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1.  An electrophysiological index of changes in risk decision-making strategies 
Neuropsychologia  2013;51(8):1397-1407.
Human decision-making is significantly modulated by previously experienced outcomes. Using event-related potentials (ERPs), we examined whether ERP components evoked by outcome feedbacks could serve as biomarkers to signal the influence of current outcome evaluation on subsequent decision-making. In this study, eighteen adult volunteers participated in a simple monetary gambling task, in which they were asked to choose between two options that differed in risk. Their decisions were immediately followed by outcome presentation. Temporospatial principle component analysis (PCA) was applied to the outcome-onset locked ERPs in the -200 – 1000 ms time window. The PCA factors that approximated classical ERP components (P2, feedback-related negativity, P3a, & P3b) in terms of time course and scalp distribution were tested for their association with subsequent decision-making strategies. Our results revealed that a fronto-central PCA factor approximating the classical P3a was related to changes of decision-making strategies on subsequent trials. The decision to switch between high- and low-risk options resulted in a larger P3a relative to the decision to retain the same choice. According to the results, we suggest the amplitude of the fronto-central P3a is an electrophysiological index of the influence of current outcome on subsequent risk decision-making. Furthermore, the ERP source analysis indicated that the activations of the frontopolar cortex and sensorimotor cortex were involved in subsequent changes of strategies, which enriches our understanding of the neural mechanisms of adjusting decision-making strategies based on previous experience.
doi:10.1016/j.neuropsychologia.2013.04.014
PMCID: PMC3989206  PMID: 23643796
decision-making; outcome evaluation; event-related potential (ERP); principal components analysis (PCA); P3 component
2.  Reactive Oxygen Species and Autophagy Associated Apoptosis and Limitation of Clonogenic Survival Induced by Zoledronic Acid in Salivary Adenoid Cystic Carcinoma Cell Line SACC-83 
PLoS ONE  2014;9(6):e101207.
Salivary adenoid cystic carcinoma is an epithelial tumor in the head and neck region. Despite its slow growth, patients with salivary adenoid cystic carcinoma exhibit poor long term survival because of a high rate of distant metastasis. Lung and bone are common distant metastasis sites. Zoledronic acid, a third generation bisphosphonate, has been used for tumor-induced osteolysis due to bone metastasis and has direct antitumor activity in several human neoplasms. Here, we observed that zoledronic acid inhibited salivary adenoid cystic carcinoma cell line SACC-83 xenograft tumor growth in nude mice. In vitro, zoledronic acid induced apoptosis and reduced clonogenic survival in SACC-83. Flow cytometry and western blotting indicated that the cell cycle was arrested at G0/G1. Zoledronic acid treatment upregulated reactive oxygen species as well as the autophagy marker protein LC-3B. Reactive oxygen species scavenger N-acetylcysteine and autophagy antagonist 3-methyladenine decreased zoledronic acid-induced apoptosis and increased clonogenic survival. Silencing of the autophagy related gene Beclin-1 also decreased zoledronic acid-induced apoptosis and inhibition of clonogenic formation. In addition, isobolographic analysis revealed synergistic effects on apoptosis when zoledronic acid and paclitaxel/cisplatin were combined. Taken together, our results suggest that zoledronic acid induced apoptosis and reduced clonogenic survival via upregulation of reactive oxygen species and autophagy in the SACC-83 cell line. Thus, zoledronic acid should be considered a promising drug for the treatment of salivary adenoid cystic carcinoma.
doi:10.1371/journal.pone.0101207
PMCID: PMC4071064  PMID: 24963720
3.  Brain Potentials and Repetition Effects During Encoding and Retrieval of Words 
Neuroreport  2008;19(14):1365-1368.
