| 1. |
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| 2. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
-
Journal article (peer-reviewed)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 3. |
- Aad, G, et al.
(author)
-
- 2015
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swepub:Mat__t
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| 4. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
-
Research review (peer-reviewed)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 5. |
- Dong, Yi-Min, et al.
(author)
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Development and Validation of a Nomogram for Assessing Survival in Patients With COVID-19 Pneumonia
- 2021
-
In: Clinical Infectious Diseases. - : Oxford University Press. - 1058-4838 .- 1537-6591. ; 72:4, s. 652-660
-
Journal article (peer-reviewed)abstract
- Background. The outbreak of coronavirus disease 2019 (COVID-19) has spread worldwide and continues to threaten peoples' health as well as put pressure on the accessibility of medical systems. Early prediction of survival of hospitalized patients will help in the clinical management of COVID-19, but a prediction model that is reliable and valid is still lacking. Methods. We retrospectively enrolled 628 confirmed cases of COVID-19 using positive RT-PCR tests for SARS-CoV-2 in Tongji Hospital, Wuhan, China. These patients were randomly grouped into a training (60%) and a validation (40%) cohort. In the training cohort, LASSO regression analysis and multivariate Cox regression analysis were utilized to identify prognostic factors for in-hospital survival of patients with COVID-19. A nomogram based on the 3 variables was built for clinical use. AUCs, concordance indexes (C-index), and calibration curves were used to evaluate the efficiency of the nomogram in both training and validation cohorts. Results. Hypertension, higher neutrophil-to-lymphocyte ratio, and increased NT-proBNP values were found to be significantly associated with poorer prognosis in hospitalized patients with COVID-19. The 3 predictors were further used to build a prediction nomogram. The C-indexes of the nomogram in the training and validation cohorts were 0.901 and 0.892, respectively. The AUC in the training cohort was 0.922 for 14-day and 0.919 for 21-day probability of in-hospital survival, while in the validation cohort this was 0.922 and 0.881, respectively. Moreover, the calibration curve for 14- and 21-day survival also showed high coherence between the predicted and actual probability of survival. Conclusions. We built a predictive model and constructed a nomogram for predicting in-hospital survival of patients with COVID-19. This model has good performance and might be utilized clinically in management of COVID-19.
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| 6. |
- Dong, Yi-Min, et al.
(author)
-
Reply to Collins et al
- 2021
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In: Clinical Infectious Diseases. - : Oxford University Press. - 1058-4838 .- 1537-6591. ; 73:3, s. 558-559
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Journal article (other academic/artistic)
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| 7. |
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| 8. |
- Yang, Anning, et al.
(author)
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Homocysteine accelerates hepatocyte autophagy by upregulating TFEB via DNMT3b-mediated DNA hypomethylation
- 2023
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In: Acta Biochimica et Biophysica Sinica. - : China Science Publishing & Media Ltd.. - 1672-9145. ; 55:8, s. 1184-1192
-
Journal article (peer-reviewed)abstract
- Autophagy plays a critical role in the physiology and pathophysiology of hepatocytes. High level of homocysteine (Hcy) promotes autophagy in hepatocytes, but the underlying mechanism is still unknown. Here, we investigate the relationship between Hcy-induced autophagy level and the expression of nuclear transcription factor EB (TFEB). The results show that Hcy-induced autophagy level is mediated by upregulation of TFEB. Silencing of TFEB decreases the level of autophagy-related protein LC3BII/I and increases p62 expression level in hepatocytes after exposure to Hcy. Moreover, the effect of Hcy on the expression of TFEB is regulated by hypomethylation of the TFEB promoter catalyzed by DNA methyltransferase 3b (DNMT3b). In summary, this study shows that Hcy can activate autophagy by inhibiting DNMT3b-mediated DNA methylation and upregulating TFEB expression. These findings provide another new mechanism for Hcy-induced autophagy in hepatocytes.
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| 9. |
- Zhang, S. -N, et al.
(author)
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Introduction to the high energy cosmic-radiation detection (HERD) facility onboard China's future space station
- 2017
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In: Proceedings of Science. - : Sissa Medialab Srl.
-
Conference paper (peer-reviewed)abstract
- The High Energy cosmic-Radiation Detection (HERD) facility is one of several space astronomy payloads onboard China's Space Station, which is planned for operation starting around 2025 for about 10 years. The main scientific objectives of HERD are searching for signals of dark matter annihilation products, precise cosmic electron (plus positron) spectrum and anisotropy measurements up to 10 TeV, precise cosmic ray spectrum and composition measurements up to the knee energy, and high energy gamma-ray monitoring and survey. HERD is composed of a 3-D cubic calorimeter (CALO) surrounded by microstrip silicon trackers (STKs) from five sides except the bottom. CALO is made of about 7,500 cubes of LYSO crystals, corresponding to about 55 radiation lengths and 3 nuclear interaction lengths, respectively. The top STK microstrips of six X-Y layers are sandwiched with tungsten converters to make precise directional measurements of incoming electrons and gamma-rays. In the baseline design, each of the four side STKs is made of only three layers microstrips. All STKs will also be used for measuring the charge and incoming directions of cosmic rays, as well as identifying back scattered tracks. With this design, HERD can achieve the following performance: energy resolution of 1% for electrons and gamma-rays beyond 100 GeV and 20% for protons from 100 GeV to 1 PeV; electron/proton separation power better than 10-5; effective geometrical factors of >3 m2sr for electron and diffuse gamma-rays, >2 m2sr for cosmic ray nuclei. R&D is under way for reading out the LYSO signals with optical fiber coupled to image intensified IsCMOS and CALO prototype of 250 LYSO crystals.
