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Li Q, Hou W, Li L, Xu J, Ren Y, Zou K, Tian R, Sun X. Measuring quality of reporting in systematic reviews of diagnostic test accuracy studies in medical imaging: comparison of PRISMA-DTA and PRISMA. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2023; 61:257-266. [PMID: 36633905 DOI: 10.1002/uog.26043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 06/24/2022] [Accepted: 07/18/2022] [Indexed: 05/27/2023]
Abstract
OBJECTIVES To compare the reporting quality measured by the Preferred Reporting Items for Systematic Reviews and Meta-Analyses of Diagnostic Test Accuracy studies (PRISMA-DTA) vs the original PRISMA checklist for systematic reviews of diagnostic test accuracy studies in imaging and survey the use of PRISMA-DTA by researchers and endorsement by journals. METHODS Systematic reviews of DTA studies published in 2020 and 2021 in Quartile 1 and Quartile 3 medical imaging journals (defined by Journal Citation Reports) were identified through PubMed. The reporting of each systematic review was assessed using PRISMA-DTA, PRISMA-2009 and PRISMA-2020. The item scores and overall score were compared among the three checklists. We also examined checklist adoption by the included systematic reviews and surveyed checklist endorsement from author instructions of included journals. RESULTS A total of 173 systematic reviews from 66 journals were included. The use of PRISMA-DTA, compared with PRISMA-2009 and PRISMA-2020, identified more issues in the reporting of title (proportion of systematic reviews with proper reporting, 27.2% vs 98.8% vs 98.8%), abstract (39.3% vs 97.1% vs 64.7%), eligibility criteria (67.6% vs 94.2% vs 94.2%), search (28.9% vs 72.3% vs 28.9%), definitions for data extraction (14.5% vs 91.9% vs 91.9%), diagnostic accuracy measures (38.2% vs 93.6% vs 93.6%), synthesis of results (28.9% vs 89.6% vs 73.4%) and results of individual studies (40.5% vs 80.3% vs 80.3%). The overall median reporting score measured by PRISMA-DTA (72.0% (interquartile range (IQR), 66.7-77.8%)) was lower than that measured by PRISMA-2009 (88.9% (IQR, 84.0-92.6%)) and similar to that measured by PRISMA-2020 (74.1% (IQR, 66.7-77.8%)). Additionally, PRISMA-DTA was used by only 43 (24.9%) systematic reviews and endorsed by two (3.0%) journals. These trends remained consistent for reviews published in journals with diverse scientific impact. CONCLUSIONS The use of PRISMA-DTA may identify more reporting inadequacies compared with the original PRISMA checklists when assessing diagnostic test accuracy systematic reviews, especially in critical sections such as title, abstract and methods. However, this tool is not commonly used by researchers and is inadequately endorsed by imaging journals. Our findings suggest a strong need to use PRISMA-DTA for reporting of diagnostic test accuracy systematic reviews by authors and its endorsement by journals. © 2022 International Society of Ultrasound in Obstetrics and Gynecology.
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Wei M, Chen A, Zhang J, Ren Y. Novel Oxygen-Dependent Degradable Immunotoxin Regulated by the Ubiquitin-Proteasome System Reduces Nonspecific Cytotoxicity. Mol Pharm 2023; 20:90-100. [PMID: 36305716 DOI: 10.1021/acs.molpharmaceut.2c00503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The use of bacterial toxins as antitumor agents has received considerable attention. Immunotoxins based on antigen recognition of single-chain antibodies have been widely explored for cancer therapy. Despite their impressive killing effect on tumor cells, immunotoxins still display unspecific toxicity with undesired side effects. High levels of hypoxia-inducible factor 1α (HIF-1α) are well-known indicators of hypoxia in cancer cells. In this study, different linkers were employed to fuse the immunotoxin DAB389-4D5 scFv (DS) with the oxygen-dependent degradation domain (ODDD) of HIF-1α, a domain selectively facilitating the accumulation of HIF-1α under hypoxia, to construct the oxygen-dependent degradable immunotoxin DS-ODDD (DSO). The engineered fusion protein DSO-2 containing a linker (G4S)3 possesses the best killing effect on cancer cells under hypoxia and displayed considerably reduced nonspecific toxicity to normal cells under normoxic conditions. Flow cytometry, immunofluorescence, and immunoblot analyses demonstrated that DSO-2 was degraded via the ubiquitin-proteasome pathway regulated by the oxygen-sensitive mechanism. Western blot analysis indicated that the degradation of DSO-2 significantly decreased the activation of apoptosis-related molecules in normal cells. The engineered immunotoxin with oxygen-sensing properties developed herein is a potential therapeutic agent for cancer treatment.