Using Event-Related Potentials (ERPs), the present study utilized a study-test paradigm to investigate the existence of a common mechanism underlying repeated learning effects during encoding and retrieval. Results showed repeated learning effects occurred in both encoding and retrieval. However, the effect of encoding appeared earlier and lasted longer than that of retrieval. Furthermore, the effect of implicit retrieval appeared earlier than that of explicit retrieval. The main scalp distributions of the repetition effects related to both encoding and retrieval occurred at parietal and central sites. Both ERP repetition effects manifested significantly larger and positive-going ERP response of repeated words compared to the words’ first appearance. The ERP repetition effects support the hypothesis that there is common learning-related automatic processing during encoding and retrieval.
doi:10.1097/WNR.0b013e32830c8dda
PMCID: PMC4058855  PMID: 18766012
encoding; retrieval; implicit memory test; explicit memory test; repetition enhancement
4.  Diversity in early crustal evolution: 4100 Ma zircons in the Cathaysia Block of southern China 
Scientific Reports  2014;4:5143.
Zircons are crucial to understanding the first 500 Myr of crustal evolution of Earth. Very few zircons of this age (>4050 Ma) have been found other than from a ~300 km diameter domain of the Yilgarn Craton, Western Australia. Here we report SIMS U-Pb and O isotope ratios and trace element analyses for two ~4100 Ma detrital zircons from a Paleozoic quartzite at the Longquan area of the Cathaysia Block. One zircon (207Pb/206Pb age of 4127 ± 4 Ma) shows normal oscillatory zonation and constant oxygen isotope ratios (δ18O = 5.8 to 6.0‰). The other zircon grain has a ~4100 Ma magmatic core surrounded by a ~4070 Ma metamorphic mantle. The magmatic core has elevated δ18O (7.2 ± 0.2‰), high titanium concentration (53 ± 3.4 ppm) and a positive cerium anomaly, yielding anomalously high calculated oxygen fugacity (FMQ + 5) and a high crystallization temperature (910°C). These results are unique among Hadean zircons and suggest a granitoid source generated from dry remelting of partly oxidizing supracrustal sediments altered by surface waters. The ~4100 Ma dry melting and subsequent ~4070 Ma metamorphism provide new evidence for the diversity of the Earth's earliest crust.
doi:10.1038/srep05143
PMCID: PMC4042129  PMID: 24888297
5.  Anxiety and Outcome Evaluation: The Good, the Bad and the Ambiguous 
Biological psychology  2010;85(2):200-206.
Previous research has indicated that anxious individuals are more prone to evaluate ambiguous information as negative compared to non-anxious individuals. The feedback-related negativity (FRN) component of event-related brain potential (ERP) has been shown to be sensitive to outcome evaluation. The current ERP study aimed to test the hypothesis that the FRNs associated with ambiguous outcomes and negative outcomes are different between high trait-anxiety (HTA) and low trait-anxiety (LTA) individuals. The FRN was measured as a difference wave created across conditions. We found significantly different FRN responses between high-anxious and low-anxious participants in ambiguous outcome condition, as well as in negative outcome condition. Moreover, the HTA group’s FRN responses under the ambiguous outcome condition were larger than the negative outcome condition. Nevertheless, the FRN following neutral outcome did not show any difference between the two groups. The present results support the idea that there is link between individual differences in anxiety and ambiguous outcome evaluation, which possibly reflects the adaptive function of anxiety. Additionally, the results indicate that the mechanisms underlying the evaluation of neutral outcomes and ambiguous outcomes might be different from each other.
doi:10.1016/j.biopsycho.2010.07.001
PMCID: PMC4041009  PMID: 20619312
Anxiety; Decision-making; Outcome Evaluation; Feedback-Related Negativity (FRN); Ambiguous Outcome; Neutral Outcome; Guessing Activity
6.  Resting EEG Discrimination of Early Stage Alzheimer’s Disease from Normal Aging Using Inter-Channel Coherence Network Graphs 
Annals of biomedical engineering  2013;41(6):10.1007/s10439-013-0788-4.
