| 1. |
- Nyberg, Lena, 1979, et al.
(författare)
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A single-step competitive binding assay for mapping of single DNA molecules
- 2012
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Ingår i: Biochemical and Biophysical Research Communications - BBRC. - : Elsevier BV. - 0006-291X .- 1090-2104. ; 417:1, s. 404-408
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Tidskriftsartikel (refereegranskat)abstract
- Optical mapping of genomic DNA is of relevance for a plethora of applications such as scaffolding for sequencing and detection of structural variations as well as identification cif pathogens like bacteria and viruses. For future clinical applications it is desirable to have a fast and robust mapping method based on as few steps as possible. We here demonstrate a single-step method to obtain a DNA barcode that is directly visualized using nanofluidic devices and fluorescence microscopy. Using a mixture of YOYO-1, a bright DNA dye, and netropsin, a natural antibiotic with very high AT specificity, we obtain a DNA map with a fluorescence intensity profile along the DNA that reflects the underlying sequence. The netropsin binds to AT-tetrads and blocks these binding sites from YOYO-1 binding which results in lower fluorescence intensity from AT-rich regions of the DNA. We thus obtain a DNA barcode that is dark in AT-rich regions and bright in GC-rich regions with kilobasepair resolution. We demonstrate the versatility of the method by obtaining a barcode on DNA from the phage T4 that captures its circular permutation and agrees well with its known sequence.
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| 2. |
- Al-Husseini, Ali, et al.
(författare)
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Long-term postural control in elite athletes following mild traumatic brain injury
- 2022
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Ingår i: Frontiers in Neurology. - : Frontiers Media S.A.. - 1664-2295. ; 13
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Tidskriftsartikel (refereegranskat)abstract
- Background: Traumas to the head and neck are common in sports and often affects otherwise healthy young individuals. Sports-related concussions (SRC), defined as a mild traumatic brain injury (mTBI), may inflict persistent neck and shoulder pain, and headache, but also more complex symptoms, such as imbalance, dizziness, and visual disturbances. These more complex symptoms are difficult to identify with standard health care diagnostic procedures.Objective: To investigate postural control in a group of former elite athletes with persistent post-concussive symptoms (PPCS) at least 6 months after the incident.Method: Postural control was examined using posturography during quiet stance and randomized balance perturbations with eyes open and eyes closed. Randomized balance perturbations were used to examine motor learning through sensorimotor adaptation. Force platform recordings were converted to reflect the energy used to maintain balance and spectrally categorized into total energy used, energy used for smooth corrective changes of posture (i.e., <0.1 Hz), and energy used for fast corrective movements to maintain balance (i.e., >0.1 Hz).Results: The mTBI group included 20 (13 males, mean age 26.6 years) elite athletes with PPCS and the control group included 12 athletes (9 males, mean age 26.4 years) with no history of SRC. The mTBI group used significantly more energy during balance perturbations than controls: +143% total energy, p = 0.004; +122% low frequency energy, p = 0.007; and +162% high frequency energy, p = 0.004. The mTBI subjects also adapted less to the balance perturbations than controls in total (18% mTBI vs. 37% controls, p = 0.042), low frequency (24% mTBI vs. 42% controls, p = 0.046), and high frequency (6% mTBI vs. 28% controls, p = 0.040). The mTBI subjects used significantly more energy during quiet stance than controls: +128% total energy, p = 0.034; +136% low-frequency energy, p = 0.048; and +109% high-frequency energy, p = 0.015.Conclusion: Athletes with previous mTBI and PPCS used more energy to stand compared to controls during balance perturbations and quiet stance and had diminished sensorimotor adaptation. Sports-related concussions are able to affect postural control and motor learning.
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| 3. |
- Altuntas Vural, Ceren, 1980, et al.
(författare)
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Life after use: circular supply chains for second-life of electric vehicle batteries
- 2024
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Ingår i: Production Planning and Control. - 0953-7287 .- 1366-5871. ; In Press
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Tidskriftsartikel (refereegranskat)abstract
- Despite the increasing interest in second-life of electric vehicle batteries, the characteristics of supply chains to support such products are yet to be developed. The purpose of this paper is to investigate the key supply chain characteristics required to effectively accommodate circular models for second-life electric vehicle batteries. Through a longitudinal case study, we map possible application areas and customer segments, necessary key activities, and potential actors that might emerge in future supply chains for these products. The findings are discussed in relation to product-oriented, use-oriented, and result-oriented circular models. The suggested circular models and their comparisons provide insights into how different supply chain dimensions are configured for different circular business models, and the advantages, disadvantages, and prerequisites associated by each model.
