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| 2. |
- Forrest, ARR, et al.
(författare)
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A promoter-level mammalian expression atlas
- 2014
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 507:7493, s. 462-
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Tidskriftsartikel (refereegranskat)
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| 3. |
- Noguchi, S, et al.
(författare)
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FANTOM5 CAGE profiles of human and mouse samples
- 2017
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Ingår i: Scientific data. - : Springer Science and Business Media LLC. - 2052-4463. ; 4, s. 170112-
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Tidskriftsartikel (refereegranskat)abstract
- In the FANTOM5 project, transcription initiation events across the human and mouse genomes were mapped at a single base-pair resolution and their frequencies were monitored by CAGE (Cap Analysis of Gene Expression) coupled with single-molecule sequencing. Approximately three thousands of samples, consisting of a variety of primary cells, tissues, cell lines, and time series samples during cell activation and development, were subjected to a uniform pipeline of CAGE data production. The analysis pipeline started by measuring RNA extracts to assess their quality, and continued to CAGE library production by using a robotic or a manual workflow, single molecule sequencing, and computational processing to generate frequencies of transcription initiation. Resulting data represents the consequence of transcriptional regulation in each analyzed state of mammalian cells. Non-overlapping peaks over the CAGE profiles, approximately 200,000 and 150,000 peaks for the human and mouse genomes, were identified and annotated to provide precise location of known promoters as well as novel ones, and to quantify their activities.
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| 4. |
- Ramilowski, JA, et al.
(författare)
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Functional annotation of human long noncoding RNAs via molecular phenotyping
- 2020
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Ingår i: Genome research. - : Cold Spring Harbor Laboratory. - 1549-5469 .- 1088-9051. ; 30:7, s. 1060-1072
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Tidskriftsartikel (refereegranskat)abstract
- Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression of 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense oligonucleotides targeting the same lncRNAs exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected genes and pathways. Here, we disseminate the largest-to-date lncRNA knockdown data set with molecular phenotyping (over 1000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for ZNF213-AS1 and lnc-KHDC3L-2.
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| 9. |
- Baumann, I., et al.
(författare)
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Do cognitively stimulating activities affect the association between retirement timing and cognitive functioning in old age?
- 2022
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Ingår i: Ageing & Society. - : Cambridge University Press. - 0144-686X .- 1469-1779. ; 42:2, s. 306-330
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Tidskriftsartikel (refereegranskat)abstract
- In response to the rising financial pressure on old-age pension systems in industrialised economies, many European countries plan to increase the eligibility age for retirement pensions. We used data from Sweden to examine whether (and if so, how) retirement after age 65 - the eligibility age for basic pension - compared to retiring earlier affects older adults' (between ages 70 and 85) cognitive functioning. Using a propensity score matching (PSM) approach, we addressed the selection bias potentially introduced by non-random selection into either early or late retirement. We also examined average and heterogeneous treatment effects (HTEs). HTEs were evaluated for different levels of cognitive stimulation from occupational activities before retirement and from leisure activities after retirement. We drew from a rich longitudinal data-set linking two nationally representative Swedish surveys with a register data-set and found that, on average, individuals who retire after age 65 do not have a higher level of cognitive functioning than those who retire earlier. Similarly, we did not observe HTEs from occupational activities. With respect to leisure activities, we found no systematic effects on cognitive functioning among those working beyond age 65. We conclude that, in general, retirement age does not seem to affect cognitive functioning in old age. Yet, the rising retirement age may put substantial pressure on individuals who suffer from poor health at the end of their occupational career, potentially exacerbating social- and health-related inequalities among older people.
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| 12. |
- Lennartsson, Anders, 1980, et al.
