Automated cell type identification is a key computational challenge in single‐cell RNA‐sequencing (scRNA‐seq) data. To capitalise on the large collection of well‐annotated scRNA‐seq datasets, we ...developed scClassify, a multiscale classification framework based on ensemble learning and cell type hierarchies constructed from single or multiple annotated datasets as references. scClassify enables the estimation of sample size required for accurate classification of cell types in a cell type hierarchy and allows joint classification of cells when multiple references are available. We show that scClassify consistently performs better than other supervised cell type classification methods across 114 pairs of reference and testing data, representing a diverse combination of sizes, technologies and levels of complexity, and further demonstrate the unique components of scClassify through simulations and compendia of experimental datasets. Finally, we demonstrate the scalability of scClassify on large single‐cell atlases and highlight a novel application of identifying subpopulations of cells from the Tabula Muris data that were unidentified in the original publication. Together, scClassify represents state‐of‐the‐art methodology in automated cell type identification from scRNA‐seq data.
Synopsis
scClassify is a multiscale classification framework based on ensemble learning and cell type hierarchies, enabling sample size estimation required for accurate cell type classification and joint classification of cells using multiple references.
scClassify performs multiscale cell type classification based on cell type hierarchies constructed from single or multiple reference datasets.
It implements a post‐hoc clustering procedure for discovering novel cell types from cells that are unassigned due to the absence of their types in the reference data.
It enables the estimation of the number of cells required in a reference dataset to accurately discriminate a given cell type in a cell type hierarchy.
Application to large atlas datasets such as Tabula Muris demonstrates its ability to refine cell types and identify cells from sub‐populations.
scClassify is a multiscale classification framework based on ensemble learning and cell type hierarchies, enabling sample size estimation required for accurate cell type classification and joint classification of cells using multiple references.
This study aimed to investigate differences in the gel matrix of aerobic granular sludge and normal aerobic flocculent sludge. From both types of sludge that fed with the same municipal sewage, the ...functional gel-forming exopolysaccharides, alginate-like exopolysaccharides, were isolated. These two exopolysaccharides were chemically fractionated, and investigated by FT-IR spectroscopy. The isolated polymers were made into a gel by calcium addition and the mechanical properties of these reconstituted gels were measured by a low load compression tester. The viscoelastic behavior of the gels was described by a generalized Maxwell model. The alginate-like exopolysaccharides derived from aerobic granules had significantly higher amount of poly(guluronic acid) blocks but lower amount of poly(guluronic acid-manuronic acid) blocks in the chemical structure, while the alginate-like exopolysaccharides derived from aerobic flocculent sludge had equal amount of poly(guluronic acid) blocks and poly(guluronic acid-manuronic acid) blocks. These differences result in a perfect gel-forming capability of alginate-like exopolysaccharides derived from aerobic granules and bestowed this exopolysaccharides gel a stronger mechanical property as compared to alginate-like exopolysaccharides derived from aerobic flocculent sludge. The different chemical and mechanical properties of these two exopolysaccharides contributed to the distinguished characteristics between aerobic granular sludge and aerobic flocculent sludge.
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► Alginate-like EPS exist in both aerobic flocculent and granular sludge. ► Ca-alginate-like EPS gels reflect the morphologies of flocs and granules. ► Chemical structures of alginate-like EPS from flocs and granules are different. ► Alginate-like EPS gel derived from aerobic granules is mechanically stronger.
Objectives
Frailty is a significant public health and clinical issue among the elder population. This study aimed to evaluate the nutritional status and renal function in relation to frailty among ...elderly Taiwanese.
Design
We administered community-based health surveys to the elder population in Chiayi County, Taiwan, from 2017 to 2019.
Measurements
We measured nutritional status (including serum albumin and total protein levels), renal function (including serum blood urea nitrogen, creatinine, urine protein, and urine creatinine levels), hand grip strength (GS) and calculated appendicular muscle mass (AMM).