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Zhou Y, Zhu X, Ren Y, Hui Y. Distribution of Cheyletus mites in dust samples. THE EUROPEAN ZOOLOGICAL JOURNAL 2022. [DOI: 10.1080/24750263.2022.2126533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Zhou Y, Shao Z, Dai G, Li X, Xiang Y, Jiang S, Zhang Z, Ren Y, Zhu Z, Fan C, Zhang G. Pathogenic infection characteristics and risk factors for bovine respiratory disease complex based on the detection of lung pathogens in dead cattle in northeast China. J Dairy Sci 2022; 106:589-606. [DOI: 10.3168/jds.2022-21929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 08/12/2022] [Indexed: 11/07/2022]
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Wang H, Li X, Xu L, Ren Y, Deng W, Feng H, Yang Z, Ma S, Ni Q, Kuang Y. The Feasibility of Quad-Modal PET/SPECT/Spectral-CT/CBCT On-Board Imaging in a Small-Animal Radiation Therapy Platform. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Zhu Y, Chen Y, Yu JH, Domier C, Yu G, Liu X, Kramer G, Ren Y, Diallo A, Luhmann NC, Li X. System-on-chip approach microwave imaging reflectometer on DIII-D tokamak. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2022; 93:113509. [PMID: 36461457 DOI: 10.1063/5.0099170] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 09/08/2022] [Indexed: 06/17/2023]
Abstract
System-on-chip millimeter wave integrated circuit technology is used on the two-dimensional millimeter-wave imaging reflectometer (MIR) upgrade for density fluctuation imaging on the DIII-D tokamak fusion plasma. Customized CMOS chips have been successfully developed for the transmitter module and receiver module array, covering the 55-75 GHz working band. The transmitter module has the capability of simultaneously launching eight tunable probe frequencies (>0 dBm output power each). The receiver enclosure contains 12 receiver modules in two vertical lines. The quasi-optical local oscillator coupling of previous MIR systems has been replaced with an internal active frequency multiplier chain for improved local oscillator power delivery and flexible installation in a narrow space together with improved shielding against electromagnetic interference. The 55-75 GHz low noise amplifier, used between the receiver antenna and the first-stage mixer, significantly improves module sensitivity and suppresses electronics noise. The receiver module has a 20 dB gain improvement compared with the mini-lens approach and better than -75 dBm sensitivity, and its electronics noise temperature has been reduced from 55 000 K down to 11 200 K. The V-band MIR system is developed for co-located multi-field investigation of MHD-scale fluctuations in the pedestal region with W-band electron cyclotron emission imaging on DIII-D tokamak.
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Patel U, Guruswamy T, Krzysko AJ, Charalambous H, Gades L, Wiaderek K, Quaranta O, Ren Y, Yakovenko A, Ruett U, Miceli A. High-resolution Compton spectroscopy using x-ray microcalorimeters. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2022; 93:113105. [PMID: 36461526 DOI: 10.1063/5.0092693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 10/23/2022] [Indexed: 06/17/2023]
Abstract
X-ray Compton spectroscopy is one of the few direct probes of the electron momentum distribution of bulk materials in ambient and operando environments. We report high-resolution inelastic x-ray scattering experiments with high momentum and energy transfer performed at a storage-ring-based high-energy x-ray light source facility using an x-ray transition-edge sensor (TES) microcalorimeter detector. The performance was compared with a silicon drift detector (SDD), an energy-resolving semiconductor detector, and Compton profiles were measured for lithium and cobalt oxide powders relevant to lithium-ion battery research. Spectroscopic analysis of the measured Compton profiles demonstrates the high-sensitivity to the low-Z elements and oxidation states. The line shape analysis of the measured Compton profiles in comparison with computed Hartree-Fock profiles is usually limited by the resolution of the semiconductor detector. We have characterized an x-ray TES microcalorimeter detector for high-resolution Compton scattering experiments using a bending magnet source at the Advanced Photon Source with a double crystal monochromator, providing monochromatic photon energies near 27.5 keV. The momentum resolution below 0.16 atomic units (a.u.) was measured, yielding an improvement of more than a factor of 7 over a state-of-the-art SDD for the same scattering geometry. Furthermore, the lineshapes of narrow valence and broad core electron profiles of sealed lithium metal were clearly resolved using an x-ray TES compared to smeared and broadened lineshapes observed when using the SDD. High-resolution Compton scattering using the energy-resolving area detector shown here presents new opportunities for spatial imaging of electron momentum distributions for a wide class of materials with applications ranging from electrochemistry to condensed matter physics.
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Dorkhom N, Grainger D, Ren Y. 27P Outcomes analysis of the effect of an educational activity on the knowledge and confidence of oncologists regarding emerging antibody drug conjugates for the treatment of breast cancer. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.10.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
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Ren Y, Bertoldi M, Caiani EG. Development of an IT tool to support post-market surveillance and expert panels in detecting sentinel signals relevant to serious incidents in high-risk medical devices: pilot on italian data. Eur Heart J 2022. [DOI: 10.1093/eurheartj/ehac544.2842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Introduction
The EU Medical Device Regulation 2017/745, in force since May 26th 2021, defines new rules for medical device (MD) certification and post-market surveillance (PMS). For high-risk implantable MD, in the certification process notified bodies are obliged to consult clinical Expert Panels (EP) that could decide to proceed for an extensive review of the supporting clinical data provided by the manufacturer, also in view of sentinel signals, such as significantly increased rate of reported serious incidents for a specific MD groups.