Amnestic mild cognitive impairment (MCI) is a degenerative neurological disorder at the early stage of Alzheimer’s disease (AD). This work is a pilot study aimed at developing a simple scalp-EEG-based method for screening and monitoring MCI and AD. Specifically, the use of graphical analysis of inter-channel coherence of resting EEG for the detection of MCI and AD at early stages is explored. Resting EEG records from 48 age-matched subjects (mean age 75.7 years)—15 normal controls (NC), 16 with early stage MCI, and 17 with early stage AD—are examined. Network graphs are constructed using pairwise inter-channel coherence measures for delta-theta, alpha, beta, and gamma band frequencies. Network features are computed and used in a support vector machine model to discriminate among the three groups. Leave-one-out cross-validation discrimination accuracies of 93.6% for MCI vs. NC (p<0.0003), 93.8% for AD vs. NC (p<0.0003), and 97.0% for MCI vs. AD (p<0.0003) are achieved. These results suggest the potential for graphical analysis of resting EEG inter-channel coherence as an efficacious method for noninvasive screening for MCI and early AD.
doi:10.1007/s10439-013-0788-4
PMCID: PMC3826279  PMID: 23483374
EEG-based diagnosis; early Alzheimer’s disease; mild cognitive impairment; coherence; graphical analysis
7.  Neural Basis of Emotional Decision Making in Trait Anxiety 
The Journal of Neuroscience  2013;33(47):18641-18653.
Although trait anxiety has been associated with risk decision making, whether it is related to risk per se or to the feeling of the risk, as well as the underlying neurocognitive mechanisms, remains unclear. Using a decision-making task with a manipulation of frame (i.e., written description of options as a potential gain or loss) and functional magnetic resonance imaging, we investigated the neurocognitive relationship between trait anxiety and decision making. The classic framing effect was observed: participants chose the safe option when it was described as a potential gain, but they avoided the same option when it was described as a potential loss. Most importantly, trait anxiety was positively correlated with this behavioral bias. Trait anxiety was also positively correlated with amygdala-based “emotional” system activation and its coupling with the ventromedial prefrontal cortex (vmPFC) when decisions were consistent with the framing effect, but negatively correlated with the dorsal anterior cingulate cortex (dACC)-based “analytic” system activation and its connectivity to the vmPFC when decisions ran counter to the framing effect. Our findings suggest that trait anxiety is not associated with subjective risk preference but an evaluative bias of emotional information in decision making, underpinned by a hyperactive emotional system and a hypoactive analytic system in the brain.
doi:10.1523/JNEUROSCI.1253-13.2013
PMCID: PMC3834062  PMID: 24259585
8.  Laminin 411 acts as a potent inducer of umbilical cord mesenchymal stem cell differentiation into insulin-producing cells 
Background
Diabetes mellitus (DM) is an incurable metabolic disease constituting a major threat to human health. Insulin-producing cells (IPCs) differentiated from mesenchymal stem cells (MSCs) hold great promise in the treatment of DM. The development of an efficient IPC induction system is a crucial step for the clinical application of IPCs for DM. Laminin 411 is a key component of the basement membrane and is involved in the regulation of cell differentiation; however, little is known about a role of laminin 411 in the regulation of IPC differentiation from human MSCs.
Methods
MSCs were isolated from human umbilical cord (UC-MSCs) and expanded in an in vitro culture system. UC-MSCs were then cultured in the IPC induction and differentiation medium in the presence of laminin 411. Flow cytometry, Quantitative realtime PCR, immunofluorescence staining, ELISA, Western blotting and other techniques were applied to determine IPC generation, insulin expression and related mechanisms. To evaluate potential therapeutic efficacy of IPCs induced from UC-MSCs, a type-1 diabetes (T1DM) rat model was generated using streptozotocin. Blood glucose, insulin levels, and survival of rats were monitored periodically following intravenous injection of the tested cells.
Results
Laminin 411 markedly induced the expression of the genes Foxa2 and Sox17, markers for pancreatic precursor cells, efficiently induced IPC differentiation from MSCs, and up-regulated insulin expression at both mRNA and protein levels. Furthermore, the expression of the genes known to govern insulin expression including Pdx1 and Ngn3 was markedly induced by laminin 411, which suggests that Pdx1 and Ngn3 signaling pathways are involved in laminin 411 induced-insulin expression machinery. More importantly, administration of laminin 411-induced IPCs rapidly and significantly down-regulated fasting blood glucose levels, significantly reduced the HbA1c concentration and markedly improved the symptoms and survival of T1DM rats.
