Publications by authors named "Nana Luo"

21 Publications

  • Page 1 of 1

An Interaction-Based Bayesian Network Framework for Surgical Workflow Segmentation.

Int J Environ Res Public Health 2021 06 13;18(12). Epub 2021 Jun 13.

Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan.

Recognizing and segmenting surgical workflow is important for assessing surgical skills as well as hospital effectiveness, and plays a crucial role in maintaining and improving surgical and healthcare systems. Most evidence supporting this remains signal-, video-, and/or image-based. Furthermore, casual evidence of the interaction between surgical staff remains challenging to gather and is largely absent. Here, we collected the real-time movement data of the surgical staff during a neurosurgery to explore cooperation networks among different surgical roles, namely surgeon, assistant nurse, scrub nurse, and anesthetist, and to segment surgical workflows to further assess surgical effectiveness. We installed a zone position system (ZPS) in an operating room (OR) to effectively record high-frequency high-resolution movements of all surgical staff. Measuring individual interactions in a closed, small area is difficult, and surgical workflow classification has uncertainties associated with the surgical staff in terms of their varied training and operation skills, patients in terms of their initial states and biological differences, and surgical procedures in terms of their complexities. We proposed an interaction-based framework to recognize the surgical workflow and integrated a Bayesian network (BN) to solve the uncertainty issues. Our results suggest that the proposed BN method demonstrates good performance with a high accuracy of 70%. Furthermore, it semantically explains the interaction and cooperation among surgical staff.
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http://dx.doi.org/10.3390/ijerph18126401DOI Listing
June 2021

Accurate Tumor Segmentation via Octave Convolution Neural Network.

Front Med (Lausanne) 2021 19;8:653913. Epub 2021 May 19.

The State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, China.

Three-dimensional (3D) liver tumor segmentation from Computed Tomography (CT) images is a prerequisite for computer-aided diagnosis, treatment planning, and monitoring of liver cancer. Despite many years of research, 3D liver tumor segmentation remains a challenging task. In this paper, we propose an effective and efficient method for tumor segmentation in liver CT images using encoder-decoder based octave convolution networks. Compared with other convolution networks utilizing standard convolution for feature extraction, the proposed method utilizes octave convolutions for learning multiple-spatial-frequency features, thus can better capture tumors with varying sizes and shapes. The proposed network takes advantage of a fully convolutional architecture which performs efficient end-to-end learning and inference. More importantly, we introduce a deep supervision mechanism during the learning process to combat potential optimization difficulties, and thus the model can acquire a much faster convergence rate and more powerful discrimination capability. Finally, we integrate octave convolutions into the encoder-decoder architecture of UNet, which can generate high resolution tumor segmentation in one single forward feeding without post-processing steps. Both architectures are trained on a subset of the LiTS (Liver Tumor Segmentation) Challenge. The proposed approach is shown to significantly outperform other networks in terms of various accuracy measures and processing speed.
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http://dx.doi.org/10.3389/fmed.2021.653913DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8169966PMC
May 2021

New global aerosol fine-mode fraction data over land derived from MODIS satellite retrievals.

Environ Pollut 2021 May 8;276:116707. Epub 2021 Feb 8.

Department of Atmospheric and Oceanic Science and ESSIC, University of Maryland, College Park, MD, 20740, USA. Electronic address:

The space-borne measured fine-mode aerosol optical depth (fAOD) is a gross index of column-integrated anthropogenic particulate pollutants, especially over the populated land. The fAOD is the product of the AOD and the fine-mode fraction (FMF). While there exist numerous global AOD products derived from many different satellite sensors, there have been much fewer, if any, global FMF products with a quality good enough to understand their spatiotemporal variations. This is key to understanding the global distribution and spatiotemporal variations of air pollutants, as well as their impacts on global environmental and climate changes. Modifying our newly developed retrieval algorithm to the latest global-scale Moderate Resolution Imaging Spectroradiometer (MODIS) aerosol product (Collection 6.1), a global 10-year FMF product is generated and analyzed here. We first validate the product through comparisons with the FMF derived from Aerosol Robotic Network (AERONET) measurements. Among our 169,313 samples, the satellite-derived FMFs agreed with the AERONET spectral deconvolution algorithm (SDA)-retrieved FMFs with a root-mean-square error (RMSE) of 0.22. Analyzed using this new product are the global patterns and interannual and seasonal variations of the FMF over land. In general, the FMF is large (>0.80) over Mexico, Myanmar, Laos, southern China, and Africa and less than 0.5 in the Sahelian and Sudanian zones of northern Africa. Seasonally, higher FMF values occur in summer and autumn. The linear trend in the satellite-derived and AERONET FMFs for different countries was explored. The upward trend in the FMFs was particularly strong over Australia since 2008. This study provides a new global view of changes in FMFs using a new satellite product that could help improve our understanding of air pollution around the world.
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http://dx.doi.org/10.1016/j.envpol.2021.116707DOI Listing
May 2021