Purpose
1) To develop an ICT tool to automatically collect and display in an aggregated way the accessible curated regulatory information on MD alerts and recalls to capture possible trends in reported incidents that could be used both for scientific analysis and as information source to EP. 2) To conduct a pilot feasibility study on the Italian data, characterized already by the same European Medical Device Nomenclature (EMDN), organized in a multi-level hierarchical tree code to define a MD, as it will be used in Europe.
Methods
Web scraping was used to retrieve data of 7622 safety notices (SN) from 2009 to 2021 from the Italian Ministry of Health website. The EMDN code was missing in 68% of cases: to retrieve it, the MD best match was searched within a separate public list of about 1.5M MD on the Italian market containing the EMDN code, using Natural Language Processing techniques and pairwise entity resolution with Cosine similarity to identify similar manufacturers and MD. The performance of this approach was tested on the 2440 SN for which the EMDN code was available as gold standard. A mash up was then performed to integrate data, and to present it to the final user through a graphical interface.
Results
The implemented entity resolution method was able to correctly assign the correct manufacturer to the MD in each SN in 99% of the cases. Moreover, the correct EMDN code at level 1 (22 categories available) was assigned in 2382 SN (97.62%), at level 2 (146 anatomical or functional groups available) in 2366 SN (96.97%), at level 3 (multiple types available) in 2304 SN (94.45%). The developed interface (Figure 1) allows querying the database by manufactures, devices, type of SN (1a), and selecting the EMDN nomenclature up to the fourth level (1b). As a result, the relevant information is shown, including trends over the selected period and the link to the SN on the original website (2).
Conclusions
The proposed approach was able to cope with the uncompleteness of the publicly available data in the SN, thus allowing proper matching of MD with its EMDN code up to level 3 with very good performance. In this way, grouping of SN relevant to a specific MD category/group/type could be used as possible sentinel for increased rates in reported serious incidents in high-risk MD. Extension of this approach to aggregate SN from other EU nations could result in an effective support tool in PMS.
Funding Acknowledgement
Type of funding sources: Public grant(s) – EU funding. Main funding source(s): EU Horizon 2020 - Project CORE-MD
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Feng P, Wu J, Ren Y, Zhang L, Cao J, Yang L. Early pregnancy regulates the expression of prolactin and its receptor in the thymus, the liver, the spleen and lymph nodes in sheep. Domest Anim Endocrinol 2022; 81:106731. [PMID: 35635981 DOI: 10.1016/j.domaniend.2022.106731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 11/17/2022]
Abstract
As a pituitary hormone, prolactin (PRL) is also synthesized by immune system cells, and exerts its effects on the immune system by binding to its receptor (PRLR) via endocrine and paracrine/autocrine pathways. The immune organs adapt to the presence of fetal alloantigens during pregnancy, and the immune system is composed of primary organs and secondary organs. The objective of this study is to analyze the effects of early pregnancy on expression of PRL and PRLR in maternal immune organs in sheep. In this study, the thymus, lymph node, the spleen and the liver were sampled at day 16 of the estrous cycle, and at days 13, 16, and 25 of pregnancy in ewes. Expression of PRL and PRLR was analyzed through quantitative real-time PCR, Western blot and immunohistochemistry. Our data showed that there were an upregulation of PRL and PRLR in the thymus, lymph node and the spleen, and a downregulation in the liver during early pregnancy in ewes. In conclusion, it is reported for the first time that early pregnancy has tissue specific effects on expression of PRL isoform and PRLR isoform in the thymus, lymph node, the spleen and the liver, which may be owing to these organs exerting different functions during early pregnancy, and necessary for the successful pregnancy in sheep.
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Liu X, Domier CW, Dannenberg J, Zhu Y, Sirigiri JR, Ren Y, Stratton B, Luhmann NC. The National Spherical Torus Experiment-Upgrade poloidal high-k scattering system pitch angle design modifications. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2022; 93:103509. [PMID: 36319363 DOI: 10.1063/5.0099912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/23/2022] [Indexed: 06/16/2023]
Abstract
A 693 GHz, eight-channel, poloidal high-k (k refers to wavenumber) collective scattering system is under development for the National Spherical Torus Experiment-Upgrade device. It will replace the previous 280 GHz, five-channel, tangential scattering system to study high-k electron density fluctuations, thereby providing a measurement of the kθ-spectrum of both electron temperature gradient and ion temperature gradient modes. A tool is under development to calculate the wavenumber that exists in the presence of strong magnetic pitch angles. We use this tool to motivate a new receiver optical design for significantly improved performance, details of which are presented herein.
