Biomedical subjects

Shuying Liu

Publications and source records attributed to Shuying Liu.

At least 19 recordsLinked to original sources

PubMed2026

OmniExtract: an automatic data extraction tool based on large language model and prompt engineering.

Extracting structured information from documents or scientific papers is crucial for data sharing and retrieval. Recent advances in large language models (LLMs) have demonstrated strong capabilities in language understanding, and a number of LLM-based tools have been developed for extraction-oriented tasks. However, it's still difficult to find a universal and user-friendly tool for various practical extraction tasks. To address this challenge, we propose OmniExtract, an automatic data extraction tool with user-friendly configuration files that can adapt to various data extraction tasks. OmniExtract employs a prompt optimization method to refine task-specific prompts and achieve high extraction performance. It also supports comprehensive data extraction from both documents and tables, making it applicable to a broad range of data sources. Evaluation results show that OmniExtract obtains a high accuracy ~90% for three datasets. Furthermore, two additional data extraction applications of OmniExtract in real-world scenarios have been presented, achieving an accuracy of 92.21% and ~90% precision and recall, respectively. Specifically, OmniExtract can handle tabular files of various sizes and formats, and achieve over 99% precision and recall on table information extraction tasks. The data reliability performance shows that OmniExtract is a valuable tool for database updating. An online testing service is available at https://ngdc.cncb.ac.cn/omniextract/. The service can be deployed locally with the code in https://github.com/wyb39/OmniExtract.

Large Language Models↗

PubMed2024

Binary vector copy number engineering improves Agrobacterium-mediated transformation.

The copy number of a plasmid is linked to its functionality, yet there have been few attempts to optimize higher-copy-number mutants for use across diverse origins of replication in different hosts. We use a high-throughput growth-coupled selection assay and a directed evolution approach to rapidly identify origin of replication mutations that influence copy number and screen for mutants that improve Agrobacterium-mediated transformation (AMT) efficiency. By introducing these mutations into binary vectors within the plasmid backbone used for AMT, we observe improved transient transformation of Nicotiana benthamiana in four diverse tested origins (pVS1, RK2, pSa and BBR1). For the best-performing origin, pVS1, we isolate higher-copy-number variants that increase stable transformation efficiencies by 60-100% in Arabidopsis thaliana and 390% in the oleaginous yeast Rhodosporidium toruloides. Our work provides an easily deployable framework to generate plasmid copy number variants that will enable greater precision in prokaryotic genetic engineering, in addition to improving AMT efficiency.

Genetic Vectors↗

PubMed2006

Of spiders and crabs: the emergence of lysophospholipids and their metabolic pathways as targets for therapy in cancer.

Lysophosphatidic acid (LPA) and sphingosine 1-phosphate (S1P), two small lysophospholipids, are potent inducers of many of the hallmarks of cancer including cell proliferation, survival, migration, invasion, and neovascularization in in vitro and in vivo tumor models. Furthermore, the enzymes metabolizing LPA and S1P and their receptors are aberrant in multiple cancer lineages and exhibit transforming activity altering patterns and targets for metastasis. Several recent studies show the remarkable activity of new chemical genomics and/or potential novel drugs in preclinical models. Combined with the physiologic and pathophysiologic activities of LPA and S1P, these studies suggest the implementation of preclinical and clinical evaluation of LPA and S1P as therapeutic targets.

Animals↗

PubMed2006

Structural features of the L-argininamide-binding DNA aptamer studied with ESI-FTMS.

The 24-mer DNA aptamer of Harada and Frankel (Harada, K.; Frankel, A. D. EMBO J. 1995, 14, 5798-5811) that binds L-argininamide (L-Arm) was studied by electrospray ionization Fourier transform mass spectrometry (ESI-FTMS). This DNA folds into a stem and loop such that the loop is able to engulf L-Arm. As controls, two derivatives of the same base composition, one with the same stem but a scrambled loop and the other with no ability to form a secondary structure, were studied. The two DNAs that could fold into stem-loop structures showed a more negatively charged distribution of ions than the linear control. This tendency was preserved in the presence of ligand; complexes expected to have more secondary structure had ions with more negative charges. Distinct species corresponding to no, one, and two bound L-Arm molecules were observed for each DNA. The fractional peak intensities were fit to a straightforward binding model and binding constants were obtained. Thus, ESI-FTMS can provide both qualitative and quantitative data regarding the structure of DNA and its interactions with noncovalent ligands.