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| 10. |
- Zhang, S. N., et al.
(author)
-
The high energy cosmic-radiation detection (HERD) facility onboard China's Space Station
- 2014
-
In: Proceedings of SPIE - The International Society for Optical Engineering. - : SPIE. - 9780819496126
-
Conference paper (peer-reviewed)abstract
- The High Energy cosmic-Radiation Detection (HERD) facility is one of several space astronomy payloads of the cosmic lighthouse program onboard China's Space Station, which is planned for operation starting around 2020 for about 10 years. The main scientific objectives of HERD are indirect dark matter search, precise cosmic ray spectrum and composition measurements up to the knee energy, and high energy gamma-ray monitoring and survey. HERD is composed of a 3-D cubic calorimeter (CALO) surrounded by microstrip silicon trackers (STKs) from five sides except the bottom. CALO is made of about 104 cubes of LYSO crystals, corresponding to about 55 radiation lengths and 3 nuclear interaction lengths, respectively. The top STK microstrips of seven X-Y layers are sandwiched with tungsten converters to make precise directional measurements of incoming electrons and gamma-rays. In the baseline design, each of the four side SKTs is made of only three layers microstrips. All STKs will also be used for measuring the charge and incoming directions of cosmic rays, as well as identifying back scattered tracks. With this design, HERD can achieve the following performance: energy resolution of 1% for electrons and gamma-rays beyond 100 GeV, 20% for protons from 100 GeV to 1 PeV; electron/proton separation power better than 10-5; effective geometrical factors of >3 m2sr for electron and diffuse gamma-rays, >2 m2sr for cosmic ray nuclei. R and D is under way for reading out the LYSO signals with optical fiber coupled to image intensified CCD and the prototype of one layer of CALO.
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| 11. |
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| 12. |
- Abeysinghe, Kasun S., et al.
(author)
-
Total mercury and methylmercury concentrations over a gradient of contamination in earthworms living in rice paddy soil
- 2017
-
In: Environmental Toxicology and Chemistry. - : Wiley. - 0730-7268 .- 1552-8618. ; 36:5, s. 1202-1210
-
Journal article (peer-reviewed)abstract
- Mercury (Hg) deposited from emissions or from local contamination, can have serious health effects on humans and wildlife. Traditionally, Hg has been seen as a threat to aquatic wildlife, because of its conversion in suboxic conditions into bioavailable methylmercury (MeHg), but it can also threaten contaminated terrestrial ecosystems. In Asia, rice paddies in particular may be sensitive ecosystems. Earthworms are soil-dwelling organisms that have been used as indicators of Hg bioavailability; however, the MeHg concentrations they accumulate in rice paddy environments are not well known. Earthworm and soil samples were collected from rice paddies at progressive distances from abandoned mercury mines in Guizhou, China, and at control sites without a history of Hg mining. Total Hg (THg) and MeHg concentrations declined in soil and earthworms as distance increased from the mines, but the percentage of THg that was MeHg, and the bioaccumulation factors in earthworms, increased over this gradient. This escalation in methylation and the incursion of MeHg into earthworms may be influenced by more acidic soil conditions and higher organic content further from the mines. In areas where the source of Hg is deposition, especially in water-logged and acidic rice paddy soil, earthworms may biomagnify MeHg more than was previously reported. It is emphasized that rice paddy environments affected by acidifying deposition may be widely dispersed throughout Asia.
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| 13. |
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| 14. |
- Chen, Zhibin, et al.
(author)
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Summary of the 3rd International Workshop on Gas-Dynamic Trap based Fusion Neutron Source (GDT-FNS)
- 2022
-
In: Nuclear Fusion. - : IOP Publishing. - 0029-5515 .- 1741-4326. ; 62:6
-
Journal article (peer-reviewed)abstract
- The 3rd International Workshop on Gas-Dynamic Trap-based Fusion Neutron Source (GDT-FNS) was held through the hybrid mode on 13-14 September 2021 in Hefei, China, jointly organized by the Hefei Institutes of Physical Science (HFIPS), Chinese Academy of Sciences (CAS), and the Budker Institute of Nuclear Physics (BINP), Russian Academy of Sciences (RAS). It followed the 1st GDT-FNS Workshop held in November 2018 in Hefei, China, and the 2nd taking place in November 2019 in Novosibirsk, Russian Federation. With the financial support from CAS and China Association for Science and Technology (CAST), this workshop was attended by more than 80 participants representing 20 institutes and universities from seven countries, with oral presentations broadcast via the Zoom conferencing system. Twenty-two presentations were made with topics covering design and key technologies, simulation and experiments, steady-state operation, status of the ALIANCE project, multi applications of neutron sources, and other concepts (Tokamaks, Mirrors, FRC, Plasma Focus, etc). The workshop consensus was made including the establishment of the ALIANCE International Working Group. The next GDT-FNS workshop is planned to be held in May 2022 in Novosibirsk.
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| 15. |
- Duanmu, Lin, et al.
(author)
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Relationship between Human Thermal Comfort and Indoor Thermal Environment Parameters in Various Climatic Regions of China
- 2017
-
In: Procedia Engineering. - : Elsevier BV. - 1877-7058 .- 1877-7058. ; 205, s. 2871-2878
-
Conference paper (peer-reviewed)abstract
- Architectural design is based on the reliability and rationality of construction standards. The thermal comfort standard is a very important part of construction standards. In this study, Chinese researches about the field survey of various areas were summarized. The distribution range of thermal comfo rt temperature and neutral temperature were obtained by using the PMV evaluation index. The neutral temperature of different types of buildings in different seasons was summarized. Its relationship with indoor parameters was analyzed in detail. These findings provide a basis for the formulation of building specifications and architectural design in future.
