| 1. |
- Sampson, Joshua N., et al.
(author)
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Analysis of Heritability and Shared Heritability Based on Genome-Wide Association Studies for 13 Cancer Types
- 2015
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In: Journal of the National Cancer Institute. - : Oxford University Press (OUP). - 0027-8874 .- 1460-2105. ; 107:12
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Journal article (peer-reviewed)abstract
- Background: Studies of related individuals have consistently demonstrated notable familial aggregation of cancer. We aim to estimate the heritability and genetic correlation attributable to the additive effects of common single-nucleotide polymorphisms (SNPs) for cancer at 13 anatomical sites. Methods: Between 2007 and 2014, the US National Cancer Institute has generated data from genome-wide association studies (GWAS) for 49 492 cancer case patients and 34 131 control patients. We apply novel mixed model methodology (GCTA) to this GWAS data to estimate the heritability of individual cancers, as well as the proportion of heritability attributable to cigarette smoking in smoking-related cancers, and the genetic correlation between pairs of cancers. Results: GWAS heritability was statistically significant at nearly all sites, with the estimates of array-based heritability, h(l)(2), on the liability threshold (LT) scale ranging from 0.05 to 0.38. Estimating the combined heritability of multiple smoking characteristics, we calculate that at least 24% (95% confidence interval [CI] = 14% to 37%) and 7% (95% CI = 4% to 11%) of the heritability for lung and bladder cancer, respectively, can be attributed to genetic determinants of smoking. Most pairs of cancers studied did not show evidence of strong genetic correlation. We found only four pairs of cancers with marginally statistically significant correlations, specifically kidney and testes (rho = 0.73, SE = 0.28), diffuse large B-cell lymphoma (DLBCL) and pediatric osteosarcoma (rho = 0.53, SE = 0.21), DLBCL and chronic lymphocytic leukemia (CLL) (rho = 0.51, SE = 0.18), and bladder and lung (rho = 0.35, SE = 0.14). Correlation analysis also indicates that the genetic architecture of lung cancer differs between a smoking population of European ancestry and a nonsmoking Asian population, allowing for the possibility that the genetic etiology for the same disease can vary by population and environmental exposures. Conclusion: Our results provide important insights into the genetic architecture of cancers and suggest new avenues for investigation.
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| 2. |
- Abbafati, Cristiana, et al.
(author)
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- 2020
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Journal article (peer-reviewed)
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| 3. |
- Dou, Shihan, et al.
(author)
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Decorrelate Irrelevant, Purify Relevant : Overcome Textual Spurious Correlations from a Feature Perspective
- 2022
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Conference paper (peer-reviewed)abstract
- Natural language understanding (NLU) models tend to rely on spurious correlations (i.e., dataset bias) to achieve high performance on in-distribution datasets but poor performance on out-of-distribution ones. Most of the existing debiasing methods often identify and weaken these samples with biased features (i.e., superficial surface features that cause such spurious correlations). However, down-weighting these samples obstructs the model in learning from the non-biased parts of these samples. To tackle this challenge, in this paper, we propose to eliminate spurious correlations in a fine-grained manner from a feature space perspective. Specifically, we introduce Random Fourier Features and weighted re-sampling to decorrelate the dependencies between features to mitigate spurious correlations. After obtaining decorrelated features, we further design a mutual-information-based method to purify them, which forces the model to learn features that are more relevant to tasks. Extensive experiments on two well-studied NLU tasks demonstrate that our method is superior to other comparative approaches.
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| 4. |
- Chen, Peilin, et al.
(author)
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Fabrication of a silver nanoparticle-coated collagen membrane with anti-bacterial and anti-inflammatory activities for guided bone regeneration
- 2018
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In: Biomedical materials. - 1748-6041. ; 13:6
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Journal article (peer-reviewed)abstract
- Alveolar bone loss is a common problem that affects dental implant placement. A barrier between the bone substitute and gingiva that can prevent fibro-tissue ingrowth, bacterial infection and induce bone formation is a key factor in improving the success of alveolar ridge reconstruction. This study aims to develop a bioactive collagen barrier material for guided bone regeneration, that is coupled with anti-bacterial and anti-inflammatory properties. We have evaluated two silver coating methods and found controllable and precise coating achieved by sonication compared with sputtering. The optimized AgNP-coated collagen membrane exhibited excellent anti-bacterial effects against Staphylococcus aureus (S. aureus) and Pseudomonas aeruginosa (P. aeruginosa) with limited cellular toxicity. It also displayed effective anti-inflammatory effects by reducing the expression and release of inflammatory cytokines including IL-6 and TNF-alpha. Additionally, AgNP-coated collagen membranes were able to induce osteogenic differentiation of mesenchymal stem cells that guide bone regeneration. These findings demonstrate the potential application of AgNP-coated collagen membranes to prevent infection after bone graft introduction in alveolar ridge reconstruction.
