| 1. |
- Abarenkov, Kessy, et al.
(författare)
-
Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard – a report from a May 23-24, 2016 workshop (Gothenburg, Sweden)
- 2016
-
Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 16, s. 1-15
-
Tidskriftsartikel (refereegranskat)abstract
- Recent molecular studies have identified substantial fungal diversity in indoor environments. Fungi and fungal particles have been linked to a range of potentially unwanted effects in the built environment, including asthma, decay of building materials, and food spoilage. The study of the built mycobiome is hampered by a number of constraints, one of which is the poor state of the metadata annotation of fungal DNA sequences from the built environment in public databases. In order to enable precise interrogation of such data – for example, “retrieve all fungal sequences recovered from bathrooms” – a workshop was organized at the University of Gothenburg (May 23-24, 2016) to annotate public fungal barcode (ITS) sequences according to the MIxS-Built Environment annotation standard (http://gensc.org/mixs/). The 36 participants assembled a total of 45,488 data points from the published literature, including the addition of 8,430 instances of countries of collection from a total of 83 countries, 5,801 instances of building types, and 3,876 instances of surface-air contaminants. The results were implemented in the UNITE database for molecular identification of fungi (http://unite.ut.ee) and were shared with other online resources. Data obtained from human/animal pathogenic fungi will furthermore be verified on culture based metadata for subsequent inclusion in the ISHAM-ITS database (http://its.mycologylab.org).
|
|
| 2. |
- Sepehri, Sobhan, 1986, et al.
(författare)
-
Volume-amplified magnetic bioassay integrated with microfluidic sample handling and high-Tc SQUID magnetic readout
- 2018
-
Ingår i: APL Bioengineering. - : AIP Publishing. - 2473-2877. ; 2:1
-
Tidskriftsartikel (refereegranskat)abstract
- A bioassay based on a high-Tc superconducting quantum interference device (SQUID) reading out functionalized magnetic nanoparticles (fMNPs) in a prototype microfluidic platform is presented. The target molecule recognition is based on volume amplification using padlock-probe-ligation followed by rolling circle amplification (RCA). The MNPs are functionalized with single-stranded oligonucleotides, which give a specific binding of the MNPs to the large RCA coil product, resulting in a large change in the amplitude of the imaginary part of the ac magnetic susceptibility. The RCA products from amplification of synthetic Vibrio cholera target DNA were investigated using our SQUID ac susceptibility system in microfluidic channel with an equivalent sample volume of 3 μl. From extrapolation of the linear dependence of the SQUID signal versus concentration of the RCA coils, it is found that the projected limit of detection for our system is about 1.0 e5 RCA coils (0.2e−18 mol), which is equivalent to 66 fM in the 3 μl sample volume. This ultra-high magnetic sensitivity and integration with microfluidic sample handling are critical steps towards magnetic bioassays for rapid detection of DNA and RNA targets at the point of care.
|
|
| 3. |
- Öhman, Sebastian, 1991-, et al.
(författare)
-
Selective kinetic growth and role of local coordination in forming Al2TiO5-based coatings at lower temperatures
- 2021
-
Ingår i: Materials Advances. - : Royal Society of Chemistry. - 2633-5409. ; 2:17, s. 5737-5751
-
Tidskriftsartikel (refereegranskat)abstract
- Negative thermal expansion is an elusive property found among certain materials, whose potential applications have remained limited due to the many challenges faced in their synthesis. Herein, we report the successful formation of aluminium titanate-based coatings (Al2TiO5), a material renowned for its low-to-negative thermal expansion, by the co-deposition of aluminium-isopropoxide and titanium-isopropoxide in a hot-wall chemical vapour deposition instrument. While coatings grown at 450 °C were amorphous as-deposited, a short-range order into the Al2TiO5-phase was found and analysed by using Raman spectroscopy. Upon subsequent annealing at 700 °C for 3 hours, crystalline coatings were achieved without forming any binary phases. The selective synthesis of the Al2TiO5 phase is ascribed to the precursors’ inherent chemical similarities, resulting in a kinetic targeting of this phase and a short-range homogeneity, entailing its preferred crystallisation. The role of local coordination is expressed by demonstrating the formation of intergrowth phases ascribed to lower coordinating interstices in the compound. Both the formation and crystallisation temperatures reported herein, as well as the timescales needed for the synthesises, are considerably lower than any conventional adopted solid-state techniques used so far to attain the Al2TiO5 phase.
|
|
| 4. |
- Sepehri, Sobhan, 1986, et al.
