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result(s) for
"Sun, Tianyi"
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Statistics or biology: the zero-inflation controversy about scRNA-seq data
by
Li, Jingyi Jessica
,
Song, Dongyuan
,
Sun, Tianyi
in
Animal Genetics and Genomics
,
Benchmarking
,
Bioinformatics
2022
Researchers view vast zeros in single-cell RNA-seq data differently: some regard zeros as biological signals representing no or low gene expression, while others regard zeros as missing data to be corrected. To help address the controversy, here we discuss the sources of biological and non-biological zeros; introduce five mechanisms of adding non-biological zeros in computational benchmarking; evaluate the impacts of non-biological zeros on data analysis; benchmark three input data types: observed counts, imputed counts, and binarized counts; discuss the open questions regarding non-biological zeros; and advocate the importance of transparent analysis.
Journal Article
scDesign2: a transparent simulator that generates high-fidelity single-cell gene expression count data with gene correlations captured
by
Li, Jingyi Jessica
,
Li, Wei Vivian
,
Song, Dongyuan
in
Animal Genetics and Genomics
,
Animals
,
Bioinformatics
2021
A pressing challenge in single-cell transcriptomics is to benchmark experimental protocols and computational methods. A solution is to use computational simulators, but existing simulators cannot simultaneously achieve three goals: preserving genes, capturing gene correlations, and generating any number of cells with varying sequencing depths. To fill this gap, we propose scDesign2, a transparent simulator that achieves all three goals and generates high-fidelity synthetic data for multiple single-cell gene expression count-based technologies. In particular, scDesign2 is advantageous in its transparent use of probabilistic models and its ability to capture gene correlations via copulas.
Journal Article
Highly stretchable and transparent nanomesh electrodes made by grain boundary lithography
2014
Foldable photoelectronics and muscle-like transducers require highly stretchable and transparent electrical conductors. Some conducting oxides are transparent, but not stretchable. Carbon nanotube films, graphene sheets and metal-nanowire meshes can be both stretchable and transparent, but their electrical resistances increase steeply with strain <100%. Here we present highly stretchable and transparent Au nanomesh electrodes on elastomers made by grain boundary lithography. The change in sheet resistance of Au nanomeshes is modest with a one-time strain of ~160% (from ~21 Ω per square to ~67 Ω per square), or after 1,000 cycles at a strain of 50%. The good stretchability lies in two aspects: the stretched nanomesh undergoes instability and deflects out-of-plane, while the substrate stabilizes the rupture of Au wires, forming distributed slits. Larger ratio of mesh-size to wire-width also leads to better stretchability. The highly stretchable and transparent Au nanomesh electrodes are promising for applications in foldable photoelectronics and muscle-like transducers.
One of the key components in stretchable electronics is the electrical conductors, which need to show a low electrical resistance even when strained. Here, by using sacrificial grain boundaries as a fabrication template, Guo and colleagues fabricate highly transparent gold nanomesh electrodes with exceptionally high stretchability.
Journal Article
Path to net zero is critical to climate outcome
by
Ocko, Ilissa B.
,
Hamburg, Steven P.
,
Sturcken, Elizabeth
in
704/106/694/2786
,
704/106/694/682
,
Carbon dioxide
2021
Net zero greenhouse gas targets have become a central element for climate action. However, most company and government pledges focus on the year that net zero is reached, with limited awareness of how critical the emissions pathway is in determining the climate outcome in both the near- and long-term. Here we show that different pathways of carbon dioxide and methane—the most prominent long-lived and short-lived greenhouse gases, respectively—can lead to nearly 0.4 °C of warming difference in midcentury and potential overshoot of the 2 °C target, even if they technically reach global net zero greenhouse gas emissions in 2050. While all paths achieve the Paris Agreement temperature goals in the long-term, there is still a 0.2 °C difference by end-of-century. We find that early action to reduce both emissions of carbon dioxide and methane simultaneously leads to the best climate outcomes over all timescales. We therefore recommend that companies and countries supplement net zero targets with a two-basket set of interim milestones to ensure that early action is taken for both carbon dioxide and methane. A one-basket approach, such as the standard format for Nationally Determined Contributions, is not sufficient because it can lead to a delay in methane mitigation.