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| 5. |
- Fan, Zheyong, et al.
(author)
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GPUMD: A package for constructing accurate machine-learned potentials and performing highly efficient atomistic simulations
- 2022
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In: Journal of Chemical Physics. - : AIP Publishing. - 1089-7690 .- 0021-9606. ; 157:11
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Journal article (peer-reviewed)abstract
- We present our latest advancements of machine-learned potentials (MLPs) based on the neuroevolution potential (NEP) framework introduced in Fan et al. [Phys. Rev. B 104, 104309 (2021)] and their implementation in the open-source package gpumd. We increase the accuracy of NEP models both by improving the radial functions in the atomic-environment descriptor using a linear combination of Chebyshev basis functions and by extending the angular descriptor with some four-body and five-body contributions as in the atomic cluster expansion approach. We also detail our efficient implementation of the NEP approach in graphics processing units as well as our workflow for the construction of NEP models and demonstrate their application in large-scale atomistic simulations. By comparing to state-of-the-art MLPs, we show that the NEP approach not only achieves above-average accuracy but also is far more computationally efficient. These results demonstrate that the gpumd package is a promising tool for solving challenging problems requiring highly accurate, large-scale atomistic simulations. To enable the construction of MLPs using a minimal training set, we propose an active-learning scheme based on the latent space of a pre-trained NEP model. Finally, we introduce three separate Python packages, viz., gpyumd, calorine, and pynep, that enable the integration of gpumd into Python workflows.
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| 6. |
- Feigin, Valery L., et al.
(author)
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Global, regional, and national burden of stroke and its risk factors, 1990-2019 : a systematic analysis for the Global Burden of Disease Study 2019
- 2021
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In: Lancet Neurology. - : Elsevier. - 1474-4422 .- 1474-4465. ; 20:10, s. 795-820
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Journal article (peer-reviewed)abstract
- Background Regularly updated data on stroke and its pathological types, including data on their incidence, prevalence, mortality, disability, risk factors, and epidemiological trends, are important for evidence-based stroke care planning and resource allocation. The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) aims to provide a standardised and comprehensive measurement of these metrics at global, regional, and national levels. Methods We applied GBD 2019 analytical tools to calculate stroke incidence, prevalence, mortality, disability-adjusted life-years (DALYs), and the population attributable fraction (PAF) of DALYs (with corresponding 95% uncertainty intervals [UIs]) associated with 19 risk factors, for 204 countries and territories from 1990 to 2019. These estimates were provided for ischaemic stroke, intracerebral haemorrhage, subarachnoid haemorrhage, and all strokes combined, and stratified by sex, age group, and World Bank country income level. Findings In 2019, there were 12.2 million (95% UI 11.0-13.6) incident cases of stroke, 101 million (93.2-111) prevalent cases of stroke, 143 million (133-153) DALYs due to stroke, and 6.55 million (6.00-7.02) deaths from stroke. Globally, stroke remained the second-leading cause of death (11.6% [10.8-12.2] of total deaths) and the third-leading cause of death and disability combined (5.7% [5.1-6.2] of total DALYs) in 2019. From 1990 to 2019, the absolute number of incident strokes increased by 70.0% (67.0-73.0), prevalent strokes increased by 85.0% (83.0-88.0), deaths from stroke increased by 43.0% (31.0-55.0), and DALYs due to stroke increased by 32.0% (22.0-42.0). During the same period, age-standardised rates of stroke incidence decreased by 17.0% (15.0-18.0), mortality decreased by 36.0% (31.0-42.0), prevalence decreased by 6.0% (5.0-7.0), and DALYs decreased by 36.0% (31.0-42.0). However, among people younger than 70 years, prevalence