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| 2. |
- 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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| 3. |
- Kristanl, Matej, et al.
(författare)
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The Seventh Visual Object Tracking VOT2019 Challenge Results
- 2019
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Ingår i: 2019 IEEE/CVF INTERNATIONAL CONFERENCE ON COMPUTER VISION WORKSHOPS (ICCVW). - : IEEE COMPUTER SOC. - 9781728150239 ; , s. 2206-2241
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Konferensbidrag (refereegranskat)abstract
- The Visual Object Tracking challenge VOT2019 is the seventh annual tracker benchmarking activity organized by the VOT initiative. Results of 81 trackers are presented; many are state-of-the-art trackers published at major computer vision conferences or in journals in the recent years. The evaluation included the standard VOT and other popular methodologies for short-term tracking analysis as well as the standard VOT methodology for long-term tracking analysis. The VOT2019 challenge was composed of five challenges focusing on different tracking domains: (i) VOT-ST2019 challenge focused on short-term tracking in RGB, (ii) VOT-RT2019 challenge focused on "real-time" short-term tracking in RGB, (iii) VOT-LT2019 focused on long-term tracking namely coping with target disappearance and reappearance. Two new challenges have been introduced: (iv) VOT-RGBT2019 challenge focused on short-term tracking in RGB and thermal imagery and (v) VOT-RGBD2019 challenge focused on long-term tracking in RGB and depth imagery. The VOT-ST2019, VOT-RT2019 and VOT-LT2019 datasets were refreshed while new datasets were introduced for VOT-RGBT2019 and VOT-RGBD2019. The VOT toolkit has been updated to support both standard short-term, long-term tracking and tracking with multi-channel imagery. Performance of the tested trackers typically by far exceeds standard baselines. The source code for most of the trackers is publicly available from the VOT page. The dataset, the evaluation kit and the results are publicly available at the challenge website(1).
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| 4. |
- Kristan, Matej, et al.
(författare)
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The Visual Object Tracking VOT2016 Challenge Results
- 2016
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Ingår i: COMPUTER VISION - ECCV 2016 WORKSHOPS, PT II. - Cham : SPRINGER INT PUBLISHING AG. - 9783319488813 - 9783319488806 ; , s. 777-823
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Konferensbidrag (refereegranskat)abstract
- The Visual Object Tracking challenge VOT2016 aims at comparing short-term single-object visual trackers that do not apply pre-learned models of object appearance. Results of 70 trackers are presented, with a large number of trackers being published at major computer vision conferences and journals in the recent years. The number of tested state-of-the-art trackers makes the VOT 2016 the largest and most challenging benchmark on short-term tracking to date. For each participating tracker, a short description is provided in the Appendix. The VOT2016 goes beyond its predecessors by (i) introducing a new semi-automatic ground truth bounding box annotation methodology and (ii) extending the evaluation system with the no-reset experiment.
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| 5. |
- Xu, Heng, et al.
(författare)
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Editorial: Some Thoughts on Reviewing for Information Systems Research and Other Leading Information Systems Journals
- 2023
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Ingår i: Information Systems Research. - : INFORMS. - 1526-5536 .- 1047-7047. ; 34:4, s. 1321-1338
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Peer review of research before publication is both an essential and an integral part of scientific knowledge production. For reputable journals, the peer review process distinguishes knowledge claims in journal articles from those in sources with unknown or varying veracity. The peer review process assures readers that the published work is credible (i.e., conducted in line with prescribed norms of research) and meets a certain threshold with respect to contributions and potential impact. Leading journals are perceived as such not only because the best research is submitted to them but also because of the efforts of the best reviewers and editors in evaluating and, when applicable, developing the initially submitted manuscripts1 to publishable form. The sustained quality of reviews is critical for journals such as Information Systems Research (ISR). With the number of submissions to ISR growing each year, as well as an explicit policy of encouraging and celebrating inclusive excellence (Sarker 2023), there is a need for more reviewers for the journal (and the discipline, more generally) who have the necessary expertise to evaluate submitted papers, who understand and are attuned to the norms of the different traditions and genres of work submitted, and who know how to craft reviews that ensure the review process supports effective knowledge production. In this editorial, we draw on the expertise of some of the experienced associate editors (AEs) at ISR2 who represent different research traditions to provide guidance on how ISR reviewers can contribute reviews that AEs and authors are likely to find valuable. The primary audience of this editorial is Ph.D. students and early career scholars who occasionally review for, or seek to review for, ISR and similar journals. Although experienced reviewers likely know most of what we will say in the next few pages, we are hopeful that the editorial can provide a useful recapitulation of characteristics of reviews that are appreciated by ISR editors, irrespective of the reviewers’ experience. Finally, revisiting what reviewers look for in manuscripts can prove helpful for authors submitting papers to journals such as ISR. Before proceeding, we would like to acknowledge the efforts of editors and editorial board members from various journals who have organized reviewer development workshops (e.g., Rai 2019, Whitley 2023), and reflections on the review process and effective reviews by notable scholars in our discipline (e.g., Lee 1995; Saunders 2005a, b; Straub 2009; Kohli and Straub 2011; Davison 2015; Rai 2016; Leidner et al. 2022); see Table 1. Our editorial does not seek to supplant this accumulated wisdom but seeks to add nuances to the various guidelines that have been offered in the past. We illustrate key points with examples from various research traditions.