New interpretable deep learning model to monitor real-time PM concentrations from satellite data.

Environ Int 2020 11 10;144:106060. Epub 2020 Sep 10.

Department of Atmospheric and Oceanic Sciences and ESSIC, University of Maryland, College Park, MD, USA. Electronic address:

Particulate matter with a mass concentration of particles with a diameter less than 2.5 μm (PM) is a key air quality parameter. A real-time knowledge of PM is highly valuable for lowering the risk of detrimental impacts on human health. To achieve this goal, we developed a new deep learning model-EntityDenseNet to retrieve ground-level PM concentrations from Himawari-8, a geostationary satellite providing high temporal resolution data. In contrast to the traditional machine learning model, the new model has the capability to automatically extract PM spatio-temporal characteristics. Validation across mainland China demonstrates that hourly, daily and monthly PM retrievals contain the root-mean-square errors of 26.85, 25.3, and 15.34 μg/m, respectively. In addition to a higher accuracy achievement when compared with various machine learning inversion methods (backpropagation neural network, extreme gradient boosting, light gradient boosting machine, and random forest), EntityDenseNet can "peek inside the black box" to extract the spatio-temporal features of PM. This model can show, for example, that PM levels in the coastal city of Tianjin were more influenced by air from Hebei than Beijing. Further, EntityDenseNet can still extract the seasonal characteristics that demonstrate that PM is more closely related within three month groups over mainland China: (1) December, January and February, (2) March, April and May, (3) July, August and September, even without meteorological information. EntityDenseNet has the ability to obtain high temporal resolution satellite-based PM data over China in real-time. This could act as an important tool to improve our understanding of PM spatio-temporal features.
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http://dx.doi.org/10.1016/j.envint.2020.106060DOI Listing
November 2020

In vivo immunological response of exposure to PEGylated graphene oxide via intraperitoneal injection.

J Mater Chem B 2020 08;8(31):6845-6856

State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P. R. China.

Polyethylene glycol functionalization is believed to have the capacity of endowing nanomaterials with stealth characteristics, which can diminish the arrest by macrophages and adverse immunological response. However, our previous study provided evidences that polyethylene glycol-functionalized graphene oxide (GOP) stimulated a strong immunological response to macrophages despite non-internalization in vitro, raising safety concerns and potential immunostimulation use of GOP. In light of this finding, we herein systematically study the in vivo immunological response upon the exposure to GOP via intraperitoneal injection. Taking cytokines production, cell types in the peritoneal fluid, biochemical index, hematology and histopathology as in vivo indicators, we demonstrate that GOP still remains the stealth-but-activating capacity on macrophages in a time and dose-dependent manner. Specifically, the immune response can be significantly elevated after a single high-dose injection, indicating that GOP can be a new candidate adjuvant for immunotherapy. For multiple low dose injections, the immune response is gentle, temporary, and tolerable, which manifests the biocompatibility of GOP in general drug delivery. The above results can thus provide guidance for safe and rational use of GOP for various biomedical applications.
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http://dx.doi.org/10.1039/d0tb00499eDOI Listing
August 2020

Short and medium-chain chlorinated paraffins in serum from residents aged from 50 to 84 in Jinan, China: Occurrence, composition and association with hematologic parameters.

Sci Total Environ 2020 Aug 19;728:137998. Epub 2020 Apr 19.

