| 1. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 2. |
- Kanoni, Stavroula, et al.
(författare)
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Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis.
- 2022
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Ingår i: Genome biology. - : Springer Science and Business Media LLC. - 1474-760X .- 1465-6906 .- 1474-7596. ; 23:1
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Tidskriftsartikel (refereegranskat)abstract
- Genetic variants within nearly 1000 loci are known to contribute to modulation of blood lipid levels. However, the biological pathways underlying these associations are frequently unknown, limiting understanding of these findings and hindering downstream translational efforts such as drug target discovery.To expand our understanding of the underlying biological pathways and mechanisms controlling blood lipid levels, we leverage a large multi-ancestry meta-analysis (N=1,654,960) of blood lipids to prioritize putative causal genes for 2286 lipid associations using six gene prediction approaches. Using phenome-wide association (PheWAS) scans, we identify relationships of genetically predicted lipid levels to other diseases and conditions. We confirm known pleiotropic associations with cardiovascular phenotypes and determine novel associations, notably with cholelithiasis risk. We perform sex-stratified GWAS meta-analysis of lipid levels and show that 3-5% of autosomal lipid-associated loci demonstrate sex-biased effects. Finally, we report 21 novel lipid loci identified on the X chromosome. Many of the sex-biased autosomal and X chromosome lipid loci show pleiotropic associations with sex hormones, emphasizing the role of hormone regulation in lipid metabolism.Taken together, our findings provide insights into the biological mechanisms through which associated variants lead to altered lipid levels and potentially cardiovascular disease risk.
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| 3. |
- Scott, Robert A., et al.
(författare)
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Large-scale association analyses identify new loci influencing glycemic traits and provide insight into the underlying biological pathways
- 2012
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 44:9, s. 991-1005
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Tidskriftsartikel (refereegranskat)abstract
- Through genome-wide association meta-analyses of up to 133,010 individuals of European ancestry without diabetes, including individuals newly genotyped using the Metabochip, we have increased the number of confirmed loci influencing glycemic traits to 53, of which 33 also increase type 2 diabetes risk (q < 0.05). Loci influencing fasting insulin concentration showed association with lipid levels and fat distribution, suggesting impact on insulin resistance. Gene-based analyses identified further biologically plausible loci, suggesting that additional loci beyond those reaching genome-wide significance are likely to represent real associations. This conclusion is supported by an excess of directionally consistent and nominally significant signals between discovery and follow-up studies. Functional analysis of these newly discovered loci will further improve our understanding of glycemic control.
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| 4. |
- Ahlberg, Patrik, 1985-
(författare)
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Graphene Implementation Study in Semiconductor Processing
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Graphene, with its two-dimensional nature and unique properties, has for over a decade captured enormous interests in both industry and academia. This work tries to answer the question of what would happen to graphene when it is subjected to various processing conditions and how this would affect the graphene functionality. The focus is placed on its ability to withstand different thin-film deposition environments with regard to the implementation of graphene in two application areas: as a diffusion barrier and in electronic devices.With single-layer graphene films grown in-house by means of chemical vapor deposition (CVD), four techniques among the well-established thin-film deposition methods are studied in detail: atomic layer deposition (ALD), evaporation, sputter-deposition and spray-deposition. And in this order, these methods span a large range of kinetic impact energies from low to high. Graphene is known to have a threshold displacement energy of 22 eV above which carbon atoms are ejected from the lattice. Thus, ALD and evaporation work with energies below this threshold, while sputtering and spraying may involve energies above. The quality of the graphene films undergone the various depositions is mainly evaluated using Raman spectroscopy.Spray deposition of liquid alloy Ga-In-Sn is shown to require a stack of at least 4 layers of graphene in order to act as an effective barrier to the Ga diffusion after the harsh spray-processing. Sputter-deposition is found to benefit from low substrate temperature and high chamber pressure (thereby low kinetic impact energy) so as to avoid damaging the graphene. Reactive sputtering should be avoided. Evaporation is non-invasiveness with low kinetic impact energy and graphene can be subjected to repeated evaporation and removal steps without losing its integrity. With ALD, the effects on graphene are of different nature and they are investigated in the field-effect-transistor (FET) configuration. The ALD process for deposition of Al2O3 films is found to remove undesired dopants from the prior processing and the Al2O3 films are shown to protect the graphene channel from doping by oxygen. When the substrate is turned hydrophobic by chemical treatment prior to graphene transfer-deposition, a unipolar transistor behavior is obtained.
