| 1. |
- Kilic, Nuzhet I., et al.
(author)
-
Two-Photon Polymerization Printing with High Metal Nanoparticle Loading
- 2023
-
In: ACS Applied Materials and Interfaces. - : American Chemical Society (ACS). - 1944-8244 .- 1944-8252. ; 15:42, s. 49794-49804
-
Journal article (peer-reviewed)abstract
- Two-photon polymerization (2PP) is an efficient technique to achieve high-resolution, three-dimensional (3D)-printed complex structures. However, it is restricted to photocurable monomer combinations, thus presenting constraints when aiming at attaining functionally active resist formulations and structures. In this context, metal nanoparticle (NP) integration as an additive can enable functionality and pave the way to more dedicated applications. Challenges lay on the maximum NP concentrations that can be incorporated into photocurable resist formulations due to the laser-triggered interactions, which primarily originate from laser scattering and absorption, as well as the limited dispersibility threshold. In this study, we propose an approach to address these two constraints by integrating metallic Rh NPs formed ex situ, purposely designed for this scope. The absence of surface plasmon resonance (SPR) within the visible and near-infrared spectra, coupled with the limited absorption value measured at the laser operating wavelength (780 nm), significantly limits the laser-induced interactions. Moreover, the dispersibility threshold is increased by engineering the NP surface to be compatible with the photocurable resin, permitting us to achieve concentrations of up to 2 wt %, which, to our knowledge, is significantly higher than the previously reported limit (or threshold) for embedded metal NPs. Another distinctive advantage of employing Rh NPs is their role as promising contrast agents for X-ray fluorescence (XRF) bioimaging. We demonstrated the presence of Rh NPs within the whole 2PP-printed structure and emphasized the potential use of NP-loaded 3D-printed nanostructures for medical devices.
|
|
| 2. |
- Vasicek, Jakub, et al.
(author)
-
Finding haplotypic signatures in proteins
- 2023
-
In: GigaScience. - : Oxford University Press (OUP). - 2047-217X. ; 12
-
Journal article (peer-reviewed)abstract
- Background: The nonrandom distribution of alleles of common genomic variants produces haplotypes, which are fundamental in medical and population genetic studies. Consequently, protein-coding genes with different co-occurring sets of alleles can encode different amino acid sequences: protein haplotypes. These protein haplotypes are present in biological samples and detectable by mass spectrometry, but they are not accounted for in proteomic searches. Consequently, the impact of haplotypic variation on the results of proteomic searches and the discoverability of peptides specific to haplotypes remain unknown. Findings: Here, we study how common genetic haplotypes influence the proteomic search space and investigate the possibility to match peptides containing multiple amino acid substitutions to a publicly available data set of mass spectra. We found that for 12.42% of the discoverable amino acid substitutions encoded by common haplotypes, 2 or more substitutions may co-occur in the same peptide after tryptic digestion of the protein haplotypes. We identified 352 spectra that matched to such multivariant peptides, and out of the 4,582 amino acid substitutions identified, 6.37% were covered by multivariant peptides. However, the evaluation of the reliability of these matches remains challenging, suggesting that refined error rate estimation procedures are needed for such complex proteomic searches. Conclusions: As these procedures become available and the ability to analyze protein haplotypes increases, we anticipate that proteomics will provide new information on the consequences of common variation, across tissues and time.
|
|
| 3. |
- Yang, Zhijian, et al.
(author)
-
Genetic Landscape of the ACE2 Coronavirus Receptor
- 2022
-
In: Circulation. - : Ovid Technologies (Wolters Kluwer Health). - 0009-7322 .- 1524-4539. ; 30:SUPPL 1, s. 36-36
-
Journal article (peer-reviewed)abstract
- Background: SARS-CoV-2, the causal agent of COVID-19, enters human cells using the ACE2 (angiotensin-converting enzyme 2) protein as a receptor. ACE2 is thus key to the infection and treatment of the coronavirus. ACE2 is highly expressed in the heart and respiratory and gastrointestinal tracts, playing important regulatory roles in the cardiovascular and other biological systems. However, the genetic basis of the ACE2 protein levels is not well understood.Methods: We have conducted the largest genome-wide association meta-analysis of plasma ACE2 levels in >28 000 individuals of the SCALLOP Consortium (Systematic and Combined Analysis of Olink Proteins). We summarize the cross-sectional epidemiological correlates of circulating ACE2. Using the summary statistics-based high-definition likelihood method, we estimate relevant genetic correlations with cardiometabolic phenotypes, COVID-19, and other human complex traits and diseases. We perform causal inference of soluble ACE2 on vascular disease outcomes and COVID-19 severity using mendelian randomization. We also perform in silico functional analysis by integrating with other types of omics data.Results: We identified 10 loci, including 8 novel, capturing 30% of the heritability of the protein. We detected that plasma ACE2 was genetically correlated with vascular diseases, severe COVID-19, and a wide range of human complex diseases and medications. An X-chromosome cis-protein quantitative trait loci-based mendelian randomization analysis suggested a causal effect of elevated ACE2 levels on COVID-19 severity (odds ratio, 1.63 [95% CI, 1.10-2.42]; P=0.01), hospitalization (odds ratio, 1.52 [95% CI, 1.05-2.21]; P=0.03), and infection (odds ratio, 1.60 [95% CI, 1.08-2.37]; P=0.02). Tissue- and cell type-specific transcriptomic and epigenomic analysis revealed that the ACE2 regulatory variants were enriched for DNA methylation sites in blood immune cells.Conclusions: Human plasma ACE2 shares a genetic basis with cardiovascular disease, COVID-19, and other related diseases. The genetic architecture of the ACE2 protein is mapped, providing a useful resource for further biological and clinical studies on this coronavirus receptor.
