148 research outputs found
Synthesis and properties of triplex-forming oligonucleotides containing 2'-modified nucleoside analogues
No full textTriplex-forming oligonucleotides (TFOs) bind to the major groove of the DNA duplex via the Hoogsteen interactions to generate triple helices. Potential applications of triplex technology are in regulation of gene expression, site-directed gene-knockout, mutation correction and as tools in molecular biotechnology. The presence of 2’-modified nucleosides in therapeutic oligonucleotides inhibits enzymatic degradation in vivo. Therefore such sugar modifications have the potential to improve the biological activity of TFOs. We have synthesized the phosphoramidite monomers of six 2’-modified nucleosides from D-ribose via 1-O-methyl-3,5-di-O-benzyl-?-D-ribofuranoside. Three of these are N-linked nucleosides: 2’-O-methoxyethyl-5-propargylamino-uridine (MEPU), 2’-O methoxyethyl-5-methyl-cytidine (MOE-5-MeC) and 2’-O-aminoethylthymidine (AE-T); and three are C-linked nucleosides: 3-methyl-2-amino-pyrdine-2’-O-methyl-ribonucleoside (Me-MAP), 3-methyl-2- amino-pyrdine-2’-O-methoxyethyl-ribonucleoside (MOE-MAP) and 3-methyl-2- amino-pyrdine-2’-O-aminoethyl-ribonucleoside (AE-MAP). These monomers were incorporated into a number of oligonucleotides, on which the biophysical and biochemical studies have been performed. TFOs containing the N-nucleoside (MEPU) showed high duplex affinity and strong nuclease resistance. Studies on two C-nucleosides (Me-MAP and MOE-MAP) revealed that their triplex stability was determined by the sequence context. The incorporation of Me-MAP and MOE-MAP into oligonucleotides renders them much more resistant to the degradation by serum nucleobases compared to their 2’-deoxy derivative (dMAP) and 2’-deoxycytidine (dC). AE-MAP is a promising triplex stabilizer, which not only shows the highest triplex stabilization, but also displays an impressive resistance to enzymatic degradatio
MAGEC_2024
No full textMAGEC (Magma And Gas Equilibrium Calculator)
Author: Chenguang Sun
Copyright, 2025
This Matlab program calculates the equilibrium distribution of C-H-O-S volatiles (H2, H2O, CO, CO2, CH4, H2S, SO2, S2, COS, O2) in gas-melt coupled systems.
Updates on April 27, 2025:
1. Added additional options for CO2 and H2O solubility models
2. Corrected CO solubility models
If you use this program for your publications, please cite the following references:
1. Sun, C. and Yao, L., 2024. Redox equilibria of iron in low-to high-silica melts: A simple model and its applications to CHOS degassing. Earth and Planetary Science Letters, 638, p.118742. [Note: This is the reference for MAGEC_2024 with new Fe- and S-redox models and flexible setting options.]
2. Sun, C. and Lee, C.T.A., 2022. Redox evolution of crystallizing magmas with CHOS volatiles and its implications for atmospheric oxygenation. Geochimica et Cosmochimica Acta, 338, pp.302-321. [Note: This is the reference for the first version of MAGEC.]
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How to run the program:
1. Input T/P/logfO2 (or Fe3+/FeT) and compositions in the input file (.xlsx).
Make sure you use different names for the input and output files.
The batch data could be polybaric/isobaric/adiabatic degassing.
