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| 2. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)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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| 3. |
- Schweinsberg, Martin, et al.
(author)
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Same data, different conclusions : Radical dispersion in empirical results when independent analysts operationalize and test the same hypothesis
- 2021
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In: Organizational Behavior and Human Decision Processes. - : Elsevier BV. - 0749-5978 .- 1095-9920. ; 165, s. 228-249
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Journal article (peer-reviewed)abstract
- In this crowdsourced initiative, independent analysts used the same dataset to test two hypotheses regarding the effects of scientists' gender and professional status on verbosity during group meetings. Not only the analytic approach but also the operationalizations of key variables were left unconstrained and up to individual analysts. For instance, analysts could choose to operationalize status as job title, institutional ranking, citation counts, or some combination. To maximize transparency regarding the process by which analytic choices are made, the analysts used a platform we developed called DataExplained to justify both preferred and rejected analytic paths in real time. Analyses lacking sufficient detail, reproducible code, or with statistical errors were excluded, resulting in 29 analyses in the final sample. Researchers reported radically different analyses and dispersed empirical outcomes, in a number of cases obtaining significant effects in opposite directions for the same research question. A Boba multiverse analysis demonstrates that decisions about how to operationalize variables explain variability in outcomes above and beyond statistical choices (e.g., covariates). Subjective researcher decisions play a critical role in driving the reported empirical results, underscoring the need for open data, systematic robustness checks, and transparency regarding both analytic paths taken and not taken. Implications for orga-nizations and leaders, whose decision making relies in part on scientific findings, consulting reports, and internal analyses by data scientists, are discussed.
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| 4. |
- Timopheev, A. A., et al.
(author)
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Effect of interaction in the magnetization reversal relaxation of superparamagnetic granulaR CoFeB -SiO2 FILMS
- 2009
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In: Magnetism and Magnetic Materials. - : Scientific.Net. ; , s. 213-216
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Conference paper (peer-reviewed)abstract
- In order to study the magnetic interactions influence on the relaxation processes in superparamagnetic media, the magnetostatic measurements were carried out for the granular (CoFeB)x-(SiO2)1-x films with x values near percolation threshold. The observed temperature dependences of the coercivity for the samples magnetized along in-plane easy axis have shown two parts linear on √T with different inclination angles, which cross each other at the blocking temperature (Tb). The first part of the curve, which corresponds to the temperature range below T b, depends on the measuring time and is related to the thermal activation nature of magnetization reversal process in the blocked superparamagnetic state. Second part of the curve, which corresponds to the temperature range above Tb, is practically independent on the measuring time and is related to existence of correlated state of superparamagnetic grains moments, i.e. to superferromagnetic state. The method of the magnetization reversal curves simulation based on the numerical solving of kinetic equation has been applied to explain the experimental results.
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| 5. |
- Muus, Christoph, et al.
(author)
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Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics
- 2021
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In: Nature Medicine. - : Springer Science and Business Media LLC. - 1078-8956 .- 1546-170X. ; 27:3, s. 546-559
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Journal article (peer-reviewed)abstract
- Angiotensin-converting enzyme 2 (ACE2) and accessory proteases (TMPRSS2 and CTSL) are needed for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cellular entry, and their expression may shed light on viral tropism and impact across the body. We assessed the cell-type-specific expression of ACE2, TMPRSS2 and CTSL across 107 single-cell RNA-sequencing studies from different tissues. ACE2, TMPRSS2 and CTSL are coexpressed in specific subsets of respiratory epithelial cells in the nasal passages, airways and alveoli, and in cells from other organs associated with coronavirus disease 2019 (COVID-19) transmission or pathology. We performed a meta-analysis of 31 lung single-cell RNA-sequencing studies with 1,320,896 cells from 377 nasal, airway and lung parenchyma samples from 228 individuals. This revealed cell-type-specific associations of age, sex and smoking with expression levels of ACE2, TMPRSS2 and CTSL. Expression of entry factors increased with age and in males, including in airway secretory cells and alveolar type 2 cells. Expression programs shared by ACE2(+)TMPRSS2(+) cells in nasal, lung and gut tissues included genes that may mediate viral entry, key immune functions and epithelial-macrophage cross-talk, such as genes involved in the interleukin-6, interleukin-1, tumor necrosis factor and complement pathways. Cell-type-specific expression patterns may contribute to the pathogenesis of COVID-19, and our work highlights putative molecular pathways for therapeutic intervention. An integrated analysis of over 100 single-cell and single-nucleus transcriptomics studies illustrates severe acute respiratory syndrome coronavirus 2 viral entry gene coexpression patterns across different human tissues, and shows association of age, smoking status and sex with viral entry gene expression in respiratory cell populations.