Journal Article
Role of Stochastic Atmospheric Forcing from the South and North Pacific in Tropical Pacific Decadal Variability
2019
Stochastic variability of internal atmospheric modes, known as teleconnection patterns, drives large-scale patterns of low-frequency SST variability in the extratropics. To investigate how the decadal component of this stochastically driven variability in the South and North Pacific affects the tropical Pacific and contributes to the observed basinwide pattern of decadal variability, a suite of climate model experiments was conducted. In these experiments, the models are forced with constant surface heat flux anomalies associated with the decadal component of the dominant atmospheric modes, particularly the Pacific–South American (PSA) and North Pacific Oscillation (NPO) patterns. Both the PSA and NPO modes induce basinwide SST anomalies in the tropical Pacific and beyond that resemble the observed interdecadal Pacific oscillation. The subtropical SST anomalies forced by the PSA and NPO modes propagate to the equatorial Pacific mainly through the wind–evaporation–SST feedback. This atmospheric bridge is stronger from the South Pacific than the North Pacific due to the northward displacement of the intertropical convergence zone and the associated northward advection of momentum anomalies. The equatorial ocean dynamics is also more strongly influenced by atmospheric circulation changes induced by the PSA mode than the NPO mode. In the PSA experiment, persistent and zonally coherent wind stress curl anomalies over the South Pacific affect the zonal mean depth of the equatorial thermocline and weaken the equatorial SST anomalies resulting from the atmospheric bridge. This oceanic adjustment serves as a delayed negative feedback and may be important for setting the time scales of tropical Pacific decadal variability.
Journal Article
The relationships between the campus built environment and walking activity
2024
Despite the gradual development of students’ sedentary habits and associated health problems, only a few studies have extensively and systematically measured campus built environments (CBE) and their impact on street walking activity. This study explores the association between CBEs and pedestrian volume (PV). Comprehensive questionnaires, field audits, and GIS were used to measure the CBE variables and PV of 892 street segments on eight Chinese campuses in Tianjin. We used negative binomial regression models without spatial autocorrelations to investigate the relationship between the CBEs and PV. The findings indicated that campus Walk Score, facility and residential land ratio, campus design qualities, sidewalk conditions, street amenities, and other streetscape features were positively associated with PV. This study presents implications for campus research and planning practices in designing a pedestrian-friendly, sustainable, and healthy campus.
Journal Article
Acting rapidly to deploy readily available methane mitigation measures by sector can immediately slow global warming
by
Oppenheimer, Michael
,
Mauzerall, Denise L
,
Hamburg, Steven P
in
Carbon dioxide
,
Carbon dioxide emissions
,
Climate action
2021
Methane mitigation is essential for addressing climate change, but the value of rapidly implementing available mitigation measures is not well understood. In this paper, we analyze the climate benefits of fast action to reduce methane emissions as compared to slower and delayed mitigation timelines. We find that the scale up and deployment of greatly underutilized but available mitigation measures will have significant near-term temperature benefits beyond that from slow or delayed action. Overall, strategies exist to cut global methane emissions from human activities in half within the next ten years and half of these strategies currently incur no net cost. Pursuing all mitigation measures now could slow the global-mean rate of near-term decadal warming by around 30%, avoid a quarter of a degree centigrade of additional global-mean warming by midcentury, and set ourselves on a path to avoid more than half a degree centigrade by end of century. On the other hand, slow implementation of these measures may result in an additional tenth of a degree of global-mean warming by midcentury and 5% faster warming rate (relative to fast action), and waiting to pursue these measures until midcentury may result in an additional two tenths of a degree centigrade by midcentury and 15% faster warming rate (relative to fast action). Slow or delayed methane action is viewed by many as reasonable given that current and on-the-horizon climate policies heavily emphasize actions that benefit the climate in the long-term, such as decarbonization and reaching net-zero emissions, whereas methane emitted over the next couple of decades will play a limited role in long-term warming. However, given that fast methane action can considerably limit climate damages in the near-term, it is urgent to scale up efforts and take advantage of this achievable and affordable opportunity as we simultaneously reduce carbon dioxide emissions.
