dissociation-confounding-influences-expectancy-integrative-difficulty

Dissociation of the Confounding Influences of Expectancy and Integrative Difficulty Residing in Anomalous Sentences in Event-related Potential Studies

The confounding factors of unexpectedness and semantic integration difficulty naturally residing in anomalous sentences in language studies make it ...

interaction-between-phonological-semantic-processes-visual-word

Interaction between Phonological and Semantic Processes in Visual Word Recognition using Electrophysiology

Controversies have always existed in research related to reading abilities; on whether printed words are perceived in a feedforward manner based on ...

Tsinghua University

Our method concentrates on and constructs the distinguished single gene network. An integrated method was proposed based on linear programming and a decomposition procedure with integrated analysis of the significant function cluster using Kappa statistics and fuzzy heuristic clustering. We tested this method to identify ATF2 regulatory network module using data of 45 samples from the same GEO dataset. The results demonstrate the effectiveness of such integrated way in terms of developing novel prognostic markers and therapeutic targets.

Integrative decomposition procedure and Kappa statistics for the distinguished single molecular network construction and analysis.

Studies were done on analysis of biological processes in the same high expression (fold change ≥2) activated PTHLH feedback-mediated cell adhesion gene ontology (GO) network of human hepatocellular carcinoma (HCC) compared with the corresponding low expression activated GO network of no-tumor hepatitis/cirrhotic tissues (HBV or HCV infection). Activated PTHLH feedback-mediated cell adhesion network consisted of anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolism, cell adhesion, cell differentiation, cell-cell signaling, G-protein-coupled receptor protein signaling pathway, intracellular transport, metabolism, phosphoinositide-mediated signaling, positive regulation of transcription, regulation of cyclin-dependent protein kinase activity, regulation of transcription, signal transduction, transcription, and transport in HCC. We proposed activated PTHLH coupling feedback phosphoinositide to G-protein receptor signal-induced cell adhesion network. Our hypothesis was verified by the different activated PTHLH feedback-mediated cell adhesion GO network of HCC compared with the corresponding inhibited GO network of no-tumor hepatitis/cirrhotic tissues, or the same compared with the corresponding inhibited GO network of HCC. Activated PTHLH coupling feedback phosphoinositide to G-protein receptor signal-induced cell adhesion network included BUB1B, GNG10, PTHR2, GNAZ, RFC4, UBE2C, NRXN3, BAP1, PVRL2, TROAP, and VCAN in HCC from GEO dataset using gene regulatory network inference method and our programming.

Activated PTHLH coupling feedback phosphoinositide to G-protein receptor signal-induced cell adhesion network in human hepatocellular carcinoma by systems-theoretic analysis.

In the present study, a comparison of the biological processes and gene ontology (GO) in human hepatocellular carcinoma (HCC) with high expression (fold change ≥2) of amelogenin Y-linked (AMELY)-activated upstream regulation networks with non-tumor hepatitis/cirrhotic tissues (HBV or HCV infection) with low expression of activated networks was performed. The principle biological processes involved in non-tumor hepatitis/cirrhotic tissues include positive regulation of mismatch repair, regulation of transcription from RNA polymerase II promoters, negative regulation of cell-cell adhesion, protein ubiquitinatin and protein catabolism. The main biological processes involved in the development of HCC include positive regulation of calcium ion transport into the cytosol, cell proliferation, DNA replication, fibroblast proliferation, immune response, microtubule polymerization and protein secretion. Specific transcription from RNA polymerase II promoters, regulation of angiogenesis, cell growth, protein metabolism, Wnt receptor signaling pathways, negative regulation of endothelial cell differentiation, microtubule depolymerization, peptidase activity and progression through the cell cycle are also involved. Positive regulation of transcription is involved in both processes. An activated AMELY-coupled upstream positive regulation of immune response-mediated protein secretion to Wnt signaling and calcium into cytosol-induced regulation of cell growth and angiogenesis in HCC is proposed. The AMELY upstream regulation molecular network model was constructed with BUB1B, CST6, ESM1, HOXA5, LEF1, MAPT, MYBL2, NOTCH3, PLA2G1B, PROK1, ROBO1, SCML2 and UBE2C in HCC from a Gene Expression Omnibus (GEO) dataset by gene regulation network inference methods and our programming methods.

Activated amelogenin Y-linked (AMELY) regulation and angiogenesis in human hepatocellular carcinoma by biocomputation.