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| 16. |
- Li, Xiaoting, et al.
(author)
-
"Mix-Then-On-Demand-Complex" : In Situ Cascade Anionization and Complexation of Graphene Oxide for High-Performance Nanofiltration Membranes
- 2021
-
In: ACS Nano. - : American Chemical Society (ACS). - 1936-0851 .- 1936-086X. ; 15:3, s. 4440-4449
-
Journal article (peer-reviewed)abstract
- Assembling two-dimensional (2D) materials by polyelectrolyte often suffers from inhomogeneous microstructures due to the conventional mixing-and-simultaneous-complexation procedure (mix-and-complex) in aqueous solution. Herein a mix-then-on-demand-complex concept via on-demand in situ cascade anionization and ionic complexation of 2D materials is raised that drastically improves structural order in 2D assemblies, as exemplified by classical graphene oxide (GO)-based ultrathin membranes. Specifically, in dimethyl sulfoxide, the carboxylic acid-functionalized GO sheets (COOH-GOs) were mixed evenly with a cationic poly(ionic liquid) (PIL) and upon filtration formed a well-ordered layered composite membrane with homogeneous distribution of PIL chains in it; next, whenever needed, it was alkali-treated to convert COOH-GO in situ into its anionized state COO--GO that immediately complexed ionically with the surrounding cationic PIL chains. This mix-then-on-demand-complex concept separates the ionic complexation of GO and polyelectrolytes from their mixing step. By synergistically combining the PIL-induced hydrophobic confinement effect and supramolecular interactions, the as-fabricated nanofiltration membranes carry interface transport nanochannels between GO and PIL, reaching a high water permeability of 96.38 L m(-2) h(-1) bar(-1) at a maintained excellent dye rejection 99.79% for 150 h, exceeding the state-of-the-art GO-based hybrid membranes. The molecular dynamics simulations support the experimental data, confirming the interface spacing between GO and PIL as the water transport channels.
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| 17. |
- Lin, Jia, et al.
(author)
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Pressure-induced semiconductor-to-metal phase transition of a charge-ordered indium halide perovskite
- 2019
-
In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 116:47, s. 23404-23409
-
Journal article (peer-reviewed)abstract
- Phase transitions in halide perovskites triggered by external stimuli generate significantly different material properties, providing a great opportunity for broad applications. Here, we demonstrate an In-based, charge-ordered (In+/In3+) inorganic halide perovskite with the composition of Cs2In(I)In(III)Cl-6 in which a pressure-driven semiconductor-to-metal phase transition exists. The single crystals, synthesized via a solid-state reaction method, crystallize in a distorted perovskite structure with space group I4/m with a = 17.2604(12) angstrom, c = 11.0113(16) angstrom if both the strong reflections and superstructures are considered. The supercell was further confirmed by rotation electron diffraction measurement. The pressure-induced semiconductor-to-metal phase transition was demonstrated by high-pressure Raman and absorbance spectroscopies and was consistent with theoretical modeling. This type of charge-ordered inorganic halide perovskite with a pressure-induced semiconductor-to-metal phase transition may inspire a range of potential applications.
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| 18. |
- Liu, Wei, et al.
(author)
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Coherent dynamics of multi-spin V-B(-) center in hexagonal boron nitride
- 2022
-
In: Nature Communications. - : Nature Portfolio. - 2041-1723. ; 13:1
-
Journal article (peer-reviewed)abstract
- Hexagonal boron nitride (hBN) has recently been demonstrated to contain optically polarized and detected electron spins that can be utilized for implementing qubits and quantum sensors in nanolayered-devices. Understanding the coherent dynamics ofmicrowave driven spins in hBN is of crucial importance for advancing these emerging new technologies. Here, we demonstrate and study the Rabi oscillation and related phenomena of a negatively charged boron vacancy (V-B(-)) spin ensemble in hBN. We report on different dynamics of the V-B(-) spins at weak and strong magnetic fields. In the former case the defect behaves like a single electron spin system, while in the latter case it behaves like a multi-spin system exhibiting multiple-frequency dynamical oscillation as beat in the Ramsey fringes. We also carry out theoretical simulations for the spin dynamics of V-B(-) and reveal that the nuclear spins can be driven via the strong electron nuclear coupling existing in V-B(-) center, which can be modulated by the magnetic field and microwave field.
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| 19. |
- Lu, Shen-ning, et al.
(author)
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Application of an innovative grid-based surveillance strategy to ensure elimination and prevent reintroduction of malaria in high-risk border communities in China
- 2022
-
In: BMC Public Health. - : Springer Nature. - 1471-2458. ; 22:1
-
Journal article (peer-reviewed)abstract
- Grid management is a grassroots governance strategy widely implemented in China since 2004 to improve the government's efficiency to actively find and solve problems among populated regions. A grid-based strategy surveillancing high-risk groups, including mobile and migrant populations (MMPs), in the China-Myanmar border region has played an indispensable role in promoting and consolidating the malaria elimination efforts by tracking and timely identification of potential importation or re-establishment of malaria among MMPs. A sequential mixed methods was implementated to explore the operational mechanism and best practices of the grid-based strategy including through the focus group discussions (FGDs), comparison of before and after the implementation of a grid-based strategy in the field sites, and data collection from the local health system.This paper distills the implementation mechanism and highlights the role of the grid-based strategy in the elimination and prevention of re-establishment of malaria transmission.
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| 20. |
- Miao, Quan, et al.