Aptamers, Nucleotide↗

PubMed2006

Impaired dendritic-cell function in ectodermal dysplasia with immune deficiency is linked to defective NEMO ubiquitination.

Ectodermal dysplasia with immune deficiency (EDI) is caused by alterations in NEMO (nuclear factor [NF]-kappaB essential modulator). Most genetic mutations are located in exon 10 and affect the C-terminal zinc finger domain. However, the biochemical mechanism by which they cause immune dysfunction remains undetermined. In this report, we investigated the effect of a cysteine-to-arginine mutation (C417R) found in the NEMO zinc finger domain on dendritic cell (DC) function. Following CD40 stimulation of DCs prepared from 2 unrelated patients with the NEMO C417R mutation, we found NEMO ubiquitination was absent, and this was associated with preserved RelA but absent c-Rel activity. As a consequence, CD40 stimulated EDI DCs failed to synthesize the c-Rel-dependent cytokine interleukin-12, had impaired up-regulation of costimulatory molecules, and failed to support allogeneic lymphocyte proliferation in vitro. In contrast, EDI DCs stimulated with the TLR4 ligand lipopolysaccharide (LPS) showed normal downstream NF-kappaB activity, DC maturation, and NEMO ubiquitination. These findings show for the first time how mutations in the zinc finger domain of NEMO can lead to pathway specific defects in NEMO ubiquitination and thus immune deficiency.

Arginine↗

PubMed2006

Lysophosphatidic acid is a major regulator of growth-regulated oncogene alpha in ovarian cancer.

Growth-regulated oncogene alpha (GROalpha), a member of the chemokine superfamily, is commonly expressed in transformed cells and contributes to angiogenesis and tumorigenesis. Here, we report that increased GROalpha levels are detected in the plasma and ascites of ovarian cancer patients. Ovarian cancer cell lines in culture express and secrete GROalpha. However, when they are starved in serum-free medium, ovarian cancer cells ceased producing GROalpha, suggesting that GROalpha is not constitutively expressed but rather is produced in response to exogenous growth factors in ovarian cancer cells. The prototype peptide growth factors present in serum such as platelet-derived growth factor, insulin-like growth factor I, and insulin do not stimulate GROalpha production by ovarian cancer cells. In contrast, lysophosphatidic acid (LPA), a glycerol backbone phospholipid mediator present in serum and ascites of ovarian cancer patients, is a potent inducer of GROalpha expression in ovarian cancer cell lines. Treatment of ovarian cancer cells with LPA leads to transcriptional activation of the GROalpha gene promoter and robust accumulation of GROalpha protein in culture supernatants. The action of LPA on GROalpha expression is mediated by LPA receptors, particularly the LPA(2) receptor in that ectopic expression of these receptors restores the LPA-dependent GROalpha production in nonresponsive cells. Down-regulation of LPA(2) expression by small interfering RNA (siRNA) in ovarian cancer cells desensitizes GROalpha production in response to LPA. The effect of serum on GROalpha production is also significantly decreased by siRNA inhibition of LPA(2) expression. These studies identify LPA as a primary regulator of GROalpha expression in ovarian cancer.

Ascites↗

PubMed2006

Analysis of strychnos alkaloids using electrospray ionization Fourier transform ion cyclotron resonance multi-stage tandem mass spectrometry.

The fragmentations of four strychnos alkaloids have been investigated by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS) in the positive ion mode. Experiments using multi-stage tandem mass spectrometry (ESI-FT-ICR-MSn) allowed us to obtain precise elemental compositions of product ions at high mass resolution. The experimental data demonstrated that the nitrogen bridge and the coordinated oxygen atom on the nitrogen bridge in the alkaloid compounds were the active sites in the MS2 fragmentations. The loss of CH3 or the OCH3 group in those alkaloids, which have an OCH3 substituent, was the dominant fragmentation mode in the MS3 fragmentations. Logical fragmentation schemes for strychnos alkaloids have been proposed and these should be useful for the identification of these compounds.

Alkaloids↗

PubMed2006

Generation and characterization of monoclonal antibodies to human keratinocyte growth factor receptor.