7 anterior gradient homolog 2 (AGR2)-inhibited different molecular mutual positive correlation network was constructed in lung adenocarcinoma compared with human normal adjacent tissues by 17 overlapping molecules of 358 GRNInfer and 19 Pearson (AGR2 CC⩽-0.25). Based on GO, KEGG, GenMAPP, BioCarta and disease databases, we determined AGR2-mediated lung adenocarcinoma metastasis through repression with cytoskeleton of MAST1; steroid metabolism of SOAT2; humoral immune response of POU2AF1; interferon alpha-inducible of IFI6; immunoglobulin of IGKC_3, CTA_246H3.1. Thus we proposed AGR2-mediated lung adenocarcinoma metastasis novel mechanism network through repression with interferon coupling cytoskeleton to steroid metabolism-dependent humoral immune response.

AGR2-mediated lung adenocarcinoma metastasis novel mechanism network through repression with interferon coupling cytoskeleton to steroid metabolism-dependent humoral immune response.

48 different Pearson mutual-positive-correlation epidermal growth factor receptor (EGFR_1)-activatory molecular feedback, up- and down-stream network was constructed from 171 overlapping of 366 GRNInfer and 223 Pearson under EGFR_1 CC ≥0.25 in high lung adenocarcinoma compared with low human normal adjacent tissues. Our identified EGFR_1 inside-out upstream activated molecular network showed SLC2A1 (solute carrier family 2 (facilitated glucose transporter) member 1), CCNB2 (cyclin B2), HMMR (hyaluronan-mediated motility receptor (RHAMM)), KIF11 (kinesin family member 11), NUSAP1 (nucleolar and spindle associated protein 1), PRC1 (protein regulator of cytokinesis 1), UBE2C (ubiquitin-conjugating enzyme E2C) in high lung adenocarcinoma. EGFR_1 inside-out upstream activated terms network includes intracellular, membrane fraction, cytoplasm, plasma membrane, integral to membrane, basolateral plasma membrane, transmembrane transport, nucleus, cytosol, cell surface; T cell homeostasis, inflammation; microtubule cytoskeleton, embryonic development (sensu Mammalia), cell cycle, mitosis, thymus development, cell division, regulation of cell cycle, Contributed--cellular process--Hs cell cycle KEGG, cytokinesis, M phase, M phase of mitotic cell cycle, estrogen-responsive protein Efp controls cell cycle and breast tumors growth, cell motility, locomotion, locomotory behavior, neoplasm metastasis, spindle pole, spindle microtubule, microtubule motor activity, microtubule-based movement, mitotic spindle organization and biogenesis, mitotic centrosome separation, spindle pole body organization and biogenesis, microtubule-based process, microtubule, cytokinesis after mitosis, mitotic chromosome condensation, establishment of mitotic spindle localization, positive regulation of mitosis, mitotic spindle elongation, spindle organization and biogenesis, positive regulation of exit from mitosis, regulation of cell proliferation, positive regulation of cell proliferation based on integrative GO, KEGG, GenMAPP, BioCarta and disease databases in high lung adenocarcinoma. Therefore, we propose high EGFR_1 inside-out activated inflammation-induced motility through SLC2A1-CCNB2-HMMR-KIF11-NUSAP1-PRC1-UBE2C in lung adenocarcinoma. 

High EGFR_1 Inside-Out Activated Inflammation-Induced Motility through SLC2A1-CCNB2-HMMR-KIF11-NUSAP1-PRC1-UBE2C.

Eighteen different Pearson mutual-positive-correlation BIK-activatory molecular feedback upstream and downstream networks were constructed from 79 overlapping of 376 GRNInfer and 98 Pearson under BIK CC ≥ 0.25 in low normal adjacent tissues of Taiwan compared with high lung adenocarcinoma. Our identified BIK interactive total feedback molecular network showed FUT3 [fucosyltransferase 3 (galactoside 3(4)-L-fucosyltransferase Lewis blood group)], PMM2 (phosphomannomutase 2), SQSTM1 (sequestosome 1), SFN_2 [REX2 RNA exonuclease 2 homolog (S. cerevisiae)] and ZNF384 (zinc finger protein 384) in low normal adjacent tissues of lung adenocarcinoma. BIK interactive total feedback terms included mitochondrial envelope, endomembrane system, integral to membrane, Golgi apparatus, cytoplasm, nucleus, cytosol, intracellular signaling cascade, mitochondrion, extracellular space, inflammation, immune response, apoptosis, cell differentiation, cell cycle, regulation of cell cycle, cell proliferation, estrogen-responsive protein Efp controls cell cycle and breast tumors growth, induction or regulation of apoptosis based on integrative GO, KEGG, GenMAPP, BioCarta and disease databases in low normal adjacent tissues of lung adenocarcinoma. Therefore, we propose low BIK outside-inside-out interactive inflammation immune-induced transcription-dependent apoptosis through FUT3-PMM2-SQSTM1-SFN-ZNF384 in normal adjacent tissues of lung adenocarcinoma.