(author)
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Numerical analysis on optical limiting performance of a series of phthalocyanines for nanosecond pulses
- 2012
-
In: Journal of Physics B. - : IOP Publishing. - 0953-4075 .- 1361-6455. ; 45:8, s. 085402-
-
Journal article (peer-reviewed)abstract
- The optical limiting properties of a series of peripherally substituted phthalocyanines with different central metals and axial chloride ligand for nanosecond pulses have been studied by solving numerically the two-dimensional paraxial field equation together with the rate equations using the Crank-Nicholson method. It is shown that all of these compounds exhibit good optical limiting behaviour, and phthalocyanines with heavier central metals have better optical limiting performance due to the faster intersystem crossing caused by the enhanced spin-orbit coupling. The major mechanism of optical limiting for long pulses is the sequential (singlet-singlet)x( triplet-triplet) nonlinear absorption. Dynamics of populations is characterized mainly by the effective transfer time of the population from the ground state to the lowest triplet state. The long lifetime of the triplet state is important but not determinant. In addition, the performance of optical limiting strongly depends on the thickness and concentration of the absorber.
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| 21. |
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| 22. |
- Miao, Quan, et al.
(author)
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Rotational Doppler Effect : A Probe for Molecular Orbitals Anisotropy
- 2015
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In: The Journal of Physical Chemistry Letters. - : American Chemical Society (ACS). - 1948-7185. ; 6:9, s. 1568-1572
-
Journal article (peer-reviewed)abstract
- The vibrationally resolved X-ray photoelectron spectra of X-2 Sigma(+)(g)(3 sigma(-1)(g)) and B-2 Sigma(+)(u)(2 sigma(-1)(u)) states of N-2(+) were recorded for different photon energies and orientations of the polarization vector. Clear dependencies of the spectral line widths on the X-ray polarization as well as on the symmetry of the final electronic states are observed. Contrary to the translational Doppler, the rotational Doppler broadening is sensitive to the photoelectron emission anisotropy. On the basis of theoretical modeling, we suggest that the different rotational Doppler broadenings observed for gerade and ungerade final states result from a Young's double-slit interference phenomenon.
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| 23. |
- Mohammed, Abdelsalam, et al.
(author)
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Raman Scattering at Resonant or Near-Resonant Conditions : A Generalized Short-Time Approximation
- 2012
-
In: Chinese Journal of Chemical Physics. - : AIP Publishing. - 1674-0068 .- 2327-2244. ; 25:1, s. 31-47
-
Journal article (peer-reviewed)abstract
- We investigate the dynamics of resonant Raman scattering in the course of the frequency detuning. The dephasing in the time domain makes the scattering fast when the photon energy is tuned from the absorption resonance. This makes frequency detuning to act as a camera shutter with a regulated scattering duration and provides a practical tool of controlling the scattering time in ordinary stationary measurements. The theory is applied to resonant Raman spectra of a couple of few-mode model systems and to trams-1,3,5-hexatriene and guanine-cytosine (G-C) Watson-Crick base pairs (DNA) molecules. Besides some particular physical effects, the regime of fast scattering leads to a simplification of the spectrum as well as to the scattering theory itself. Strong overtones appear in the Raman spectra when the photon frequency is tuned in the resonant region, while in the mode of fast scattering, the overtones are gradually quenched when the photon frequency is tuned more than one vibrational quantum below the first a,absorption resonance. The detuning front the resonant region thus leads to a strong purification of the Raman spectrum from the contamination by higher overtones and soft modes and purifies the spectrum also in terms of avoidance of dissociation and interfering fluorescence decay of the resonant state. This makes frequency detuning a very useful practical tool in the analysis of the resonant Raman spectra of complex systems and considerably improves the prospects for using the Raman effect for detection of foreign substances at ultra-low concentrations.
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| 24. |
- Park, Jong-Sun, et al.
(author)
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Auroral electrojet activity for long-duration radial interplanetary magnetic field events
- 2023
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In: Journal of Geophysical Research - Space Physics. - : American Geophysical Union (AGU). - 2169-9380 .- 2169-9402. ; 128:3
-
Journal article (peer-reviewed)abstract
- In this paper, we provide statistical evidence that the level of solar wind-magnetosphere-ionosphere (SW-M-I) coupling is weaker under radial (Sun-Earth component dominant) interplanetary magnetic field (IMF) conditions than non-radial IMF conditions. This is performed by analyzing auroral electrojet activity (using SuperMAG auroral electrojet indices) in the sunlit and dark ionospheres for long-duration (at least 4 hr) radial IMF events and comparing against the same for long-duration azimuthal (dusk-dawn component dominant) IMF events. We show that the north-south IMF component (IMF Bz) plays a crucial role in controlling the level of auroral electrojet activity as a negative half-wave rectifier even for both IMF orientation categories. However, it is found that the magnitudes of the auroral electrojet indices are generally lower for radial IMF than for azimuthal IMF under similar sets of solar wind (radial bulk velocity and number density) and IMF Bz conditions, regardless of whether these indices are derived in the sunlit or dark regions. Moreover, the efficiency of coupling functions is lower for radial IMF than for azimuthal IMF, implying that increased coupling strength due to the azimuthal IMF component alone cannot well explain weaker auroral electrojets during radial IMF periods. Lastly, the contribution of the radial IMF component itself to auroral electrojet activity is also lower compared to the azimuthal IMF component. Our results suggest that the level of SW-M-I coupling characterized by auroral electrojet activity can be modulated by the radial IMF component, although the effect of this component is weaker than the other two IMF components.
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| 25. |
- Park, Jong-Sun, et al.