Keratinocyte growth factor receptor (KGFR) and fibroblast growth factor receptor (FGFR) 2c share identical amino acid sequences, except for a 46-amino acid domain in the extracellular region. Monoclonal antibodies (MAbs) specific to KGFR have not been reported nor are commercially available. In this study, we generated murine MAbs specific to KGFR in non-obese diabetic (NOD) mice using a modified Repeated Immunizations at Multiple Sites (RIMMS) technology. Stable cell lines expressing the full-length human KGFR or FGFR2c were produced to facilitate the identification of KGFR-specific MAbs. Following the initial screening of hybridoma clones with a fluorescence-based, confocal cell detection method and ELISA, KGFR-specific MAbs were selected and confirmed by flow cytometry and Western blot analyses. Antagonistic MAbs were identified using a cell-based functional assay. These KGFR MAbs will be important reagents for studying the biological function and tissue distribution of this receptor in normal and pathological conditions.

Amino Acid Sequence↗

PubMed2006

Structure identification of a prenylflavonol glycoside from Epimedium koreanum by electrospray ionization tandem mass spectrometry.

A novel prenylflavonol glycoside, named acetylicariin, has been isolated from the aerial parts of Epimedium koreanum Nakai. The structure has been identified by electrospray ionization multi-stage tandem mass spectrometry (ESI-MSn) and other chemical evidence, which has been elucidated as 8-prenylkaempferol-4'-methoxyl-3-O-alpha-L-rhamnopyranosyl-7-O-beta-D-(2"-O-acetyl)glucopyranoside.

Epimedium↗

PubMed2005

Isolation and purification of acteoside and isoacteoside from Plantago psyllium L. by high-speed counter-current chromatography.

Two isomeric phenylethanoid glycosides, acteoside and isoacteoside were isolated and purified from the seeds of Plantago psyllium L. for the first time by high-speed counter-current chromatography (HSCCC) using a solvent system consisting of ethyl acetate-water (1:1, v:v). By injecting 200 mg of the n-butanol extract of P. psyllium for five consecutive times, the two-step HSCCC procedure yielded a total of 165 mg of acteoside and 17.5 mg of isoacteoside from 978 mg extract. The recovery rates for acteoside and isoacteoside were 90 and 84%, respectively, and the purities were 98 and 94%, respectively. The HSCCC fractions were analyzed by HPLC and the structures were identified by UV, LC-APCI-MS in negative ion mode, and confirmed by NMR experiments.

Chromatography, High Pressure Liquid↗

PubMed2004

Structural analyses of protoberberine alkaloids in medicine herbs by using ESI-FT-ICR-MS and HPLC-ESI-MS(n).

The Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FT-ICR-MS) using sustained off-resonance irradiation (SORI)/collision-induced dissociation (CID) method at high mass resolution has been first applied to investigate the characteristic fragment ions of four protoberberine alkaloids in medicine herbs. The ESI-FT-ICR SORI-CID experiment results demonstrate that the unambiguous elemental composition of fragment ions can be obtained at high mass resolution, then the logical fragmentation pathways of the protoberberine alkaloids has been proposed. The characteristic fragment ions of CID and MS(n) of protoberberine alkaloids have been discussed, which are specific and useful for the identification of some protoberberine alkaloid compounds. Then, the extracts of four kinds of medicine herbs have been analyzed by HPLC-ESI-MS(n). According to these characteristic fragmentation pathways, the retention time (t(R)) of HPLC and mass spectra of product ion, the structures of six kinds of protoberberine alkaloids have been identified. And, in the present paper, the selected ion monitoring (SIM) method has been used to separate and identify the alkaloid isomers.

Alkaloids↗

PubMed2004

Glycogen synthase kinase 3beta is a negative regulator of growth factor-induced activation of the c-Jun N-terminal kinase.