|
|
| 4. |
- Abbaszadeh Shahri, Abbas, et al.
(author)
-
Normalizing Large Scale Sensor-Based MWD Data : An Automated Method toward A Unified Database
- 2024
-
In: Sensors. - : MDPI AG. - 1424-8220. ; 24:4
-
Journal article (peer-reviewed)abstract
- In the context of geo-infrastructures and specifically tunneling projects, analyzing the large-scale sensor-based measurement-while-drilling (MWD) data plays a pivotal role in assessing rock engineering conditions. However, handling the big MWD data due to multiform stacking is a time-consuming and challenging task. Extracting valuable insights and improving the accuracy of geoengineering interpretations from MWD data necessitates a combination of domain expertise and data science skills in an iterative process. To address these challenges and efficiently normalize and filter out noisy data, an automated processing approach integrating the stepwise technique, mode, and percentile gate bands for both single and peer group-based holes was developed. Subsequently, the mathematical concept of a novel normalizing index for classifying such big datasets was also presented. The visualized results from different geo-infrastructure datasets in Sweden indicated that outliers and noisy data can more efficiently be eliminated using single hole-based normalizing. Additionally, a relational unified PostgreSQL database was created to store and automatically transfer the processed and raw MWD as well as real time grouting data that offers a cost effective and efficient data extraction tool. The generated database is expected to facilitate in-depth investigations and enable application of the artificial intelligence (AI) techniques to predict rock quality conditions and design appropriate support systems based on MWD data.
|
|
| 5. |
- Bjureland, William, 1987-, et al.
(author)
-
Dimensionering av sprutbetongförstärkning för lösa block med sannolikhetsbaserade metoder
- 2020
-
Conference paper (pop. science, debate, etc.)abstract
- Användning av sannolikhetsbaserade metoder för dimensionering av bergförstärkning är ett tillvägagångssätt som är accepterat i Eurokoderna. Vid dimensionering med dessa metoder beaktas osäkerheter stringent genom att ansätta sannolikhetsfördelningar för relevanta parametrar. Konstruktionens säkerhet säkerställs genom att verifiera att sannolikheten att överskrida bärförmågan är lägre än den i Eurokoderna kravställda brottsannolikheten. För tillämpning av sannolikhetsbaserade metoder för dimensionering av sprutbetongförstärkning för lösa block har ett problem varit att data saknats för att kunna beskriva relevanta parametrar med representativa sannolikhetsfördelningar. Dessutom samverkar de olika brottmoderna och måste därför betraktas ur ett systemperspektiv, vilket inte beaktats i tidigare studier. I denna artikel presenteras resultatet av ett doktorandprojekt med finansiering av SBUF, BeFo, SVC och SKB. Baserat på ovanstående aspekter presenteras en metodik för dimensionering av sprutbetongförstärkning för lösa block med sannolikhetsbaserade metoder. Inledningsvis presenteras sannolikhetsfördelningar för sprutbetongens parametrar baserat på en stor mängd analyserade data från Citybanan. Därefter presenteras den utvecklade dimensioneringsmetodiken, vilken bygger på att en initial dimensionering av sprutbetongen utförs innan tunneldrivningen påbörjas och att den applicerade sprutbetongens bärförmåga därefter verifieras med hjälp av kontrollmätningar från fält och Bayesiansk statistik.
|
|
| 6. |
- Bjureland, William, 1987-, et al.