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| 6. |
- Bortolini, C., et al.
(författare)
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Atomic Structure of Amyloid Crystals
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- A deep understanding of the self-assembly and crystallization of biomolecules as highly ordered biomaterials is crucial to enable the design and the generation of complex functional systems for cutting-edge applications in nanotechnology and biomedicine. In this work, we determined the atomic structure of Aβ16-20 crystals, a fragment of amyloid-β which aberrant folding is linked to the etiology of Alzheimer’s disease, the most common cause of dementia. We detailed the hierarchical aggregation mechanism of Aβ16-20 into highly ordered crystals and revealed that the self-assembly is reversible, leading to the formation of oligomers as an intermediate. Our structural investigation combined with molecular dynamics simulations highlights how a combination of favorable non-covalent interactions drives the efficient fast self-assembly and enhanced stability. We studied the chemical and surface properties of amyloid crystals, including their mechanical properties and their capability to transmit light; the long-rang order of Aβ16-20 crystals enables them to be used as optical waveguide materials for biologically based modulation and sensing. Our results shed new light on pathogenic amyloid assembly at the atomic level and reveal the potential of amyloid crystals for applications in nanotechnology.
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| 7. |
- Chen, Jingjing, et al.
(författare)
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FishBuddy : Promoting Student Engagement in Self-Paced Learning through Wearable Sensing
- 2017
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Ingår i: 2017 IEEE INTERNATIONAL CONFERENCE ON SMART COMPUTING (SMARTCOMP). - : IEEE. - 9781509065172 ; , s. 211-219
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Konferensbidrag (refereegranskat)abstract
- Student engagement is crucial for successful self-paced learning. Feeling isolated during self-paced learning with neither adequate supervision nor intervention by teachers may cause negative emotions such as anxiety. Such emotions may in turn significantly weaken students' motivation to engage in learning activities. In this paper, we develop a self-paced learning environment (FishBuddy) that aims to reduce anxiety and promote student engagement. We construct and implement a physiologically-state-aware performance-evaluation model for identifying potentially fruitful moments of intervention when students show frustration during learning activities using an Apple Watch application that measures heart rate and alerts the student to watch a visualization of his or her own physiological state. We have conducted an experiment with 20 first-year undergraduate students, randomly separated into an experimental group and a control group, who carry out online, self-paced English grammar exercises. The students in the experimental group used FishBuddy and those in the control group did not. The self-reports from both groups show that FishBuddy significantly reduced reported experiences of anxiety and isolation in the experiment. Further to this, students who used FishBuddy were engaged longer with the exercises. The average scores on the exercises between the two groups, however, were not significantly different.
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| 8. |
- Clabbers, Max T. B., et al.