School of Environmental Science and Engineering, Shandong University, Binhai Road 72, Qingdao, 266237, China. Electronic address:

Human exposure to chlorinated paraffins (CPs) has been expected and assessed by external pathways considering their pervasive environmental occurrence. However, the deficiency of external exposure assessment in characterizing human burden is unavoidable. In addition, the associations between health outcomes and CP contents in human biospecimen are rarely assessed. In this study, we reported the occurrence and homologue profiles of short-chain chlorinated paraffins (SCCPs) and medium-chain chlorinated paraffins (MCCPs) in serum samples from 145 residents aged from 50 to 84 in Jinan, Shandong Province of China using quadrupole time-of-flight high-resolution mass spectrometry coupled with atmospheric pressure chemical ionization source operated in negative ion mode (APCI-qTOF-HRMS). The associations between serum CP concentrations and hematologic parameters were further analyzed by linear regression. We identified high level of ∑SCCPs (median = 107 ng/g wet weight, ww; 13,800 ng/g lipid, lw), ∑MCCPs (median = 134 ng/g ww; 15,200 ng/g lw) and elevated ∑MCCPs/∑SCCPs (median = 1.12) in serum of the studied population. C-CPs and C-CPs were the most abundant SCCP and MCCP groups, respectively. While the predominant chlorine homologues among SCCPs and MCCPs were Cl-CPs. ∑SCCPs, ∑MCCPs, ∑MCCPs/∑SCCPs and the homologue patterns presented no significant variance among age, sex and BMI groups. Further explorations suggested that perturbation of hematologic homeostasis could be induced by CP exposure in a sex-specific way, reflected by significant negative associations of serum SCCP and MCCP concentrations in lipid weight basis with sex-specific hematologic parameters. This study suffered from some limitations and should be interpreted with caution. However, the CP burdens of residents in China and the subsequent health risks must be underscored.
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http://dx.doi.org/10.1016/j.scitotenv.2020.137998DOI Listing
August 2020

TCOF1 pathogenic variants identified by Whole-exome sequencing in Chinese Treacher Collins syndrome families and hearing rehabilitation effect.

Orphanet J Rare Dis 2019 07 15;14(1):178. Epub 2019 Jul 15.

Department of Otolaryngology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.

Background: Treacher Collins syndrome (TCS, OMIM 154500) is an autosomal disorder of craniofacial development with an incidence rate of 1/50,000 live births. Although TCOF1, POLR1D, and POLR1C, have been identified as the pathogenic genes for about 90% TCS patients, the pathogenic variants of about 8-11% cases remain unknown. The object of this study is to describe the molecular basis of 14 clinically diagnosed TCS patients from four families using Whole-exome sequencing (WES) followed by Sanger sequencing confirmation, and to analyze the effect of bone conduction hearing rehabilitation in TCS patients with bilateral conductive hearing loss.

Results: Four previously unreported heterozygous pathogenic variants (c.3047-2A > G, c.2478 + 5G > A, c.489delC, c.648delC) were identified in the TCOF1 gene, one in each of the four families. Sanger sequencing in family members confirmed co-segregation of the identified TCOF1 variants with the phenotype. The mean pure-tone threshold improvements measured 3 months after hearing intervention were 28.8 dB for soft-band BAHA, 36.6 ± 2.0 dB for Ponto implantation, and 27.5 dB SPL for Bonebridge implantation. The mean speech discrimination improvements measured 3 months after hearing intervention in a sound field with a presentation level of 65 dB SPL were 44%, 51.25 ± 5.06, and 58%, respectively. All six patients undergoing hearing rehabilitation in this study got a satisfied hearing improvement.

Conclusions: WES combined with Sanger sequencing enables the molecular diagnosis of TCS and may detect other unknown causative genes. Bone conduction hearing rehabilitation may be an optimal option for TCS patients with bilateral conductive hearing loss.
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http://dx.doi.org/10.1186/s13023-019-1136-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6631538PMC
July 2019

Characteristics of atmospheric fungi in particle growth events along with new particle formation in the central North China Plain.

Sci Total Environ 2019 Sep 21;683:389-398. Epub 2019 May 21.