(author)
-
Influence of spatially varying thickness on load-bearing capacity of shotcrete
- 2020
-
In: Tunnelling and Underground Space Technology. - : Elsevier. - 0886-7798 .- 1878-4364. ; 98
-
Journal article (peer-reviewed)abstract
- A common approach to verify a shotcrete layer's ability to secure blocks that can exist between rockbolts in a tunnel is to use analytical calculations. For this situation, an attractive approach to account for variability in the shotcrete parameters is to use reliability-based methods. Variability can then be accounted for by assigning suitable probability distributions to all relevant input parameters. Structural safety can be ensured by verifying that the probability of limit exceedance is smaller than an acceptable target probability of failure. However, even though analytical calculations and reliability-based methods can be used to design shotcrete support, one of the commonly made basic assumptions is that the load-bearing capacity of the shotcrete is governed by the spatial average of the input parameters. Thus, the spatial variability of the parameters are neglected. As a result, if the capacity is governed by the lowest value of a certain parameter, this assumption is non-conservative. In this paper, we present a novel approach in which the minimum of either the spatial average of a shotcrete slab of varying thickness, or the spatial average along the periphery of a loose block of that same slab, is used to estimate the load-bearing capacity of the shotcrete in a tunnel. The approach is based on results from numerical simulations of a shotcrete slab that we perform to investigate the effect that a spatially varying thickness has on the flexural load-bearing capacity of the slab. The results from the simulations show that the shotcrete's flexural load-bearing capacity might be overestimated when using the spatial average of shotcrete thickness between four rockbolts in design. Using the presented approach, the spatial variability of shotcrete thickness can be accounted for in practical design of tunnels without complex and time-consuming numerical simulations.
|
|
| 7. |
- Bjureland, William
(author)
-
Reliability-based design of rock tunnel support
- 2020
-
Doctoral thesis (other academic/artistic)abstract
- Since 2009, design of rock tunnels can be performed in accordance with the Eurocodes, which allows that different design methodologies are applied, such as design by calculation or design using the observational method. To account for uncertainties in design, the Eurocode states that design by calculation should primarily be performed using the partial factor method or reliability-based methods. The basic principle of both of these methods is that it shall be assured that a structure’s resisting capacity is larger than the load acting on the structure, with sufficiently high probability. Even if this might seem straightforward, the practical application of limit state design to rock tunnel support has only been studied to a limited extent.The overall aim of this project has been to develop reliability-based methods for environmental and economic optimization of rock tunnel support, with a special focus on shotcrete support. To achieve this, this thesis aims to: (1) assess the applicability of the partial factor method and reliability-based methods for design of shotcrete support, exclusively or in combination with the observational method, (2) quantify the magnitude and uncertainty of the shotcrete’s input parameters, and (3) assess the influence from spatial variability on shotcrete’s load-bearing capacity and judge the correctness of the assumption that the load-bearing capacity of the support is governed by the mean values of its input parameters.The thesis shows that the partial factor method is not suitable, and in some cases not applicable, to use in design of rock tunnel support. Instead, the thesis presents a reliability-based design methodology for shotcrete in rock tunnels with respect to loose blocks between rockbolts and a design methodology for shotcrete lining based on a combination of the observational method and reliability-based methods. The presented design methodologies enable optimization of the shotcrete support and shotcrete lining by stringently accounting for uncertainties related to input data throughout the design process. The thesis also discusses the limited knowledge that we as an industry sometimes have in our calculation models and the clarifications that should be made in future revisions of the Eurocode related to target reliability and the definition of failure.
|
|
| 8. |
- Chadwick, D., et al.
(author)
-
Digital inclusion and participation of people with intellectual disabilities during COVID-19 : A rapid review and international bricolage
- 2022
-
In: Journal of Policy and Practice in Intellectual Disabilities. - : Wiley. - 1741-1122 .- 1741-1130. ; 19:3, s. 242-256
-
Journal article (peer-reviewed)abstract
- The COVID-19 pandemic has meant a rapid transfer of everyday activities to the online world. Information and communication technologies (ICTs) have become more embedded than ever in people's lives. This investigation addresses how this change has affected the lives of people with intellectual disabilities (ID). A two-step design was used. A rapid review was conducted on empirical studies published between January 2019 and June 2021. Search terms related to ID, ICT use and COVID-19. A qualitative international bricolage was also conducted corresponding to author nationalities. Data gathered from the review and bricolage were analysed separately using thematic analysis and relationally synthesised. Digital solutions to provide access to COVID-19 information and guidance seemed inadequate but were seldom empirically studied. Digital poverty, literacy and exclusion remain significant issues for people with ID internationally. People and their carers experienced reduced and removed service provision, loneliness and impoverished daily lives during the pandemic; amelioration of which was facilitated by digital solutions. One solution often used was videoconferencing. Prior experience of digital participation, adequate finances, connection, support and digital literacy mentoring for both people with ID and those providing services and support facilitated digital inclusion. Digital exclusion during COVID-19 was exacerbated by sociopolitical, structural, individual and support-related barriers. Although awareness of digital exclusion appears to have been raised, the extent to which this has led to action and change remains unclear. Despite digital exclusion and digital participation benefitting continuation of life, social and emotional well-being and autonomy, COVID-19 has not provided the impetus to eradicate digital poverty for people with ID. Governmental support, digital education, creativity and problem solving are required to enable people with ID the human right to be included in the digital world at this essential time and into the future.