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| 5. |
- Arachchige, Erandi C.W.Subasinghe, et al.
(författare)
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A global assessment of the species composition and effectiveness of watermelon pollinators and the management strategies to inform effective pollination service delivery
- 2023
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Ingår i: Basic and Applied Ecology. - : Elsevier BV. - 1439-1791. ; 66, s. 50-62
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Forskningsöversikt (refereegranskat)abstract
- For most food crops the identity and efficiency of pollinators across key growing regions remains a significant knowledge gap that needs to be addressed before we can develop crop-specific approaches for pollination service delivery. Here, we conducted a systematic literature review and meta-analysis on watermelon (Citrullus lanatus (Thunb. Matsum. & Nakai)), a globally important fruit crop, to identify the floral visitors and their efficiency across different growing regions. We found that 265 insect species visit watermelon flowers (including 5 orders, 18 families and 75 genera) across 17 countries and 6 continents. Bees and flies were the most abundant flower visitors overall, but show distinct regional differences. Honey bees were the majority visitor in 53% of growing regions (range: 0 – 94%), whilst wild bee species were more abundant in 42% of regions (range: 3.4 – 100%). Honey bees and other bees were equally effective at depositing pollen on stigmas, but varied in effectiveness for fruit set and seed set. Pollination data from global studies appear to be limited for the largest-scale watermelon producers, namely: China, Turkey, and India, with the majority (56%) of data available from North America. This synthesis identified four key themes for improving pollination in watermelon: increasing honey bee densities on crops where local polices and environmental conditions are suitable; introducing other managed pollinators; identifying key wild pollinator taxa to encourage within crops; and improving local and landscape management practices to support pollinators.
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| 6. |
- Axelsson, S., et al.
(författare)
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Theoretical and experimental investigations of three-terminal carbon nanotube nanorelays
- 2005
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Ingår i: New J. Phys. - : IOP Publishing. - 1367-2630. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- We present theoretical and experimental investigations of three-terminal nanoelectromechanical relays based on suspended carbon nanotubes. A charge is induced in the nanotube by applying a voltage to an underlying gate electrode thus inducing the nanotube to bend and make contact with a drain electrode. Such devices have potential applications as fast switches, logic devices, memory elements and pulse generators. We describe two modes of operation: a contact mode where the nanotube makes physical contact with the drain electrode and a non-contact mode where electrical contact between the nanotube and the drain electrode is made via a field emission current.
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| 7. |
- Bengtsson, Stefan, 1961, et al.
(författare)
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Carbon-based nanoelectromechanical devices
- 2011
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Ingår i: International Journal of High Speed Electronics and Systems. - 1793-6438. ; 20:1, s. 195-204
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Tidskriftsartikel (refereegranskat)abstract
- Carbon-based nanoelectromechanical devices are approaching applications in electronics. Switches based on individual carbon nanotubes deliver record low off-state leakage currents. Arrays of vertically aligned carbon nanotubes or nanofibers can be fabricated to constitute varactors. Very porous, low density arrays of quasi-vertically aligned arrays of carbon nanotubes behave mechanically as a single unit with very unusual material properties.
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| 8. |
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| 9. |
- Berndt, Sonja I., et al.
(författare)
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Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture
- 2013
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 45:5, s. 501-U69
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Tidskriftsartikel (refereegranskat)abstract
- Approaches exploiting trait distribution extremes may be used to identify loci associated with common traits, but it is unknown whether these loci are generalizable to the broader population. In a genome-wide search for loci associated with the upper versus the lower 5th percentiles of body mass index, height and waist-to-hip ratio, as well as clinical classes of obesity, including up to 263,407 individuals of European ancestry, we identified 4 new loci (IGFBP4, H6PD, RSRC1 and PPP2R2A) influencing height detected in the distribution tails and 7 new loci (HNF4G, RPTOR, GNAT2, MRPS33P4, ADCY9, HS6ST3 and ZZZ3) for clinical classes of obesity. Further, we find a large overlap in genetic structure and the distribution of variants between traits based on extremes and the general population and little etiological heterogeneity between obesity subgroups.