rates increased by 22.0% (21.0-24.0) and incidence rates increased by 15.0% (12.0-18.0). In 2019, the age-standardised stroke-related mortality rate was 3.6 (3.5-3.8) times higher in the World Bank low-income group than in the World Bank high-income group, and the age-standardised stroke-related DALY rate was 3.7 (3.5-3.9) times higher in the low-income group than the high-income group. Ischaemic stroke constituted 62.4% of all incident strokes in 2019 (7.63 million [6.57-8.96]), while intracerebral haemorrhage constituted 27.9% (3.41 million [2.97-3.91]) and subarachnoid haemorrhage constituted 9.7% (1.18 million [1.01-1.39]). In 2019, the five leading risk factors for stroke were high systolic blood pressure (contributing to 79.6 million [67.7-90.8] DALYs or 55.5% [48.2-62.0] of total stroke DALYs), high body-mass index (34.9 million [22.3-48.6] DALYs or 24.3% [15.7-33.2]), high fasting plasma glucose (28.9 million [19.8-41.5] DALYs or 20.2% [13.8-29.1]), ambient particulate matter pollution (28.7 million [23.4-33.4] DALYs or 20.1% [16.6-23.0]), and smoking (25.3 million [22.6-28.2] DALYs or 17.6% [16.4-19.0]). Interpretation The annual number of strokes and deaths due to stroke increased substantially from 1990 to 2019, despite substantial reductions in age-standardised rates, particularly among people older than 70 years. The highest age-standardised stroke-related mortality and DALY rates were in the World Bank low-income group. The fastest-growing risk factor for stroke between 1990 and 2019 was high body-mass index. Without urgent implementation of effective primary prevention strategies, the stroke burden will probably continue to grow across the world, particularly in low-income countries.
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| 7. |
- He, Wei, et al.
(author)
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China's Terrestrial Carbon Sink Over 2010–2015 Constrained by Satellite Observations of Atmospheric CO2 and Land Surface Variables
- 2022
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In: Journal of Geophysical Research: Biogeosciences. - 2169-8953. ; 127:2
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Journal article (peer-reviewed)abstract
- The magnitude and distribution of China's terrestrial carbon sink remain uncertain due to insufficient constraints at large scales, whereby satellite data offer great potential for reducing the uncertainty. Here, we present two carbon sink estimates for China constrained either by satellite CO2 column concentrations (XCO2) within the Global Carbon Assimilation System or by remotely sensed soil moisture and Fraction of Absorbed Photosynthetically Active Radiation (FAPAR) in addition to in situ CO2 observations within the Carbon Cycle Data Assimilation System. They point to a moderate size of carbon sinks of 0.34 ± 0.14 (mean ± unc.) and 0.43 ± 0.09 PgC/yr during 2010–2015, which are supported by an inventory-based estimate for forest and soil carbon sink (0.26 PgC/yr) and fall in the range of contemporary ensemble atmospheric inversions (0.25–0.48 PgC/yr). They also agree reasonably well on interannual variations, which reflect the carbon sink anomalies induced by regional droughts in southwest China. Furthermore, their spatial distributions are broadly consistent that of the forest inventory-based estimate, indicating that the largest carbon sinks locate in central and eastern China. Their estimates for forest carbon sink coincide fairly well with the inventory-based estimate across different regions, especially when aggregated to the north and south of China. Although enhanced recently by afforestation, China's carbon sink was also significantly weakened by regional droughts, which were often not fully represented in previous in situ CO2-based inversions due to insufficient observations. Our results suggest that satellite-based atmospheric CO2 and land surface observations are vital in characterizing terrestrial net carbon fluxes at regional scales.
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| 8. |
- Hu, Yutao, et al.
(author)
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TreeCen : Building Tree Graph for Scalable Semantic Code Clone Detection
- 2022
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In: iWOAR 2022. - New York, NY, USA : Association for Computing Machinery (ACM).