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| 6. |
- Ahmad, Amais, et al.
(author)
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IMI – Oral biopharmaceutics tools project – Evaluation of bottom-up PBPK prediction success part 4 : Prediction accuracy and software comparisons with improved data and modelling strategies
- 2020
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In: European journal of pharmaceutics and biopharmaceutics. - : Elsevier BV. - 0939-6411 .- 1873-3441. ; 156, s. 50-63
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Journal article (peer-reviewed)abstract
- Oral drug absorption is a complex process depending on many factors, including the physicochemical properties of the drug, formulation characteristics and their interplay with gastrointestinal physiology and biology. Physiological-based pharmacokinetic (PBPK) models integrate all available information on gastro-intestinal system with drug and formulation data to predict oral drug absorption. The latter together with in vitro-in vivo extrapolation and other preclinical data on drug disposition can be used to predict plasma concentration-time profiles in silico. Despite recent successes of PBPK in many areas of drug development, an improvement in their utility for evaluating oral absorption is much needed. Current status of predictive performance, within the confinement of commonly available in vitro data on drugs and formulations alongside systems information, were tested using 3 PBPK software packages (GI-Sim (ver.4.1), Simcyp® Simulator (ver.15.0.86.0), and GastroPlusTM (ver.9.0.00xx)). This was part of the Innovative Medicines Initiative (IMI) Oral Biopharmaceutics Tools (OrBiTo) project.Fifty eight active pharmaceutical ingredients (APIs) were qualified from the OrBiTo database to be part of the investigation based on a priori set criteria on availability of minimum necessary information to allow modelling exercise. The set entailed over 200 human clinical studies with over 700 study arms. These were simulated using input parameters which had been harmonised by a panel of experts across different software packages prior to conduct of any simulation. Overall prediction performance and software packages comparison were evaluated based on performance indicators (Fold error (FE), Average fold error (AFE) and absolute average fold error (AAFE)) of pharmacokinetic (PK) parameters.On average, PK parameters (Area Under the Concentration-time curve (AUC0-tlast), Maximal concentration (Cmax), half-life (t1/2)) were predicted with AFE values between 1.11 and 1.97. Variability in FEs of these PK parameters was relatively high with AAFE values ranging from 2.08 to 2.74. Around half of the simulations were within the 2-fold error for AUC0-tlast and around 90% of the simulations were within 10-fold error for AUC0-tlast. Oral bioavailability (Foral) predictions, which were limited to 19 APIs having intravenous (i.v.) human data, showed AFE and AAFE of values 1.37 and 1.75 respectively. Across different APIs, AFE of AUC0-tlast predictions were between 0.22 and 22.76 with 70% of the APIs showing an AFE > 1. When compared across different formulations and routes of administration, AUC0-tlast for oral controlled release and i.v. administration were better predicted than that for oral immediate release formulations. Average predictive performance did not clearly differ between software packages but some APIs showed a high level of variability in predictive performance across different software packages. This variability could be related to several factors such as compound specific properties, the quality and availability of information, and errors in scaling from in vitro and preclinical in vivo data to human in vivo behaviour which will be explored further. Results were compared with previous similar exercise when the input data selection was carried by the modeller rather than a panel of experts on each in vitro test. Overall, average predictive performance was increased as reflected in smaller AAFE value of 2.8 as compared to AAFE value of 3.8 in case of previous exercise.
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| 7. |
- Jacoby, Nori, et al.