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Wang YF, Ren Y, Zhu CF, Qian L, Yang Q, Deng WM, Zou LY, Liu Z, Luo DH. Optimising diffusion-weighted imaging of the thyroid gland using dedicated surface coil. Clin Radiol 2022; 77:e791-e798. [PMID: 36096939 DOI: 10.1016/j.crad.2022.07.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 07/06/2022] [Accepted: 07/08/2022] [Indexed: 11/03/2022]
Abstract
AIM To assess the feasibility of applying field-of-view (FOV) optimised and constrained undistorted single-shot (FOCUS) diffusion-weighted imaging (DWI) in the thyroid gland by comparing its image quality with conventional DWI (C-DWI) qualitatively and quantitatively using a dedicated surface coil exclusively designed for the thyroid gland at 3 T magnetic resonance imaging (MRI). MATERIALS AND METHODS In this prospective study, 32 healthy volunteers who had undergone 3 T the thyroid gland MRI with FOCUS-DWI and C-DWI were enrolled. Two independent reviewers assessed the overall image quality, artefacts, sharpness, and geometric distortion based on a five-point Likert scale. The signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR), and apparent diffusion coefficient (ADC) were quantified for both sequences. Interobserver agreement, qualitative scores, and quantitative parameters were compared between two sequences. RESULTS Agreement between the two readers was good for FOCUS-DWI (κ = 0.714-0.778) and moderate to good for C-DWI (κ = 0.525-0.672) in qualitative image quality assessment. Qualitatively, image quality (overall image quality, artefacts, sharpness, and geometric distortion) was significantly better in FOCUS-DWI than that in the C-DWI (all p<0.05); however, quantitatively, FOCUS-DWI had significantly lower SNRs (p<0.001) and CNRs (p=0.012) compared with C-DWI. The ADC value on FOCUS-DWI was significantly higher than that on C-DWI (p<0.001). CONCLUSION FOCUS-DWI depicted the thyroid gland with significantly better image quality qualitatively and less ghost artefacts, but had significantly lower SNR and CNR quantitatively, compared with C-DWI, suggesting that both DWI sequences have advantages and could be chosen for different purposes.
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Karamat U, Yang R, Ren Y, Lu Y, Li N, Zhao J. Comprehensive In Silico Characterization and Expression Pro-Filing of DA1/DAR Family Genes in Brassica rapa. Genes (Basel) 2022; 13:genes13091577. [PMID: 36140744 PMCID: PMC9498896 DOI: 10.3390/genes13091577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/24/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022] Open
Abstract
The DA1/DAR family genes have been shown to play important roles in regulating organ size and plant biomass in the model plant Arabidopsis and several crops. However, this family has not been characterized in Brassica rapa (B. rapa). In this study, we identified 17 DA1&DAR genes from B. rapa. Phylogenetic analysis indicated that these genes are classified into four groups. Structural and motif analysis of BrDA1&DARs discovered that the genes within the same group have similar exon-intron structures and share an equal number of conserved motifs except for BrDAR6.3 from group IV, which contains two conserved motifs. Cis-regulatory elements identified four phytohormones (Salicylic acid, Abscisic acid, Gibberellin, and auxin) and three major abiotic (Light, Low temperature, and drought) responsive elements. Further, six br-miRNAs named br-miR164a, br-miR164b, br-miR164c, br-miR164d, br-miRN360, and br-miRN366 were found which target BrDAR6.1, BrDA1.4, and BrDA1.5. BrDA1&DAR genes were highly expressed in stem, root, silique, flower, leaf, and callus tissues. Moreover, qRT-PCR analyses indicated that some of these genes were responsive to abiotic stresses or phytohormone treatments. Our findings provide a foundation for further genetic and physiological studies of BrDA1&DARs in B. rapa.
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Zhao M, Li Y, Wang F, Ren Y, Wei D. A CRISPRi mediated self-inducible system for dynamic regulation of TCA cycle and improvement of itaconic acid production in Escherichia coli. Synth Syst Biotechnol 2022; 7:982-988. [PMID: 35782485 PMCID: PMC9213231 DOI: 10.1016/j.synbio.2022.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 11/17/2022] Open
Abstract
Itaconic acid (ITA), an effective alternative fossil fuel, derives from the bypass pathway of the tricarboxylic acid (TCA) cycle. Therefore, the imbalance of metabolic flux between TCA cycle and ITA biosynthetic pathway seriously limits the production of ITA. The optimization of flux distribution between biomass and production has the potential to the productivity of ITA. Based on the previously constructed strain Escherichia coli MG1655 Δ1-SAS-3 (ITA titer: 1.87 g/L), a CRISPRi-mediated self-inducible system (CiMS), which contained a responsive module based on the ITA biosensor YpItcR/P ccl and a regulative CRISPRi-mediated interferential module, was developed to regulate the flux of the TCA cycle and to enhance the capacity of the strain to produce ITA. First, a higher ITA-yielding strain, Δ4-P rmd -SAS-3 (ITA titer: 3.20 g/L), derived from Δ1-SAS-3, was constructed by replacing the promoter P J23100 , for the expression of ITA synthesis genes, with P rmd and knocking out the three bypass genes poxB, pflB, and ldhA. Subsequently, the CiMS was used to inhibit the expression of key genes icd, pykA, and sucCD to dynamically balance the metabolic flux between TCA cycle and ITA biosynthetic pathway during the ITA production stage. The constructed strain Δ4-P rmd -SAS-3 under the dynamic regulation of the CiMS, showed a 23% increase in the ITA titer, which reached 3.93 g/L. This study indicated that CiMS was a practical strategy to dynamically and precisely regulated the metabolic flux in microbial cell factories.