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Conference paper (peer-reviewed)abstract
- Code clone detection is an important research problem that has attracted wide attention in software engineering. Many methods have been proposed for detecting code clone, among which text-based and token-based approaches are scalable but lack consideration of code semantics, thus resulting in the inability to detect semantic code clones. Methods based on intermediate representations of codes can solve the problem of semantic code clone detection. However, graph-based methods are not practicable due to code compilation, and existing tree-based approaches are limited by the scale of trees for scalable code clone detection. In this paper, we propose TreeCen, a scalable tree-based code clone detector, which satisfies scalability while detecting semantic clones effectively. Given the source code of a method, we first extract its abstract syntax tree (AST) based on static analysis and transform it into a simple graph representation (i.e., tree graph) according to the node type, rather than using traditional heavyweight tree matching. We then treat the tree graph as a social network and adopt centrality analysis on each node to maintain the tree details. By this, the original complex tree can be converted into a 72-dimensional vector while containing comprehensive structural information of the AST. Finally, these vectors are fed into a machine learning model to train a detector and use it to find code clones. We conduct comparative evaluations on effectiveness and scalability. The experimental results show that TreeCen maintains the best performance of the other six state-of-the-art methods (i.e., SourcererCC, RtvNN, DeepSim, SCDetector, Deckard, and ASTNN) with F1 scores of 0.99 and 0.95 on BigCloneBench and Google Code Jam datasets, respectively. In terms of scalability, TreeCen is about 79 times faster than the other state-of-the-art tree-based semantic code clone detector (ASTNN), about 13 times faster than the fastest graph-based approach (SCDetector), and even about 22 times faster than the one-time trained token-based detector (RtvNN).
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| 9. |
- Li, Suyang, et al.
(author)
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Highly homogeneous bimetallic core-shell Au@Ag nanoparticles with embedded internal standard fabrication using a microreactor for reliable quantitative SERS detection
- 2023
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In: Materials Chemistry Frontiers. - : Royal Society of Chemistry (RSC). - 2052-1537. ; 7:6, s. 1100-1109
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Journal article (peer-reviewed)abstract
- Bimetallic gold core-silver shell (Au@Ag) surface-enhanced Raman scattering tags draw broad interest in the fields of biological and environmental analyses. Herein, an efficient hybrid microfluidic chip was designed to prepare uniform Au@Ag core-shell nanoparticles, and DTNB was used as the internal standard tag molecule to prepare Au@DTNB@Ag for SERS detection. Homogeneous core-shell nanoparticles with a particle size of 90 nm were prepared by mixing a silver precursor and a gold core in a microfluidic chip. The relative standard deviation (RSD) of the particle size distribution was close to 10%, and the detection limit of 4-MBA was as low as 10-10 M. In order to solve the influence of SERS signal fluctuation, a uniform Au@DTNB@Ag core-molecule-shell structure was synthesized in a microfluidic chip, and the characteristic peak of the analyte was corrected by the relative intensity of the DTNB characteristic peak (1335 cm−1). The experimental results showed that the SERS detection was achieved with high reproducibility, and the SERS peak intensity had a good linear correlation with the concentration. The homogeneous SERS substrate prepared using a microfluidic chip has potential for sensitive and reliable detection of environmental chemical contaminants.
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| 10. |
- Liu, Huizeng, et al.
(author)
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Estimating ultraviolet reflectance from visible bands in ocean colour remote sensing
- 2021
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In: Remote Sensing of Environment. - : Elsevier BV. - 0034-4257 .- 1879-0704. ; 258
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Journal article (peer-reviewed)abstract
- In recent years, ultraviolet (UV) bands have received increasing attention from the ocean colour remote sensing community, as they may contribute to improving atmospheric correction and inherent optical properties (IOPs) retrieval. However, most ocean colour satellite sensors do not have UV bands, and the accurate retrieval of UV remote sensing reflectance (Rrs) from UV satellite data is still a challenge. In order to address this problem, this study proposes a hybrid approach for estimating UV Rrs from the visible bands. The approach was implemented with two popular ocean colour satellite sensors, i.e. GCOM-C SGLI and Sentinel-3 OLCI. In situ Rrs collected globally and simulated Rrs spectra were used to develop UV Rrs retrieval models, and UV Rrs values at 360, 380 and 400 nm were estimated from visible Rrs spectra. The performances of the established models were evaluated using in situ Rrs and satellite data, and applied to a semi-analytical algorithm for IOPs retrieval. The results showed that: (i) UV Rrs retrieval models had low uncertainties with mean absolute percentage differences (MAPD) less than 5%; (ii) the model assessment with in situ Rrs showed high accuracy (r = 0.92–1.00 and MAPD = 1.11%–10.95%) in both clear open ocean and optically complex waters; (iii) the model assessment with satellite data indicated that model-estimated UV Rrs were more consistent with in situ values than satellite-derived UV Rrs; and (iv) model-estimated UV Rrs may improve the decomposition accuracy of absorption coefficients in semi-analytical IOPs algorithm. Thus, the proposed method has great potentials for reconstructing UV Rrs data and improving IOPs retrieval for historical satellite sensors, and might also be useful for UV-based atmospheric correction algorithms.