(författare)
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MyD88 TIR domain higher-order assembly interactions revealed by microcrystal electron diffraction and serial femtosecond crystallography
- 2021
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- MyD88 and MAL are Toll-like receptor (TLR) adaptors that signal to induce pro-inflammatory cytokine production. We previously observed that the TIR domain of MAL (MALTIR) forms filaments in vitro and induces formation of crystalline higher-order assemblies of the MyD88 TIR domain (MyD88TIR). These crystals are too small for conventional X-ray crystallography, but are ideally suited to structure determination by microcrystal electron diffraction (MicroED) and serial femtosecond crystallography (SFX). Here, we present MicroED and SFX structures of the MyD88TIR assembly, which reveal a two-stranded higher-order assembly arrangement of TIR domains analogous to that seen previously for MALTIR. We demonstrate via mutagenesis that the MyD88TIR assembly interfaces are critical for TLR4 signaling in vivo, and we show that MAL promotes unidirectional assembly of MyD88TIR. Collectively, our studies provide structural and mechanistic insight into TLR signal transduction and allow a direct comparison of the MicroED and SFX techniques.
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| 9. |
- Colyn Bwanika, Henri, et al.
(författare)
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Limiting the Effects of Radiation Damage in MicroED through Dose Selection during Data Processing
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Microcrystal electron diffraction (MicroED), also known as three-dimensional electron diffraction (3D ED), allows collection of diffraction data from submicron-sized crystals under low electron dose conditions, typically around 5-6 e-Å-2 in total. Despite having several advantages of MicroED over most conventional X-ray crystallographic techniques, susceptibility to radiation damage is a big problem that remains to be solved. Similar to X-ray crystallography, radiation damage to the macromolecular crystal structures in MicroED manifests in two forms, the global damage that affects the overall crystal lattice order and the site-specific damage that affects highly sensitive residues and moieties in macromolecules. In this study, we investigated data processing strategies that could be used to limit the effects of radiation damage to the crystal even when data collection is performed at high electron doses. During MicroED data collection, radiation damage increases with the number of acquired ED frames because the accumulated electron dose increases. To limit the damage, we propose to process only the first few frames of a dataset with a certain low dose cutoff. Data collected from several crystals and processed in this way can be merged to increase completeness and subsequently be used for structure refinement. According to our results, this approach improves the resolution of the data, the data statistics, the structure determination, and the quality of the final structure. The suggested approach could be especially useful in MicroED structure-based drug discovery where atomic resolution structures will provide detailed information about ligand-protein binding properties, which are essential during library screening and hit identification.
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| 10. |
- de las Fuentes, Lisa, et al.
(författare)
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Gene-educational attainment interactions in a multi-ancestry genome-wide meta-analysis identify novel blood pressure loci
- 2021
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Ingår i: Molecular Psychiatry. - : Springer Nature. - 1359-4184 .- 1476-5578. ; 26:6, s. 2111-2125
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Tidskriftsartikel (refereegranskat)abstract
- Educational attainment is widely used as a surrogate for socioeconomic status (SES). Low SES is a risk factor for hypertension and high blood pressure (BP). To identify novel BP loci, we performed multi-ancestry meta-analyses accounting for gene-educational attainment interactions using two variables, “Some College” (yes/no) and “Graduated College” (yes/no). Interactions were evaluated using both a 1 degree of freedom (DF) interaction term and a 2DF joint test of genetic and interaction effects. Analyses were performed for systolic BP, diastolic BP, mean arterial pressure, and pulse pressure. We pursued genome-wide interrogation in Stage 1 studies (N = 117 438) and follow-up on promising variants in Stage 2 studies (N = 293 787) in five ancestry groups. Through combined meta-analyses of Stages 1 and 2, we identified 84 known and 18 novel BP loci at genome-wide significance level (P < 5 × 10-8). Two novel loci were identified based on the 1DF test of interaction with educational attainment, while the remaining 16 loci were identified through the 2DF joint test of genetic and interaction effects. Ten novel loci were identified in individuals of African ancestry. Several novel loci show strong biological plausibility since they involve physiologic systems implicated in BP regulation. They include genes involved in the central nervous system-adrenal signaling axis (ZDHHC17, CADPS, PIK3C2G), vascular structure and function (GNB3, CDON), and renal function (HAS2 and HAS2-AS1, SLIT3). Collectively, these findings suggest a role of educational attainment or SES in further dissection of the genetic architecture of BP.
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