(författare)
-
Characterization of Binding of Magnetic Nanoparticles to Rolling Circle Amplification Products by Turn-On Magnetic Assay
- 2019
-
Ingår i: Biosensors-Basel. - : MDPI AG. ; 9:3
-
Tidskriftsartikel (refereegranskat)abstract
- The specific binding of oligonucleotide-tagged 100 nm magnetic nanoparticles (MNPs) to rolling circle products (RCPs) is investigated using our newly developed differential homogenous magnetic assay (DHMA). The DHMA measures ac magnetic susceptibility from a test and a control samples simultaneously and eliminates magnetic background signal. Therefore, the DHMA can reveal details of binding kinetics of magnetic nanoparticles at very low concentrations of RCPs. From the analysis of the imaginary part of the DHMA signal, we find that smaller MNPs in the particle ensemble bind first to the RCPs. When the RCP concentration increases, we observe the formation of agglomerates, which leads to lower number of MNPs per RCP at higher concentrations of RCPs. The results thus indicate that a full frequency range of ac susceptibility observation is necessary to detect low concentrations of target RCPs and a long amplification time is not required as it does not significantly increase the number of MNPs per RCP. The findings are critical for understanding the underlying microscopic binding process for improving the assay performance. They furthermore suggest DHMA is a powerful technique for dynamically characterizing the binding interactions between MNPs and biomolecules in fluid volumes.
|
|
| 5. |
- Zambrano, Jesús, et al.
(författare)
-
Optimal steady-state design of zone volumes of bioreactors with Monod growth kinetics
- 2015
-
Ingår i: Biochemical Engineering Journal. - : Elsevier BV. - 1369-703X .- 1873-295X. ; 100, s. 59-66
-
Tidskriftsartikel (refereegranskat)abstract
- This paper deals with steady-state analysis and design of bioreactors consisting of a number of completely stirred tank reactors (CSTRs) in series. The study is confined to one consumed (substrate) and one consuming constituent (biomass). The specific microbial growth rate is assumed to be described by Monod kinetics. The death of biomass is assumed to be negligible. Two optimal design problems for a large number of CSTRs in series are studied: to minimize the effluent substrate concentration for a given total volume, and to minimize the total volume for a given effluent substrate concentration. As an appealing alternative to solve these problems numerically, it is proposed to consider the asymptotic case where the number of CSTRs tends to infinity. This is shown to correspond to one CSTR in series with a plug flow reactor (PFR). A CSTR with a sufficient large volume is needed to avoid wash-out of the biomass. The main result is that both design problems for the CSTR + PFR configuration have the same solution with respect to the optimal volume of the CSTR, which is given as an explicit function of the incoming substrate concentration, the volumetric flow rate and the coefficients of the Monod growth rate function. Numerical results indicate that the plug flow approach may be used as a feasible design procedure even for a reasonably low number of CSTRs in series.
|
|
| 6. |
- Sepehri, Sobhan, 1986, et al.
(författare)
-
Homogeneous Differential Magnetic Assay
- 2019
-
Ingår i: Acs Sensors. - : American Chemical Society (ACS). - 2379-3694. ; 4:9, s. 2381-2388
-
Tidskriftsartikel (refereegranskat)abstract
- Assays are widely used for detection of various targets, including pathogens, drugs, and toxins. Homogeneous assays are promising for the realization of point-of-care diagnostics as they do not require separation, immobilization, or washing steps. For low concentrations of target molecules, the speed and sensitivity of homogeneous assays have hitherto been limited by slow binding kinetics, time-consuming amplification steps, and the presence of a high background signal. Here, we present a homogeneous differential magnetic assay that utilizes a differential magnetic readout that eliminates previous limitations of homogeneous assays. The assay uses a gradiometer sensor configuration combined with precise microfluidic sample handling. This enables simultaneous differential measurement sample containing a synthesized Vibrio cholerae target and a negative control sample, which reduces the background signal and increases the readout speed. Very low concentrations of targets down to femtomolar levels are thus detectable without any additional amplification of the number of targets. Our homogeneous differential magnetic assay method opens new possibilities for rapid and highly sensitive diagnostics at the point of care.
|
|
| 7. |
- Aartsen, M. G., et al.
