficile infections (rCDI). Mounting evidence suggests that bacteriophages (phages) play a key role in successful FMT treatment by restoring the dysbiotic bacterial GM. As a refinement to FMT, removing the bacterial component of donor feces by sterile filtration, also referred to as fecal virome transplantation (FVT), decreases the risk of invasive infections caused by bacteria. However, eukaryotic viruses and prophage-encoded virulence factors remain a safety issue. Recent in vivo studies show how cascading effects are initiated when phage communities are transferred to the gut by e.g. FVT, which leads to changes in the GM composition, host metabolome, and improve host health such as alleviating symptoms of obesity and type-2-diabetes (T2D). In this review, we discuss the promises and limitations of FVT along with the perspectives of using FVT to treat various diseases associated with GM dysbiosis., (© FEMS 2020.)
- Published
- 2020
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19. Suppression of Coherence Collapse in Semiconductor Fano Lasers.
- Author
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Rasmussen TS, Yu Y, and Mork J
- Abstract
We show that semiconductor Fano lasers strongly suppress dynamic instabilities induced by external optical feedback. A comparison with conventional Fabry-Perot lasers shows orders of magnitude improvement in feedback stability and in many cases even total suppression of coherence collapse, which is of major importance for applications in integrated photonics. The laser dynamics are analyzed using a generalization of the Lang-Kobayashi model for semiconductor lasers with external feedback, and an analytical expression for the critical feedback level is derived.
- Published
- 2019
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20. Sporofaciens musculi gen. nov., sp. nov., a novel bacterium isolated from the caecum of an obese mouse.
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Rasmussen TS, Streidl T, Hitch TCA, Wortmann E, Deptula P, Kofoed MVW, Riedel T, Neumann-Schaal M, Hansen M, Nielsen DS, Clavel T, and Vogensen FK
- Abstract
A bacterial strain, designated WCA-9-b2
T , was isolated from the caecal content of an 18-week-old obese C57BL/6NTac male mouse. According to phenotypic analyses, the isolate was rod-shaped, strictly anaerobic, spore-forming, non-motile and Gram-stain-positive, under the conditions tested. Colonies were irregular and non-pigmented. Analysis of the 16S rRNA gene sequence indicated that the isolate belonged to the order Clostridiales with Dorea longicatena ATCC 27755T (94.9 % sequence identity), Ruminococcus gnavus ATCC 29149T (94.8%) and Clostridium scindens ATCC 35704T (94.3%) being the closest relatives. Whole genome sequencing showed an average nucleotide identity <74.23 %, average amino acid identity <64.52-74.67 % and percentage of conserved proteins values <50 % against the nine closest relatives ( D. longicatena , Ruminococcus gnavus , C. scindens , Dorea formicigenerans , Ruminococcus lactaris , Clostridium hylemonae , Merdimonas faecis , Faecalicatena contorta and Faecalicatena fissicatena ). The genome-based G+C content of genomic DNA was 44.4 mol%. The major cellular fatty acids were C16 : 0 (24.5%), C18 : 1 cis 9 (19.8 %), C16 : 0 DMA (11.7%), C18 : 0 (8.4%) and C14 : 0 (6.6%). Respiratory quinones were not detected. The predominant metabolic end products of glucose fermentation were acetate and succinate. Production of CO2 and H2 were detected. Based on these data, we propose that strain WCA-9-b2T represents a novel species within a novel genus, for which the name Sporofaciens musculi gen. nov., sp. nov. is proposed. The type strain is WCA-9-b2T (=DSM 106039T =CECT 30156T ).- Published
- 2019
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21. Mouse Vendor Influence on the Bacterial and Viral Gut Composition Exceeds the Effect of Diet.
