| 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. |
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| 3. |
- Lensink, Marc F., et al.
(författare)
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Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment
- 2023
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Ingår i: Proteins. - : WILEY. - 0887-3585 .- 1097-0134.
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Tidskriftsartikel (refereegranskat)abstract
- We present the results for CAPRI Round 54, the 5th joint CASP-CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo-trimers, 13 heterodimers including 3 antibody-antigen complexes, and 7 large assemblies. On average similar to 70 CASP and CAPRI predictor groups, including more than 20 automatics servers, submitted models for each target. A total of 21 941 models submitted by these groups and by 15 CAPRI scorer groups were evaluated using the CAPRI model quality measures and the DockQ score consolidating these measures. The prediction performance was quantified by a weighted score based on the number of models of acceptable quality or higher submitted by each group among their five best models. Results show substantial progress achieved across a significant fraction of the 60+ participating groups. High-quality models were produced for about 40% of the targets compared to 8% two years earlier. This remarkable improvement is due to the wide use of the AlphaFold2 and AlphaFold2-Multimer software and the confidence metrics they provide. Notably, expanded sampling of candidate solutions by manipulating these deep learning inference engines, enriching multiple sequence alignments, or integration of advanced modeling tools, enabled top performing groups to exceed the performance of a standard AlphaFold2-Multimer version used as a yard stick. This notwithstanding, performance remained poor for complexes with antibodies and nanobodies, where evolutionary relationships between the binding partners are lacking, and for complexes featuring conformational flexibility, clearly indicating that the prediction of protein complexes remains a challenging problem.
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| 4. |
- Li, J., et al.
(författare)
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Study of silicon nitride inner spacer formation in process of gate-all-around nano-transistors
- 2020
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Ingår i: Nanomaterials. - : MDPI AG. - 2079-4991. ; 10:4
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Tidskriftsartikel (refereegranskat)abstract
- Stacked SiGe/Si structures are widely used as the units for gate-all-around nanowire transistors (GAA NWTs) which are a promising candidate beyond fin field effective transistors (FinFETs) technologies in near future. These structures deal with a several challenges brought by the shrinking of device dimensions. The preparation of inner spacers is one of the most critical processes for GAA nano-scale transistors. This study focuses on two key processes: Inner spacer film conformal deposition and accurate etching. The results show that low pressure chemical vapor deposition (LPCVD) silicon nitride has a good film filling effect; a precise and controllable silicon nitride inner spacer structure is prepared by using an inductively coupled plasma (ICP) tool and a new gas mixtures of CH2F2/CH4/O2/Ar. Silicon nitride inner spacer etch has a high etch selectivity ratio, exceeding 100:1 to Si and more than 30:1 to SiO2. High anisotropy with an excellent vertical/lateral etch ratio exceeding 80:1 is successfully demonstrated. It also provides a solution to the key process challenges of nano-transistors beyond 5 nm node. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.
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| 5. |
- Archambault, Alexi N., et al.
(författare)
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Cumulative Burden of Colorectal Cancer Associated Genetic Variants Is More Strongly Associated With Early-Onset vs Late-Onset Cancer
- 2020
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Ingår i: Gastroenterology. - : Elsevier BV. - 0016-5085 .- 1528-0012. ; 158:5, s. 1274-1286.e12
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND & AIMS: Early-onset colorectal cancer (CRC, in persons younger than 50 years old) is increasing in incidence; yet, in the absence of a family history of CRC, this population lacks harmonized recommendations for prevention. We aimed to determine whether a polygenic risk score (PRS) developed from 95 CRC-associated common genetic risk variants was associated with risk for early-onset CRC.METHODS: We studied risk for CRC associated with a weighted PRS in 12,197 participants younger than 50 years old vs 95,865 participants 50 years or older. PRS was calculated based on single nucleotide polymorphisms associated with CRC in a large-scale genome-wide association study as of January 2019. Participants were pooled from 3 large consortia that provided clinical and genotyping data: the Colon Cancer Family Registry, the Colorectal Transdisciplinary Study, and the Genetics and Epidemiology of Colorectal Cancer Consortium and were all of genetically defined European descent. Findings were replicated in an independent cohort of 72,573 participants.RESULTS: Overall associations with CRC per standard deviation of PRS were significant for early-onset cancer, and were stronger compared with late-onset cancer (P for interaction = .01); when we compared the highest PRS quartile with the lowest, risk increased 3.7-fold for early-onset CRC (95% CI 3.28-4.24) vs 2.9-fold for late-onset CRC (95% CI 2.80-3.04). This association was strongest for participants without a first-degree family history of CRC (P for interaction = 5.61 x 10(-5)). When we compared the highest with the lowest quartiles in this group, risk increased 4.3-fold for early-onset CRC (95% CI 3.61-5.01) vs 2.9-fold for late-onset CRC (95% CI 2.70-3.00). Sensitivity analyses were consistent with these findings.CONCLUSIONS: In an analysis of associations with CRC per standard deviation of PRS, we found the cumulative burden of CRC-associated common genetic variants to associate with early-onset cancer, and to be more strongly associated with early-onset than late-onset cancer, particularly in the absence of CRC family history. Analyses of PRS, along with environmental and lifestyle risk factors, might identify younger individuals who would benefit from preventive measures.