Low BIK outside-inside-out interactive inflammation immune-induced transcription-dependent apoptosis through FUT3-PMM2-SQSTM1-SFN-ZNF384.

Breast cancer 1 (BRCA1) and E2F transcription factor 1 (E2F1) are related to metabolism and cell cycle regulation. However, the corresponding mechanism is not clear in HCC. High BRCA1 direct pathway was constructed with 11 molecules from E2F1 feedback-interactive network in HCC by GRNInfer based on 39 Pearson mutual positive corelation CC ≥0.25 molecules with E2F1. Integration of GRNInfer with GO, KEGG, BioCarta, GNF_U133A, UNIGENE_EST, Disease, GenMAPP databases by DAVID and MAS 3.0, E2F1 feedback-interactive BRCA1 indirect mitochondrion to cytosol pathway was identified as upstream LAPTM4B activation, feedback UNG, downstream BCAT1-HIST1H2AD-TK1 reflecting protein, and DNA binding with enrichment of small molecule metabolism; The corresponding BRCA1 indirect membrane to cytosol pathway as upstream CCNB2-NUSAP1 activation, feedback TTK-HIST1H2BJ-CENPF, downstream MCM4-TK1 reflecting ATP, and microtubule binding with enrichment of CD4+T-related cell cycle regulation in HCC. Therefore, we propose that E2F1 interactive with BRCA1 pathway induces HCC two different small molecule metabolism or cell cycle regulation via mitochondrion or CD4+T to cytosol. Knowledge analysis demonstrates our E2F1 feedback-interactive BRCA1 pathway wide disease distribution and reflects a novel common one of tumor and cancer.

E2F1 interactive with BRCA1 pathway induces HCC two different small molecule metabolism or cell cycle regulation via mitochondrion or CD4+T to cytosol.

It remains an open question whether the amplitude of N400 reflects combinatory postlexical semantic integration processing. To examine the issue, we repeatedly presented strictly simplified, N400-eliciting three-word structures for seven times, mixed with their plausible counterparts, followed immediately by a much more enriched and informative sentence containing two keywords of the incongruous structure, for the purpose of reinitiating semantic integration processing. Event-related potentials were recorded and compared at the first, fourth, seventh, and eighth time. It was found that multiple repetitions attenuated the N400 effect to almost nonexistent and that the follow-up semantic integration reinitiating sentence did not recover N400 amplitude. The results suggest that combinatory postlexical semantic integration does not significantly modulate N400 amplitude, and provide evidence for noncombinatory processes underlying N400 such as automatic spreading activation and expectancy/prediction.

N400 amplitude does not recover from disappearance after repetitions despite reinitiated semantic integration difficulty.

Orthographic processing is crucial in reading. For the Chinese language, sub-lexical processing has already taken place at radical level. Previous literature reported early position-specific radical representations and later position-general radical representations, implying a possible separating process of abstract position information irrespective of radicals per se from radical representations during orthographic processing. However, it remains largely unclear whether the abstract pattern of spatial arrangement of radicals can be rapidly extracted, and if so, whether this extraction takes place at the visual cortex, the very first processing center. As the visual cortex is documented to actively participate in orthographic processing, it may also play a role in the possible extraction of abstract orthographic patterns of Chinese characters. Hence, we hypothesize that abstract orthographic patterns of Chinese characters are covertly extracted at the visual cortex during reading. In this study, we investigated whether the visual cortex could rapidly extract abstract structural patterns of Chinese characters, using the event-related potential (ERP) technique. We adopted an active oddball paradigm with two types of deviant stimuli different only in one feature, structural or tonal, from standard stimuli; in each of the two sessions, subjects focused conscious attention on one feature and neglected the other. We observed that the ERPs recorded at occipital electrodes responded differentially to standard and structural deviant stimuli in both sessions, especially within the time range of the occipital P200 component. Then, we extracted three source waves arising from different levels of the visual cortex. Early response differences (from 88 to 456 ms after stimulus onset) were observed between the source waves, probably arising from left primary/secondary and bilateral associative visual cortices, in response to standard and deviant stimuli that violated abstract structural patterns, whether subjects focused their attention on the character structure or not. This suggests rapid extraction of abstract structural patterns of Chinese characters in the visual cortex, no matter the abstract structural pattern was explicit or implicit to subjects. Note that the source waves arising from right primary/secondary visual cortices in response to standard and structural deviant stimuli did not differ at all, indicating that this extraction of the abstract structural pattern of Chinese characters was left-lateralized. Besides, no difference was observed between source waves originating from any level of the visual cortex to standard and deviant stimuli that violated abstract tonal patterns, until 768 ms when a late effect related to conscious detection of targets occurred at higher levels of the visual cortex. Note that at late stages (later than 698 ms after stimulus onset), responses arising from bilateral associative visual cortices to standard and target stimuli differed for both sessions, no matter the structural or tonal feature was attended to. Our findings support the primitive intelligence of visual cortex to rapidly extract abstract orthographic patterns of Chinese characters that might be engaged in further lexical processing. Our findings also suggest that this rapid extraction can take place implicitly during reading.

