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Article ; Online: Large-Scale Glass-Transition Temperature Prediction with an Equivariant Neural Network for Screening Polymers.

Long, Zheng / Lu, Hongmei / Zhang, Zhimin

ACS omega

2024 Volume 9, Issue 5, Page(s) 5452–5462

Abstract: The practically infinite chemical and morphological space of polymers makes them pervasive with applications in materials science but challenges the rational discovery of new materials with favorable properties. Polymer informatics aims to accelerate ... ...

Abstract	The practically infinite chemical and morphological space of polymers makes them pervasive with applications in materials science but challenges the rational discovery of new materials with favorable properties. Polymer informatics aims to accelerate materials design through property prediction and large-scale virtual screening. In this study, a new method (Lieconv-Tg) has been developed to predict glass-transition temperature (Tg) values from repeating units of polymers based on Lieconv, which is equivariant with transformations from any specified Lie group. The introduction of equivariance allows the prediction of molecular properties from their 3D structures, independent of orientation and position. A total of 27,659 homopolymers with Tg values were collected from PolyInfo, and a standard data set containing 7166 polymers (named data set_Tg) was created for training a robust Lieconv-Tg model. Using the 3D coordinates as input, Lieconv-Tg performs better than Edge-Conditioned Convolution (ECC), and the mean absolute error (MAE) is significantly reduced by ∼6 from ∼30 to ∼24 on both the validation set and the test set, and the
Language	English
Publishing date	2024-01-26
Publishing country	United States
Document type	Journal Article
ISSN	2470-1343
ISSN (online)	2470-1343
DOI	10.1021/acsomega.3c06843
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Article ; Online: GCMSFormer: A Fully Automatic Method for the Resolution of Overlapping Peaks in Gas Chromatography-Mass Spectrometry.

Guo, Zixuan / Fan, Yingjie / Yu, Chuanxiu / Lu, Hongmei / Zhang, Zhimin

Analytical chemistry

2024 Volume 96, Issue 15, Page(s) 5878–5886

Abstract: Gas chromatography-mass spectrometry (GC-MS) is one of the most important instruments for analyzing volatile organic compounds. However, the complexity of real samples and the limitations of chromatographic separation capabilities lead to coeluting ... ...

Abstract	Gas chromatography-mass spectrometry (GC-MS) is one of the most important instruments for analyzing volatile organic compounds. However, the complexity of real samples and the limitations of chromatographic separation capabilities lead to coeluting compounds without ideal separation. In this study, a Transformer-based automatic resolution method (GCMSFormer) is proposed to resolve mass spectra from GC-MS peaks in an end-to-end manner, predicting the mass spectra of components directly from the raw overlapping peaks data. Furthermore, orthogonal projection resolution (OPR) was integrated into GCMSFormer to resolve minor components. The GCMSFormer model was trained, validated, and tested using 100,000 augmented data. It achieves 99.88% of the bilingual evaluation understudy (BLEU) value on the test set, significantly higher than the 97.68% BLEU value of the baseline sequence-to-sequence model long short-term memory (LSTM). GCMSFormer was also compared with two nondeep learning resolution tools (MZmine and AMDIS) and two deep learning resolution tools (PARAFAC2 with DL and MSHub/GNPS) on a real plant essential oil GC-MS data set. Their resolution results were compared on evaluation metrics, including the number of compounds resolved, mass spectral match score, correlation coefficient, explained variance, and resolution speed. The results demonstrate that GCMSFormer has better resolution performance, higher automation, and faster resolution speed. In summary, GCMSFormer is an end-to-end, fast, fully automatic, and accurate method for analyzing GC-MS data of complex samples.
Language	English
Publishing date	2024-04-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.3c05772
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Article: The influence of policy design on club good provisions: A study of for-profit shopping mall roof gardens in Shanghai

Lu, Hongmei / Ryan, Robert L.