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| 4. |
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| 5. |
- Bivik, Caroline, et al.
(författare)
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Novel Genes Involved in Controlling Specification of Drosophila FMRFamide Neuropeptide Cells
- 2015
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Ingår i: Genetics. - : Genetics Society of America. - 0016-6731 .- 1943-2631. ; 200:4, s. 1229-1244
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Tidskriftsartikel (refereegranskat)abstract
- The expression of neuropeptides is often extremely restricted in the nervous system, making them powerful markers for addressing cell specification . In the developing Drosophila ventral nerve cord, only six cells, the Ap4 neurons, of some 10,000 neurons, express the neuropeptide FMRFamide (FMRFa). Each Ap4/FMRFa neuron is the last-born cell generated by an identifiable and well-studied progenitor cell, neuroblast 5-6 (NB5-6T). The restricted expression of FMRFa and the wealth of information regarding its gene regulation and Ap4 neuron specification makes FMRFa a valuable readout for addressing many aspects of neural development, i.e., spatial and temporal patterning cues, cell cycle control, cell specification, axon transport, and retrograde signaling. To this end, we have conducted a forward genetic screen utilizing an Ap4-specific FMRFa-eGFP transgenic reporter as our readout. A total of 9781 EMS-mutated chromosomes were screened for perturbations in FMRFa-eGFP expression, and 611 mutants were identified. Seventy-nine of the strongest mutants were mapped down to the affected gene by deficiency mapping or whole-genome sequencing. We isolated novel alleles for previously known FMRFa regulators, confirming the validity of the screen. In addition, we identified novel essential genes, including several with previously undefined functions in neural development. Our identification of genes affecting most major steps required for successful terminal differentiation of Ap4 neurons provides a comprehensive view of the genetic flow controlling the generation of highly unique neuronal cell types in the developing nervous system.
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| 6. |
- Bostanci, Nagihan, et al.
(författare)
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Dysbiosis of the Human Oral Microbiome During the Menstrual Cycle and Vulnerability to the External Exposures of Smoking and Dietary Sugar.
- 2021
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Ingår i: Frontiers in Cellular and Infection Microbiology. - : Frontiers Media SA. - 2235-2988. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- Physiological hormonal fluctuations exert endogenous pressures on the structure and function of the human microbiome. As such, the menstrual cycle may selectively disrupt the homeostasis of the resident oral microbiome, thus compromising oral health. Hence, the aim of the present study was to structurally and functionally profile the salivary microbiome of 103 women in reproductive age with regular menstrual cycle, while evaluating the modifying influences of hormonal contraceptives, sex hormones, diet, and smoking. Whole saliva was sampled during the menstrual, follicular, and luteal phases (n = 309) of the cycle, and the participants reported questionnaire-based data concerning their life habits and oral or systemic health. No significant differences in alpha-diversity or phase-specific clustering of the overall microbiome were observed. Nevertheless, the salivary abundances of genera Campylobacter, Haemophilus, Prevotella, and Oribacterium varied throughout the cycle, and a higher species-richness was observed during the luteal phase. While the overall community structure maintained relatively intact, its functional properties were drastically affected. In particular, 11 functional modules were differentially abundant throughout the menstrual cycle, including pentose phosphate metabolism, and biosynthesis of cobalamin and neurotransmitter gamma-aminobutyric acid. The menstrual cycle phase, but not oral contraceptive usage, was accountable for greater variations in the metabolic pathways of the salivary microbiome. Further co-risk factor analysis demonstrated that Prevotella and Veillonella were increased in current smokers, whereas high dietary sugar consumption modified the richness and diversity of the microbiome during the cycle. This is the first large study to systematically address dysbiotic variations of the oral microbiome during the course of menstrual cycle, and document the additive effect of smoking and sugar consumption as environmental risk factors. It reveals the structural resilience and functional adaptability of the oral microbiome to the endogenous hormonal pressures of the menstrual cycle, while revealing its vulnerability to the exogenous exposures of diet and smoking.
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| 7. |
- Braekeveldt, Noémie, et al.