Results
The study recruited 3739 participants (2139 women). Participants of both sexes with normal GS had higher serum albumin levels and lower urine protein/creatinine ratios (UPCRs). For the men with normal and weak GS, serum albumin levels were 4.15 ± 0.2 and 4.10 ± 0.2 g/dL (p < 0.01), and UPCRs were 123.1 ± 219.6 and 188.7 ± 366.2 (p < 0.001), respectively. GS was positively correlated with serum albumin and urine creatinine levels (r = 0.136 and 0.177, both p < 0.001). AMM was also positively correlated with serum albumin and urine creatinine levels (r = 0.078 and 0.091, both p < 0.001). In the multivariate regression model, for every 1 g/dL increase in serum albumin level, there was a 1.9 and 1.7-kg increase in GS for men and women (p < 0.05 and p < 0.01), respectively. The final model for predicting GS included age, albumin, BUN, and UPCR (urine creatinine for women) which presented a variance of 22.1% and 13.8%, respectively.
Conclusion
Proper dietary nutritional intake and maintaining renal function are key elements for preventing frailty among elder population in Taiwan.
Summary
A considerable proportion of stroke survivors are prescribed with proton pump inhibitors (PPIs). Our study indicated that PPI use is associated with an increased risk of osteoporosis, hip ...fracture, and vertebral fracture in stroke patients. The risk tends to increase as the cumulative doses of PPIs increase.
Introduction
A considerable proportion of stroke survivors are prescribed with proton pump inhibitors (PPIs). Our study investigated the association between PPI use and the risk of osteoporosis and fracture among stroke survivors.
Methods
A population-based propensity-matched retrospective cohort study was conducted using the National Health Insurance Research Database in Taiwan. Patients diagnosed with a new stroke between 2000 and 2012 were identified. After propensity score matching, 10,596 patients were enrolled, and 5298 patients were each assigned to the PPI user and non-user groups. Hazard ratios (HRs) were calculated for the risk of osteoporosis, hip fracture, and vertebral fractures according to PPI use or non-use. Sensitivity analyses were conducted to evaluate the dose effects of PPI.
Results
PPI use after stroke was associated with an increased risk of osteoporosis, hip fracture, or vertebral fracture, with an adjusted HR (aHR) of 1.28 (
P
< 0.001). The aHRs were also significant for each outcome: osteoporosis, 1.26 (
P
< 0.001); hip fracture, 1.18 (
P
= 0.048); vertebral fracture, 1.33 (
P
< 0.001). A pattern of dose effect was identified. For any event (osteoporosis/hip fracture/vertebral fracture), the aHR for PPI use of 1–90, 91–365, and > 365 cDDDs was 1.22 (
P
< 0.001), 1.27 (
P
< 0.001), and 1.66 (
P
< 0.001), respectively. For each outcome, the highest dose was associated with the highest risk, with aHR of 1.79 (
P
< 0.001), 1.41 (
P
= 0.039), and 1.82 (
P
< 0.001) for osteoporosis, hip fracture, and vertebral fracture, respectively. Age- and sex-stratified analyses revealed similar patterns.
Conclusions
PPI use is associated with an increased risk of osteoporosis, hip fracture, and vertebral fracture in stroke patients.
Although copper is essential for plant growth and development and plays an important role in many physiological processes, excess copper, resulting from industrial development and population ...expansion in the recent decades, leads to environmental pollution and has been a cause of wide concern for the adverse effects on photosynthesis, metabolism and growth of plants.
The growth properties (e.g. fresh weight, root length, height), photosynthetic properties (e.g. gas exchange, chlorophyll a fluorescence, chlorophyll content) and the physiological index (e.g. activity of antioxidant enzymes and osmotic regulators) of Eichhornia crassipes were assessed under various Cu2+ concentrations in hydroponic experiments.
The growth of E. crassipes was negatively affected by Cu2+ treatments, especially at higher Cu2+ concentrations; the Cu2+ treatments resulted in decreased photosynthesis because of a decrease in leaf chlorophyll content and damage to PSII functions, except the oxygen‐evolving complex. The physiological tolerance of E. crassipes to Cu2+ relies on osmotic regulation, anti‐lipid peroxidation and improved antioxidant properties.
The results indicate that E. crassipes could be considered as a phytoremediation agent for Cu2+ pollution in aquatic environments. However, the benefit of E. crassipes for Cu2+ removal in a highly polluted aquatic environment will be limited, but it will be effective in remediating sites with low pollution (≤5 mg·l−1). The present results could provide not only a basis for understanding the effects of pollutants on photosynthesis in plants under heavy metal stress but also provide a basis for choosing plants for phytoremediation.