Land use policy. 2022 Oct., v. 121

2022

Abstract: Greenspace provision in high-density metropolises is often constrained by land shortage; market-based tools show the potential to solve the problem. Privately-owned public greenspace is a type of club goods provided by private developers to club members ... ...

Abstract	Greenspace provision in high-density metropolises is often constrained by land shortage; market-based tools show the potential to solve the problem. Privately-owned public greenspace is a type of club goods provided by private developers to club members with non-rival but excludable beneﬁts. Club goods are for-profit, and their sustainability, or the long-term ability to deliver high-quality services, entails appropriate policy design. This paper explores how policy design influences club good’s sustainable provision, exemplified by the new developments of for-profit shopping-mall roof gardens in Shanghai, China. Such gardens established by developers to serve mall customers are club goods, providing ecosystem services and becoming significant compensation for urban greenspace shortage. Through field investigations and in-depth interviews, authors find that the current green-roof policy design increased roof gardens’ quantity but not quality and brought about gaps in legitimacy, profitability, and non-compliance. This research concludes that (1) general policy design can boost club good production; (2) more tailored policy design, including cross-department collaboration and tailored policymaking, are indispensable to improve clubs’ sustainability. This study suggests that policy designers take club good’s intrinsic characteristics into consideration and address the legitimacy, profitability, and compliance problems, which will enable market-based tools to be better utilized in public-goods provision.
Keywords	compliance ; ecosystems ; green roofs ; land policy ; profitability ; China
Language	English
Dates of publication	2022-10
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	852476-2
ISSN	0264-8377
ISSN	0264-8377
DOI	10.1016/j.landusepol.2022.106340
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Quantitative Mass Spectrometry Imaging with Liquid Microjunction Surface Sampling.

Wu, Qian / Lu, Hongmei

Methods in molecular biology (Clifton, N.J.)

2021 Volume 2437, Page(s) 181–194

Abstract: Mass spectrometry imaging (MSI) could provide chemical spatial distribution within a diverse range of samples, but absolute quantitation with those techniques is still challenging. Recent years, ambient liquid extraction-based MSI techniques, such as ... ...

Abstract	Mass spectrometry imaging (MSI) could provide chemical spatial distribution within a diverse range of samples, but absolute quantitation with those techniques is still challenging. Recent years, ambient liquid extraction-based MSI techniques, such as liquid microjunction surface sampling (LMJSS), have been largely developed and were found to be favorable to quantitation by directly doping standards in the extraction solvent. Here, we describe the detailed experimental protocols and the data processing methods for quantitative MSI with LMJSS. The new methods could have absolute quantitative MSI of both endogenous lipids and small metabolites from tissue samples.
MeSH term(s)	Diagnostic Imaging ; Lipids ; Mass Spectrometry ; Solvents
Chemical Substances	Lipids ; Solvents
Language	English
Publishing date	2021-12-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2030-4_13
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Article ; Online: Lewis Acidic Metal-Organic Framework Assisted Ambient Liquid Extraction Mass Spectrometry Imaging for Enhancing the Coverage of Poorly Ionizable Lipids in Brain Tissue.

Lv, Yuanxia / Zhao, Zhihao / Long, Zheng / Yu, Chuanxiu / Lu, Hongmei / Wu, Qian

Analytical chemistry

2024 Volume 96, Issue 3, Page(s) 1073–1083

Abstract: The spatial distribution of lipidomes in tissues is of great importance in studies of living processes, diseases, and therapies. Mass spectrometry imaging (MSI) has become a critical technique for spatial lipidomics. However, MSI of low-abundance or ... ...