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Zhang K, Pan T, Wang L, Wang H, Ren Y, Wei D. Screening and characterization of a nitrilase with significant nitrile hydratase activity. Biotechnol Lett 2022; 44:1163-1173. [PMID: 36050605 DOI: 10.1007/s10529-022-03291-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 08/09/2022] [Indexed: 11/28/2022]
Abstract
PURPOSE We screened nitrilases with significant nitrile hydratase activity to exploit their potential in benzylic amide biosynthesis. We also investigated the factors affecting their hydration activity to support further research on benzylic amide production by nitrilase. METHODS A sequence-based screening method using previously reported crucial positions identified to be essential for amide-forming capacity of nitrilase (referred to as "amide-formation hotspots") as molecular probes to identify putative amide-forming nitrilases. RESULTS Based on the previously reported "amide-formation hotspots," we identified a nitrilase NitPG from Paraburkholderia graminis DSM 17151 that could produce a significant amount of mandelamide toward mandelonitrile and exhibited general hydration activity toward various benzylic nitriles. The time-course experiment with NitPG demonstrated that amide was also a true reaction product of nitrilase, suggesting that the nitrile catalysis by amide-forming nitrilase could be a post-transition state bifurcation-mediated enzymatic reaction. Further research demonstrated that low temperature, metal ion addition, and specific substrate structure could profoundly improve the amide formation capability of nitrilase. CONCLUSIONS NitPG with broad hydration activity is a potential candidate for the enzymatic synthesis of benzylic amides for biotechnological applications. Studying the effect of nitrilase hydration activity could promote our understanding of the factors that influence amide and acid distribution.
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Wan S, Zhang TT, Chen T, Zhang D, Mo D, Xu J, Tian HM, Ren Y. [Primary pigmented nodular adrenal disease: a report of three cases]. ZHONGHUA NEI KE ZA ZHI 2022; 61:944-947. [PMID: 35922222 DOI: 10.3760/cma.j.cn112138-20211031-00760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
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Xu JF, Cen YX, Tang SS, Ren Y, Lyu WG. [IL-1β inhibitor sensitizes to olaparib in homologous recombination deficiency proficient ovarian cancer cells]. ZHONGHUA FU CHAN KE ZA ZHI 2022; 57:519-529. [PMID: 35902786 DOI: 10.3760/cma.j.cn112141-20220509-00307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Objective: To investigate the inhibitory effect of combined strategy of poly adenosine diphosphate ribose polymerase (PARP) inhibitor and interleukin-1β (IL-1β) inhibitor on homologous recombination deficiency (HRD)-proficient ovarian cancer cells. Methods: (1) HRD-proficient ovarian cancer cell lines OVCAR3 and CAOV3 were treated with PARP inhibitor olaparib. Screening by RNA sequencing analysis, the expression level of IL-1β was validated by enzyme-linked immunosorbent assay (ELISA) and western blot. (2) The dose-response curves of IL-1β inhibitor diacerein were evaluated by cell counting kit-8 (CCK-8) assays in OVCAR3 and CAOV3 cells. CCK-8 assays were further applied to determine the viabilities of OVCAR3 and CAOV3 cells. (3) To evaluate the synergistic effects of olaparib and IL-1β inhibitor in vivo, the transplanted ovarian cancer model was constructed. BALB/c-nude mice (n=16) were injected intraperitoneally with 1×107 OVACR3 cells labelled with luciferase (OVCAR3-Luc). Immunohistochemistry (IHC) assay was performed to determine nuclear antigen associated with cell proliferation (Ki-67) expression. (4) Blood routine tests, kidney and liver function tests were performed to analyze the toxic reaction of different drug treatments. The potential drug-induced injuries of vital organs including heart, liver, spleen, lungs and kidneys of nude mice were determined by hematoxylin-eosin (HE) staining. Results: (1) The RNA sequencing results showed that the mRNA level of IL-1β was the most significantly increased among the 25 differentially expressed genes in OVCAR3 cells treated with olaparib, compared to the negative control group. Olaparib treatment significantly promoted the secretion and expression of IL-1β protein in both OVACR3 and CAOV3 cells by ELISA [(36.2±3.5) and (49.5±3.5) pg/ml, respectively; all P<0.001] and western bolt (2.87±0.37 and 2.05±0.08, respectively; all P<0.01). (2) The half maximal inhibitory concentration (IC50) value of IL-1β