| 1. |
- 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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| 2. |
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| 3. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)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. |
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- 2019
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Journal article (peer-reviewed)
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| 5. |
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The Seventeenth Data Release of the Sloan Digital Sky Surveys : Complete Release of MaNGA, MaStar, and APOGEE-2 Data
- 2022
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In: Astrophysical Journal Supplement Series. - : Institute of Physics (IOP). - 0067-0049 .- 1538-4365. ; 259:2
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Journal article (peer-reviewed)abstract
- This paper documents the seventeenth data release (DR17) from the Sloan Digital Sky Surveys; the fifth and final release from the fourth phase (SDSS-IV). DR17 contains the complete release of the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey, which reached its goal of surveying over 10,000 nearby galaxies. The complete release of the MaNGA Stellar Library accompanies this data, providing observations of almost 30,000 stars through the MaNGA instrument during bright time. DR17 also contains the complete release of the Apache Point Observatory Galactic Evolution Experiment 2 survey that publicly releases infrared spectra of over 650,000 stars. The main sample from the Extended Baryon Oscillation Spectroscopic Survey (eBOSS), as well as the subsurvey Time Domain Spectroscopic Survey data were fully released in DR16. New single-fiber optical spectroscopy released in DR17 is from the SPectroscipic IDentification of ERosita Survey subsurvey and the eBOSS-RM program. Along with the primary data sets, DR17 includes 25 new or updated value-added catalogs. This paper concludes the release of SDSS-IV survey data. SDSS continues into its fifth phase with observations already underway for the Milky Way Mapper, Local Volume Mapper, and Black Hole Mapper surveys.
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| 6. |
- Abbasi, Rasha, et al.
(author)
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IceCube search for neutrinos from GRB 221009A
- 2023
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In: Proceedings of 38th International Cosmic Ray Conference (ICRC 2023). - : Sissa Medialab Srl.
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Conference paper (peer-reviewed)abstract
- GRB 221009A is the brightest Gamma Ray Burst (GRB) ever observed. The observed extremelyhigh flux of high and very-high-energy photons provide a unique opportunity to probe the predictedneutrino counterpart to the electromagnetic emission. We have used a variety of methods to searchfor neutrinos in coincidence with the GRB over several time windows during the precursor, promptand afterglow phases of the GRB. MeV scale neutrinos are studied using photo-multiplier ratescalers which are normally used to search for galactic core-collapse supernovae neutrinos. GeVneutrinos are searched starting with DeepCore triggers. These events don’t have directionallocalization, but instead can indicate an excess in the rate of events. 10 GeV - 1 TeV and >TeVneutrinos are searched using traditional neutrino point source methods which take into accountthe direction and time of events with DeepCore and the entire IceCube detector respectively. The>TeV results include both a fast-response analysis conducted by IceCube in real-time with timewindows of T0 − 1 to T0 + 2 hours and T0 ± 1 day around the time of GRB 221009A, as well asan offline analysis with 3 new time windows up to a time window of T0 − 1 to T0 + 14 days, thelongest time period we consider. The combination of observations by IceCube covers 9 ordersof magnitude in neutrino energy, from MeV to PeV, placing upper limits across the range forpredicted neutrino emission.
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| 7. |
- Chau, Michael, et al.
(author)
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The synovial microenvironment suppresses chondrocyte hypertrophy and promotes articular chondrocyte differentiation
- 2022
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In: NPJ Regenerative medicine. - : Nature Publishing Group. - 2057-3995. ; 7:1
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Journal article (peer-reviewed)abstract
- During the development of the appendicular skeleton, the cartilaginous templates undergo hypertrophic differentiation and remodels into bone, except for the cartilage most adjacent to joint cavities where hypertrophic differentiation and endochondral bone formation are prevented, and chondrocytes instead form articular cartilage. The mechanisms that prevent hypertrophic differentiation and endochondral bone formation of the articular cartilage have not been elucidated. To explore the role of the synovial microenvironment in chondrocyte differentiation, osteochondral allografts consisting of articular cartilage, epiphyseal bone, and growth plate cartilage from distal femoral epiphyses of inbred Lewis rats expressing enhanced green fluorescent protein from a ubiquitous promoter were transplanted either in inverted or original (control) orientation to matching sites in wildtype littermates, thereby allowing for tracing of transplanted cells and their progenies. We found that no hypertrophic differentiation occurred in the growth plate cartilage ectopically placed at the joint surface. Instead, the transplanted growth plate cartilage, with time, remodeled into articular cartilage. This finding suggests that the microenvironment at the articular surface inhibits hypertrophic differentiation and supports articular cartilage formation. To explore this hypothesis, rat chondrocyte pellets were cultured with and without synoviocyte-conditioned media. Consistent with the hypothesis, hypertrophic differentiation was inhibited and expression of the articular surface marker lubricin (Prg4) was dramatically induced when chondrocyte pellets were exposed to synovium- or synoviocyte-conditioned media, but not to chondrocyte- or osteoblast-conditioned media. Taken together, we present evidence for a novel mechanism by which synoviocytes, through the secretion of a factor or factors, act directly on chondrocytes to inhibit hypertrophic differentiation and endochondral bone formation and promote articular cartilage formation. This mechanism may have important implications for articular cartilage development, maintenance, and regeneration.