Abstract	The spatial distribution of lipidomes in tissues is of great importance in studies of living processes, diseases, and therapies. Mass spectrometry imaging (MSI) has become a critical technique for spatial lipidomics. However, MSI of low-abundance or poorly ionizable lipids is still challenging because of the ion suppression from high-abundance lipids. Here, a metal-organic framework (MOF) Zr
MeSH term(s)	Metal-Organic Frameworks ; Mass Spectrometry/methods ; Phospholipids ; Diagnostic Imaging ; Brain ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
Chemical Substances	Metal-Organic Frameworks ; Phospholipids
Language	English
Publishing date	2024-01-11
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.3c03690
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Article ; Online: Photocatalytic degradation-based ambient mass spectrometry imaging for enhancing detection coverage of poorly-ionizable lipidomes.

Zhou, Yongchang / Wu, Qian / Zhao, Zhihao / Wang, Yang / Lu, Hongmei

Talanta

2023 Volume 270, Page(s) 125564

Abstract: Localization of lipidomes and tracking their spatial changes in tissues by mass spectrometry imaging (MSI) plays an important role in unveiling the mechanisms of living processes, diseases and therapeutic treatments. However, it is always challenging to ... ...

Abstract	Localization of lipidomes and tracking their spatial changes in tissues by mass spectrometry imaging (MSI) plays an important role in unveiling the mechanisms of living processes, diseases and therapeutic treatments. However, it is always challenging to achieve direct MSI of poorly-ionizable lipids, such as glycolipids and glycerolipids, due to the strong ion suppression and isobaric peaks interference from high-abundance phosphatidylcholines (PCs) in tissues. Here we developed a photocatalytic degradation-based ambient liquid extraction MSI method to largely enhance the detection coverage of poorly-ionizable lipids by rapid online removal of PCs in MSI. Phospholipids were found to be selectively photodegraded on TiO
MeSH term(s)	Lipidomics ; Mass Spectrometry/methods ; Diagnostic Imaging ; Glycolipids ; Ceramides ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
Chemical Substances	Glycolipids ; Ceramides
Language	English
Publishing date	2023-12-18
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1500969-5
ISSN	1873-3573 ; 0039-9140
ISSN (online)	1873-3573
ISSN	0039-9140
DOI	10.1016/j.talanta.2023.125564
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Article ; Online: Two cases of measles after vaccination with measles mumps and rubella combined live attenuated vaccine

SHEN Jinhua / HU Tajing / CHEN Wenhua / QIAN Jingxian / LU Hongmei

Shanghai yufang yixue, Vol 34, Iss 5, Pp 446-

2022 Volume 447

Abstract: Measles is an acute respiratory infectious disease caused by the measles virus. It is highly infectious and easy to occur in children. It causes many serious complications such as tracheitis， otitis media and pneumonia. Since the promotion of the measles ...

Abstract	Measles is an acute respiratory infectious disease caused by the measles virus. It is highly infectious and easy to occur in children. It causes many serious complications such as tracheitis， otitis media and pneumonia. Since the promotion of the measles vaccine in China， the measles epidemic has been effectively controlled. From June 1， 2020， the immunization procedure of measles-containing vaccine for children in Shanghai has been adjusted to one dose of measles， mumps and rubella combined live attenuated vaccine （MMR） at the age of 8 months， 18 months and 6 years. There is generally no local reaction after the injection of the MMR vaccine. A few individuals may have transient fever and scattered rash， which generally fade away by themselves. However， because it is a live vaccine， it may cause vaccine related diseases in extremely rare cases. This paper reports two cases of measles after vaccination with the MMR vaccine.
Keywords	measles ; measles，mumps and rubella combined live attenuated vaccine （mmr） ; measles igm antibody ; nucleotide sequencing of measles virus sample ; vaccine strain ; Medicine ; R
Subject code	630
Language	Chinese
Publishing date	2022-05-01T00:00:00Z
Publisher	Shanghai Preventive Medicine Association
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Monitoring of adverse reaction of Haemophilus influenzae type b vaccine in Songjiang District， Shanghai

SHEN Jinhua / GU Shikang / CHEN Wenhua / ZHU Qi / LU Hongmei

Shanghai yufang yixue, Vol 34, Iss 11, Pp 1129-

2022 Volume 1133

Abstract: ObjectiveTo determine the reporting rate of adverse reaction of Haemophilus influenzae type b （Hib） containing vaccine in Songjiang District from 2016 to 2020， so as to provide evidence for the inclusion of Hib vaccine in children's immunization planning ...