2. Modify the "settings" in the input file.
3. Open [Run_MAGEC_2024_v2.m] in Matlab
4. Go to [Editor] Tab in Matlab and click [Run] button.
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2?-aminoethoxy-2-amino-3-methylpyridine in triplex-forming oligonucleotides: high affinity, selectivity and resistance to enzymatic degradation
No full textThe phosphoramidite monomer of the C-nucleoside 2?-aminoethoxy-2-amino-3-methylpyridine (AE-MAP) has been synthesized for the first time and incorporated into triplex-forming oligonucleotides (TFOs). Ultraviolet melting and DNase I footprinting studies show that AE-MAP is a potent triplex-stabilizing monomer that is selective for GC base pairs. TFOs containing AE-MAP bind with high affinity to duplexes but only weakly to single stranded DNA. In addition, AE-MAP confers high nuclease resistance on oligonucleotides. TFOs containing AE-MAP have potential for gene knock-out and gene expression studies.<br/
2?-Substituted 2-amino-3-methylpyridine ribonucleosides in triplex-forming oligonucleotides: triplex stability is determined by chemical environment
No full textA new synthetic route to the phosphoramidite monomer of 2-amino-3-methyl-5-(2?-O-methyl-?-D-ribofuranosyl)pyridine (Me-MAP) and its 2?-O-methoxyethyl analogue (MOE-MAP) has been established using D-ribose and 2-amino-3-methyl-5-bromopyridine as precursors. Ultraviolet melting and DNase I footprinting studies indicate that the triplex stabilizing properties of 2?-modified MAPs are determined by the conformation of the entire oligonucleotide backbone. Me-MAP confers a higher triplex stability than 2?-deoxycytidine whereas triplex stabilization by MOE-MAP is similar to that of dC. Incorporation of Me-MAP or MOE-MAP into oligonucleotides renders them dramatically more resistant to degradation by serum nucleases than incorporation of 2-amino-3-methyl-5-(2?-deoxy-?-D-ribofuranosyl)pyridine (dMAP) or dC.<br/
"Yi zhuan" "sheng sheng" si xiang yan jiu =: On the Idea of shengsheng in the commentaries of Yi
No full textPh.D.The thesis aims to investigate the idea of Shengsheng (continuous creation) in the Commentaries of Yi and its development in the history of Confucian philosophy. The investigation consists of four parts. The first part starts by discussing the literal meaning of the character Sheng in the oracle bone script and the Chinese bronze inscriptions. It then examines the idea of Shengsheng in the ancient Chinese classics, especially its textual context in the Commentaries of Yi . Accordingly, we will answer the following questions one by one: What is Shengsheng ? How can it actualize? How is the idea adopted by other Pre Qin thoughts? The second part focuses on the understanding of the idea in Han Confucianism. It takes Zhouyi Qianzhaodu and the Zheng Xuan interpretation as illustrative examples. Here we see how another idea Qi has been introduced to interpret Sheng sheng as the origin and process of actualization in both the natural world and human community. The third part moves to the development of the idea in Northern Song Confucianism and explores how the Confucian scholars at that time further elaborated the idea as an essential of moral metaphysics. The final part studies the thought of Xiong Shili to show how Xiong draws from Buddhism and Confucian philosophy to develop a critical inquiry into the idea and hence argues its modern relevance.本文以《易傳》「生生」觀念為研究對象。全文分為四部分，第一部分由考察甲骨、金文中「生」字之原義開始，依次分析並討論了早期文獻中所見之「生生」觀念及《易傳》所論「生生」之本義，包括何為《易傳》所論之「生生」，據《易傳》之說 ，「 生生」將何以實現，以及《易傳》「生生」觀念與先秦諸子思想之關係。第二部分通過以《周易乾鑿度》為切入點，考察了經學時代下學者們對《易傳》「生生」觀念的最有代表性的若干理解，包括據《乾鑿度》之理解 ，「 生生」當如何實現於天地萬物及人類社會之中，以及鄭康成所作之《乾鑿度注》之中包含的對「生生」 所以實現之根本與歷程的另一種思考。第三部分通過將北宋五子的詮釋作為典範，考察了理學思維下《易傳》「生生」觀念之詮釋理論的一般理論框架，包括理學思維下的「生生」之本質及「生生」之道德義之豁顯。第四部分則通過將熊十力《新唯識論（語體文本）》中關於《易傳》「生生」觀之詮釋作為代表，考察了現代哲學視域下的《易傳》「生生」觀念。竇晨光."2019年8月".Parallel title from added title page.Thesis Ph.D. Chinese University of Hong Kong 2019.Includes bibliographical references (leaves 334-340).Abstracts in Chinese and English.Title from PDF title page (viewed on February 23, 2022).Dou Chenguang