State Key Laboratory of Remote Sensing Science, College of Global Change and Earth System Science, Beijing Normal University, Beijing 100875, China. Electronic address:

The importance of fungi as cloud condensation nuclei (CCN) and ice-forming nuclei (IN) has been recognized for some researches. Particle growth along with new particle formation (NPF) play a joint role in modulating the CCN number concentration. Although fungi can accelerate the coalescence by large particles, the specific contribution and characteristics of atmospheric fungi for particle growth, especially during NPF events, is poorly understood. In this study, aerosol size distribution data and air samples were collected at Xingtai, a suburban site in the central North China Plain, from 1 May to 1 June 2016. Using DNA sequence-based methods, atmospheric fungal communities were identified and quantified. Significant differences in fungal communities between particle growth events along with new particle formation (PGE-NPF) and non-PGE-NPF events are found, especially for the Ascomycota and Basidiomycota phyla, and the Dothideomycetes, Saccharomycetes, and Tremellomycetes classes. At the genus level, five fungal communities were significantly different under PGE-NPF and non-PGE-NPF conditions, i.e., the Cladosporium, Capnodiales, Mrakia, Saccharomycetales and Trichocomaceae genera. The air mass source not only had an impact on NPF and the particle growth process, but also on the characteristics of the fungal communities. The fungal genus communities of Cladosporium, Capnodiales, Trichocomaceae, Mrakia, and Saccharomycetales may contribute to NPF and the particle growth process.
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http://dx.doi.org/10.1016/j.scitotenv.2019.05.299DOI Listing
September 2019

Short-chain chlorinated paraffins in soil, sediment, and seawater in the intertidal zone of Shandong Peninsula, China: Distribution and composition.

Chemosphere 2019 Apr 21;220:452-458. Epub 2018 Dec 21.

Environmental Research Institute, Shandong University, Binhai Road 72, Qingdao, 266237, China. Electronic address:

Short-chain chlorinated paraffins (SCCPs) are components of chlorinated paraffins (CPs) with high persistence, bioaccumulation potential, and toxicity, and SCCPs have been listed on Stockholm Convention as persistent organic pollutants. In this work, we investigated the distribution and homologue group patterns of SCCPs in the intertidal zone of the Shandong Peninsula, which is surrounded by the Bohai Sea (BS) and Yellow Sea (YS). Total SCCP concentrations (ΣSCCPs) in the samples from the sites along the coast of BS were 64.14-452.9 ng/g (mean = 181.0 ng/g), which were higher than those of the YS (17.59-155.5 ng/g, mean = 108.5 ng/g). ΣSCCPs were generally higher in intertidal sediments than in coastal soils along the BS, which could be ascribed to local industrial emissions through river runoff and mid-estuarine maximum phenomenon that resulted from seawater intrusion. In contrast, the opposite trend was observed along the YS. The contribution of shorter chain (C) and lower chlorinated (Cl) SCCP congeners was higher when the sampling sites were more proximal to the sea than heavier ones because of their greater potential for long-range transportation. Similar homologue group patterns were observed in the intertidal zone of Shandong, thus indicating a uniform use of commercial CP mixtures. High SCCP concentrations and similar homologue group patterns as those of the STP effluent were observed in seawater samples, thus suggesting that massive insufficiently purified or nonpurified industrial effluents were discharged into the BS.
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http://dx.doi.org/10.1016/j.chemosphere.2018.12.063DOI Listing
April 2019

Exploration of Antigen Induced CaCO Nanoparticles for Therapeutic Vaccine.

Small 2018 04 22;14(14):e1704272. Epub 2018 Feb 22.

State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, P. R. China.

Therapeutic vaccines possess particular advantages and show promising potential to combat burdening diseases, such as acquired immunodeficiency syndrome, hepatitis, and even cancers. An efficient therapeutic vaccine would strengthen the immune system and eventually eliminate target cells through cytotoxic T lymphocytes (CTLs). Unfortunately, insufficient efficacy in triggering such an adaptive immune response is a problem that remains unsolved. To achieve efficient cellular immunity, antigen-presenting cells must capture and further cross-present disease-associated antigens to CD8 T cells via major histocompatibility complex I molecules. Here, a biomimetic strategy is developed to fabricate hierarchical [email protected] nanoparticles ([email protected], ≈500 nm) under the templating effect of antigen OVA. Taking advantage of the unique physicochemical properties of crystalline vaterite, cluster structure, and high loading, [email protected] can efficiently ferry cargo antigen to dendritic cells and blast lysosomes for antigen escape to the cytoplasm. In addition, the first evidence that the physical stress from generated CO induces autophagy through the LC3/Beclin 1 pathways is presented. These outcomes cooperatively promote antigen cross-presentation, elicit CD8 T cell proliferation, ignite a potent and specific CTL response, and finally achieve prominent tumor therapy effects.
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http://dx.doi.org/10.1002/smll.201704272DOI Listing
April 2018

Early re-staging and molecular subtype shift surveillance of locally recurrent or metastatic breast cancer: A new PET/CT integrated precise algorithm.