(författare)
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Reversible Guest Binding in a Non-Porous FeII Coordination Polymer Host Toggles Spin Crossover
- 2015
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Ingår i: Chemistry - A European Journal. - : Wiley. - 1521-3765 .- 0947-6539. ; 21:45, s. 16066-16072
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Tidskriftsartikel (refereegranskat)abstract
- Formation of either a dimetallic compound or a 1D coordination polymer of adiponitrile adducts of [Fe(bpte)]2+ (bpte=[1,2-bis(pyridin-2-ylmethyl)thio]ethane) can be controlled by the choice of counteranion. The iron(II) atoms of the bis(adiponitrile)-bridged dimeric complex [Fe2(bpte)2(μ2-(NC(CH2)4CN)2](SbF6)4 (2) are low spin at room temperature, as are those in the polymeric adiponitrile-linked acetone solvate polymer {[Fe(bpte)(μ2-NC(CH2)4CN)](BPh4)2 Me2CO} (3Me2CO). On heating 3Me2CO to 80°C, the acetone is abruptly removed with an accompanying purple to dull lavender colour change corresponding to a conversion to a high-spin compound. Cooling reveals that the desolvate 3 shows hysteretic and abrupt spin crossover (SCO) S=0虠S=2 behaviour centred at 205K. Non-porous 3 can reversibly absorb one equivalent of acetone per iron centre to regenerate the same crystalline phase of 3Me2CO concurrently reinstating a low-spin state.
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| 16. |
- Skogar, O, et al.
(författare)
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"Effects of Tactile Touch on pain, sleep and health related quality of life in Parkinsons disease with chronic pain": A randomized, controlled and prospective study
- 2013
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Ingår i: European Journal of Integrative Medicine. - : Elsevier. - 1876-3820 .- 1876-3839. ; 5:2, s. 141-152
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Tidskriftsartikel (refereegranskat)abstract
- Introduction: Parkinsons disease (PD) is often associated with chronic PD related pain. Complementary medicine are widely used but randomized, controlled and prospective studies of the effects are sparse. less thanbrgreater than less thanbrgreater thanAims of the study: To compare the effects of Tactile Touch (TT) with Rest to Music (RTM) in PD patients with chronic pain and to describe effects within groups. less thanbrgreater than less thanbrgreater thanPatients and methods: A 34 week controlled randomized and prospective trial compared the effects of TT with RTM in 45 (29 TT and 16 RTM) patients with PD and chronic pain. The whole body tactile stimulation method was performed for each individual patient by the same therapist for 10 times during the first 8 weeks. The RTM group received the same therapy except for the tactile stimulation. Pharmacotherapy was kept unchanged. Participants were assessed at pre- and post-intervention for pain, sleep patterns and health related quality of life (HRQoL). less thanbrgreater than less thanbrgreater thanResults: Differences between TT and RTM groups were few. Total PDSS significantly improved within the TT but not in the RTM-group. No significant differences between groups were seen in pain parameters, although significant improvements were seen within the TT-group after the intervention period. There were significant improvements within both groups in HRQoL and between groups in the items physical role and social functioning 4 weeks after screening. less thanbrgreater than less thanbrgreater thanConclusions: No significant differences between the TT and RTM groups were seen. Only in single aspects did patients with PD and chronic pain have more benefit more from CAM therapy with TT in combination with RTM.
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| 17. |
- Skogar, Ö, et al.
(författare)
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Diurnal salivary cortisol concentrations in Parkinson’s disease: increased total secretion and morning cortisol concentrations
- 2011
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Ingår i: International Journal of General Medicine. - Macclesfield, UK : Dove Medical Press Ltd.. - 1178-7074. ; 18, s. 494-494
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Tidskriftsartikel (refereegranskat)abstract
- Background:Parkinson’s disease (PD) is a chronic neurodegenerative disorder. There is limited knowledge about the function of the hypothalamic-pituitary-adrenal axis in PD. The primary aim of this prospective study was to analyze diurnal salivary cortisol concentrations in patients with PD and correlate these with age, gender, body mass index (BMI), duration of PD, and pain. The secondary aim was to compare the results with a healthy reference group.Methods:Fifty-nine PD patients, 35 women and 24 men, aged 50–79 years, were recruited. The reference group comprised healthy individuals matched for age, gender, BMI, and time point for sampling. Salivary cortisol was collected at 8 am, 1 pm, and 8 pm, and 8 am the next day using cotton-based Salivette ®tubes and analyzed using Spectria®Cortisol I125. A visual analog scale was used for estimation of pain.Results:The median cortisol concentration was 16.0 (5.8–30.2) nmol/L at 8 am, 5.8 (3.0–16.4) at 1 pm, 2.8 (1.6–8.0) at 8 pm, and 14.0 (7.5–28.7) at 8 am the next day. Total secretion and rate of cortisol secretion during the day (8 am–8 pm) and the concentration of cortisol on the next morning were lower (12.5 nmol/L) in the reference group. No significant correlations with age, gender, BMI, duration of PD, Hoehn and Yahr score, Unified Parkinson’s Disease Rating Scale III score, gait, pain, or cortisol concentrations were found.Conclusion:The neurodegenerative changes in PD does not seem to interfere with the hypothalamic-pituitary-adrenal axis. Salivary cortisol concentrations in PD patients were increased in the morning compared with the reference group, and were not influenced by motor dysfunction, duration of disease, or coexistence of chronic or acute pain.
