| 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. |
- 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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| 3. |
- Ademuyiwa, Adesoji O., et al.
(author)
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Determinants of morbidity and mortality following emergency abdominal surgery in children in low-income and middle-income countries
- 2016
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In: BMJ Global Health. - : BMJ Publishing Group Ltd. - 2059-7908. ; 1:4
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Journal article (peer-reviewed)abstract
- Background: Child health is a key priority on the global health agenda, yet the provision of essential and emergency surgery in children is patchy in resource-poor regions. This study was aimed to determine the mortality risk for emergency abdominal paediatric surgery in low-income countries globally.Methods: Multicentre, international, prospective, cohort study. Self-selected surgical units performing emergency abdominal surgery submitted prespecified data for consecutive children aged <16 years during a 2-week period between July and December 2014. The United Nation's Human Development Index (HDI) was used to stratify countries. The main outcome measure was 30-day postoperative mortality, analysed by multilevel logistic regression.Results: This study included 1409 patients from 253 centres in 43 countries; 282 children were under 2 years of age. Among them, 265 (18.8%) were from low-HDI, 450 (31.9%) from middle-HDI and 694 (49.3%) from high-HDI countries. The most common operations performed were appendectomy, small bowel resection, pyloromyotomy and correction of intussusception. After adjustment for patient and hospital risk factors, child mortality at 30 days was significantly higher in low-HDI (adjusted OR 7.14 (95% CI 2.52 to 20.23), p<0.001) and middle-HDI (4.42 (1.44 to 13.56), p=0.009) countries compared with high-HDI countries, translating to 40 excess deaths per 1000 procedures performed.Conclusions: Adjusted mortality in children following emergency abdominal surgery may be as high as 7 times greater in low-HDI and middle-HDI countries compared with high-HDI countries. Effective provision of emergency essential surgery should be a key priority for global child health agendas.
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| 4. |
- Bairagi, Samiran, et al.
(author)
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Formation of quaternary Zn(AlxGa1−x)2O4 epilayers driven by thermally induced interdiffusion between spinel ZnGa2O4 epilayer and Al2O3 substrate
- 2023
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In: Materials Today Advances. - : Elsevier. - 2590-0498. ; 20
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Journal article (peer-reviewed)abstract
- Zinc aluminogallate, Zn(AlxGa1−x)2O4 (ZAGO), a single-phase spinel structure, offers considerable potential for high-performance electronic devices due to its expansive compositional miscibility range between aluminum (Al) and gallium (Ga). Direct growth of high-quality ZAGO epilayers however remains problematic due to the high volatility of zinc (Zn). This work highlights a novel synthesis process for high-quality epitaxial quaternary ZAGO thin films on sapphire substrates, achieved through thermal annealing of a ZnGa2O4 (ZGO) epilayer on sapphire in an ambient air setting. In-situ annealing x-ray diffraction measurements show that the incorporation of Al in the ZGO epilayer commenced at 850 °C. The Al content (x) in ZAGO epilayer gradually increased up to around 0.45 as the annealing temperature was raised to 1100 °C, which was confirmed by transmission electron microscopy (TEM) and energy dispersive x-ray spectroscopy. X-ray rocking curve measurement revealed a small full width at half maximum value of 0.72 °, indicating the crystal quality preservation of the ZAGO epilayer with a high Al content. However, an epitaxial intermediate �–(AlxGa1−x)2O3 layer (� - AGO) was formed between the ZAGO and sapphire substrate. This is believed to be a consequence of the interdiffusion of Al and Ga between the ZGO thin film and sapphire substrate. Using density functional theory, the substitution cost of Ga in sapphire was determined to be about 0.5 eV lower than substitution cost of Al in ZGO. Motivated by this energetically favorable substitution, a formation mechanism of the ZAGO and AGO layers was proposed. Spectroscopic ellipsometry studies revealed an increase in total thickness of the film from 105.07 nm (ZGO) to 147.97 nm (ZAGO/AGO) after annealing to 1100 °C, which were corroborated using TEM. Furthermore, an observed increase in the direct (indirect) optical bandgap from 5.06 eV (4.7 eV) to 5.72 eV (5.45 eV) with an increasing Al content in the ZAGO layer further underpins the formation of a quaternary ZAGO alloy with a tunable composition.
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| 5. |
- Chang, Jui-Che, et al.