Cancer Lett 2018 04 11;418:221-229. Epub 2018 Jan 11.

Department of Nuclear Medicine & Minnan PET Center, Xiamen Cancer Hospital, The First Affiliated Hospital of Xiamen University, Xiamen, China. Electronic address:

Recurrent breast cancer poses considerable diagnostic and therapeutic challenges for clinic. Clinical suspicion of recurrence must be first confirmed by imaging studies. Then re-biopsy of suspected recurrence and metastasis in patients with breast cancer is recommended in the practice guidelines of the National Comprehensive Cancer Network (NCCN) and European Society for Medical Oncology (ESMO) to confirm whether the molecular subtype changes. It may change the individual treatment plan directly. Our research provided an integrated algorithm for locally recurrent or distant metastatic breast cancer, including early relapse detection and subsequently a new practical PET/CT imaging guide biopsy approach for surveilling molecular subtype shifts of the recurrent breast cancer. In our results, F-FDG PET/CT appears to be more sensitive and accurate than conventional imaging technologies in early detecting locally recurrent or metastatic breast cancer. PET/CT-guided percutaneous FDG-avid target biopsies offers a new integrated precise re-biopsy algorithm for pathologic confirm and surveillance of molecular subtype shifts of the recurrent breast cancer. The precise algorithm for breast cancer recurrence and metastasis can be established in one stop, opening a window of opportunity for breast cancer patients to improve precise individual therapy and prolong survival.
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http://dx.doi.org/10.1016/j.canlet.2018.01.019DOI Listing
April 2018

Biomimetically Engineered Demi-Bacteria Potentiate Vaccination against Cancer.

Adv Sci (Weinh) 2017 10 15;4(10):1700083. Epub 2017 Jun 15.

State Key Laboratory of Biochemical Engineering Institute of Process Engineering Chinese Academy of Sciences 1 North 2nd Street Zhongguancun, Haidian District Beijing 100190 P. R. China.

Failure in enhancing antigen immunogenicity has limited the development of cancer vaccine. Inspired by effective immune responses toward microorganisms, demi-bacteria (DB) from are engineered as carriers for cancer vaccines. The explored hydrothermal treatment enables the to preserve optimal pathogen morphology with intrinsic mannose receptor agonist. Meanwhile, the treated can be further endowed with ideal hollow/porous structure for efficient accommodation of antigen and adjuvant, such as CpG. Therefore, this optimal engineered nanoarchitecture allows multiple immunostimulatory elements integrate in a pattern closely resembling that of bacterial pathogens. Such pathogen mimicry greatly enhances antigen uptake and cross-presentation, resulting in stronger immune activation suitable for cancer vaccines. Indeed, DB-based biomimetic vaccination in mice induces synergistic cellular and humoral immune responses, achieving potent therapeutic and preventive effects against cancer. Application of microorganism-sourced materials thus presents new opportunities for potent cancer therapy.
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http://dx.doi.org/10.1002/advs.201700083DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5644226PMC
October 2017

PEGylated graphene oxide elicits strong immunological responses despite surface passivation.

Nat Commun 2017 02 24;8:14537. Epub 2017 Feb 24.

State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China.