(författare)
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Patient-derived xenograft models reveal intratumor heterogeneity and temporal stability in neuroblastoma
- 2018
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Ingår i: Cancer Research. - 0008-5472. ; 78:20, s. 5958-5969
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Tidskriftsartikel (refereegranskat)abstract
- Patient-derived xenografts (PDX) and the Avatar, a single PDX mirroring an individual patient, are emerging tools in preclinical cancer research. However, the consequences of intratumor heterogeneity for PDX modeling of biomarkers, target identification, and treatment decisions remain underexplored. In this study, we undertook serial passaging and comprehensive molecular analysis of neuroblastoma orthotopic PDXs, which revealed strong intrinsic genetic, transcriptional, and phenotypic stability for more than 2 years. The PDXs showed preserved neuroblastoma-associated gene signatures that correlated with poor clinical outcome in a large cohort of patients with neuroblastoma. Furthermore, we captured spatial intratumor heterogeneity using ten PDXs from a single high-risk patient tumor. We observed diverse growth rates, transcriptional, proteomic, and phosphoproteomic profiles. PDX-derived transcriptional profiles were associated with diverse clinical characteristics in patients with high-risk neuroblastoma. These data suggest that high-risk neuroblastoma contains elements of both temporal stability and spatial intratumor heterogeneity, the latter of which complicates clinical translation of personalized PDX-Avatar studies into preclinical cancer research.
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| 8. |
- Brorsson, Joakim, 1988, et al.
(författare)
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Efficient Calculation of the Lattice Thermal Conductivity by Atomistic Simulations with Ab Initio Accuracy
- 2022
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Ingår i: Advanced Theory and Simulations. - : Wiley. - 2513-0390. ; 5:2
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Tidskriftsartikel (refereegranskat)abstract
- High-order force constant expansions can provide accurate representations of the potential energy surface relevant to vibrational motion. They can be efficiently parametrized using quantum mechanical calculations and subsequently sampled at a fraction of the cost of the underlying reference calculations. Here, force constant expansions are combined via the hiphive package with GPU-accelerated molecular dynamics simulations via the GPUMD package to obtain an accurate, transferable, and efficient approach for sampling the dynamical properties of materials. The performance of this methodology is demonstrated by applying it both to materials with very low thermal conductivity (Ba8Ga16Ge30, SnSe) and a material with a relatively high lattice thermal conductivity (monolayer-MoS2). These cases cover both situations with weak (monolayer-MoS2, SnSe) and strong (Ba8Ga16Ge30) pho renormalization. The simulations also enable to access complementary information such as the spectral thermal conductivity, which allows to discriminate the contribution by different phonon modes while accounting for scattering to all orders. The software packages described here are made available to the scientific community as free and open-source software in order to encourage the more widespread use of these techniques as well as their evolution through continuous and collaborative development.
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| 9. |
- Dahl, Caroline, et al.
(författare)
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Ekosystemtjänsternas bidrag till god urban livsmiljö
- 2017
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Ekosystemtjänster uppmärksammas alltmer som ett viktigt inslag för en hållbar utveckling av städer och samhällen. Dessa handlar inte bara om ett miljö- och biodiversitetsperspektiv, utan också om hur ekosystemen bidrar till människans livsmiljö och stadens attraktivitet, samt de praktiska och rekreativa nyttor som befintlig och anlagd natur kan skapa i den byggda miljön.Denna rapport har tillkommit på Naturvårdsverkets initiativ, vilka också delvis har finansierat den. Arbetet har sammanfallit med ett opinionsbildande projekt, projektlett av Tankesmedjan Movium ochfinansierat av Vinnova, kallat Påverkansplattform för urbana ekosystemtjänster. Båda dessa aktiviteterhar efterfrågat kartläggning av nuläget och redovisningar av lärande exempel, varför vi har valt att arbeta integrerat med aktiviteterna. I rapporten har vi försökt att kombinera generella reflektioner med konkreta exempel. Vi har också valt att hämta lärdomar från såväl praktik som akademi och har bjudit in några av de ledande forskarna från Sveriges lantbruksuniversitet att utifrån sin forskningshorisont kommentera sådant som vi tycker oss kunna konstatera i praktiken. Det kan