inhibitor was determined as follows: 75 μmol/L for OVACR3 cells and 100 μmol/L for CAOV3 cells. The treatments were divided into four groups including control group, olaparib monotherapy group, IL-1β inhibitor monotherapy group and the combination therapy group. The cell viabilities of each group in OVCAR3 and CAOV3 were determined by CCK-8 assay. The data in each group were showed as follows for OVCAR3 and CAOV3 cells: (100.0±0.4)% and (100.0±3.5)% in control group; (63.1±6.2)% and (63.3±3.8)% in olaparib monotherapy group; (61.6±4.7)% and (63.8±3.5)% in IL-1β inhibitor monotherapy group; and (32.9±5.2)% and (30.0±1.3)% in the combination therapy group. The viability assay showed that the combined strategy exhibited a significant inhibition effect on OVACR3 and CAOV3 cells, compared to the monotherapy group and the control group (all P<0.01). (3) All mice with transplanted tumors of HRD-proficient ovarian cancer cells were randomly divided into four groups, and treated with four different treatments as mentioned above, respectively. After 4 weeks (on day 29), the vivo fluorescence imaging were determined. The results showed that the amount of fluorescence of transplanted tumors was mostly decreased in the combination therapy group [(0.5±0.4)×1010 p/s], compared to the control group [(4.2±1.0)×1010 p/s] or the groups treated with any single drug [(3.1±0.9)×1010, (2.2±0.9)×1010 p/s; all P<0.05]. Mice were then sacrificed under anesthesia, and all transplanted tumors detached and weighed for further investigation. The weight of transplanted tumors was significantly decreased in the combination therapy group [(0.09±0.03) g], compared to that in control group [(0.25±0.05) g] or groups treated with any single drug [(0.17±0.03), (0.19±0.04) g; all P<0.05]. The measurement of the expression of Ki-67 showed that it was significantly decreased in the combination therapy group (0.33±0.10), compared to that in the control group (1.00±0.20) or monotherapy groups (0.76±0.07, 0.77±0.12; all P<0.05). (4) There were no significant differences of body weights, blood routine test, renal and liver function tests among mice with different treatments (all P>0.05). Moreover, no significant injuries were observed in the vital organs among the four groups. Conclusions: The combination of olaparib and IL-1β inhibitor synergistically exhibits significant cytotoxicity in HRD-proficient ovarian cancer cells. Moreover, the blood routine and blood biochemistry results confirmed the biosafety of the combination of olaparib and IL-1β inhibitor.
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Song Z, Zhang M, Ren Y, Iang B. [Improved Mayo Endoscopic Score has a higher value for evaluating clinical severity of ulcerative colitis]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2022; 42:997-1005. [PMID: 35869761 DOI: 10.12122/j.issn.1673-4254.2022.07.05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To assess the value of Improved Mayo Endoscopic Score (IMES) for evaluation of the clinical severity of ulcerative colitis (UC). METHODS We retrospectively analyzed the clinical and endoscopic data of 167 patients diagnosed with UC in Beijing Tsinghua Changgung Hospital from January, 2015 to November, 2021. The severity of endoscopic lesions was determined by Mayo Endoscopic Score (MES, 0-3 points) and the Ulcerative Colitis Endoscopic Index of Severity (UCEIS) score (0-8 points), and the scope of endoscopic lesions was evaluated based on the Montreal classification system. The IMES was established by combining the MES with the Montreal classification. RESULTS The IMSE showed stronger correlations with modified Truelove and Witts Disease Severity, Mayo score and partial Mayo score (r=0.712, 0.784, and 0.703, respectively) than MES (r=0.642, 0.754, and 0.604, respectively), Montreal classification (r=0.598, 0.628, and 0.603, respectively) and UCEIS (r= 0.670, 0.767, and 0.677, respectively). ROC curve analysis showed that IMES was superior to MES, Montreal and UCEIS in diagnosis of severe and moderate- to-severe UC. IMES also showed stronger correlations with the laboratory indicators including CRP (r=0.583), WBC (r=0.235), HB (r=-0.280), PLT (r=0.352), ALB (r=-0.396) and ESR (r=0.471) than MES and Montreal classification. An IMES score of 5 was of greater value than a MES score of 3, E3, and UCEIS≥6 for predicting the administration of systemic hormones, immunosuppressants, or surgery in the near future. CONCLUSION IMES can better reflect the clinical severity of UC and has good correlations with the laboratory indicators of the patients.