Engineered nanomaterials promise to transform medicine at the bio-nano interface. However, it is important to elucidate how synthetic nanomaterials interact with critical biological systems before such products can be safely utilized in humans. Past evidence suggests that polyethylene glycol-functionalized (PEGylated) nanomaterials are largely biocompatible and elicit less dramatic immune responses than their pristine counterparts. We here report results that contradict these findings. We find that PEGylated graphene oxide nanosheets (nGO-PEGs) stimulate potent cytokine responses in peritoneal macrophages, despite not being internalized. Atomistic molecular dynamics simulations support a mechanism by which nGO-PEGs preferentially adsorb onto and/or partially insert into cell membranes, thereby amplifying interactions with stimulatory surface receptors. Further experiments demonstrate that nGO-PEG indeed provokes cytokine secretion by enhancing integrin β-related signalling pathways. The present results inform that surface passivation does not always prevent immunological reactions to 2D nanomaterials but also suggest applications for PEGylated nanomaterials wherein immune stimulation is desired.
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http://dx.doi.org/10.1038/ncomms14537DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5333105PMC
February 2017

Low molecular weight glutenin subunit gene Glu-B3h confers superior dough strength and breadmaking quality in wheat (Triticum aestivum L.).

Sci Rep 2016 06 7;6:27182. Epub 2016 Jun 7.

College of Life Science, Capital Normal University, Beijing 100048, China.

Low molecular weight glutenin subunit is one of the important quality elements in wheat (Triticum aestivum L.). Although considerable allelic variation has been identified, the functional properties of individual alleles at Glu-3 loci are less studied. In this work, we performed the first comprehensive study on the molecular characteristics and functional properties of the Glu-B3h gene using the wheat cultivar CB037B and its Glu-B3 deletion line CB037C. The results showed that the Glu-B3h deletion had no significant effects on plant morphological or yield traits, but resulted in a clear reduction in protein body number and size and main quality parameters, including inferior mixing property, dough strength, loaf volume, and score. Molecular characterization showed that the Glu-B3h gene consists of 1179 bp, and its encoded B-subunit has a longer repetitive domain and an increased number of α-helices, as well as higher expression, which could contribute to superior flour quality. The SNP-based allele-specific PCR markers designed for the Glu-B3h gene were developed and validated with bread wheat holding various alleles at Glu-B3 locus, which could effectively distinguish the Glu-B3h gene from others at the Glu-B3 locus, and have potential applications for wheat quality improvement through marker-assisted selection.
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http://dx.doi.org/10.1038/srep27182DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4895167PMC
June 2016

GIS-based multielement source analysis of dustfall in Beijing: A study of 40 major and trace elements.

Chemosphere 2016 Jun 8;152:123-31. Epub 2016 Mar 8.

College of Resource Environment and Tourism, Capital Normal University, Beijing, China. Electronic address:

Dust, as an important carrier of inorganic and organic pollutants, daily exposes to human without any protection. It affects our health adversely, especially its chemical elements and ions. In this research, we investigated the chemical characteristics of dustfall in Beijing, specifically in terms of 40 major and trace elements, and presented semi-quantitative evaluations of the relative local and remote contributions. In total, 58 samples were collected in Beijing and nearby cities during 2013-2014 "the winter heating period". Using multiple statistical methods and GIS techniques, we obtained the relative similarities among certain elements and identified their pollution sources (from local or nearby cities). And more interestingly, the relative contributions of nearby cities can be calculated by the Hysplit4 backward-trajectory model. In addition, the correlation analysis for the 40 elements in dust and soil indicated that traffic restricted interchange between them; the city center, with the heaviest traffic, had the most significant influence. Finally, the resulting source apportionment was examined and modified using land use data and terrain information. We hope it can provide a strong basis for the environmental protection and risk assessment.
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http://dx.doi.org/10.1016/j.chemosphere.2016.02.099DOI Listing
June 2016

Molecular characterization and evolutionary origins of farinin genes in Brachypodium distachyon L.

J Appl Genet 2016 Aug 30;57(3):287-303. Epub 2015 Oct 30.

College of Life Science, Capital Normal University, Beijing, 100048, China.