Conclusions
Our results demonstrate that laminin 411 acts as a potent differentiation inducer of IPCs from UC-MSCs via the Pdx1 and Ngn3 signaling pathways. Moreover, transfusion of laminin 411 induced-IPCs more efficiently improves symptoms and survival of T1DM rats. These novel finding highlights a potential clinical application of laminin 411 induced-IPCs in the treatment of T1DM, which calls for further studies.
doi:10.1186/1479-5876-12-135
PMCID: PMC4040110  PMID: 24885418
Laminin 411; Mesenchymal stem cell; Insulin-producing cell
9.  Identifying Gastric Cancer Related Genes Using the Shortest Path Algorithm and Protein-Protein Interaction Network 
BioMed Research International  2014;2014:371397.
Gastric cancer, as one of the leading causes of cancer related deaths worldwide, causes about 800,000 deaths per year. Up to now, the mechanism underlying this disease is still not totally uncovered. Identification of related genes of this disease is an important step which can help to understand the mechanism underlying this disease, thereby designing effective treatments. In this study, some novel gastric cancer related genes were discovered based on the knowledge of known gastric cancer related ones. These genes were searched by applying the shortest path algorithm in protein-protein interaction network. The analysis results suggest that some of them are indeed involved in the biological process of gastric cancer, which indicates that they are the actual gastric cancer related genes with high probability. It is hopeful that the findings in this study may help promote the study of this disease and the methods can provide new insights to study various diseases.
doi:10.1155/2014/371397
PMCID: PMC3963223  PMID: 24729971
11.  Neonatal Desensitization Supports Long-Term Survival and Functional Integration of Human Embryonic Stem Cell-Derived Mesenchymal Stem Cells in Rat Joint Cartilage Without Immunosuppression 
Stem Cells and Development  2012;22(1):90-101.
Immunological response hampers the investigation of human embryonic stem cells (hESCs) or their derivates for tissue regeneration in vivo. Immunosuppression is often used after surgery, but exhibits side effects of significant weight loss and allows only short-term observation. The purpose of this study was to investigate whether neonatal desensitization supports relative long-term survival of hESC-derived mesenchymal stem cells (hESC-MSCs) and promotes cartilage regeneration. hESC-MSCs were injected on the day of birth in rats. Six weeks after neonatal injection, a full-thickness cylindrical cartilage defect was created and transplanted with a hESC-MSC-seeded collagen bilayer scaffold (group d+s+c) or a collagen bilayer scaffold (group d+s). Rats without neonatal injection were transplanted with the hESC-MSC-seeded collagen bilayer scaffold to serve as controls (group s+c). Cartilage regeneration was evaluated by histological analysis, immunohistochemical staining, and biomechanical test. The role of hESC-MSCs in cartilage regeneration was analyzed by CD4 immunostaining, cell death detection, and visualization of human cells in regenerated tissues. hESC-MSCs expressed CD105, CD73, CD90, CD29, and CD44, but not CD45 and CD34, and possessed trilineage differentiation potential. Group d+s+c exhibited greater International Cartilage Repair Society (ICRS) scores than group d+s or group s+c. Abundant collagen type II and improved mechanical properties were detected in group d+s+c. There were less CD4+ inflammatory cell infiltration and cell death at week 1, and hESC-MSCs were found to survive as long as 8 weeks after transplantation in group d+s+c. Our study suggests that neonatal desensitization before transplantation may be an efficient way to develop a powerful tool for preclinical study of human cell-based therapies in animal models.