The c-Jun N-terminal kinase (JNK)/stress activated protein kinase is preferentially activated by stress stimuli. Growth factors, particularly ligands for G protein-coupled receptors, usually induce only modest JNK activation, although they may trigger marked activation of the related extracellular signal-regulated kinase. In the present study, we demonstrated that homozygous disruption of glycogen synthase kinase 3beta (GSK-3beta) dramatically sensitized mouse embryonic fibroblasts (MEFs) to JNK activation induced by lysophosphatidic acid (LPA) and sphingosine-1-phosphate, two prototype ligands for G protein-coupled receptors. To a lesser degree, a lack of GSK-3beta also potentiated JNK activation in response to epidermal growth factor. In contrast, the absence of GSK-3beta decreased UV light-induced JNK activation. The increased JNK activation induced by LPA in GSK-3beta null MEFs was insufficient to trigger apoptotic cell death or growth inhibition. Instead, the increased JNK activation observed in GSK-3beta-/- MEFs was associated with an increased proliferative response to LPA, which was reduced by the inhibition of JNK. Ectopic expression of GSK-3beta in GSK-3beta-negative MEFs restrained LPA-triggered JNK phosphorylation and induced a concomitant decrease in the mitogenic response to LPA compatible with GSK-3beta through the inhibition of JNK activation, thus limiting LPA-induced cell proliferation. Mutation analysis indicated that GSK-3beta kinase activity was required for GSK-3beta to optimally inhibit LPA-stimulated JNK activation. Thus GSK-3beta serves as a physiological switch to specifically repress JNK activation in response to LPA, sphingosine-1-phosphate, or the epidermal growth factor. These results reveal a novel role for GSK-3beta in signal transduction and cellular responses to growth factors.

3T3 Cells↗

PubMed2004

Studies on the flavones using liquid chromatography-electrospray ionization tandem mass spectrometry.

Fragmentation pathways of nine flavone compounds have been studied by using electrospray ionization multi-stage tandem mass spectrometry (ESI-MSn). Analyzing the product ion spectra of flavonoids and aglycones, we observed some diagnostic neutral losses, such as CH3, H2O, residue of glucose and gluconic acid, which are very useful for the identification of the functional groups in the structures. Furthermore, specific retro Diels-Alder (RDA) fragments for flavones with different hydroxyl substitution have also been discussed. The information is helpful for the rapid identification of the location site of hydroxyl substitution on flavones. Fragmentation pathways of C-glycosidic flavonoid have also been discussed using ESI-MSn, demonstrating ions [M-H-60]-, [M-H-90]-, [M-H-120]- are characteristic ions of C-glycosidic flavonoid. According to the fragmentation mechanism of mass spectrometry and HPLC-MS data, the structures of seven flavones in Scutellaria baicalensis Georgi have been identified on-line without time-consuming isolation. The HPLC-ESI-MSn method for analyzing constituents in the Scutellaria baicalensis Georgi has been established.

Chromatography, High Pressure Liquid↗

PubMed2004

Lysophosphatidic acid production and action: validated targets in cancer?

The completion of the human genome project, the evolution of transcriptional profiling and the emergence of proteomics have focused attention on these areas in the pathophysiology and therapy of cancer. The role of lysophospholipids as potential mediators in cancer pathophysiology, screening and management has taken a major leap forward with the recent cloning of several enzymes involved in the metabolism of lysophospholipids. Lysophospholipids, although small molecules, contain a high "informational" content. Differences include the nature of the phosphate head group, the regiochemistry of the fatty acyl chain on the glyceryl backbone, the presence of ether versus ester linkages to the backbone, and the length and saturation of the fatty acyl or alkyl chain. This informational content is sufficient to result in a marked structure function activity relationship at their cognate receptors. Thus the emerging discipline of "functional lipidomics" is likely to prove as important as genomics and proteomics in terms of early diagnosis, prognosis, and therapy. Lysophospholipid levels are elevated in vivo in a number of pathophysiological states including ascitic fluid from ovarian cancer patients indicating a role in the pathophysiology of this devastating disease. Although controversial, levels of specific lysophospholipids may be altered in the blood of cancer patients providing a potential mechanism for early diagnosis. Several of the enzymes involved in the metabolism of lysophospholipids are aberrant in ovarian and other cancers. Further, the enzymes are active in the interstitial space, rendering them readily accessible to the effects of inhibitors including antibodies, proteins, and small molecules. In support of a role for lysophospholipids in the pathophysiology of cancer, expression of receptors for lysophospholipids is also aberrant in cancer cells from multiple different lineages. All of the cell surface receptors for lysophospholipids belong to the G protein coupled receptor family. As over 40% of all drugs in current use target this family of receptors, lysophospholipid receptors are highly "druggable." Indeed, a number of highly specific agonists and antagonists of lysophospholipid receptors have been identified. A number are in preclinical evaluation as therapeutics. We look forward to the next several years when the role of lysophospholipids in physiology and the pathophysiology and management of cancer and other diseases are fully elucidated.

Animals↗

PubMed2004

Characterization of non-covalent complexes of rutin with cyclodextrins by electrospray ionization tandem mass spectrometry.