Farinins are one of the oldest members of the gluten family in wheat and Aegilops species, and they influence dough properties. Here, we performed the first detailed molecular genetic study on farinin genes in Brachypodium distachyon L., the model species for Triticum aestivum. A total of 51 b-type farinin genes were cloned and characterized, including 27 functional and 24 non-functional pseudogenes from 14 different B. distachyon accessions. All genes were highly similar to those previously reported from wheat and Aegilops species. The identification of deduced amino acid sequences showed that b-type farinins across Triticeae genomes could be classified as b1-, b2-, b3-, and b4-type farinins; however, B. distachyon had only b3- and b4-type farinins. Real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) revealed that farinin genes are transcribed into mRNA in B. distachyon at much lower levels than in Triticeae, despite the presence of cis-acting elements in promoter regions. Phylogenetic analysis suggested that Brachypodium farinins may have closer relationships with common wheat and further confirmed four different types of b-type farinins in Triticeae and Brachypodium genomes, corresponding to b1, b2, b3 (group 1), and b4 (group 2). A putative evolutionary origin model of farinin genes in Brachypodium, Triticum, and the related species suggests that all b-type farinins diverged from their common ancestor ~3.2 million years ago (MYA). The b3 and b4 types could be considered older in the farinin family. The results explain the loss of b1- and b2-type farinin alleles in Brachypodium.
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http://dx.doi.org/10.1007/s13353-015-0316-3DOI Listing
August 2016

Exploration of graphene oxide as an intelligent platform for cancer vaccines.

Nanoscale 2015 Dec 30;7(47):19949-57. Epub 2015 Sep 30.

National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China.

We explored an intelligent vaccine system via facile approaches using both experimental and theoretical techniques based on the two-dimensional graphene oxide (GO). Without extra addition of bio/chemical stimulators, the microsized GO imparted various immune activation tactics to improve the antigen immunogenicity. A high antigen adsorption was acquired, and the mechanism was revealed to be a combination of electrostatic, hydrophobic, and π-π stacking interactions. The "folding GO" acted as a cytokine self-producer and antigen reservoir and showed a particular autophagy, which efficiently promoted the activation of antigen presenting cells (APCs) and subsequent antigen cross-presentation. Such a "One but All" modality thus induced a high level of anti-tumor responses in a programmable way and resulted in efficient tumor regression in vivo. This work may shed light on the potential use of a new dimensional nano-platform in the development of high-performance cancer vaccines.
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http://dx.doi.org/10.1039/c5nr04986eDOI Listing
December 2015

Surface-engineered graphene navigate divergent biological outcomes toward macrophages.

ACS Appl Mater Interfaces 2015 Mar 26;7(9):5239-47. Epub 2015 Feb 26.

National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences , Beijing, 100190, PR China.

The "nano-bio" interface profoundly shapes the interaction between cells and nanomaterials and can even decide a cell's fate. As a nascent two-dimensional material, graphene has many unique attributes and is proposed to be a promising candidate for biomedical applications. Thus, for graphene-based applications, it is necessary to clarify how the graphene surface navigates biological outcomes when encountering "janitorial" cells (macrophages). For this purpose, we synthesized nanographene oxide (nGO) and engineered the surface with polyethylene glycol (PEG), bovine serum albumin (BSA), and poly(ether imide) (PEI). In contrast to pristine nGO, decoration with PEG and BSA hindered endocytosis and improved their benignancy toward macrophages. Contrarily, nGO-PEI commenced with favorable endocytosis but then suffered stagnation due to compromised macrophage viability. To unravel the underlying mechanisms regulating these diverse macrophage fates, we built a stepwise analysis. Compared to the others, nGO-PEI tended to interact electrostatically with mitochondria after their cellular internalization. Such an unexpected encounter disrupted the normal potential and integrity of mitochondria and then elicited an alteration in reactive oxygen species and cytochrome c. These responses further initiated the activation of the caspase family and ultimately dictated cells to undergo apoptosis. The advances described above will complement our knowledge of graphene functionality and serve to guide its application in biotechnological applications.
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http://dx.doi.org/10.1021/am5084607DOI Listing
March 2015

Mapping dustfall distribution in urban areas using remote sensing and ground spectral data.

Sci Total Environ 2015 Feb 26;506-507:604-12. Epub 2014 Nov 26.

Department of Land Surveying and Geo-Informatics, The Hong Kong Polytechnic University, Hong Kong; College of Resource Environment and Tourism, Capital Normal University, Beijing, China.