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Steegman R, Hogeveen F, Schoeman A, Ren Y. Cone beam computed tomography volumetric airway changes after orthognathic surgery: a systematic review. Int J Oral Maxillofac Surg 2022; 52:60-71. [PMID: 35788289 DOI: 10.1016/j.ijom.2022.05.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 05/22/2022] [Accepted: 05/31/2022] [Indexed: 10/17/2022]
Abstract
The aim of this systematic review was to provide a structured overview of three-dimensional airway volume changes in relation to various orthognathic surgeries. Clinical human studies performing pre- and postoperative three-dimensional airway volume assessments to investigate volumetric changes of the airway after orthognathic surgery were included. Pre-determined inclusion and exclusion criteria were applied in an extensive search of the PubMed, Embase, and Web of Science electronic databases. The cut-off date was set to January 1, 2022. Forty-one articles reporting retrospective and prospective case-control and case series studies were included. All studies were determined to be of medium quality (moderate risk of bias). The included studies were categorized by type of intervention. Pre- and postoperative volumes were extracted from the available data, and volume changes as a percentage of the preoperative levels were calculated. Isolated mandibular setback surgery generally decreased the airway volume. Isolated maxillary or mandibular advancement, bimaxillary advancement, and surgically assisted maxillary expansion generally increased the airway volume in the total airway and oropharynx, among which the effect of bimaxillary advancement surgery appeared most significant. High heterogeneity exists in the terminology and definitions of the airway and its segments. A more uniform methodology for airway volume measurement is needed to provide an insight into the impact on the airway of specific types of surgical intervention. In conclusion, airway volumes are affected after orthognathic surgery, which may be of clinical significance, especially in patients who are predisposed to obstructive sleep apnoea.
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Petkov V, Peralta JE, Aoun B, Ren Y. Atomic structure and Mott nature of the insulating charge density wave phase of 1T-TaS 2. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2022; 34:345401. [PMID: 35688141 DOI: 10.1088/1361-648x/ac77cf] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
Using x-ray pair distribution function (PDF) analysis and computer modeling, we explore structure models for the complex charge density wave (CDW) phases of layered 1T-TaS2that both well capture their atomic-level features and are amenable to electronic structure calculations. The models give the most probable position of constituent atoms in terms of 3D repetitive unit cells comprising a minimum number of Ta-S layers. Structure modeling results confirm the emergence of star-of-David (SD) like clusters of Ta atoms in the high-temperature incommensurate (IC) CDW phase and show that, contrary to the suggestions of recent studies, the low-temperature commensurate (C) CDW phase expands upon cooling thus reducing lattice strain. The C-CDW phase is also found to preserve the stacking sequence of Ta-S layers found in the room temperature, nearly commensurate (NC) CDW phase to a large extent. DFT based on the PDF refined model shows that bulk C-CDW 1T-TaS2also preserves the insulating state of individual layers of SD clusters, favoring the Mott physics description of the metal-to-insulator (NC-CDW to C-CDW) phase transition in 1T-TaS2. Our work highlights the importance of using precise crystal structure models in determining the nature of electronic phases in complex materials.
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Li Y, Zhao M, Wei D, Zhang J, Ren Y. Photocontrol of Itaconic Acid Synthesis in Escherichia coli. ACS Synth Biol 2022; 11:2080-2088. [PMID: 35638258 DOI: 10.1021/acssynbio.2c00014] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Metabolic engineering aims to control cellular metabolic flow and maximize the production of a product of interest. Photocontrol of the activities of proteins is an effective method for accurately regulating metabolic pathways. In this study, we inserted the photosensor light-oxygen-voltage-sensing domain 2 of Avena sativa (AsLOV2) into selected sites of isocitrate dehydrogenase (IDH), the key enzyme in the competitive pathway of itaconic acid (ITA) synthesis, to construct photoswitchable IDH-AsLOV2 (ILOVs). These engineered light-sensitive proteins were used to regulate the metabolic flux of the tricarboxylic acid (TCA) cycle in Escherichia coli to improve ITA production. The engineered fusion proteins ILOV2, ILOV3, ILOV6, and ILOV7 exhibited effective reversibility under the oscillation of darkness and blue light illumination in vitro. The efficacies of the intracellular photoswitches were evaluated, and an optimal photocontrol strategy was established in vivo. The ITA titer was significantly enhanced to 3.30 g/L for strain ITAΔ43, which displayed superior photoswitchable potency for ITA production compared with the strains that completely deleted the icd gene. The photocontrol strategy developed here can be extended for process optimization and titer improvement of other high-value bioengineering chemicals.
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Zhang S, Ren Y. The Mediating Role of a Xu-Argument Based Iterative Translation Continuation Task in the Dynamic Relationships Between Translation Learning Anxiety and Foreign Language Learning Proficiency and Translation Strategies. Front Psychol 2022; 13:916597. [PMID: 35712187 PMCID: PMC9196630 DOI: 10.3389/fpsyg.2022.916597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 05/09/2022] [Indexed: 12/04/2022] Open
Abstract
Growing interest has been shown in the effects of the xu-argument based translation continuation task, which have been mainly explored via the linguistic dimension. The current study, using a pretest-intervention-posttest design, investigated the dynamic relationships among translation learning anxiety, foreign language learning proficiency, and English-Chinese translation strategies under an iterative translation continuation task (ITCT) that lasted 13 turns. The results yielded from 134 student translators showed a significant increase in their translation strategies comprehension and production, with those with a medium level of translation learning anxiety and foreign language learning proficiency achieving the most. It also showed that the significant partial mediating effect of translation learning anxiety between foreign language learning proficiency and the production of translation strategies in the pre-test became insignificant in the post-test, and the insignificant correlation between the comprehension and production of translation strategies in the pre-test became significant in the post-test. The dynamic relationships among translation learning anxiety, foreign language learning proficiency, and translation strategies confirmed the mediating role of the ITCT in attenuating the impact of higher level of translation learning anxiety and lower level of foreign language learning proficiency on the comprehension and use of translation strategies, though its effects could be different for student translators with different levels of translation anxiety and proficiency as measured by different assessments.