(author)
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Commonality and variation in mental representations of music revealed by a cross-cultural comparison of rhythm priors in 15 countries
- 2024
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In: Nature Human Behaviour. - : Springer Nature. - 2397-3374. ; 8:5, s. 846-877
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Journal article (peer-reviewed)abstract
- Music is present in every known society but varies from place to place. What, if anything, is universal to music cognition? We measured a signature of mental representations of rhythm in 39 participant groups in 15 countries, spanning urban societies and Indigenous populations. Listeners reproduced random ‘seed’ rhythms; their reproductions were fed back as the stimulus (as in the game of ‘telephone’), such that their biases (the prior) could be estimated from the distribution of reproductions. Every tested group showed a sparse prior with peaks at integer-ratio rhythms. However, the importance of different integer ratios varied across groups, often reflecting local musical practices. Our results suggest a common feature of music cognition: discrete rhythm ‘categories’ at small-integer ratios. These discrete representations plausibly stabilize musical systems in the face of cultural transmission but interact with culture-specific traditions to yield the diversity that is evident when mental representations are probed across many cultures.
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| 8. |
- Rashid, A. U., et al.
(author)
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Numerical simulation model development and comparative analysis of low-voltage SiC BJT for compact modeling
- 2019
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In: 2019 IEEE 7th Workshop on Wide Bandgap Power Devices and Applications, WiPDA 2019. - : Institute of Electrical and Electronics Engineers Inc.. ; , s. 137-142
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Conference paper (peer-reviewed)abstract
- The paper presents a comprehensive investigation of the key differences between the characteristics of Si and SiC low-voltage (LV) BJT. The purpose of this investigation is to identify the special characteristics of SiC LV BJT which will require changes in the parameter extraction sequence of the conventional compact models. Characteristics of LV SiC bipolar devices fabricated in KTH's ion-implantation-free process are compared with a similar Si BJT characteristics. The investigation proves that key differences arrive from the low intrinsic carrier concentration, high contact resistance, and the presence of interfacial trap states in the SiO2/SiC interface. To verify the claims, TCAD deck for LV SiC bipolar device has been developed. TCAD simulation results clearly indicate the importance of interface trap states and, comparatively, large internal resistance in the base region. It also verifies the very low current of SiC BJT at the operating voltage range of Si BJT, which is difficult to measure with curve tracers.
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| 9. |
- Abadei, S., et al.
(author)
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DC field dependent properties of Na0.5K0.5NbO3/SiO2/Si structures at millimeter-wave frequencies
- 2001
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In: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 78:13, s. 1900-1902
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Journal article (peer-reviewed)abstract
- Dielectric properties of laser-ablated 0.5-mum-thick c-axis epitaxial Na0.5K0.5NbO3 films on high-resistivity (7.7 Omega cm) silicon SiO2/Si substrate are studied experimentally at frequencies up to 40 GHz. For measurements, planar 0.5-mum-thick gold electrodes (interdigital and straight slot) are photolithography defined on the top surface of Na0.5K0.5NbO3 films. The slot width between the electrodes is 2 or 4 mum. 13% capacitance change at 40 V dc bias and Q factor more than 15 are observed at 40 GHz, which makes the structure useful for applications in electrically tunable millimeter-wave devices.
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| 10. |
- Alex-Amor, Antonio, et al.
(author)
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Elliptical Glide-Symmetric Holey Metasurfaces for Wideband Anisotropy
- 2020
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In: 2020 14th European Conference on Antennas and Propagation (EUCAP 2020). - : Institute of Electrical and Electronics Engineers (IEEE).
-
Conference paper (peer-reviewed)abstract
- This paper presents a mode-matching technique to study the dispersive features of periodic structures composed of glide-symmetric elliptical holes. As a difference from purely numerical methods, our formulation provides physical insight on the Floquet harmonics. At the same time, the computational cost is reduced compared to general purpose commercial software. The fields inside the holes are described by means of Mathieu functions and subsequently used to compute the full 2-D dispersion diagrams. With the presented analysis, we demonstrate that glide-symmetric periodic structures with elliptical holes offer anisotropic refractive indexes over a wide range of frequencies.
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