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Rasmussen TS, de Vries L, Kot W, Hansen LH, Castro-Mejía JL, Vogensen FK, Hansen AK, and Nielsen DS
- Subjects
- Animals, Bacterial Physiological Phenomena, DNA, Bacterial analysis, DNA, Viral analysis, Diet, High-Fat adverse effects, Feces microbiology, Gastrointestinal Microbiome genetics, Male, Mice, Mice, Inbred C57BL, Models, Animal, RNA, Ribosomal, 16S genetics, Reproducibility of Results, Sequence Analysis, DNA, Virus Physiological Phenomena, Bacteria classification, Bacteria genetics, Bacteria virology, Bacteriophages classification, Bacteriophages genetics, Diet, Gastrointestinal Microbiome physiology
- Abstract
Often physiological studies using mice from one vendor show different outcome when being reproduced using mice from another vendor. These divergent phenotypes between similar mouse strains from different vendors have been assigned to differences in the gut microbiome. During recent years, evidence has mounted that the gut viral community plays a key role in shaping the gut microbiome and may thus also influence mouse phenotype. However, to date inter-vendor variation in the murine gut virome has not been studied. Using a metavirome approach, combined with 16S rRNA gene sequencing, we here compare the composition of the viral and bacterial gut community of C57BL/6N mice from three different vendors exposed to either a chow-based low-fat diet or high-fat diet. Interestingly, both the bacterial and the viral component of the gut community differed significantly between vendors. The different diets also strongly influenced both the viral and bacterial gut community, but surprisingly the effect of vendor exceeded the effect of diet. In conclusion, the vendor effect is substantial not only on the gut bacterial community but also strongly influences viral community composition. Given the effect of GM on mice phenotype, this is essential to consider for increasing reproducibility of mouse studies.
- Published
- 2019
- Full Text
- View/download PDF
22. The Gut Microbiome on a Periodized Low-Protein Diet Is Associated With Improved Metabolic Health.
- Author
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Li Z, Rasmussen TS, Rasmussen ML, Li J, Henríquez Olguín C, Kot W, Nielsen DS, and Jensen TE
- Abstract
A periodized (14 days on/14 days off) 5% low protein-high carbohydrate (pLPHC) diet protects against weight gain, improves glucose tolerance in mice and interacts with concurrent voluntary activity wheel training on several parameters including weight maintenance and liver FGF21 secretion. The gut microbiome (GM) responds to both diet and exercise and may influence host metabolism. This study compared the cecal GM after a 13.5-week intervention study in mice on a variety of dietary interventions ± concurrent voluntary exercise training in activity wheels. The diets included chronic chow diet, LPHC diet, 40 E% high protein-low carbohydrate (HPLC) diet, an obesigenic chronic high-fat diet (HFD) and the pLPHC diet. Our hypothesis was that the GM changes with pLPHC diet would generally reflect the improved metabolic health of the host and interact with concurrent exercise training. The GM analyses revealed greater abundance phylum Bacteroidetes and the genus Akkermansia on chronic and periodized LPHC and higher abundance of Oscillospira and Oscillibacter on HFD. The differences in diet-induced GM correlated strongly with the differences in a range of host metabolic health-measures. In contrast, no significant effect of concurrent exercise training was observed. In conclusion, pLPHC diet elicits substantial changes in the GM. In contrast, only subtle and non-significant effects of concurrent activity wheel exercise were observed. The pLPHC-associated microbiome may contribute to the healthier host phenotype observed in these mice.
- Published
- 2019
- Full Text
- View/download PDF
23. Effect of fecal microbiota transplantation route of administration on gut colonization and host response in preterm pigs.