doi:10.1089/scd.2012.0116
PMCID: PMC3528094  PMID: 22788986
12.  Linking brain electrical signals elicited by current outcomes with future risk decision-making 
The experience of current outcomes influences future decisions in various ways. The neural mechanism of this phenomenon may help to clarify the determinants of decision-making. In this study, thirty-nine young adults finished a risky gambling task by choosing between a high- and a low-risk option in each trial during electroencephalographic data collection. We found that risk-taking strategies significantly modulated mean amplitudes of the event-related potential (ERP) component P3, particularly at the central scalp. The event-related spectral perturbation and the inter-trial coherence measurements of the independent component analysis (ICA) data indicated that the “stay” vs. “switch” electrophysiological difference associated with subsequent decision-making was mainly due to fronto-central theta and left/right mu independent components. Event-related cross-coherence results suggested that the neural information of action monitoring and updating emerged in the fronto-central cortex and propagated to sensorimotor area for further behavior adjustment. Based on these findings of ERP and event-related oscillation (ERO) measures, we propose a neural model of the influence of current outcomes on future decisions.
doi:10.3389/fnbeh.2014.00084
PMCID: PMC3957203  PMID: 24672447
decision-making; outcome evaluation; event-related potential; event-related oscillation; time-frequency analysis; independent component analysis
13.  A novel wavelength-adjusting method in InGaN-based light-emitting diodes 
Scientific Reports  2013;3:3389.
The pursuit of high internal quantum efficiency (IQE) for green emission spectral regime is referred as “green gap” challenge. Now researchers place their hope on the InGaN-based materials to develop high-brightness green light-emitting diodes. However, IQE drops fast when emission wavelength of InGaN LED increases by changing growth temperature or well thickness. In this paper, a new wavelength-adjusting method is proposed and the optical properties of LED are investigated. By additional process of indium pre-deposition before InGaN well layer growth, the indium distribution along growth direction becomes more uniform, which leads to the increase of average indium content in InGaN well layer and results in a redshift of peak-wavelength. We also find that the IQE of LED with indium pre-deposition increases with the wavelength redshift. Such dependence is opposite to the IQE-wavelength behavior in conventional InGaN LEDs. The relations among the IQE, wavelength and the indium pre-deposition process are discussed.
doi:10.1038/srep03389
PMCID: PMC3865511  PMID: 24343166
14.  Prediction of Drugs Target Groups Based on ChEBI Ontology 
BioMed Research International  2013;2013:132724.
Most drugs have beneficial as well as adverse effects and exert their biological functions by adjusting and altering the functions of their target proteins. Thus, knowledge of drugs target proteins is essential for the improvement of therapeutic effects and mitigation of undesirable side effects. In the study, we proposed a novel prediction method based on drug/compound ontology information extracted from ChEBI to identify drugs target groups from which the kind of functions of a drug may be deduced. By collecting data in KEGG, a benchmark dataset consisting of 876 drugs, categorized into four target groups, was constructed. To evaluate the method more thoroughly, the benchmark dataset was divided into a training dataset and an independent test dataset. It is observed by jackknife test that the overall prediction accuracy on the training dataset was 83.12%, while it was 87.50% on the test dataset—the predictor exhibited an excellent generalization. The good performance of the method indicates that the ontology information of the drugs contains rich information about their target groups, and the study may become an inspiration to solve the problems of this sort and bridge the gap between ChEBI ontology and drugs target groups.
doi:10.1155/2013/132724
PMCID: PMC3853244  PMID: 24350241
15.  Valproic Acid Treatment Inhibits Hypoxia-Inducible Factor 1α Accumulation and Protects against Burn-Induced Gut Barrier Dysfunction in a Rodent Model 
PLoS ONE  2013;8(10):e77523.
Objective
Burn-induced gut dysfunction plays an important role in the development of sepsis and multiple organ dysfunction. Emerging evidence suggests that hypoxia-inducible factor-1α (HIF-1α) is critical in paracelluar barrier functions via regulating vascular endothelial growth factor (VEGF) and myosin light chain kinase (MLCK) expression. Previous studies have also demonstrated that histone deacetylase inhibitors (HDACIs) can repress HIF-1α. This study aims to examine whether valproic acid (VPA), a HDACI, protects against burn-induced gut barrier dysfunction via repressing HIF-1α-dependent upregulation of VEGF and MLCK expression.