The photosynthetic rate and growth of E. crassipes is greatly affected by Cu2+ in aquatic cultivation, and the negative effect of Cu2+ on E. crassipes is dose‐dependent, but E. crassipes might adapt to moderate Cu2+ pollution (≤ 5 mg·L‐1) through osmotic regulation, anti‐lipid peroxidation, and the improvement of its antioxidant properties.
Staphylococcus aureus may cause infections in humans from mild skin disorders to lethal pneumonia. Rapid and accurate monitoring of viable S. aureus is essential to characterize human exposure. This ...study evaluated quantitative PCR (qPCR) with propidium monoazide (PMA) to quantify S. aureus. The results showed comparable S. aureus counts between exclusively live cells and mixtures of live/dead cells by qPCR with 1.5 or 2.3 μg/mL PMA (P>.05), illustrating the ability of PMA‐qPCR to detect DNA exclusively from viable cells. Moreover, qPCR with 1.5 or 2.3 μg/mL PMA performed optimally with linearity over 103‐108 CFU/mL (R2≥0.9), whereas qPCR with 10, 23 or 46 μg/mL PMA significantly underestimated viable counts. Staphylococcus aureus and total viable bacteria were further determined with PMA‐qPCR (1.5 μg/mL) from 48 samples from a public library and two university dormitories and four from outside. Viable bacteria averaged 1.9×104 cells/m3, and S. aureus were detected in 22 (42%) samples with a mean of 4.4×103 cells/m3. The number of S. aureus and viable bacteria were positively correlated (r=.61, P<.005), and percentages of S. aureus relative to viable bacteria averaged 12‐44%. The results of field samples suggest that PMA‐qPCR can be used to quantify viable S. aureus cells.
Soil metal contamination leads to a decrease in a yield of crops and is a threat to human health. In the present study, the properties (
i.e.
, photosynthetic pigments, gas-exchange parameters, ...chlorophyll fluorescence, biomass, leaf area, leaf mass per area) of three green vegetables (
i.e.
,
Brassica chinensis
,
Chrysanthemum coronarium
,
Brassica alboglabra
) grown under various Cu treatments 0, 200, 400, and 600 mg(Cu) kg
–1
were measured and analysed. The results showed that soil Cu contamination resulted in the damage of photosynthetic pigments, negative effects on gas exchange, and hampered growth of all three vegetables. However, it did not significantly influence PSII functions of the three vegetables. It indicates that soil Cu contamination negatively affected photosynthesis particularly due to stomatal factors, but not due to the damage of photosynthetic apparatus.
Abstract
Photocatalytic formation of hydrocarbons using solar energy via artificial photosynthesis is a highly desirable renewable-energy source for replacing conventional fossil fuels. Using an
l
...-cysteine-based hydrothermal process, here we synthesize a carbon-doped SnS
2
(SnS
2
-C) metal dichalcogenide nanostructure, which exhibits a highly active and selective photocatalytic conversion of CO
2
to hydrocarbons under visible-light. The interstitial carbon doping induced microstrain in the SnS
2
lattice, resulting in different photophysical properties as compared with undoped SnS
2
. This SnS
2
-C photocatalyst significantly enhances the CO
2
reduction activity under visible light, attaining a photochemical quantum efficiency of above 0.7%. The SnS
2
-C photocatalyst represents an important contribution towards high quantum efficiency artificial photosynthesis based on gas phase photocatalytic CO
2
reduction under visible light, where the in situ carbon-doped SnS
2
nanostructure improves the stability and the light harvesting and charge separation efficiency, and significantly enhances the photocatalytic activity.
A 28 GHz 5-bit switch-type phase shifter (STPS) using 0.18 μm CMOS technology is presented for 5G mobile communication applications. Utilising a process variation insensitive transmission line-based ...bridged T-type topology for 11.25°, 22.5°, 45°, 90° 1-bit phase shifters and high-pass/low-pass network switched-path-type topology for 180° 1-bit phase shifter, the 5-bit STPS achieves ultra-low root mean square (RMS) phase error of 1.7° and low RMS amplitude error of 0.59 dB at 28 GHz with intrinsic digital phase-control mechanism. The measured insertion loss of all 32 states is 15 ± 1.5 dB at 28 GHz with zero dc consumption.
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