- Author
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Brunse A, Martin L, Rasmussen TS, Christensen L, Skovsted Cilieborg M, Wiese M, Khakimov B, Pieper R, Nielsen DS, Sangild PT, and Thymann T
- Subjects
- Animals, Animals, Newborn, Bacteria genetics, Bacteria isolation & purification, Bacteroides genetics, Bacteroides isolation & purification, Colon microbiology, Enterocolitis, Necrotizing microbiology, Enterocolitis, Necrotizing prevention & control, Enterocolitis, Necrotizing therapy, Feces microbiology, Female, Gastrointestinal Tract microbiology, Hydrogen-Ion Concentration, Pregnancy, RNA, Ribosomal, 16S genetics, Stomach microbiology, Swine, Swine Diseases microbiology, Swine Diseases prevention & control, Bacterial Adhesion, Enterocolitis, Necrotizing veterinary, Fecal Microbiota Transplantation veterinary, Gastrointestinal Microbiome physiology, Swine Diseases therapy
- Abstract
This study examined gut colonization patterns and host responses to fecal microbiota transplantation (FMT) by different administration routes after preterm birth. In two separate experiments, cesarean-delivered, preterm pigs were administered combined oral + rectal, or exclusively rectal donor feces, and compared with saline controls. After 5 days, stomach and colon bacterial compositions were determined by 16S rRNA gene amplicon sequencing, and organic acid metabolites measured. Further, gut pathology, mucosa bacterial adherence, and goblet cell density were assessed. FMT increased the relative abundance of obligate anaerobes in the colon without affecting total bacterial load. Bacteroides colonized recipients despite low abundance in the donor feces, whereas highly abundant Prevotella and Ruminococcaceae did not. Further, FMT changed carbohydrate metabolism from lactate to propionate production thereby increasing colonic pH. Besides, FMT preserved goblet cell mucin stores and reduced necrotizing enterocolitis incidence. Only rectal FMT increased the stomach-to-colon pH gradient and resistance to mucosa bacterial adhesion. Conversely, oral + rectal FMT increased bacterial adhesion, internal organ colonization, and overall mortality. Our results uncovered distinctions in bacterial colonization patterns along the gastrointestinal tract, as well as host tolerability between oral and rectal FMT administration in preterm newborns. Besides, FMT showed the potential to prevent necrotizing enterocolitis.
- Published
- 2019
- Full Text
- View/download PDF
24. Modes, stability, and small-signal response of photonic crystal Fano lasers.
- Author
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Rasmussen TS, Yu Y, and Mork J
- Abstract
Photonic crystal Fano lasers have recently been realised experimentally, showing useful properties such as pinned single-mode lasing and passive pulse generation. Here the fundamental properties of the modes of the Fano laser are analysed, showing how the laser functionality depends sensitively on the system configuration. Furthermore the laser stability is investigated and linked to the small-signal response, which shows additional dynamics that cannot be explained with a conventional rate equation model, including a damping of relaxation oscillations and a frequency modulation bandwidth that is only limited by the nanocavity response.
- Published
- 2018
- Full Text
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25. Genetic manipulation of structural color in bacterial colonies.
- Author
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Johansen VE, Catón L, Hamidjaja R, Oosterink E, Wilts BD, Rasmussen TS, Sherlock MM, Ingham CJ, and Vignolini S
- Subjects
- Bacterial Proteins genetics, Bacterial Proteins metabolism, Color, Flavobacterium growth & development, Flavobacterium metabolism, Genetic Engineering, Photons, Seaweed microbiology, Flavobacterium chemistry, Flavobacterium genetics
- Abstract
Naturally occurring photonic structures are responsible for the bright and vivid coloration in a large variety of living organisms. Despite efforts to understand their biological functions, development, and complex optical response, little is known of the underlying genes involved in the development of these nanostructures in any domain of life. Here, we used Flavobacterium colonies as a model system to demonstrate that genes responsible for gliding motility, cell shape, the stringent response, and tRNA modification contribute to the optical appearance of the colony. By structural and optical analysis, we obtained a detailed correlation of how genetic modifications alter structural color in bacterial colonies. Understanding of genotype and phenotype relations in this system opens the way to genetic engineering of on-demand living optical materials, for use as paints and living sensors., Competing Interests: The authors declare no conflict of interest.