Rapid implicit extraction of abstract orthographic patterns of Chinese characters during reading.

The present study aims to delineate the working mechanism of prediction in sentence comprehension, by disentangling the influence of the facilitated general memory retrieval from the coexistent influence of the predicted language-specific semantic and/or syntactic information for the first time. The results support that prediction might influence the downstream cognitive processing in two aspects: (1) the pre-activated information facilitates the retrieval of a matched input in memory and, (2) the pre-activated information interacts with higher-level semantic/syntactic processing. More importantly, the present findings suggest that these two types of influences seem to occur at different stages of sentence comprehension: the facilitated memory retrieval of the input modulates N400 amplitude and the latency of post-N400 late central-parietal positivity/P600, while the predicted semantic/syntactic information and/or their interactions modulate the amplitude of the late positivity. The present findings would be helpful for interpreting the underlying mechanism of observed effects in prediction studies.

Delving Into the Working Mechanism of Prediction in Sentence Comprehension: An ERP Study.

Unlike in English, the role of phonology in word recognition in Chinese is unclear. In this event-related potential experiment, we investigated the role of phonology in reading both high- and low-frequency two-character compound Chinese words. Participants executed semantic and homophone judgment tasks of the same precede-target pairs. Each pair of either high- or low-frequency words were either unrelated (control condition) or related semantically or phonologically (homophones). The induced P200 component was greater for low- than for high-frequency word-pairs both in semantic and phonological tasks. Homophones in the semantic judgment task and semantically-related words in the phonology task both elicited a smaller N400 than the control condition, word frequency-independently. However, for low-frequency words in the phonological judgment task, it was found that the semantically related pairs released a significantly larger P200 than the control condition. Thus, the semantic activation of both high- and low-frequency words may be no later than phonological activation.

ArticleTotal : 2	Year
Publication title	2019
Publication title	2021

Article	Year
Integrative decomposition procedure and Kappa statistics for the distinguished single molecular network construction and analysis. Journal of biomedicine & biotechnology\| PubMed ID: 19390583	2009
Activated PTHLH coupling feedback phosphoinositide to G-protein receptor signal-induced cell adhesion network in human hepatocellular carcinoma by systems-theoretic analysis. TheScientificWorldJournal\| PubMed ID: 22997493	2012
Activated amelogenin Y-linked (AMELY) regulation and angiogenesis in human hepatocellular carcinoma by biocomputation. Oncology letters\| PubMed ID: 23426651	2013
AGR2-mediated lung adenocarcinoma metastasis novel mechanism network through repression with interferon coupling cytoskeleton to steroid metabolism-dependent humoral immune response. Cellular immunology\| PubMed ID: 24960290	2014
High EGFR_1 Inside-Out Activated Inflammation-Induced Motility through SLC2A1-CCNB2-HMMR-KIF11-NUSAP1-PRC1-UBE2C. Journal of Cancer\| PubMed ID: 26000042	2015
Low BIK outside-inside-out interactive inflammation immune-induced transcription-dependent apoptosis through FUT3-PMM2-SQSTM1-SFN-ZNF384. Immunologic research\| PubMed ID: 26423071	2016
E2F1 interactive with BRCA1 pathway induces HCC two different small molecule metabolism or cell cycle regulation via mitochondrion or CD4+T to cytosol. Journal of cellular physiology\| PubMed ID: 28474358	2018
N400 amplitude does not recover from disappearance after repetitions despite reinitiated semantic integration difficulty. Neuroreport\| PubMed ID: 30096130	2018
Rapid implicit extraction of abstract orthographic patterns of Chinese characters during reading. PloS one\| PubMed ID: 32084247	2020
Delving Into the Working Mechanism of Prediction in Sentence Comprehension: An ERP Study. Frontiers in psychology\| PubMed ID: 33679524	2021
An ERP Study on the Role of Phonological Processing in Reading Two-Character Compound Chinese Words of High and Low Frequency. Frontiers in psychology\| PubMed ID: 33716906	2021

Minghu Jiang

Biography

JoVE Journal Publications

Other Publications