| 1. |
- Cossarizza, A., et al.
(författare)
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Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition)
- 2019
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Ingår i: European Journal of Immunology. - : Wiley. - 0014-2980 .- 1521-4141. ; 49:10, s. 1457-1973
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Tidskriftsartikel (refereegranskat)abstract
- These guidelines are a consensus work of a considerable number of members of the immunology and flow cytometry community. They provide the theory and key practical aspects of flow cytometry enabling immunologists to avoid the common errors that often undermine immunological data. Notably, there are comprehensive sections of all major immune cell types with helpful Tables detailing phenotypes in murine and human cells. The latest flow cytometry techniques and applications are also described, featuring examples of the data that can be generated and, importantly, how the data can be analysed. Furthermore, there are sections detailing tips, tricks and pitfalls to avoid, all written and peer-reviewed by leading experts in the field, making this an essential research companion.
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| 2. |
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| 3. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 4. |
- Forrest, ARR, et al.
(författare)
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A promoter-level mammalian expression atlas
- 2014
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 507:7493, s. 462-
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Tidskriftsartikel (refereegranskat)
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| 5. |
- Noguchi, S, et al.
(författare)
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FANTOM5 CAGE profiles of human and mouse samples
- 2017
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Ingår i: Scientific data. - : Springer Science and Business Media LLC. - 2052-4463. ; 4, s. 170112-
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Tidskriftsartikel (refereegranskat)abstract
- In the FANTOM5 project, transcription initiation events across the human and mouse genomes were mapped at a single base-pair resolution and their frequencies were monitored by CAGE (Cap Analysis of Gene Expression) coupled with single-molecule sequencing. Approximately three thousands of samples, consisting of a variety of primary cells, tissues, cell lines, and time series samples during cell activation and development, were subjected to a uniform pipeline of CAGE data production. The analysis pipeline started by measuring RNA extracts to assess their quality, and continued to CAGE library production by using a robotic or a manual workflow, single molecule sequencing, and computational processing to generate frequencies of transcription initiation. Resulting data represents the consequence of transcriptional regulation in each analyzed state of mammalian cells. Non-overlapping peaks over the CAGE profiles, approximately 200,000 and 150,000 peaks for the human and mouse genomes, were identified and annotated to provide precise location of known promoters as well as novel ones, and to quantify their activities.
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| 6. |
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| 7. |
- Rangelow, I. W., et al.
(författare)
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Piezoresistive and self-actuated 128-cantilever arrays for nanotechnology applications
- 2007
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Ingår i: Microelectronic Engineering. - : Elsevier BV. - 0167-9317 .- 1873-5568. ; 84:5-8, s. 1260-1264
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Tidskriftsartikel (refereegranskat)abstract
- A major limitation for future nanotechnology, particularly for bottom-up manufacturing is the non-availability of 2-dimensional massively parallel probe arrays. Scanning proximity probes are uniquely powerful tools for analysis, manipulation and bottom-up synthesis: they are capable of addressing and engineering surfaces at the atomic level and are the key to unlocking the full potential of Nanotechnology. Generic massively parallel intelligent cantilever-probe platforms is demonstrated through a number of existing and ground-breaking techniques. A packaged VLSI NEMS-chip (Very Large Scale Integrated Nano Electro Mechanical System) incorporating 128 proximal probes, fully addressable with control and readout interconnects and advanced software will be presented.
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| 8. |
- Bogaerts, Wim, et al.
(författare)
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Scaling programmable silicon photonics circuits
- 2023
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Ingår i: Silicon Photonics XVIII. - : SPIE-Intl Soc Optical Eng.
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Konferensbidrag (refereegranskat)abstract
- We give an overview the progress of our work in silicon photonic programmable circuits, covering the techn stack from the photonic chip over the driver electronics, packaging technologies all the way to the sof layers. On the photonic side, we show our recent results in large-scale silicon photonic circuits with diff tuning technologies, including heaters, MEMS and liquid crystals, and their respective electronic driving sch We look into the scaling potential of these different technologies as the number of tunable elements in a ci increases. Finally, we elaborate on the software routines for routing and filter synthesis to enable the pho programmer.
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| 9. |
- Khan, U., et al.
(författare)
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Large scale programmable photonic circuits using silicon photonic MEMS
- 2022
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Ingår i: 2022 Conference on Lasers and Electro-Optics, CLEO 2022. - : Institute of Electrical and Electronics Engineers Inc..
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Konferensbidrag (refereegranskat)abstract
- We demonstrate low-power and non-volatile MEMS actuators on an industrially established silicon photonics platform. The compact electrostatically actuated phase shifters and tunable couplers enable large-scale programmable photonic integrated circuits.
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| 10. |
- Khan, Umar, et al.
(författare)
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Low power actuators for programmable photonic processors
- 2023
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Ingår i: AI and Optical Data Sciences IV. - : SPIE-Intl Soc Optical Eng.
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Konferensbidrag (refereegranskat)abstract
- The demand for efficient actuators in photonics has peaked with increasing popularity for large-scale general-purpose programmable photonics circuits. We present our work to enhance an established silicon photonics platform with low-power micro-electromechanical (MEMS) and liquid crystal (LC) actuators to enable large-scale programmable photonic integrated circuits (PICs).
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| 11. |
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| 12. |
- Williams, K, et al.
(författare)
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Assessment of competencies by use of virtual patient technology
- 2011
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Ingår i: Academic psychiatry : the journal of the American Association of Directors of Psychiatric Residency Training and the Association for Academic Psychiatry. - : Springer Science and Business Media LLC. - 1545-7230. ; 35:5, s. 328-330
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Tidskriftsartikel (refereegranskat)
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