i något fall bli motsägelsefullt, men så är också frågan kring ekosystemtjänster i urban miljö komplext beskaffad. Som alla komplext beskaffade frågor hyser den därmed inneboende målkonflikter, åtminstone på ett generellt och övergripande plan.I rapporten konstaterar vi att det är viktigt och grundläggande att ekosystemtjänster behandlas som en tillgång för livsmiljöer i staden, och därmed också för arbetet med att planera, gestalta, anlägga och förvalta dessa miljöer. Utgångspunkten för ett sådant arbete behöver vara platsernas förutsättningar och de förväntningar som vi har på dessa miljöer. Möjligen kan det uppfattas som lite motsägelsefullt för en rapport med namnet ”Ekosystemtjänsteras bidrag till en god urban livsmiljö”, men vi är övertygande om att utgångspunkten för arbetet med ekosystemtjänster bör inte vara ekosystemtjänsterna själva, snarare en ökad platsspecifik kunskap och en ökad tydlighet kring samhällets uttalade målsättningar. Varför inleder vi med ett sådant påstående? Jo, för att påminna om att ekosystemtjänsterna utgår från oss människor och tjänsterna svarar mot våra behov. Det är alltså en slags konsumtion av tjänster som vi pratar om och som i all hållbar konsumtion handlar det om att balansera mellan tillgång och efterfrågan. Vi menar alltså att det inte alltid handlar om att maximera uttaget av en viss ekosystemtjänst, utan det handlar snarare om vilket behov som vi har identifierat på en viss plats eller i ett visst sammanhang samt hur ekosystemtjänsterna kan levererar på den platsen utifrån identifierade behov. Det är måhända en hårfin perspektivförskjutning, men vi menar att tar vi inte med oss detta synsätt in i diskussionen om ekosystemtjänster så befarar vi att vi får ett oönskat överutnyttjande av naturens ”gratistjänster”.Det pågår mycket lovvärt arbete i landet för att hitta system och verktyg som strävar efter att finna helhetssyn och mångfunktionalitet i ekosystemtjänsterna. Det finns dock en risk att verktyg blir väl generella när man försöker att fånga upp alla aspekter av hur man kan arbeta med ekosystemtjänsterna. Då riskerar implementeringsglappen också att bli för stora när generella verktyg ska appliceras på en specifik plats. Att istället lära av hur andra har gjort och ta del av varandras erfarenheter kan då vara ett värdefullt komplement och Naturvårdsverket har därför bett Tankesmedjan Movium att ta fram denna exempelsamling. Vår förhoppning är att denna rapport ska hjälpa stadsbyggnadsprocessens olika aktörer och skeden att förstå nyttan med urban natur och att ta in ekosystemtjänsterna i befintliga arbetssätt och processer.
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| 10. |
- Dawson, Victoria, et al.
(författare)
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Survival of Root-filled Teeth in Relation to Restoration and Tooth-group
- 2016
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Objectives: To compare the survival of teeth root-filled in Sweden in 2009 in relation to type of restoration and tooth-group.Methods: The database at the Swedish Social Insurance Agency containing information on treatments was used to identify all teeth in Sweden that were root-filled during 2009, by searching for the treatment codes corresponding to root-filling. The completed root-fillings could be linked to a specific tooth in a specific individual. Teeth registered as restored with a direct or indirect restoration within 6 months after completion of the root-filling were tagged and tracked until December 31st 2014. During this period, the treatment codes for extraction were registered for the identified root-filled teeth in order to construct Kaplan-Meier tooth survival analyses.Results: 248,299 teeth were registered as root-filled in Sweden in the year 2009. Of these 142,264 (57.3%) were restored with a direct restoration and 64,092 (25.8%) with an indirect restoration. Survival analysis disclosed that 5-6 years after root canal treatment 93.1% of the teeth with an indirect restoration had survived and 89.6% of the teeth with a direct restoration had survived. In the total material, irrespectively to any coronal restoration, premolars and upper anterior teeth had the highest survival (93.0% respectively 91.4%) and molars the lowest survival (87.6%). The same pattern was observed in sub-group analysis in the group of root-filled teeth with direct restorations. In the group with root-filled teeth with indirect restorations another pattern was observed; upper anterior teeth (92.6%) had a relatively lower survival, equivalent to those of molar teeth (92.6%).Conclusions: 5-6 year survival of root-filled teeth in Sweden were higher in the group with indirect restorations compared to the group with direct restoration. Root-filled upper incisors had an overall high survival, though for root-filled upper anterior teeth with indirect restorations the survival was relatively low.
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