Journal Article
Metallic nanostructures for light trapping in energy-harvesting devices
2014
Solar energy is abundant and environmentally friendly. Light trapping in solar-energy-harvesting devices or structures is of critical importance. This article reviews light trapping with metallic nanostructures for thin film solar cells and selective solar absorbers. The metallic nanostructures can either be used in reducing material thickness and device cost or in improving light absorbance and thereby improving conversion efficiency. The metallic nanostructures can contribute to light trapping by scattering and increasing the path length of light, by generating strong electromagnetic field in the active layer, or by multiple reflections/absorptions. We have also discussed the adverse effect of metallic nanostructures and how to solve these problems and take full advantage of the light-trapping effect.
Photovoltaics: light trapping
In recent years, researchers have demonstrated a number of new schemes for enhancing the absorption of light in solar cells. Chuan Fei Guo and colleagues from the University of Houston in the USA and National Center for Nanoscience and Technology of China in Beijing have now reviewed the use of metallic nanostructures for trapping light in photovoltaic devices. In particular, the presence of metallic nanoparticles in a solar cell or a solar absorber can aid light absorption by inducing strong, local field-enhancement effects or coupling to resonant plasmon modes. Such particles can also promote scattering and thus increase path lengths for light within the device. Solar cells that utilize this approach are either more efficient or substantially thinner than those that do not, thus reducing material costs and creating the opportunity for ultrathin, flexible devices.
Journal Article
Interaction effects of outdoor thermal comfort and air pollution
2025
Urban haze pollution is a major problem affecting outdoor environmental quality, thereby hindering the construction of ecological civilization and healthy urban development. The urban physical environment also affects the urban outdoor thermal environment. Both the thermal and air environment have important effects on the subjective comfort evaluations of people. In this study, four typical University Campus Green Spaces (UCGSs) in Xi’an, China, were selected to investigate the thermal and air environments in outdoor spaces. The adaptive thermal comfort due to the interaction between the outdoor thermal environment and air pollution was studied based on questionnaires and field measurements, and a strategy was developed for optimizing the thermal comfort of urban campus green space environments. The results showed that the influence of the thermal air quality environment on subjective comfort varied among different spaces. The influence of haze pollution on subjective comfort was greater in high and low-temperature environments, but less obvious in a moderate temperature environment. When the PM2.5 particle concentration was greater than 100 µg/m
3
, the evaluation of respiratory comfort was low in the high-temperature environment. The perception of air pollution was less sensitive in the thermal environment in covered road sections. Heat pollution and air pollution will affect human health to varying degrees. The outdoor thermal environment and patients with respiratory diseases are affected most by haze pollution.
Journal Article
The Preparation of Superhydrophobic Polylactic Acid Membrane with Adjustable Pore Size by Freeze Solidification Phase Separation Method for Oil–Water Separation
2023
An environmentally friendly pore size-controlled, superhydrophobic polylactic acid (PLA) membrane was successfully prepared by a simpler freeze solidification phase separation method (FSPS) and solution impregnation, which has application prospects in the field of oil–water separation. The pore size and structure of the membrane were adjusted by different solvent ratios and solution impregnation ratios. The PLA-FSPS membrane after solution impregnation (S-PLA-FSPS) had the characteristics of uniform pore size, superhydrophobicity and super lipophilicity, its surface roughness Ra was 338 nm, and the contact angle to water was 151°. The S-PLA-FSPS membrane was used for the oil–water separation. The membrane oil flux reached 16,084 L·m−2·h−1, and the water separation efficiency was 99.7%, which was much higher than that of other oil–water separation materials. In addition, the S-PLA-FSPS membrane could also be applied for the adsorption and removal of oil slicks and underwater heavy oil. The S-PLA-FSPS membrane has great application potential in the field of oil–water separation.
Journal Article