(author)
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Radial Interplanetary Magnetic Field-Induced North-South Asymmetry in the Solar Wind-Magnetosphere-Ionosphere Coupling : A Case Study
- 2022
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In: Journal of Geophysical Research - Space Physics. - : John Wiley & Sons. - 2169-9380 .- 2169-9402. ; 127:2
-
Journal article (peer-reviewed)abstract
- In this paper, we present a case study of the radial interplanetary magnetic field (IMF Bx)-induced asymmetric solar wind-magnetosphere-ionosphere (SW-M-I) coupling between the northern and southern polar caps using ground-based and satellite-based data. Under prolonged conditions of strong earthward IMF on 5 March 2015, we find significant discrepancies between polar cap north (PCN) and polar cap south (PCS) magnetic indices with a negative bay-like change in the PCN and a positive bay-like change in the PCS. The difference between these indices (PCN-PCS) reaches a minimum of −1.63 mV/m, which is approximately three times higher in absolute value than the values for most of the time on this day (within ±0.5 mV/m). The high-latitude plasma convection also shows an asymmetric feature such that there exists an additional convection cell near the noon sector in the northern polar cap, but not in the southern polar cap. Meanwhile, negative bays in the north-south component of ground magnetic field perturbations (less than 50 nT) observed in the nightside auroral region of the Northern Hemisphere are accompanied with the brightening and widening of the nightside auroral oval in the Southern Hemisphere, implying a weak, but clear energy transfer to the nightside ionosphere of both hemispheres. After the hemispheric asymmetries in the polar caps disappear, a substorm onset takes place. All these observations indicate that IMF Bx-induced single lobe reconnection that occurred in the Northern Hemisphere plays an important role in hemispheric asymmetry in the energy transfer from the solar wind to the polar cap through the magnetosphere.
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| 26. |
- Park, Jong-Sun, et al.
(author)
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Statistical features of polar cap North and South indices in response to interplanetary and terrestrial conditions : a revisit
- 2024
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In: Space Weather. - : American Geophysical Union (AGU). - 1542-7390. ; 22:4
-
Journal article (peer-reviewed)abstract
- In this study, we investigate statistical features of polar cap north (PCN) and south (PCS) indices in response to various interplanetary conditions (interplanetary magnetic field [IMF] orientation in three-dimensions) and terrestrial conditions (seasonal and magnetic local time [MLT] locations of the index stations). The concurrent PCN-PCS pairs for 1998–2002 and 2004–2018 are divided based on their sign type (positive-positive, negative-negative, negative-positive, and positive-negative PCN-PCS pairs) and time coverage (the times when both index stations are in the dawn/dusk MLT sector during northern summer/winter). Analyzing the IMF orientation dependence on the occurrence probabilities of concurrent indices and on the differences between the indices in various sign types for each time coverage reveals that the statistical features in PCN-PCS pairs obtained in the dawn MLT sector can be largely explained by the effects of the three-component IMF (related to the polar cap convection patterns) combined with season (related to the hemispheric asymmetry in solar illumination-induced ionospheric conductance). However, those obtained in the dusk MLT sector are controlled dominantly by seasonal effects rather than IMF orientation effects. Our findings indicate that PCN-PCS pair data provide local views about the solar wind-magnetosphere-ionosphere (SW-M-I) coupling system with different control efficiencies of IMF orientation and season depending on the MLT location of the stations. Therefore, introducing polar cap indices recorded simultaneously at various locations in both hemispheres and analyzing them are strongly required to infer global views of the coupled SW-M-I system in the open field regions with higher confidence.
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| 27. |
- Park, Jong-Sun, et al.
(author)
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Transpolar Arcs During a Prolonged Radial Interplanetary Magnetic Field Interval
- 2021
-
In: Journal of Geophysical Research - Space Physics. - : John Wiley & Sons. - 2169-9380 .- 2169-9402. ; 126:6
-
Journal article (peer-reviewed)abstract
- Transpolar arcs (TPAs) are believed to predominantly occur under northward interplanetary magnetic field (IMF) conditions with their hemispheric asymmetry controlled by the Sun-Earth (radial) component of the IMF. In this study, we present observations of TPAs that appear in both the northern and southern hemispheres even during a prolonged interval of radially oriented IMF. The Defense Meteorological Satellite Program (DMSP) F16 and the Thermosphere Ionosphere Mesosphere Energetics and Dynamics (TIMED) satellites observed TPAs on the dawnside polar cap in both hemispheres (one TPA structure in the southern hemisphere and two in the northern hemisphere) during an interval of nearly earthward-oriented IMF on October 29, 2005. The southern hemisphere TPA and one of the northern hemisphere TPAs are associated with electron and ion precipitation and mostly sunward plasma flow (with shears) relative to their surroundings. Meanwhile, the other TPA in the northern hemisphere is associated with an electron-only precipitation and antisunward flow relative to its surroundings. Our observations indicate the following: (a) the TPA formation is not limited to northward IMF conditions; (b) the TPAs can be located on both closed field lines rooted in the polar cap of both hemispheres and open field lines connected to the northward field lines draped over one hemisphere of the magnetopause. We believe that the TPAs presented here are the result of both indirect and direct processes of solar wind energy transfer to the high-latitude ionosphere.
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| 28. |
- Shen, Yang-mei, et al.