- Published
- 2018
- Full Text
- View/download PDF
26. Dignity as an empirical lifeworld construction-in the field of surgery in Denmark.
- Author
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Rasmussen TS and Delmar C
- Subjects
- Aged, Denmark, Female, Humans, Male, Middle Aged, Nurse-Patient Relations, Personal Autonomy, Qualitative Research, Surgical Procedures, Operative nursing, Surveys and Questionnaires, Personhood, Surgical Procedures, Operative psychology
- Abstract
Patient dignity is a complex yet central phenomenon. Disrespect for dignity can mean retention of sick role, loss of self-care and control, decreased participation and therefore influence healing. At the same time, nurses have an obligation to respect dignity, and patients expect it. In clinical practice, with the focus on efficiency and economy, dignity can be compromised. The surgical patient may be particularly vulnerable to loss of dignity, when focus is solely on surgical procedure, efficiency, and productivity. The aim of the article is to describe the characteristics of the importance of dignity perceived by four surgical patients at a university hospital in Denmark. The hermeneutic phenomenological approach of Van Manen is used to analyse and interpret data collected from in-depth semi-structured interviews. The interviews explored the lived experience with two women and two men who had undergone a surgical intervention in a Danish vascular surgery department. The thematic analysis led to the basic theme: "To be an important person" illustrated by the themes: "Being a co-player," "Over exposure," and "To swallow the bitter pill." The findings provide a better understanding of patient's perspective of dignity, which is characterized by a complex interaction of several factors. Nurses should be concerned with balancing expectations, values, and opinions to maintain dignity in nursing and create a common platform for collaboration. This collaboration makes it possible for patients to be involved and have a voice in relation to nursing, treatment, and administering of time even though it could be at the expense of the terms of the system.
- Published
- 2014
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27. Chiral pool synthesis of calystegine A3 from 2-deoxyglucose via a Brown allylation.
- Author
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Rasmussen TS and Jensen HH
- Subjects
- Alkylation, Molecular Conformation, Nortropanes chemistry, Solanaceous Alkaloids chemistry, Stereoisomerism, Deoxyglucose chemistry, Nortropanes chemical synthesis, Solanaceous Alkaloids chemical synthesis
- Abstract
Calystegine A(3) is a naturally occurring nortropane iminosugar of which there previously have been three total syntheses. Inspired by our previous work we here report on a fourth approach using 17 steps from 2-deoxy-d-glucose applying a diastereoselective allylation protocol., (Copyright © 2011 Elsevier Ltd. All rights reserved.)
- Published
- 2011
- Full Text
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28. Synthesis of uronic-noeurostegine--a potent bacterial β-glucuronidase inhibitor.
- Author
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Rasmussen TS, Koldsø H, Nakagawa S, Kato A, Schiøtt B, and Jensen HH
- Subjects
- Animals, Binding, Competitive, Cattle, Enzyme Inhibitors pharmacology, Escherichia coli drug effects, Escherichia coli enzymology, Escherichia coli Proteins metabolism, Glucuronidase metabolism, Inhibitory Concentration 50, Intestines drug effects, Intestines enzymology, Lactase metabolism, Liver drug effects, Liver enzymology, Models, Molecular, Nortropanes pharmacology, Protein Binding, Rats, Species Specificity, Trehalase antagonists & inhibitors, Trehalase metabolism, Uronic Acids chemistry, Chemistry, Pharmaceutical methods, Enzyme Inhibitors chemical synthesis, Escherichia coli Proteins antagonists & inhibitors, Glucuronidase antagonists & inhibitors, Nortropanes chemical synthesis
- Abstract
Inhibition of β-glucuronidases has recently been shown to be useful in alleviating drug toxicity for common colon cancer chemotherapeutic CPT-11 (also called Irinotecan). We have prepared a new compound of the nortropane-type, uronic-Noeurostegine, and demonstrated that this is a competitive and potent E. coli β-glucuronidase inhibitor, while inhibition of the mammalian β-glucuronidase from bovine liver was found to be less significant. Although not intended, two other compounds having N-ethyl and N-(4-hydroxybutyl) substituents were also prepared in this study due to the sluggish debenzylation in the final step. The N-substituents are believed to come from reaction with the solvents used being ethanol and THF, respectively. These compounds also inhibited the two β-glucuronidases albeit to a lesser extent compared to the parent compound. Noeurostegine and the three uronic-noeurostegines were additionally evaluated as inhibitors against a wide panel of glycosidases with the former showing potent inhibition of rat intestinal lactase and trehalase, whereas the latter was found to be inactive.