Abstract	ObjectiveTo determine the reporting rate of adverse reaction of Haemophilus influenzae type b （Hib） containing vaccine in Songjiang District from 2016 to 2020， so as to provide evidence for the inclusion of Hib vaccine in children's immunization planning and safety monitoring.MethodsThe adverse reaction data of Hib vaccination were collected through the Chinese Disease Prevention and Control Information System and presented by descriptive methods.ResultsFrom 2016 to 2020， the reporting rate of adverse reaction of various Hib-containing vaccines in Songjiang District was determined to be 747.76/105 doses， among which the rates of general reaction and abnormal reaction were 734.31/105 doses and 13.45/105 doses， respectively. The reporting rate of general reaction was significantly higher than that of abnormal reaction （χ2=1 400.18，P<0.001）. Moreover， the reporting rate of adverse reaction did not differ significantly by sex or registered residence， whereas it differed significantly by age groups （χ2=366.07，P<0.001）. Children ≥12 months old had the highest reporting rate， which was caused by higher rate of general reaction （χ2=360.48，P<0.001） compared with other age groups； in contrast， there was no difference in the reporting rate of abnormal reactions across age groups. The reporting rate of adverse reaction differed significantly across four Hib-containing vaccines （χ2=508.51，P<0.001）， among which the reporting rate of pentavalent vaccine was the highest， followed by tetravalent vaccine， and Hib vaccine and meningococcal HI vaccine. This difference was mainly caused by general reaction （χ2=499.19，P<0.001）. The reporting rate of booster Hib-containing vaccines was significantly higher than that of basic immunization （χ2=462.85，P<0.001）. Furthermore， the reporting rate differed between DTaP-Hib vaccine and DTaP-IPV-Hib vaccine by injection sites（χ2=13.63，P=0.001；χ2=78.48， P<0.001）； the reporting rate on the thigh was lower than that on the hip or upper arm. Among the 1 501 reported adverse ...
Keywords	hib vaccine ; meningococcal hi vaccine ; dtap-hib vaccine ; dtap-ipv-hib vaccine ; adverse reaction ; safety monitoring ; Medicine ; R
Subject code	660
Language	Chinese
Publishing date	2022-11-01T00:00:00Z
Publisher	Shanghai Preventive Medicine Association
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Epidemiological characteristics of varicella in Songjiang District， Shanghai from 2013 to 2021

ZHU Qi / QIAN Jingxian / SHEN Jinhua / CHEN Wenhua / SHEN Jingwen / LU Hongmei

Shanghai yufang yixue, Vol 35, Iss 7, Pp 639-

2023 Volume 643

Abstract: ObjectiveTo evaluate the effectiveness of the varicella vaccine immunization strategy in Shanghai， and to provide evidence for enhancing prevention and control measures by analyzing the incidence and trends of varicella in Songjiang District， Shanghai ... ...