(author)
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Novel gene hBiot2 is an independent prognostic factor in colorectal cancer patients
- 2012
-
In: Oncology Reports. - : Spandidos Publications. - 1021-335X .- 1791-2431. ; 27:2, s. 376-382
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Journal article (peer-reviewed)abstract
- The present study investigated the expression of the novel gene hBiot2 in colorectal cancer (CRC) and its relationships with clinicopathological variables in CRC patients. The expression of hBiot2 in 163 primary CRCs together with the corresponding normal mucosa, 36 liver metastases and 5 colon cancer cell lines was examined using real-time PCR. In situ hybridization (ISH) was performed to evaluate the localization of hBiot2 expression in CRC and normal mucosa. hBiot2 expression at the RNA level was localized in the nucleus of tumor cells and normal epithelial cells. The mean expression of hBiot2 in the CRCs (243.571 +/- 564.569) was higher compared to the normal mucosa (107.252 +/- 413.635, Pandlt;0.0001) and liver metastasis samples (42.002 +/- 40.809, P=0.0002). hBiot2 expression was increased from stages I + II to III (P=0.047), and no difference in the expression was found in stages III and IV (P=0.452). A high value of hBiot2 was associated with a poorer prognosis compared with a low value independently of gender, age, tumor site, stage and differentiation (P=0.007, RR 7.519, 95% Cl 1.729-32.704). Liver metastasis, smaller tumors, non-local recurrence and primary liver surgery alone were associated with a higher value of hBiot2 compared to larger tumors, local recurrence and repeated liver surgery (P=0.003, 0.044 and 0.026, respectively). An inverse relationship was found between hBiot2 expression and the metastatic potential of the colon cancer cell lines. Thus, increased expression of hBiot2 may be an early and interim event in the development of CRC. A higher expression of hBiot2 in primary CRC patients independently indicates a poorer prognosis.
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| 29. |
- Sullivan, Patrick F., et al.
(author)
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Leveraging base-pair mammalian constraint to understand genetic variation and human disease
- 2023
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In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 380:6643, s. 367-
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Journal article (peer-reviewed)abstract
- Thousands of genomic regions have been associated with heritable human diseases, but attempts to elucidate biological mechanisms are impeded by an inability to discern which genomic positions are functionally important. Evolutionary constraint is a powerful predictor of function, agnostic to cell type or disease mechanism. Single-base phyloP scores from 240 mammals identified 3.3% of the human genome as significantly constrained and likely functional. We compared phyloP scores to genome annotation, association studies, copy-number variation, clinical genetics findings, and cancer data. Constrained positions are enriched for variants that explain common disease heritability more than other functional annotations. Our results improve variant annotation but also highlight that the regulatory landscape of the human genome still needs to be further explored and linked to disease.
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| 30. |
- Sun, Chen, et al.
(author)
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Does gemcitabine-based combination therapy improve the prognosis of unresectable pancreatic cancer?
- 2012
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In: World Journal of Gastroenterology. - : Baishideng Publishing Group Inc.. - 1007-9327. ; 18:35, s. 4944-4958
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Journal article (peer-reviewed)abstract
- AIM: To assess whether gemcitabine-based combination therapy improves the prognosis of unresectable pancreatic cancer compared with gemcitabine treatment alone. METHODS: A quantitative up-to-date meta-analysis was undertaken to investigate the efficacy of gemcitabine-based combination treatment compared with gemcitabine monotherapy in locally advanced or metastatic pancreatic cancer. Inclusion was limited to high-quality randomized clinical trials. RESULTS: Twenty-six studies were included in the present analysis, with a total of 8808 patients recruited. The studies were divided into four subgroups based on the different kinds of cytotoxic agents, including platinum, fluoropyrimidine, camptothecin and targeted agents. Patients treated with gemcitabine monotherapy had significantly lower objective response rate [risk ratio (RR), 0.72; 95% confidence interval (CI): 0.63-0.83; P < 0.001], and lower 1-year overall survival (RR, 0.90; 95%CI: 0.82-0.99; P = 0.04). Gemcitabine monotherapy caused fewer complications, including fewer grade 3-4 toxicities: including vomiting (RR, 0.75; 95%CI: 0.62-0.89; P = 0.001), diarrhea (RR, 0.66; 95%CI: 0.49-0.89; P = 0.006), neutropenia (RR, 0.88; 95%CI: 0.72-1.06; P = 0.18), anemia (RR, 0.96; 95%CI: 0.82-1.12; P = 0.60), and thrombocytopenia (RR, 0.76; 95%CI: 0.60-0.97; P = 0.03) compared with gemcitabine combination therapies. CONCLUSION: Gemcitabine combination therapy provides a modest improvement of survival, but is associated with more toxicity compared with gemcitabine monotherapy. (C) 2012 Baishideng. All rights reserved.
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| 31. |
- Sun, Xiao-dong, et al.
(author)
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Implementing a novel capture and ligation probe-PCR method in mass screen and treatment to support malaria elimination efforts in the China-Myanmar border region
- 2023
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In: Malaria Journal. - : BioMed Central (BMC). - 1475-2875. ; 22:1
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Journal article (peer-reviewed)abstract
- BackgroundMass screening and treatment (MSAT) for malaria elimination lacks an ideal diagnostic tool to allow sensitive and affordable test of the target population in the field. This study evaluated whether Capture and Ligation Probe-PCR (CLIP-PCR) could be used in a field MSAT in Laiza City, Myanmar.MethodsOn day 0, two dried blood spots were collected from each participant. On day 1, all samples were screened for Plasmodium in a 20 m(2) laboratory with workbench, a biosafety cabinet, a refrigerator, a benchtop shaking incubator and a qPCR machine, by four technicians using CLIP-PCR with sample pooling, at a health clinic of the Chinese bordering town of Nabang. On day 2, all positives were followed up and treated.ResultsOf 15,038 persons (65% of the total population) screened, 204 (1.36%) were CLIP-PCR positives. Among them, 188, 14, and 2 were infected with Plasmodium vivax, Plasmodium falciparum, and P. vivax/P. falciparum mix, respectively. The testing capacity was 538 persons/day, with a cost of US$0.92 /person. The proportion of submicroscopic infection was 64.7%. All positive individuals received treatment within 72 h after blood collection.ConclusionUsing CLIP-PCR in MSAT in low transmission settings can support the malaria elimination efforts in the China-Myanmar border region.