The aim of this study was to utilize remote sensing and ground-based spectral data to assess dustfall distribution in urban areas. The ground-based spectral data denoted that dust has a significant impact on spectral features. Dusty leaves have an obviously lower reflectance than clean leaves in the near-infrared bands (780-1,300 nm). The correlation analysis between dustfall weight and spectral reflectance showed that spectroscopy in the 350-2,500-nm region produced useful dust information and could assist in dust weight estimation. A back propagation (BP) neutral network model was generated using spectral response functions and integrated remote sensing data to assess dustfall weight in the city of Beijing. Compared with actual dustfall weight, validation of the results showed a satisfactory accuracy with a lower root mean square error (RMSE) of 3.6g/m(2). The derived dustfall distribution in Beijing indicated that dustfall was easily accumulated and increased in the south of the city. In addition, our results showed that construction sites and low-rise buildings with inappropriate land use were two main sources of dust pollution. This study offers a low-cost and effective method for investigating detailed dustfall in an urban environment. Environmental authorities may use this method for deriving dustfall distribution maps and pinpointing the sources of pollutants in urban areas.
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http://dx.doi.org/10.1016/j.scitotenv.2014.11.036DOI Listing
February 2015

Molecular characterization and expression profiling of the protein disulfide isomerase gene family in Brachypodium distachyon L.

PLoS One 2014 18;9(4):e94704. Epub 2014 Apr 18.

College of Life Science, Capital Normal University, Beijing, China.

Protein disulfide isomerases (PDI) are involved in catalyzing protein disulfide bonding and isomerization in the endoplasmic reticulum and functions as a chaperone to inhibit the aggregation of misfolded proteins. Brachypodium distachyon is a widely used model plant for temperate grass species such as wheat and barley. In this work, we report the first molecular characterization, phylogenies, and expression profiles of PDI and PDI-like (PDIL) genes in B. distachyon in different tissues under various abiotic stresses. Eleven PDI and PDIL genes in the B. distachyon genome by in silico identification were evenly distributed across all five chromosomes. The plant PDI family has three conserved motifs that are involved in catalyzing protein disulfide bonding and isomerization, but a different exon/intron structural organization showed a high degree of structural differentiation. Two pairs of genes (BdPDIL4-1 and BdPDIL4-2; BdPDIL7-1 and BdPDIL7-2) contained segmental duplications, indicating each pair originated from one progenitor. Promoter analysis showed that Brachypodium PDI family members contained important cis-acting regulatory elements involved in seed storage protein synthesis and diverse stress response. All Brachypodium PDI genes investigated were ubiquitously expressed in different organs, but differentiation in expression levels among different genes and organs was clear. BdPDIL1-1 and BdPDIL5-1 were expressed abundantly in developing grains, suggesting that they have important roles in synthesis and accumulation of seed storage proteins. Diverse treatments (drought, salt, ABA, and H2O2) induced up- and down-regulated expression of Brachypodium PDI genes in seedling leaves. Interestingly, BdPDIL1-1 displayed significantly up-regulated expression following all abiotic stress treatments, indicating that it could be involved in multiple stress responses. Our results provide new insights into the structural and functional characteristics of the plant PDI gene family.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0094704PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3991636PMC
January 2015

The role of the lateral dimension of graphene oxide in the regulation of cellular responses.

Biomaterials 2012 Jun 28;33(16):4013-21. Epub 2012 Feb 28.

National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China.

The nanomaterial graphene oxide (GO) has attracted explosive interests in various areas. However, its performance in biological environments is still largely unknown, particularly with regard to cellular response to GO. Here we separated the GO sheets in different size and systematically investigated size effect of the GO in response to different types of cells. In terms of abilities to internalize GO, enormous discrepancies were observed in the six cell types, with only two phagocytes were found to be capable of internalizing GO. The 2 μm and 350 nm GO greatly differed in lateral dimensions, but equally contributed to the uptake amount in macrophages. Similar amounts of antibody opsonization and active Fcγ receptor-mediated phagocytosis were demonstrated the cause of this behavior. In comparison with the nanosized GO, the GO in micro-size showed divergent intracellular locations and induced much stronger inflammation responses. Present study provided insight into selective internalization, size-independent uptake, and several other biological behaviors undergone by GO. These findings might help build necessary knowledge for potential incorporation of the unique two-dimensional nanomaterial as a biomedical tool, and for avoiding potential hazards.
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http://dx.doi.org/10.1016/j.biomaterials.2012.02.021DOI Listing
June 2012