- Published
- 2011
- Full Text
- View/download PDF
29. Synthesis of N-alkylated noeurostegines and evaluation of their potential as treatment for Gaucher's disease.
- Author
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Rasmussen TS, Allman S, Twigg G, Butters TD, and Jensen HH
- Subjects
- Enzyme Assays, Humans, Inhibitory Concentration 50, Nortropanes chemistry, Nortropanes therapeutic use, Gaucher Disease drug therapy, Glucosylceramidase antagonists & inhibitors, Nortropanes chemical synthesis
- Abstract
The potent and selective inhibitor of β-glucosidases, noeurostegine, was evaluated as an inhibitor of glucocerebrosidase (GCase) to give an IC(50) value of 0.4 μM, being 250- and 150-fold better than N-butyl and N-nonyl noeurostegine, respectively. The parent noeurostegine and its N-butyl and N-nonyl alkylated congeners were also tested as pharmacological chaperones against a N370S GCase mutant. Of these, only noeurostegine, was found to increase enzyme activity, which in potency was comparable to that previously reported for isofagomine., (Copyright © 2011 Elsevier Ltd. All rights reserved.)
- Published
- 2011
- Full Text
- View/download PDF
30. Synthesis and glycosidase inhibitory activity of noeurostegine-a new and potent inhibitor of beta-glucoside hydrolases.
- Author
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Rasmussen TS and Jensen HH
- Subjects
- Catalytic Domain, Ethylenes chemistry, Glycoside Hydrolases chemistry, Glycoside Hydrolases metabolism, Nortropanes chemistry, Nortropanes pharmacology, Solanaceous Alkaloids chemistry, Solanaceous Alkaloids pharmacology, Thermotoga maritima enzymology, Enzyme Inhibitors chemical synthesis, Enzyme Inhibitors pharmacology, Glycoside Hydrolases antagonists & inhibitors, Nortropanes chemical synthesis
- Abstract
A new, stable hemi-aminal nor-tropane christened noeurostegine was synthesised in 22 steps from levoglucosan and tested for inhibitory activity against glycoside hydrolases. Sweet almond and Thermotoga maritimabeta-glucosidases, coffee bean alpha-galactosidase, and Asp. oryzaebeta-galactosidase were inhibited in the low micromolar region but significant tightening of binding to K(i) 50 nM for almond beta-glucosidase was found to occur after pre-incubation. Yeast alpha-glucosidase and E. colibeta-galactosidase were not inhibited at 1 mM.
- Published
- 2010
- Full Text
- View/download PDF
31. Adaptive partially hidden Markov models with application to bilevel image coding.
- Author
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Forchhammer S and Rasmussen TS
- Abstract
Partially hidden Markov models (PHMMs) have previously been introduced. The transition and emission/output probabilities from hidden states, as known from the HMMs, are conditioned on the past. This way, the HMM may be applied to images introducing the dependencies of the second dimension by conditioning. In this paper, the PHMM is extended to multiple sequences with a multiple token version and adaptive versions of PHMM coding are presented. The different versions of the PHMM are applied to lossless bilevel image coding. To reduce and optimize the model cost and size, the contexts are organized in trees and effective quantization of the parameters is introduced. The new coding methods achieve results that are better than the JBIG standard on selected test images, although at the cost of increased complexity. By the minimum description length principle, the methods presented for optimizing the code length may apply as guidance for training (P)HMMs for, e.g., segmentation or recognition purposes. Thereby, the PHMM models provide a new approach to image modeling.
- Published
- 1999
- Full Text
- View/download PDF
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