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| 19. |
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| 20. |
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| 21. |
- Wu, X. P., et al.
(författare)
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Alternative Cytotoxic Effects of the Postulated IGF-IR Inhibitor Picropodophyllin In Vitro
- 2013
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Ingår i: Molecular Cancer Therapeutics. - : American Association for Cancer Research (AACR). - 1535-7163 .- 1538-8514. ; 12:8, s. 1526-1536
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Tidskriftsartikel (refereegranskat)abstract
- The insulin-like growth factor-1 (IGF-I) and its receptors play an important role in transformation and progression of several malignancies. Inhibitors of this pathway have been developed and evaluated but generally performed poorly in clinical trials, and several drug candidates have been abandoned. The cyclolignan picropodophyllin (PPP) has been described as a potent and selective IGF-IR inhibitor and is currently undergoing clinical trials. We investigated PPP's activity in panels of human cancer cell lines (e. g., esophageal squamous carcinoma cell lines) but found no effects on the phosphorylation or expression of IGF-IR. Nor was the cytotoxic activity of PPP related to the presence or spontaneous phosphorylation of IGF-IR. However, its activity correlated with that of known tubulin inhibitors, and it destabilized microtubule assembly at cytotoxic concentrations also achievable in patients. PPP is a stereoisomer of podophyllotoxin (PPT), a potent tubulin inhibitor, and an equilibrium between the two has previously been described. PPPcould thus potentially act as a reservoir for the continuous generation of low doses of PPT. Interestingly, PPP also inhibited downstream signaling from tyrosine kinase receptors, including the serine/threonine kinase Akt. This effect is associated with microtubule-related downregulation of the EGF receptor, rather than the IGF-IR. These results suggest that the cytotoxicity and pAkt inhibition observed following treatment with the cyclolignan PPP in vitro result from microtubule inhibition (directly or indirectly by spontaneous PPT formation), rather than any effect on IGF-IR. It is also suggested that PPT should be used as a reference compound in all future studies on PPP. (C)2013 AACR.
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| 22. |
- Asadollahzadeh, Mohammadtaghi, et al.
(författare)
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Application of Fungal Biomass for the Development of New Polylactic Acid-Based Biocomposites
- 2022
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Ingår i: Polymers. - : MDPI AG. - 2073-4360. ; 14:9
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Tidskriftsartikel (refereegranskat)abstract
- Fungal biomass (FB), a by-product of the fermentation processes produced in large volumes, is a promising biomaterial that can be incorporated into poly(lactic acid) (PLA) to develop enhanced biocomposites that fully comply with the biobased circular economy concept. The PLA/FB composites, with the addition of triethyl citrate (TEC) as a biobased plasticizer, were fabricated by a microcompounder at 150 °C followed by injection molding. The effects of FB (10 and 20 wt %) and TEC (5, 10, and 15 wt %) contents on the mechanical, thermal and surface properties of the biocomposites were analyzed by several techniques. The PLA/FB/TEC composites showed a rough surface in their fracture section. A progressive decrease in tensile strength and Young’s modulus was observed with increasing FB and TEC, while elongation at break and impact strength started to increase. The neat PLA and biocomposite containing 10% FB and 15% TEC exhibited the lowest (3.84%) and highest (224%) elongation at break, respectively. For all blends containing FB, the glass transition, crystallization and melting temperatures were shifted toward lower values compared to the neat PLA. The incorporation of FB to PLA thus offers the possibility to overcome one of the main drawbacks of PLA, which is brittleness.
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| 23. |
- Asadollahzadeh, Mohammadtaghi, et al.