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| 10. |
- Blunden, Jessica, et al.
(författare)
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State of the Climate in 2012
- 2013
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Ingår i: Bulletin of The American Meteorological Society - (BAMS). - 0003-0007 .- 1520-0477. ; 94:8, s. S1-S258
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Tidskriftsartikel (refereegranskat)abstract
- For the first time in serveral years, the El Nino-Southern Oscillation did not dominate regional climate conditions around the globe. A weak La Ni a dissipated to ENSOneutral conditions by spring, and while El Nino appeared to be emerging during summer, this phase never fully developed as sea surface temperatures in the eastern conditions. Nevertheless, other large-scale climate patterns and extreme weather events impacted various regions during the year. A negative phase of the Arctic Oscillation from mid-January to early February contributed to frigid conditions in parts of northern Africa, eastern Europe, and western Asia. A lack of rain during the 2012 wet season led to the worst drought in at least the past three decades for northeastern Brazil. Central North America also experienced one of its most severe droughts on record. The Caribbean observed a very wet dry season and it was the Sahel's wettest rainy season in 50 years. Overall, the 2012 average temperature across global land and ocean surfaces ranked among the 10 warmest years on record. The global land surface temperature alone was also among the 10 warmest on record. In the upper atmosphere, the average stratospheric temperature was record or near-record cold, depending on the dataset. After a 30-year warming trend from 1970 to 1999 for global sea surface temperatures, the period 2000-12 had little further trend. This may be linked to the prevalence of La Ni a-like conditions during the 21st century. Heat content in the upper 700 m of the ocean remained near record high levels in 2012. Net increases from 2011 to 2012 were observed at 700-m to 2000-m depth and even in the abyssal ocean below. Following sharp decreases in to the effects of La Ni a, sea levels rebounded to reach records highs in 2012. The increased hydrological cycle seen in recent years continued, with more evaporation in drier locations and more precipitation in rainy areas. In a pattern that has held since 2004, salty areas of the ocean surfaces and subsurfaces were anomalously salty on average, while fresher areas were anomalously fresh. Global tropical cyclone activity during 2012 was near average, with a total of 84 storms compared with the 1981-2010 average of 89. Similar to 2010 and 2011, the North Atlantic was the only hurricane basin that experienced above-normal activity. In this basin, Sandy brought devastation to Cuba and parts of the eastern North American seaboard. All other basins experienced either near-or below-normal tropical cyclone activity. Only three tropical cyclones reached Category 5 intensity-all in Bopha became the only storm in the historical record to produce winds greater than 130 kt south of 7 N. It was also the costliest storm to affect the Philippines and killed more than 1000 residents. Minimum Arctic sea ice extent in September and Northern Hemisphere snow cover extent in June both reached new record lows. June snow cover extent is now declining at a faster rate (-17.6% per decade) than September sea ice extent (-13.0% per decade). Permafrost temperatures reached record high values in northernmost Alaska. A new melt extent record occurred on 11-12 July on the Greenland ice sheet; 97% of the ice sheet showed some form of melt, four times greater than the average melt for this time of year. The climate in Antarctica was relatively stable overall. The largest maximum sea ice extent since records begain in 1978 was observed in September 2012. In the stratosphere, warm air led to the second smallest ozone hole in the past two decades. Even so, the springtime ozone layer above Antarctica likely will not return to its early 1980s state until about 2060. Following a slight decline associated with the global 2 emissions from fossil fuel combustion and cement production reached a record 9.5 +/- 0.5 Pg C in 2011 and a new record of 9.7 +/- 0.5 Pg C is estimated for 2012. Atmospheric CO2 concentrations increased by 2.1 ppm in 2012, to 392.6 ppm. In spring 2012, 2 concentration exceeded 400 ppm at 7 of the 13 Arctic observation sites. Globally, other greenhouse gases including methane and nitrous oxide also continued to rise in concentration and the combined effect now represents a 32% increase in radiative forcing over a 1990 baseline. Concentrations of most ozone depleting substances continued to fall.
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