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| 6. |
- Borozan, Ivan, et al.
(författare)
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Molecular and Pathology Features of Colorectal Tumors and Patient Outcomes Are Associated with Fusobacterium nucleatum and Its Subspecies animalis
- 2022
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Ingår i: Cancer Epidemiology, Biomarkers and Prevention. - : American Association for Cancer Research. - 1055-9965 .- 1538-7755. ; 31:1, s. 210-220
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Tidskriftsartikel (refereegranskat)abstract
- Background: Fusobacterium nucleatum (F. nucleatum) activates oncogenic signaling pathways and induces inflammation to promote colorectal carcinogenesis.Methods: We characterized F. nucleatum and its subspecies in colorectal tumors and examined associations with tumor characteristics and colorectal cancer-specific survival. We conducted deep sequencing of nusA, nusG, and bacterial 16s rRNA genes in tumors from 1,994 patients with colorectal cancer and assessed associations between F. nucleatum presence and clinical characteristics, colorectal cancer-specific mortality, and somatic mutations.Results: F. nucleatum, which was present in 10.3% of tumors, was detected in a higher proportion of right-sided and advanced-stage tumors, particularly subspecies animalis. Presence of F. nucleatum was associated with higher colorectal cancer-specific mortality (HR, 1.97; P = 0.0004). This association was restricted to nonhypermutated, microsatellite-stable tumors (HR, 2.13; P = 0.0002) and those who received chemotherapy [HR, 1.92; confidence interval (CI), 1.07-3.45; P = 0.029). Only F. nucleatum subspecies animalis, the main subspecies detected (65.8%), was associated with colorectal cancer-specific mortality (HR, 2.16; P = 0.0016), subspecies vincentii and nucleatum were not (HR, 1.07; P = 0.86). Additional adjustment for tumor stage suggests that the effect of F. nucleatum on mortality is partly driven by a stage shift. Presence of F. nucleatum was associated with microsatellite instable tumors, tumors with POLE exonuclease domain mutations, and ERBB3 mutations, and suggestively associated with TP53 mutations.Conclusions: F. nucleatum, and particularly subspecies animalis, was associated with a higher colorectal cancer-specific mortality and specific somatic mutated genes.
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| 7. |
- Cai, W. L., et al.
(författare)
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Angular Dependent Auto-Oscillations by Spin-Transfer and Spin-Orbit Torques in Three-Terminal Magnetic Tunnel Junctions
- 2023
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Ingår i: Ieee Electron Device Letters. - : Institute of Electrical and Electronics Engineers (IEEE). - 0741-3106 .- 1558-0563. ; 44:5, s. 861-864
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Tidskriftsartikel (refereegranskat)abstract
- Spintronic oscillators are promising candidates for neuromorphic computing due to their true miniaturization, non-linearity and synchronization properties. However, spin torque nano-oscillators are excited by current-induced spin-transfer torque which may cause high power consumption and reliability problems. Spin Hall nano-oscillators can realize higher energy efficiency, while their relatively low power emission limits their further applications. Here, we demonstrate three-terminal magnetic tunnel junction based spin torque nano-oscillators excited by the combination of spin-transfer and spin-orbit torques under different angle configurations. Thanks to the large spin Hall angle (-0.278) of W, the ratio between threshold current density of spin-transfer and spin-orbit torques for auto-oscillations can reach 0.6, indicating their high energy efficiency. Furthermore, we observe that the ratio has a sine function dependence on the angle between the spin-polarization directions of spin-transfer and spin-orbit torques. Our work could benefit the development of high-efficiency spintronic oscillators and their large network designs.
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| 8. |
- Cao, W., et al.