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| 32. |
- Sun, Xian-qiang, et al.
(author)
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Structure-based ensemble-QSAR model : a novel approach to the study of the EGFR tyrosine kinase and its inhibitors
- 2014
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In: Acta Pharmacologica Sinica. - : Springer Science and Business Media LLC. - 1671-4083 .- 1745-7254. ; 35:2, s. 301-310
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Journal article (peer-reviewed)abstract
- Aim: To develop a novel 3D-QSAR approach for study of the epidermal growth factor receptor tyrosine kinase (EGFR TK) and its inhibitors. Methods: One hundred thirty nine EGFR TK inhibitors were classified into 3 clusters. Ensemble docking of these inhibitors with 19 EGFR TK crystal structures was performed. Three protein structures that showed the best recognition of each cluster were selected based on the docking results. Then, a novel QSAR (ensemble-QSAR) building method was developed based on the ligand conformations determined by the corresponding protein structures. Results: Compared with the 3D-QSAR model, in which the ligand conformations were determined by a single protein structure, ensemble-QSAR exhibited higher R2 (0.87) and Q2 (0.78) values and thus appeared to be a more reliable and better predictive model. Ensemble-QSAR was also able to more accurately describe the interactions between the target and the ligands. Conclusion: The novel ensemble-QSAR model built in this study outperforms the traditional 3D-QSAR model in rationality, and provides a good example of selecting suitable protein structures for docking prediction and for building structure-based QSAR using available protein structures.
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| 33. |
- Sun, Yu-Ping, et al.
(author)
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Interference between Resonant and Nonresonant Inelastic X-Ray Scattering
- 2013
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In: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 110:22, s. 223001-
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Journal article (peer-reviewed)abstract
- A detailed study of inelastic x-ray scattering from the ground state to the Σg3(3σg-13sg1) state of the O2 molecule is presented. The observed angular anisotropy shows that the vibrational excitations within this final state are strongly dependent on the polarization of the incident radiation. The analysis demonstrates that this is a manifestation of interference between resonant and direct nonresonant inelastic x-ray scattering. This interference provides a new tool to monitor nuclear dynamics by relative rotation of the polarization vectors of the incident and scattered photons.
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| 34. |
- Sun, Yu-Ping, et al.
(author)
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Shortening scattering duration by detuning purifies Raman spectra of complex systems
- 2011
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In: Chemical Physics Letters. - : Elsevier BV. - 0009-2614 .- 1873-4448. ; 511:1-3, s. 16-21
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Journal article (peer-reviewed)abstract
- We highlight Resonant Raman scattering as a dynamical process with a finite duration time that results from not only the irreversible homogeneous broadening but also the reversible dephasing caused by the detuning from the resonance, which acts as a camera shutter with a regulated scattering duration. This provides a practical tool of controlling the scattering time. We show that the typical dephasing rates in gas and condensed matter phases are not sufficiently high to make the scattering fast. The detuning from the resonance leads to a strong purification of Raman spectrum from the contamination by higher overtones and soft modes.
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| 35. |
- Sun, Yu-Ping, et al.
(author)
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Suppression of resonant auger effect with chirped x-ray free-electron laser pulse
- 2018
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In: Journal of Physics B. - : IOP PUBLISHING LTD. - 0953-4075 .- 1361-6455. ; 51:3
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Journal article (peer-reviewed)abstract
- We study the Auger effect in the presence of strong x-ray free-electron lasers (XFELs) propagating through resonant argon vapors by solving the Maxwell-Bloch equations numerically. The simulations are based on the three-level system with the carrier frequency tuned in the 2p(3/2)-4s resonance. It is shown that the Auger branching is sensitive to the pulse area and duration. The relative Auger yield can be suppressed in the course of pulse propagation due to the interplay between the Auger decay and stimulated emission. Further suppression can be achieved by chirping the initial pulse, which is more effective for the long-pulse case. In addition, the sign and magnitude of the chirp rate play important roles in pulse reshaping and Auger emission.
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| 36. |
- Termorshuizen, Jet D., et al.
(author)
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Longer-term impact of COVID-19 among individuals with self-reported eating disorders in the United States, the Netherlands, and Sweden
- 2023
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In: International Journal of Eating Disorders. - : WILEY. - 0276-3478 .- 1098-108X. ; 56:1, s. 80-90
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Journal article (peer-reviewed)abstract
- Objective We assessed eating disorder (ED) illness status, symptomatology, treatment access, anxiety, and depression in the first year of the COVID-19 pandemic among individuals with a pre-existing ED in the United States (US), the Netherlands (NL), and Sweden (SE). Methods Participants completed online surveys in April-July 2020, at the early stage of the pandemic, and one year later. At one-year follow-up, we added questions addressing retrospective changes in ED symptoms, treatment, and anxiety/depression since the start of the COVID-19 pandemic. We present descriptive statistics and assess change in ED symptomatology, treatment, and anxiety/depression among those with an active or lingering ED. Results Participants (US n = 132; NL n = 219; SE n = 702) were mostly young and female with a history of anorexia nervosa (>60% in all three countries). Across countries, respondents reported impact of COVID-19 on ED symptoms at both time points, with improvement in US and NL at one-year follow-up, and stable but less impact on ED symptoms in SE. Furthermore, at one-year follow-up, roughly half of those in treatment reported reduced treatment access and quality, and the majority of the sample reported increased anxiety and depressive mood since the start of the pandemic. Discussion Our findings suggest that the self-perceived impact of COVID-19 changed over time but remained concerning even one year after the start of the pandemic. Clinicians, community organizations, and policy makers are encouraged to address potentially changing treatment needs in the face of public health emergency events. Public Significance Our findings suggest that the impact of COVID-19 on individuals with eating disorders decreased over time but remained concerning even one year after the start of the pandemic and that the impact differed across countries. Clinicians, community organizations, and policy makers are encouraged to incorporate this knowledge to address potentially changing treatment needs in the face of public health emergency events.