Abstract	ObjectiveTo evaluate the effectiveness of the varicella vaccine immunization strategy in Shanghai， and to provide evidence for enhancing prevention and control measures by analyzing the incidence and trends of varicella in Songjiang District， Shanghai from 2013 to 2021.MethodsA descriptive analysis was conducted on 12 417 varicella cases reported in Songjiang District between 2013 and 2021. The epidemiological distribution of varicella cases was described， and the incidence rates were compared among different demographic variables， including registered residence， gender， age， and occupation.ResultsA total of 12 417 varicella cases were reported in Songjiang District from 2013 to 2021，with an average annual incidence of 77.03/105. The incidence of varicella showed an increasing trend from 2013 to 2017 （χ2trend=19.39， P<0.001）， followed by a subsequent decrease from 2017 to 2021（χ2trend=758.62， P<0.001）. Varicella cases demonstrated significant seasonal variation， with peak incidences occurring in April to May and November to January of the following year. The incidence rate among local residents was higher than that among non-local residents （χ2=2 935.58， P<0.001）. Most （38.59%） of the cases were students aged between 5 and 9 years old， accounting for 23.45% of the total cases. However， the age distribution of cases varied over the years （χ2=615.57， P<0.001）， and the incidence among children aged 5 to 9 years showed a declining trend since 2017.ConclusionThe overall incidence of varicella in Songjiang District exhibites a declining trend in recent years. Although varicella primarily affects children， there have notable changes in the age distribution. Adjustment of the immunization strategy for varicella vaccines in Shanghai effectively reduces the proportion of school-age subjects.
Keywords	varicella ; epidemiology ; analysis ; Medicine ; R
Language	Chinese
Publishing date	2023-07-01T00:00:00Z
Publisher	Shanghai Preventive Medicine Association
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Pulled Flowprobe for Ambient Liquid Extraction-Based High Spatial Resolution Mass Spectrometry Imaging with Enhanced Sensitivity and Stability

Zhao, Zhihao / Long, Zheng / Wang, Huabei / Wu, Qian / Wang, Yang / Lü, Hongmei

Analytical Chemistry. 2023 Nov. 08, v. 95, no. 46 p.16927-16935

2023

Abstract: Ambient liquid extraction techniques enable direct mass spectrometry imaging (MSI) under ambient conditions with minimal sample preparation. However, currently an integrated probe for ambient liquid extraction-based MSI with high spatial resolution, high ...

Abstract	Ambient liquid extraction techniques enable direct mass spectrometry imaging (MSI) under ambient conditions with minimal sample preparation. However, currently an integrated probe for ambient liquid extraction-based MSI with high spatial resolution, high sensitivity, and stability is still lacking. In this work, we developed a new integrated probe made of pulled coaxial capillaries, named pulled flowprobe, and compared it with the previously reported single-probe. Mass transfer kinetics in probes was first investigated. The extraction kinetic curves during probe sampling indicate a narrower and higher peak shape for the pulled flowprobe than single-probe. Computational fluid dynamics analysis reveals that in the pulled flowprobe flow velocities are lower in liquid microjunction and higher in the transferring channels, resulting in higher extraction efficiencies and reduced band diffusion compared with single-probe and other probes with a similar flow route. Results of ambient liquid extraction-based MSI of lipids in rat cerebrum show that signals of low-abundance lipids were 2–5 times higher via a pulled flowprobe than via a single-probe, and 26 more lipid species were detected on brain tissue via a pulled flowprobe than via a single-probe. The stability of MSI with the pulled flowprobe was found to be higher than that with single-probe (averaged relative standard deviation = 18% vs 80%) by imaging a lab-made uniform ink coating. Moreover, in the pulled flowprobe, no retraction of the inner capillary from outer capillary is optimal for both sensitivity and stability. The spatial resolution of the pulled flowprobe (30–40 μm) was measured to be higher than that of a comparable size single-probe by calculation with the “80–20” rule. Finally, the new pulled flowprobe was applied to high-resolution MSI of lipids in the hippocampus, and localization of several lipids to the specific cell layers in the hippocampus region was observed. Thus, this work provides an alternative easily fabricated sampling probe with enhanced sensitivity, stability, and spatial resolution, promoting the use of ambient liquid extraction-based MSI in biological and clinical research.
Keywords	analytical chemistry ; biomedical research ; cerebrum ; hippocampus ; lipids ; liquids ; mass spectrometry ; mass transfer ; rats ; standard deviation
Language	English
Dates of publication	2023-1108
Size	p. 16927-16935.
Publishing place	American Chemical Society
Document type	Article ; Online
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.3c03046
Database	NAL-Catalogue (AGRICOLA)

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