(författare)
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In Situ Study of FePt Nanoparticles-Induced Morphology Development during Printing of Magnetic Hybrid Diblock Copolymer Films
- 2022
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Ingår i: Advanced Functional Materials. - : Wiley. - 1616-301X .- 1616-3028. ; 32:4, s. 2107667-
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Tidskriftsartikel (refereegranskat)abstract
- The development of magnetic hybrid films containing diblock copolymers (DBCs) and magnetic nanoparticles (NPs) by printing is a highly promising method for scalable and low-cost fabrication. During printing, the drying and arrangement kinetics of the DBC and magnetic NPs play an important role in the film formation concerning morphology and magnetic properties. In this study, the morphology evolution of ultrahigh molecular weight DBC polystyrene-block-poly(methyl methacrylate) and magnetic iron platinum (FePt) NPs is investigated with grazing-incidence small-angle X-ray scattering (GISAXS) in situ during printing. For comparison, a pure DBC film is printed without FePt NPs under the same conditions. The GISAXS data suggest that the addition of NPs accelerates the solvent evaporation, leading to a faster film formation of the hybrid film compared to the pure film. As the solvent is almost evaporated, a metastable state is observed in both films. Compared with the pure film, such a metastable state continues longer during the printing process of the hybrid film because of the presence of FePt NPs, which inhibits the reorganization of the DBC chains. Moreover, investigations of the field-dependent magnetization and temperature-dependent susceptibility indicate that the printed hybrid film is superparamagnetic, which makes this film class promising for magnetic sensors.
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| 9. |
- Cao, Wei, et al.
(författare)
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Self-Assembly of Large Magnetic Nanoparticles in Ultrahigh Molecular Weight Linear Diblock Copolymer Films
- 2020
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Ingår i: ACS Applied Materials and Interfaces. - : AMER CHEMICAL SOC. - 1944-8244 .- 1944-8252. ; 12:6, s. 7557-7564
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Tidskriftsartikel (refereegranskat)abstract
- The development of diblock copolymer (DBC) nanocomposite films containing magnetic nanoparticles (NPs) with diameters (D) over 20 nm is a challenging task. To host large iron oxide NPs (Fe3O4, D = 27 +/- 0.6 nm), an ultrahigh molecular weight (UHMW) linear DBC polystyrene-block-poly(methyl methacrylate) (PS-b-PMMA) is used as a template in the present work. Due to hydrogen bonding between the carboxylic acid ligands of the NPs and the ester groups in PMMA, the NPs show an affinity to the PMMA block. The localization of the NPs inside the DBC is investigated as a function of the NP concentration. At low NP concentrations, NPs are located preferentially at the interface between PS and PMMA domains to minimize the interfacial tension caused by the strong segregation strength of the UHMW DBC. At high NP concentrations (>= 10 wt %), chain-like NP aggregates (a head-to-tail orientation) are observed in the PMMA domains, resulting in a change of the morphology from sphere to ellipsoid for part of the PMMA domains. Magnetic properties of the hybrid films are probed via superconducting quantum interference device magnetometry. All hybrid films show ferrimagnetism and are promising for potential applications in magnetic data storage.
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| 10. |
- Cao, Wei, et al.
(författare)
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Spray-Deposited Anisotropic Ferromagnetic Hybrid Polymer Films of PS-b-PMMA and Strontium Hexaferrite Magnetic Nanoplatelets
- 2021
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Ingår i: ACS Applied Materials and Interfaces. - : AMER CHEMICAL SOC. - 1944-8244 .- 1944-8252. ; 13:1, s. 1592-1602
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Tidskriftsartikel (refereegranskat)abstract
- Spray deposition is a scalable and cost-effective technique for the fabrication of magnetic hybrid films containing diblock copolymers (DBCs) and magnetic nanoparticles. However, it is challenging to obtain spray-deposited anisotropic magnetic hybrid films without using external magnetic fields. In the present work, spray deposition is applied to prepare perpendicular anisotropic magnetic hybrid films by controlling the orientation of strontium hexaferrite nanoplatelets inside ultra-high-molecular-weight DBC polystyrene-block-poly(methyl methacrylate) (PS-b-PMMA) films. During spray deposition, the evolution of DBC morphology and the orientation of magnetic nanoplatelets are monitored with in situ grazing-incidence small-angle X-ray scattering (GISAXS). For reference, a pure DBC film without nanoplatelets is deposited with the same conditions. Solvent-controlled magnetic properties of the hybrid film are proven with solvent vapor annealing (SVA) applied to the final deposited magnetic films. Obvious changes in the DBC morphology and nanoplatelet localization are observed during SVA. The superconducting quantum interference device data show that ferromagnetic hybrid polymer films with high coercivity can be achieved via spray deposition. The hybrid films show a perpendicular magnetic anisotropy before SVA, which is strongly weakened after SVA. The spray-deposited hybrid films appear highly promising for potential applications in magnetic data storage and sensors.
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