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| 11. |
- Radamson, Henry H., et al.
(author)
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State of the Art and Future Perspectives in Advanced CMOS Technology
- 2020
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In: Nanomaterials. - : MDPI AG. - 2079-4991. ; 10:8
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Research review (peer-reviewed)abstract
- The international technology roadmap of semiconductors (ITRS) is approaching the historical end point and we observe that the semiconductor industry is driving complementary metal oxide semiconductor (CMOS) further towards unknown zones. Today's transistors with 3D structure and integrated advanced strain engineering differ radically from the original planar 2D ones due to the scaling down of the gate and source/drain regions according to Moore's law. This article presents a review of new architectures, simulation methods, and process technology for nano-scale transistors on the approach to the end of ITRS technology. The discussions cover innovative methods, challenges and difficulties in device processing, as well as new metrology techniques that may appear in the near future.
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| 12. |
- Xu, Weidong, et al.
(author)
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Iodomethane-Mediated Organometal Halide Perovskite with Record Photoluminescence Lifetime
- 2016
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In: ACS Applied Materials and Interfaces. - : AMER CHEMICAL SOC. - 1944-8244 .- 1944-8252. ; 8:35, s. 23181-23189
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Journal article (peer-reviewed)abstract
- Organometallic lead halide perovskites are excellent light harvesters for high-efficiency photovoltaic devices. However, as the key component in these devices, a perovskite thin film with good morphology and minimal trap states is still difficult to obtain. Herein we show that by incorporating a low boiling point alkyl halide such as iodomethane (CH3I) into the precursor solution, a perovskite (CH3NH3PbI3-xClx) film with improved grain size and orientation can be easily achieved. More importantly, these films exhibit a significantly reduced amount of trap states. Record photoluminescence lifetimes of more than 4 mu s are achieved; these lifetimes are significantly longer than that of pristine CH3NH3PbI3-xClx films. Planar heterojunction solar cells incorporating these CH3I-mediated perovskites have demonstrated a dramatically increased power conversion efficiency compared to the ones using pristine CH3NH3PbI3-xClx. Photoluminescence, transient absorption, and microwave detected photoconductivity measurements all provide consistent evidence that CH3I addition increases the number of excitons generated and their diffusion length, both of which assist efficient carrier transport in the photovoltaic device. The simple incorporation of alkyl halide to enhance perovskite surface passivation introduces an important direction for future progress on high efficiency perovskite optoelectronic devices.
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| 13. |
- Zhang, Yongchao, et al.
(author)
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Online High Resolution Stochastic Radiation Radar Imaging using Sparse Covariance Fitting
- 2019
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In: IGARSS 2019 : 2019 IEEE International Geoscience and Remote Sensing Symposium - 2019 IEEE International Geoscience and Remote Sensing Symposium. - 9781538691557 - 9781538691540 ; , s. 8562-8565
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Conference paper (peer-reviewed)abstract
- Stochastic radiation radar (SRR) systems allow for the forming of radar images by transmitting stochastic signals to form the stochastic radiation field and thereby increase the target observation information to achieve high resolution imaging. In this paper, we examine the use of the online SParse Iterative Covariance-based Estimation (SPICE) algorithm to suppress the noise and improve the operational efficiency. The SPICE algorithm is based on a weighted covariance fitting criterion, and has recently been generalized to allow for an improved reconstruction performance. The used online extension can take advantage of echoes non-correlation along time, allowing for updating the imaging result through successive echo sequences. The simulation results verify the superior performance of the resulting estimator as compared to other recent SRR imaging methods.
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