(author)
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HiPIMS-grown AlN buffer for threading dislocation reduction in DC-magnetron sputtered GaN epifilm on sapphire substrate
- 2023
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In: Vacuum. - : PERGAMON-ELSEVIER SCIENCE LTD. - 0042-207X .- 1879-2715. ; 217
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Journal article (peer-reviewed)abstract
- Gallium nitride (GaN) epitaxial films on sapphire (Al2O3) substrates have been grown using reactive magnetron sputter epitaxy with a liquid Ga target. Threading dislocations density (TDD) of sputtered GaN films was reduced by using an inserted high-quality aluminum nitride (AlN) buffer layer grown by reactive high power impulse magnetron sputtering (R-HiPIMS) in a gas mixture of Ar and N2. After optimizing the Ar/N2 pressure ratio and deposition power, a high-quality AlN film exhibiting a narrow full-width at half-maximum (FWHM) value of the double-crystal x-ray rocking curve (DCXRC) of the AlN(0002) peak of 0.086° was obtained by R-HiPIMS. The mechanism giving rise the observed quality improvement is attributed to the enhancement of kinetic energy of the adatoms in the deposition process when operated in a transition mode. With the inserted HiPIMS-AlN as a buffer layer for direct current magnetron sputtering (DCMS) GaN growth, the FWHM values of GaN(0002) and (10 1‾ 1) XRC decrease from 0.321° to 0.087° and from 0.596° to 0.562°, compared to the direct growth of GaN on sapphire, respectively. An order of magnitude reduction from 2.7 × 109 cm−2 to 2.0 × 108 cm−2 of screw-type TDD calculated from the FWHM of the XRC data using the inserted HiPIMS-AlN buffer layer demonstrates the improvement of crystal quality of GaN. The result of TDD reduction using the HiPIMS-AlN buffer was also verified by weak beam dark-field (WBDF) cross-sectional transmission electron microscopy (TEM).
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| 6. |
- Ching, Tao-Chung, et al.
(author)
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The JCMT BISTRO-2 Survey: Magnetic Fields of the Massive DR21 Filament
- 2022
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In: Astrophysical Journal. - : American Astronomical Society. - 1538-4357 .- 0004-637X. ; 941:2
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Journal article (peer-reviewed)abstract
- We present 850 mu m dust polarization observations of the massive DR21 filament from the B-fields In STar-forming Region Observations (BISTRO) survey, using the POL-2 polarimeter and the SCUBA-2 camera on the James Clerk Maxwell Telescope. We detect ordered magnetic fields perpendicular to the parsec-scale ridge of the DR21 main filament. In the subfilaments, the magnetic fields are mainly parallel to the filamentary structures and smoothly connect to the magnetic fields of the main filament. We compare the POL-2 and Planck dust polarization observations to study the magnetic field structures of the DR21 filament on 0.1-10 pc scales. The magnetic fields revealed in the Planck data are well-aligned with those of the POL-2 data, indicating a smooth variation of magnetic fields from large to small scales. The plane-of-sky magnetic field strengths derived from angular dispersion functions of dust polarization are 0.6-1.0 mG in the DR21 filament and similar to 0.1 mG in the surrounding ambient gas. The mass-to-flux ratios are found to be magnetically supercritical in the filament and slightly subcritical to nearly critical in the ambient gas. The alignment between column density structures and magnetic fields changes from random alignment in the low-density ambient gas probed by Planck to mostly perpendicular in the high-density main filament probed by James Clerk Maxwell Telescope. The magnetic field structures of the DR21 filament are in agreement with MHD simulations of a strongly magnetized medium, suggesting that magnetic fields play an important role in shaping the DR21 main filament and subfilaments.
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| 7. |
- Doi, Yasuo, et al.
(author)
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The JCMT BISTRO Survey: Magnetic Fields Associated with a Network of Filaments in NGC 1333
- 2020
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In: Astrophysical Journal. - : American Astronomical Society. - 1538-4357 .- 0004-637X. ; 899:1
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Journal article (peer-reviewed)abstract
- We present new observations of the active star formation region NGC 1333 in the Perseus molecular cloud complex from the James Clerk Maxwell Telescope B-Fields In Star-forming Region Observations (BISTRO) survey with the POL-2 instrument. The BISTRO data cover the entire NGC 1333 complex (∼1.5 pc ? 2 pc) at 0.02 pc resolution and spatially resolve the polarized emission from individual filamentary structures for the first time. The inferred magnetic field structure is complex as a whole, with each individual filament aligned at different position angles relative to the local field orientation. We combine the BISTRO data with low- and high- resolution data derived from Planck and interferometers to study the multiscale magnetic field structure in this region. The magnetic field morphology drastically changes below a scale of ∼1 pc and remains continuous from the scales of filaments (∼0.1 pc) to that of protostellar envelopes (∼0.005 pc or ∼1000 au). Finally, we construct simple models in which we assume that the magnetic field is always perpendicular to the long axis of the filaments. We demonstrate that the observed variation of the relative orientation between the filament axes and the magnetic field angles are well reproduced by this model, taking into account the projection effects of the magnetic field and filaments relative to the plane of the sky. These projection effects may explain the apparent complexity of the magnetic field structure observed at the resolution of BISTRO data toward the filament network.
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| 8. |
- Eswaraiah, Chakali, et al.