(författare)
-
Computational techniques for the analysis of small signals in high-statistics neutrino oscillation experiments
- 2020
-
Ingår i: Nuclear Instruments and Methods in Physics Research Section A. - : Elsevier BV. - 0168-9002 .- 1872-9576. ; 977
-
Tidskriftsartikel (refereegranskat)abstract
- The current and upcoming generation of Very Large Volume Neutrino Telescopes - collecting unprecedented quantities of neutrino events - can be used to explore subtle effects in oscillation physics, such as (but not restricted to) the neutrino mass ordering. The sensitivity of an experiment to these effects can be estimated from Monte Carlo simulations. With the high number of events that will be collected, there is a trade-off between the computational expense of running such simulations and the inherent statistical uncertainty in the determined values. In such a scenario, it becomes impractical to produce and use adequately-sized sets of simulated events with traditional methods, such as Monte Carlo weighting. In this work we present a staged approach to the generation of expected distributions of observables in order to overcome these challenges. By combining multiple integration and smoothing techniques which address limited statistics from simulation it arrives at reliable analysis results using modest computational resources.
|
|
| 8. |
- Foda, O., et al.
(författare)
-
Overlaps of partial Neel states and Bethe states
- 2016
-
Ingår i: Journal of Statistical Mechanics. - : IOP Publishing. - 1742-5468.
-
Tidskriftsartikel (refereegranskat)abstract
- Partial Neel states are generalizations of the ordinary Neel (classical anti-ferromagnet) state that can have arbitrary integer spin. We study overlaps of these states with Bethe states. We first identify this overlap with a partial version of reflecting-boundary domain-wall partition function, and then derive various determinant representations for off-shell and on-shell Bethe states.
|
|
| 9. |
- Hägglund, Carl, 1975, et al.
(författare)
-
Plasmonic Near-Field Absorbers for Ultrathin Solar Cells
- 2012
-
Ingår i: Journal of Physical Chemistry Letters. - : American Chemical Society (ACS). - 1948-7185. ; 3:10, s. 1275-1285
-
Forskningsöversikt (refereegranskat)abstract
- If the active layer of efficient solar cells could be made 100 times thinner than in today's thin film devices, their economic competitiveness would greatly benefit. However, conventional solar cell materials do not have the optical capability to allow for such thickness reductions without a substantial loss of light absorption. To address this challenge, the use of plasmon resonances in metal nanostructures to trap light and create charge carriers in a nearby semiconductor material is an interesting opportunity. In this Perspective, recent progress with regards to ultrathin (similar to 10 nm) plasmonic nanocomposites is reviewed. Their optimal internal geometry for plasmon near-field induced absorption is discussed, and a zero thickness effective medium representation is used to optimize stacks including an Al back reflector for photovoltaics. This shows that high conversion efficiencies (>20%) are possible even when taking surface scattering effects and thin passivating layers inserted between the metal and semiconductor into account.
|
|
| 10. |
- Li, Jibiao, et al.
(författare)
-
Chemical Bonding of Unique CO on Fe(100)
- 2018
-
Ingår i: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 122:16, s. 9062-9074
-
Tidskriftsartikel (refereegranskat)abstract
- At low coverage, CO molecules are known to preferentially occupy the hollow sites of Fe(100) with considerably inclined molecular orientations. This CO configuration serves as the precursor state of CO dissociation, which is particularly important in several important catalytic reactions. In this study, we present a unique bonding picture of the precursor state from the spin, charge, and orbital perspectives. From the spin and orbital views, we show the antiferromagenetic nature of the adsorbate-metal coupling, where 2 pi magnetism prevails with a dominant spin-down channel. However, contrasting tendencies are found for the two 1 pi orbitals in two orthogonal directions: the 1 pi orbital in the vertical plane loses its symmetry, whereas the other 1 pi orbital remains intact with a preserved symmetry. The 1 pi symmetry in the vertical plane favors the 1 pi -> 2 pi* excitation mechanism owing to the partial opening up of the 1 pi symmetry. In the charge perspective, we have identified a charge transfer mechanism involving the local structural Fe-I(C)-C-O motif, in which the surface slightly charges the adsorbate with additional partial electrons located at the surface Fe atoms bonded to the carbon end, whereas the charges of the metallic atoms beneath the Fe-I(C)-C-O motif are found to be depleted. In both the adsorbate and metal sides, the depletion of s electrons serves as a good measure of orbital repulsion and delocalization. Interestingly, the carbon and oxygen ends exhibit contrasting electron affinity with the metal surface: the carbon end is attractive, whereas the oxygen end is repulsive in terms of the contrasting charge rearrangement in the bonded metallic atoms.
|
|