|
|
| 9. |
- Chen, Gefei, et al.
(author)
-
Molecular basis for different substrate-binding sites and chaperone functions of the BRICHOS domain
- 2024
-
In: Protein Science. - : Wiley. - 0961-8368 .- 1469-896X. ; 33:7
-
Journal article (peer-reviewed)abstract
- Proteins can misfold into fibrillar or amorphous aggregates and molecular chaperones act as crucial guardians against these undesirable processes. The BRICHOS chaperone domain, found in several otherwise unrelated proproteins that contain amyloidogenic regions, effectively inhibits amyloid formation and toxicity but can in some cases also prevent non-fibrillar, amorphous protein aggregation. Here, we elucidate the molecular basis behind the multifaceted chaperone activities of the BRICHOS domain from the Bri2 proprotein. High-confidence AlphaFold2 and RoseTTAFold predictions suggest that the intramolecular amyloidogenic region (Bri23) is part of the hydrophobic core of the proprotein, where it occupies the proposed amyloid binding site, explaining the markedly reduced ability of the proprotein to prevent an exogenous amyloidogenic peptide from aggregating. However, the BRICHOS-Bri23 complex maintains its ability to form large polydisperse oligomers that prevent amorphous protein aggregation. A cryo-EM-derived model of the Bri2 BRICHOS oligomer is compatible with surface-exposed hydrophobic motifs that get exposed and come together during oligomerization, explaining its effects against amorphous aggregation. These findings provide a molecular basis for the BRICHOS chaperone domain function, where distinct surfaces are employed against different forms of protein aggregation.
|
|
| 10. |
- Ehrmanntraut, Editha
(author)
-
Soil identification by vibration measurements during soil-rock sounding
- 2022
-
Licentiate thesis (other academic/artistic)abstract
- Dynamic penetration tests are frequently used as geotechnical site investigation methods. In Sweden, the main reason to choose a dynamic penetration method is to investigatedepth to bedrock, strength and deformation properties of soil, compaction, or pilingdepth. The advantage of dynamic penetration methods is that they have a betterpenetration ability than static methods and it is therefore easier to penetrate hardmaterial or rock.The most common dynamic penetration method in Sweden is soil-rock sounding. Duringsoil-rock sounding, a metal rod is drilled into the ground and measurements are taken ofdepth, drilling resistance, sinking speed, feeding force, hammer pressure, and rotationalspeed and pressure. The method is conducted in different classes with varying accuracies.Soil-rock sounding is mainly used to determine depth to bedrock, but as the drilling rodpenetrates the whole soil layer profile, there may be opportunities to gain moreknowledge about the penetrated material using the same process.The scope of this licentiate research project was to investigate whether vibrationmeasurements on the ground surface performed simultaneously with soil-rock soundingcan yield additional information about the soil layer profile and the thin layers within amaterial. Measurements were conducted in various building and infrastructure projectsin eastern Sweden between Norrköping and Stockholm/Solna and the results wereanalyzed. It was investigated whether there is a relationship between the vibration resultsand soil properties as determined by other geotechnical investigation methods in thesame area.The results show that soil-rock sounding with simultaneous vibration measurementsconstitutes a promising extension of the conventional soil-rock sounding method whichcan provide additional information about the soil layer profiles at the investigation site.Furthermore, indications can be made about overall soil layer profiles. However, thevibration signals must be adjusted due to distance attenuation before results fromdifferent depths, boreholes and sites are comparable.The different penetrated materials and their properties are correlated to the frequencycontent of the vibration signal. In this way, more information about the penetratedmaterial can be gained from the vibration measurements. The results show thatheterogeneities in the penetrated soil layer can clearly be seen in the vibration results andpatterns in these heterogeneities identified. Furthermore, the results indicate that thevibration signals can help to distinguish silt from sand/gravelly soil and boulder from rock,and the ground water table can be seen in the frequency spectrogram for granular soils.
|
|