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van Leeuwen BJ, Dijkstra PU, Dieters JA, Verbeek HPJ, Kuijpers-Jagtman AM, Ren Y. Effect of voxel size in cone-beam computed tomography on surface area measurements of dehiscences and fenestrations in the lower anterior buccal region. Clin Oral Investig 2022; 26:5663-5672. [PMID: 35513582 PMCID: PMC9474376 DOI: 10.1007/s00784-022-04521-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 04/23/2022] [Indexed: 11/26/2022]
Abstract
Objectives This study aims to assess whether different voxel sizes in cone-beam computed tomography (CBCT) affected surface area measurements of dehiscences and fenestrations in the mandibular anterior buccal region. Materials and methods Nineteen dry human mandibles were scanned with a surface scanner (SS). Wax was attached to the mandibles as a soft tissue equivalent. Three-dimensional digital models were generated with a CBCT unit, with voxel sizes of 0.200 mm (VS200), 0.400 mm (VS400), and 0.600 mm (VS600). The buccal surface areas of the six anterior teeth were measured (in mm2) to evaluate areas of dehiscences and fenestrations. Differences between the CBCT and SS measurements were determined in a linear mixed model analysis. Results The mean surface area per tooth was 88.3 ± 24.0 mm2, with the SS, and 94.6 ± 26.5 (VS200), 95.1 ± 27.3 (VS400), and 96.0 ± 26.5 (VS600), with CBCT scans. Larger surface areas resulted in larger differences between CBCT and SS measurements (− 0.1 β, SE = 0.02, p < 0.001). Deviations from SS measurements were larger with VS600, compared to VS200 (1.3 β, SE = 0.05, P = 0.009). Fenestrations were undetectable with CBCT. Conclusions CBCT imaging magnified the surface area of dehiscences in the anterior buccal region of the mandible by 7 to 9%. The larger the voxel size, the larger the deviation from SS measurements. Fenestrations were not detectable with CBCT. Clinical relevance CBCT is an acceptable tool for measuring dehiscences but not fenestrations. However, CBCT overestimates the size of dehiscences, and the degree of overestimation depends on the actual dehiscence size and CBCT voxel size employed.
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Ji D, Li J, Ren Y, Wang Y. Rational engineering in Escherichia coli for high-titer production of baicalein based on genome-scale target identification. Biotechnol Bioeng 2022; 119:1916-1925. [PMID: 35312063 DOI: 10.1002/bit.28087] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/04/2022] [Accepted: 03/16/2022] [Indexed: 11/08/2022]
Abstract
Baicalein is a bioactive flavonoid isolated from the traditional Chinese medicinal plant, Scutellaria baicalensis Georgi. Microbial synthesis of flavonoids has been intensively developed owing to the eco-friendly nature of the process. However, the titer of the flavonoids obtained is still at a low level, and effective methods to enhance these titers are lacking. In this study, the synthetic performance of baicalein-producing engineered E. coli was rationally evaluated to enhanced the expression of key enzymes. Transcriptional analyses of baicalein-overproducing strain and a control strain enabled the identification of 13 beneficial genes, including 8 genes that are seemingly irrelevant to baicalein metabolism. With the combination of the enzyme assembly and modularization strategy, the engineered DN-8 strain produced 367.8 mg/L baicalein in fed-batch fermentation, the maximum titer reported to date. This article is protected by copyright. All rights reserved.
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Liu YM, Ren Y, Jia YL, Yao MH, Zou K, Lin K, Sun X. [Exploration of construction mode of real-world data system]. ZHONGHUA LIU XING BING XUE ZA ZHI = ZHONGHUA LIUXINGBINGXUE ZAZHI 2022; 43:418-423. [PMID: 35345300 DOI: 10.3760/cma.j.cn112338-20210824-00675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Real-world data study evidence, as an important part of evaluating the safety and effectiveness of drugs and devices, has attracted increasing attention from regulatory agencies and scholars both at home and abroad, and has become an essential source of evidence to support the development and review of drugs and devices. This paper systematically discusses the process and mode of real-world data system construction based on the preliminary practical study of real-world data according to the guidelines/technical specifications issued by regulatory agencies and academic research results. This study result provides not only reference for the generation of clinical evaluation evidence to meet the regulatory requirements for innovative drugs and devices, but also reference for researchers, sponsors and regulators to carry out real-world data studies successfully.
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