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| 37. |
- Xu, Chao-Qun, et al.
(author)
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Genome sequence of Malania oleifera, a tree with great value for nervonic acid production
- 2019
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In: GigaScience. - : Oxford University Press. - 2047-217X. ; 8:2
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Journal article (peer-reviewed)abstract
- Background Malania oleifera, a member of the Olacaceae family, is an IUCN red listed tree, endemic and restricted to the Karst region of southwest China. This tree's seed is valued for its high content of precious fatty acids (especially nervonic acid). However, studies on its genetic makeup and fatty acid biogenesis are severely hampered by a lack of molecular and genetic tools. Findings We generated 51 Gb and 135Gb of raw DNA sequences, using Pacific Biosciences (PacBio) single-molecule real-time and 10x Genomics sequencing, respectively. A final genome assembly, with a scaffold N50 size of 4.65 Mb and a total length of 1.51Gb, was obtained by primary assembly based on PacBio long reads plus scaffolding with 10x Genomics reads. Identified repeats constituted approximate to 82% of the genome, and 24,064 protein-coding genes were predicted with high support. The genome has low heterozygosity and shows no evidence for recent whole genome duplication. Metabolic pathway genes relating to the accumulation of long-chain fatty acid were identified and studied in detail. Conclusions Here, we provide the first genome assembly and gene annotation for M. oleifera. The availability of these resources will be of great importance for conservation biology and for the functional genomics of nervonic acid biosynthesis.
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| 38. |
- Yang, Xinping, et al.
(author)
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Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing
- 2016
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In: Cell. - : Elsevier BV. - 0092-8674 .- 1097-4172. ; 164:4, s. 805-817
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Journal article (peer-reviewed)abstract
- While alternative splicing is known to diversify the functional characteristics of some genes, the extent to which protein isoforms globally contribute to functional complexity on a proteomic scale remains unknown. To address this systematically, we cloned full-length open reading frames of alternatively spliced transcripts for a large number of human genes and used protein-protein interaction profiling to functionally compare hundreds of protein isoform pairs. The majority of isoform pairs share less than 50% of their interactions. In the global context of interactome network maps, alternative isoforms tend to behave like distinct proteins rather than minor variants of each other. Interaction partners specific to alternative isoforms tend to be expressed in a highly tissue-specific manner and belong to distinct functional modules. Our strategy, applicable to other functional characteristics, reveals a widespread expansion of protein interaction capabilities through alternative splicing and suggests that many alternative "isoforms'' are functionally divergent (i.e., "functional alloforms'').
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| 39. |
- Yu, De-quan, et al.
(author)
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Hermiticity of Hamiltonian Matrix using the Fourier Basis Sets in Bond-Bond-Angle and Radau Coordinates
- 2016
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In: Chinese Journal of Chemical Physics. - : AIP Publishing. - 1674-0068 .- 2327-2244. ; 29:1
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Journal article (peer-reviewed)abstract
- In quantum calculations a transformed Hamiltonian is often used to avoid singularities in a certain basis set or to reduce computation time. We demonstrate for the Fourier basis set that the Hamiltonian can not be arbitrarily transformed. Otherwise, the Hamiltonian matrix becomes non-hermitian, which may lead to numerical problems. Methods for correctly constructing the Hamiltonian operators are discussed. Specific examples involving the Fourier basis functions for a triatomic molecular Hamiltonian (J=0) in bond-bond angle and Radau coordinates are presented. For illustration, absorption spectra are calculated for the OClO molecule using the time-dependent wavepacket method. Numerical results indicate that the non-hermiticity of the Hamiltonian matrix may also result from integration errors. The conclusion drawn here is generally useful for quantum calculation using basis expansion method using quadrature scheme.
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| 40. |
- Zhou, Yong, et al.
(author)
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Solvent effect on dynamical TPA and optical limiting of BDMAS molecular media for nanosecond and femtosecond laser pulses
- 2011
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In: Journal of Physics B. - : IOP Publishing. - 0953-4075 .- 1361-6455. ; 44:3, s. 035103-
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Journal article (peer-reviewed)abstract
- The dynamical two-photon absorption (TPA) cross section as well as optical limiting of a 4,4'-bis(dimethylamino) stilbene (BDMAS) molecular medium for the nanosecond and femtosecond laser pulses is studied. This molecular medium can be described by a cascade three-level model in the visible light regime. Our numerical results show that the BDMAS molecular medium exhibits a strong optical limiting behaviour. The saturation TPA in the femtosecond time domain can be observed, and materials with larger nonlinear absorption cross sections would be much easier to saturate. Due to the contribution of the two-step TPA, the dynamical TPA cross section of BDMAS for nanosecond pulses is about three orders of magnitude larger than that for ultrashort femtosecond pulses. Special attention has been paid to the solvent effects on the optimal limiting performance. With an enhancement of the polarity of solvents, the dynamical optical limiting window becomes broader. In the origin of optical limiting, the dynamical TPA cross section of BDMAS decreases when the polarity of solvents increases, which is in good agreement with the experiment.
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