(författare)
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Using spent sulfite liquor for valuable fungal biomass production by Aspergilus oryzae
- 2017
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Ingår i: Nordic Pulp & Paper Research Journal. - 0283-2631 .- 2000-0669. ; 32:4, s. 630-638
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Tidskriftsartikel (refereegranskat)abstract
- The recent and increasing interest in bioconversion of lignocellulosic wastes into value-added products has led to extensive research on various microorganisms and substrates. In this study, filamentous fungus Aspergillus oryzae was cultivated on spent sulfite liquor (SSL) from a pulp mill. The process using an airlift bioreactor (3.5 L working volume) was successfully carried out in 48 h with an airflow of 0.85 vvm (volume air per volume culture per minute) at 35°C and pH 5.5. The cultivation results showed that the fungal biomass concentration was higher in more diluted SSL. The highest and lowest fungal biomass concentrations when spore inoculation was used were 10.2 and 6.5 g/l SSL, in diluted SSL to 60 and 80%, respectively. The range of crude protein and total fat of the fungal biomass was 0.44 – 0.48 and 0.04 – 0.11 g/g biomass dry weight, respectively. All essential amino acids were present in acceptable quantities in the fungal biomass. The results obtained in this study have practical implications in that the fungus A. oryzae could be used successfully to produce fungal biomass protein using spent sulfite liquor for animal feed.
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| 24. |
- Bátori, Veronika, et al.
(författare)
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Ethanol and Protein from Ethanol Plant By-Products Using Edible Fungi Neurospora intermedia and Aspergillus oryzae
- 2015
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Ingår i: BioMed Research International. - : Hindawi Limited. - 2314-6133 .- 2314-6141. ; 2015:nov23
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Tidskriftsartikel (refereegranskat)abstract
- Feasible biorefineries for production of second-generation ethanol are difficult to establish due to the process complexity. An alternative is to partially include the process in the first-generation plants. Whole stillage, a by-product from dry-mill ethanol processes from grains, is mostly composed of undegraded bran and lignocelluloses can be used as a potential substrate for production of ethanol and feed proteins. Ethanol production and the proteins from the stillage were investigated using the edible fungi Neurospora intermedia and Aspergillus oryzae, respectively. N. intermedia produced 4.7 g/L ethanol from the stillage and increased to 8.7 g/L by adding 1 FPU of cellulase/g suspended solids. Saccharomyces cerevisiae produced 0.4 and 5.1 g/L ethanol, respectively. Under a two-stage cultivation with both fungi, up to 7.6 g/L of ethanol and 5.8 g/L of biomass containing 42% (w/w) crude protein were obtained. Both fungi degraded complex substrates including arabinan, glucan, mannan, and xylan where reductions of 91, 73, 38, and 89% (w/v) were achieved, respectively. The inclusion of the current process can lead to the production of 44,000 m(3) of ethanol (22% improvement), around 12,000 tons of protein-rich biomass for animal feed, and energy savings considering a typical facility producing 200,000 m(3) ethanol/year.
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| 25. |
- Bátori, Veronika, 1980-, et al.
(författare)
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Production of Pectin-Cellulose Biofilms: A New Approach for Citrus Waste Recycling
- 2017
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Ingår i: International Journal of Polymer Science. - : Hindawi Limited. - 1687-9422 .- 1687-9430. ; 2017, s. 1-9
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Tidskriftsartikel (refereegranskat)abstract
- While citrus waste is abundantly generated, the disposal methods used today remain unsatisfactory: they can be deleterious for ruminants, can cause soil salinity, or are not economically feasible; yet citrus waste consists of various valuable polymers. This paper introduces a novel environmentally safe approach that utilizes citrus waste polymers as a biobased and biodegradable film, for example, for food packaging. Orange waste has been investigated for biofilm production, using the gelling ability of pectin and the strength of cellulosic fibres. A casting method was used to form a film from the previously washed, dried, and milled orange waste. Two film-drying methods, a laboratory oven and an incubator shaker, were compared. FE-SEM images confirmed a smoother film morphology when the incubator shaker was used for drying. The tensile strength of the films was 31.67 ± 4.21 and 34.76 ± 2.64 MPa, respectively, for the oven-dried and incubator-dried films, which is within the range of different commodity plastics. Additionally, biodegradability of the films was confirmed under anaerobic conditions. Films showed an opaque appearance with yellowish colour.
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