Electrospray ionization tandem mass spectrometry (ESI-MS(n)) and the phase solubility method were used to characterize the gas-phase and solution-phase non-covalent complexes between rutin (R) and alpha-, beta- and gamma-cyclodextrins (CDs). The direct correlation between mass spectrometric results and solution-phase behavior is thus revealed. The order of the 1 : 1 association constants (K(c)) of the complexes between R and the three CDs in solution calculated from solubility diagrams is in good agreement with the order of their relative peak intensities and relative collision-induced dissociation (CID) energies of the complexes under the same ESI-MS(n) condition in both the positive and negative ion modes. Not only the binding stoichiometry but also the relative stabilities and even binding sites of the CD-R complexes can be elucidated by ESI-MS(n). The diagnostic fragmentation of CD-R complexes, with a significant contribution of covalent fragmentation of rutin leaving the quercetin (Q) moiety attached to the CDs, provides convincing evidence for the formation of inclusion complexes between R and CDs. The diagnostic fragment ions can be partly confirmed by the complexes between Q and CDs. The gas-phase stability order of the deprotonated CD-R complexes is beta-CD-R > alpha-CD-R > gamma-CD/R; beta-CD seems to bind R more strongly than the other CDs.

Cyclodextrins↗

PubMed2004

Structural elucidation and identification of alkaloids in Rhizoma Coptidis by electrospray ionization tandem mass spectrometry.

Simple, convenient, sensitive and accurate analytical methods are needed for the structural characterization and identification of alkaloid components in Rhizoma Coptidis in traditional Chinese herbal medicine, which has important bioactivity. In this work, the identification of alkaloid compounds in Rhizoma Coptidis was investigated by obtaining molecular mass information using electrospray ionization mass spectrometry (ESI-MS). Multi-stage tandem mass spectrometric (ESI-MS(n)) data for the alkaloid compounds were used for detailed structural characterization, then structure information was obtained by comparison of the fragmentation mechanisms of both alkaloids in Rhizoma Coptidis and standard samples of berberine, palmatine, coptisine and jatrorrhizine by MS. Based on the results obtained, the structure of a novel compound was elucidated. The results of the experiments demonstrate that ESI-MS(n) is a sensitive, selective and effective tool for the rapid determination of alkaloids in Rhizoma Coptidis.

Berberine↗

PubMed2004

High resolution mass spectrometric alveolar proteomics: identification of surfactant protein SP-A and SP-D modifications in proteinosis and cystic fibrosis patients.

In the present study, one- and two-dimensional gel electrophoresis combined with high resolution Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS) have been applied as powerful approaches for the proteome analysis of surfactant proteins SP-A and SP-D, including identification of structurally modified and truncation forms, in bronchoalveolar lavage fluid from patients with cystic fibrosis, chronic bronchitis and pulmonary alveolar proteinosis. Highly sensitive micropreparation techniques were developed for matrix-assisted laser desorption/ionization (MALDI) FT-ICR MS analysis which provided the identification of surfactant proteins at very low levels. Owing to the high resolution, FT-ICR MS was found to provide substantial advantages for the structural identification of surfactant proteins from complex biological matrices with high mass determination accuracy. Several protein bands corresponding to SP-A and SP-D were identified by MALDI-FT-ICR MS after electrophoretic separation by one- and two-dimensional gel electrophoresis, and provided the identification of structural modifications (hydroxy-proline) and degradation products. The high resolution mass spectrometric proteome analysis should facilitate the unequivocal identification of subunits, aggregations, modifications and degradation products of surfactant proteins and hence contribute to the understanding of the mechanistic basis of lung disease pathogenesis.

Bronchoalveolar Lavage Fluid↗

PubMed2004

Multiple-stage tandem mass spectrometry for differentiation of isomeric saponins.

Four isomers of steroidal saponins were differentiated using multiple-stage tandem mass spectrometry combined with electrospray ionization (ESI-MS(n)). With the addition of lithium salt, the [M+Li](+) ions of saponins were observed in the ESI spectra. MS(n) spectra of these [M+Li](+) ions provided detailed structural information and allowed differentiation of the four isomeric saponins. The cross-ring cleavage ions from the saccharide chains of the saponins could be used as diagnostic ions for information concerning the linkage of the sugar moieties of the saponins. The masses of the X, A, Y and C type fragment ions formed from [M+Li](+) ions of the isomeric saponins provided information defining the methyl group locations.

Binding Sites↗