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| 8. |
- Chau, Pui Hing, et al.
(author)
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Visits to the accident and emergency department in hot season of a city with subtropical climate: association with heat stress and related meteorological variables
- 2022
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In: International journal of biometeorology. - : Springer Nature. - 0020-7128 .- 1432-1254. ; 66:10, s. 1955-1971
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Journal article (peer-reviewed)abstract
- Background Literature reporting the association between heat stress defined by universal thermal climate index (UTCI) and emergency department visits is mainly conducted in Europe. This study aimed to investigate the association between heat stress, as defined by the UTCI, and visits to the accident and emergency department (AED) in Hong Kong, which represents a subtropical climate region.Methods A retrospective study involving 13,438,846 AED visits in the public sector from May 2000 to September 2016, excluding 2003 and 2009, was conducted in Hong Kong. Age-sex-specific ANCOVA models of daily AED rates on heat stress and prolonged heat stress, adjusting for air quality, prolonged poor air quality, typhoon, rainstorm, year, day of the week, public holiday, summer vacation, and fee charging, were used.Results On a day with strong heat stress (32.1 °C ≤ UTCI ≤ 38.0 °C), the AED visit rate (per 100,000) increased by 0.9 (95% CI: 0.5, 1.3) and 1.7 (95% CI: 1.3, 2.1) for females and males aged 19–64 and 4.1 (95% CI: 2.7, 5.4) and 4.1 (95% CI: 2.6, 5.6) for females and males aged ≥ 65, while keeping other variables constant. On a day with very strong heat stress (38.1 °C ≤ UTCI ≤ 46.0 °C), the corresponding rates increased by 0.6 (95% CI: 0.1, 1.2), 2.2 (95% CI: 1.7, 2.7), 4.9 (95% CI: 3.1, 6.7), and 4.7 (95% CI: 2.7, 6.6), respectively. The effect size of heat stress associated with AED visit rates was negligible among those aged ≤ 18. Heat stress showed the greatest effect size for males aged 19–64 among all subgroups.Conclusion Biothermal condition from heat stress was associated with the health of the citizens in a city with a subtropical climate and reflected in the increase of daily AED visit. Public health recommendations have been made accordingly for the prevention of heat-related AED visits.
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| 9. |
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| 10. |
- Lai, Eric T. C., et al.
(author)
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Perception of extreme hot weather and the corresponding adaptations among older adults and service providers–A qualitative study in Hong Kong
- 2023
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In: Frontiers in Public Health. - : Frontiers Media S.A.. - 2296-2565. ; 11
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Journal article (peer-reviewed)abstract
- Background: Extreme hot weather events are happening with increasing frequency, intensity and duration in Hong Kong. Heat stress is related to higher risk of mortality and morbidity, with older adults being particularly vulnerable. It is not clear whether and how the older adults perceive the increasingly hot weather as a health threat, and whether community service providers are aware and prepared for such future climate scenario.Methods: We conducted semi-structure interviews with 46 older adults, 18 staff members of community service providers and two district councilors of Tai Po, a north-eastern residential district of Hong Kong. Transcribed data were analyzed using thematic analysis until data saturation was reached.Results: It was agreed upon among the older adult participants that the weather in recent years has become increasingly hot and this led to some health and social problems for them, although some participants perceived that hot weather did not have any impact in their daily lives and they were not vulnerable. The community service providers and district councilors reported that there is a lack of relevant services in the community to support the older adults in hot weather; and there is generally a lack of public education regarding the heat-health issue.Conclusions: Heatwaves are affecting older adults' health in Hong Kong. Yet, discussions and education effort regarding the heat-health issue in the public domain remain scarce. Multilateral efforts are urgently needed to co-create a heat action plan to improve community awareness and resilience.
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