(author)
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The JCMT BISTRO Survey: Revealing the Diverse Magnetic Field Morphologies in Taurus Dense Cores with Sensitive Submillimeter Polarimetry
- 2021
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In: Astrophysical Journal Letters. - : American Astronomical Society. - 2041-8213 .- 2041-8205. ; 912:2
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Journal article (peer-reviewed)abstract
- We have obtained sensitive dust continuum polarization observations at 850 μm in the B213 region of Taurus using POL-2 on SCUBA-2 at the James Clerk Maxwell Telescope as part of the B-fields in STar-forming Region Observations (BISTRO) survey. These observations allow us to probe magnetic field (B-field) at high spatial resolution (∼2000 au or ∼0.01 pc at 140 pc) in two protostellar cores (K04166 and K04169) and one prestellar core (Miz-8b) that lie within the B213 filament. Using the Davis-Chandrasekhar-Fermi method, we estimate the B-field strengths in K04166, K04169, and Miz-8b to be 38 ± 14, 44 ± 16, and 12 ± 5 μG, respectively. These cores show distinct mean B-field orientations. The B-field in K04166 is well ordered and aligned parallel to the orientations of the core minor axis, outflows, core rotation axis, and large-scale uniform B-field, in accordance with magnetically regulated star formation via ambipolar diffusion taking place in K04166. The B-field in K04169 is found to be ordered but oriented nearly perpendicular to the core minor axis and large-scale B-field and not well correlated with other axes. In contrast, Miz-8b exhibits a disordered B-field that shows no preferred alignment with the core minor axis or large-scale field. We found that only one core, K04166, retains a memory of the large-scale uniform B-field. The other two cores, K04169 and Miz-8b, are decoupled from the large-scale field. Such a complex B-field configuration could be caused by gas inflow onto the filament, even in the presence of a substantial magnetic flux.
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| 9. |
- Horng, Ray-Hua, et al.
(author)
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Growth and Characterization of Sputtered InAlN Nanorods on Sapphire Substrates for Acetone Gas Sensing
- 2024
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In: Nanomaterials. - : MDPI. - 2079-4991. ; 14:1
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Journal article (peer-reviewed)abstract
- The demand for highly sensitive and selective gas sensors has been steadily increasing, driven by applications in various fields such as environmental monitoring, healthcare, and industrial safety. In this context, ternary alloy indium aluminum nitride (InAlN) semiconductors have emerged as a promising material for gas sensing due to their unique properties and tunable material characteristics. This work focuses on the fabrication and characterization of InAlN nanorods grown on sapphire substrates using an ultra-high vacuum magnetron sputter epitaxy with precise control over indium composition and explores their potential for acetone-gas-sensing applications. Various characterization techniques, including XRD, SEM, and TEM, demonstrate the structural and morphological insights of InAlN nanorods, making them suitable for gas-sensing applications. To evaluate the gas-sensing performance of the InAlN nanorods, acetone was chosen as a target analyte due to its relevance in medical diagnostics and industrial processes. The results reveal that the InAlN nanorods exhibit a remarkable sensor response of 2.33% at 600 ppm acetone gas concentration at an operating temperature of 350 degrees C, with a rapid response time of 18 s. Their high sensor response and rapid response make InAlN a viable candidate for use in medical diagnostics, industrial safety, and environmental monitoring.
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| 10. |
- Hwang, Jihye, et al.
(author)
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The JCMT BISTRO Survey: A Spiral Magnetic Field in a Hub-filament Structure, Monoceros R2
- 2022
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In: Astrophysical Journal. - : American Astronomical Society. - 1538-4357 .- 0004-637X. ; 941:1
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Journal article (peer-reviewed)abstract
- We present and analyze observations of polarized dust emission at 850 μm toward the central 1 × 1 pc hub-filament structure of Monoceros R2 (Mon R2). The data are obtained with SCUBA-2/POL-2 on the James Clerk Maxwell Telescope (JCMT) as part of the B-fields in Star-forming Region Observations survey. The orientations of the magnetic field follow the spiral structure of Mon R2, which are well described by an axisymmetric magnetic field model. We estimate the turbulent component of the magnetic field using the angle difference between our observations and the best-fit model of the underlying large-scale mean magnetic field. This estimate is used to calculate the magnetic field strength using the Davis–Chandrasekhar–Fermi method, for which we also obtain the distribution of volume density and velocity dispersion using a column density map derived from Herschel data and the C18O (J = 3 - 2) data taken with HARP on the JCMT, respectively. We make maps of magnetic field strengths and mass-to-flux ratios, finding that magnetic field strengths vary from 0.02 to 3.64 mG with a mean value of 1.0 ± 0.06 mG, and the mean critical mass-to-flux ratio is 0.47 ± 0.02. Additionally, the mean Alfvén Mach number is 0.35 ± 0.01. This suggests that, in Mon R2, the magnetic fields provide resistance against large-scale gravitational collapse, and the magnetic pressure exceeds the turbulent pressure. We also investigate the properties of each filament in Mon R2. Most of the filaments are aligned along the magnetic field direction and are magnetically subcritical.
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