Synthesis and properties of triplex-forming oligonucleotides containing 2'-O-(2-methoxyethyl)-5-(3-aminoprop-1-ynyl)-uridine
No full text2'-O-(2-Methoxyethyl)-5-(3-aminoprop-1-ynyl)-uridine phosphoramidite (MEPU) has been synthesized from d-ribose and 5-iodouracil and incorporated into triplex-forming oligonucleotides (TFOs) by automated solid-phase oligonucleotide synthesis. The TFOs gave very high triplex stability with their target duplexes as measured by ultraviolet/fluorescence melting and DNase I footprinting. The incorporation of MEPU into TFOs renders them resistant to degradation by serum nucleases.<br/
FVM and XCT Measurement of Surface Texture of Additively Manufactured Parts
No full textFocus variation microscopy (FVM) and X-ray computed tomography (XCT) are two popular technologies employed to measure the surface texture of additively manufactured components. The impacts of various influence factors of these two measurement techniques on surface texture measurement are investigated, respectively. A twostage surface registration program is developed to allow the accurate comparison of surface topographies measured by two instruments at the same location on the surface. The associated surface texture parameters Sa, Sq, Ssk, and Sku are also compared. The results indicate XCT can capture reentrant features, while FVM can capture more details. However, XCT measurement is limited in its resolution and FVM measurement is restricted by the line-of-sight constraint. The surface parameters of two measurement techniques are closer in the cases where surface texture of the parts is highe
Causal Confirmation Measures: From Simpson’s Paradox to COVID-19
Get PDFWhen we compare the influences of two causes on an outcome, if the conclusion from every group is against that from the conflation, we think there is Simpson’s Paradox. The Existing Causal Inference Theory (ECIT) can make the overall conclusion consistent with the grouping conclusion by removing the confounder’s influence to eliminate the paradox. The ECIT uses relative risk difference Pd = max(0, (R − 1)/R) (R denotes the risk ratio) as the probability of causation. In contrast, Philosopher Fitelson uses confirmation measure D (posterior probability minus prior probability) to measure the strength of causation. Fitelson concludes that from the perspective of Bayesian confirmation, we should directly accept the overall conclusion without considering the paradox. The author proposed a Bayesian confirmation measure b* similar to Pd before. To overcome the contradiction between the ECIT and Bayesian confirmation, the author uses the semantic information method with the minimum cross-entropy criterion to deduce causal confirmation measure Cc = (R − 1)/max(R, 1). Cc is like Pd but has normalizing property (between −1 and 1) and cause symmetry. It especially fits cases where a cause restrains an outcome, such as the COVID-19 vaccine controlling the infection. Some examples (about kidney stone treatments and COVID-19) reveal that Pd and Cc are more reasonable than D; Cc is more useful than Pd
Hydrophobicity engineering of hierarchically ordered SiO2/Fe-N-C catalyst with optimized triple-phase boundary for boosting oxygen reduction reaction
Get PDF202511 bcchVersion of RecordOthersThis work is financially supported by the National Key Research and Development Program of China (No. 2022YFE0138900), the National Natural Science Foundation of China (No. 21972017), the Shanghai Sailing Program (22YF1400700)， the Chenguang Program of Shanghai Education Development Foundation and Shanghai Municipal Education Commission (22CGA37), the Fundamental Research Funds for the Central Universities and Graduate Student Innovation Fund of Donghua University (CUSF-DH-D-2024035), and the Fundamental Research Funds for the Central Universities (2232022D-18).PublishedC
Synthesis of hierarchical SAPO-11 using phosphoric acid-treated aluminosilicate zeolite as precursor
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