Methods
Rats were subjected to third degree 55% TBSA burns and treated with/ without VPA (300mg/kg). Intestinal barrier dysfunction was evaluated by permeability of intestinal mucosa to fluorescein isothiocyanate (FITC)-dextran and histologic evaluation. Histone acetylation, tight junction protein zonula occludens 1 (ZO-1), VEGF, MLCK and HIF-1α were measured. In addition, CaCO2 cells were transfected with siRNA directed against HIF-1α and were stimulated with CoCl2 (1mM) for 24 hours with/without VPA (2mM) followed by analysis of HIF-1α, MLCK, VEGF and ZO-1.
Results
Burn insults resulted in a significant increase in intestinal permeability and mucosal damage, accompanied by a significant reduction in histone acetylation, ZO-1, upregulation of VEGF, MLCK expression, and an increase in HIF-1α accumulation. VPA significantly attenuated the increase in intestinal permeability, mucosa damage, histone deacetylation and changes in ZO-1 expression. VPA also attenuated the increased VEGF, MLCK and HIF-1α protein levels. VPA reduced HIF-1α, MLCK and VEGF production and prevented ZO-1 loss in CoCl2-stimulated Caco-2 cells. Moreover, transfection of siRNA directed against HIF-1α led to inhibition of MLCK and VEGF production, accompanied by upregulation of ZO-1.
Conclusions
These results indicate that VPA can protect against burn-induced gut barrier dysfunction. These protective effects may be due to its inhibitory action on HIF-1α, leading to a reduction in intestinal VEGF and MLCK expression and minimizing ZO-1 degradation.
doi:10.1371/journal.pone.0077523
PMCID: PMC3798300  PMID: 24147016
16.  Composite diffuse large B-cell lymphoma and classical Hodgkin’s lymphoma of the stomach: Case report and literature review 
The combination of classical Hodgkin’s lymphoma (cHL) and non-Hodgkin lymphoma coexisting in the same patient is not common, especially in one extranodal location. Here we present a rare case of composite diffuse large B-cell lymphoma (DLBCL) and cHL occurring simultaneously in the stomach of a 53-year-old female who presented with upper abdominal discomfort and gas pain. Surgery was performed and the disease was diagnosed pathologically as composite lymphoma of DLBCL and cHL using hematoxylin-eosin and immunohistochemical staining. Epstein-Barr virus (EBV) infection was not detected by in situ hybridization for EBV-encoded RNA or immunohistochemistry for EBV latent membrane protein-1. Polymerase chain reaction analysis from the two distinct components of the tumor demonstrated clonal immunoglobulin κ light chain gene rearrangements. The patient died approximately 11 mo after diagnosis in spite of receiving eight courses of the CHOP and two courses of the rituximab-CHOP (RCHOP) chemotherapy regimen. This case report showed that the two distinct components, DLBCL and cHL, appeared to originate from the same clonal progenitor cell, and that EBV infection was not essential for transformation during the course of tumorigenesis.
doi:10.3748/wjg.v19.i37.6304
PMCID: PMC3787365  PMID: 24115832
Composite lymphoma; Diffuse large B-cell lymphoma; Hodgkin’s lymphoma; Stomach
17.  The Interaction of Arousal and Valence in Affective Priming: Behavioral and Electrophysiological Evidence 
Brain research  2012;1474:60-72.
The affective priming paradigm has been studied extensively and applied in many fields during the past two decades. Most research thus far has focused on the valence dimension. Whether emotional arousal influences affective priming remains poorly understood. The present study demonstrates how arousal impacts evaluation of affective words using reaction time and event-related potential (ERP) measures. Eighteen younger subjects evaluated pleasantness of target words after seeing affective pictures as primes. The participants’ responses were faster and/or more accurate for valence-congruent trials than for incongruent trials, particularly with high-arousal stimuli. An ERP affective priming effect (N400) also occurred mainly in high-arousing stimulus pairs. In addition, whereas valence congruency influenced both the N400 and the LPP, arousal congruency influenced only the LPP, suggesting that arousal congruency mainly modulates post-semantic processes, but valence congruency effects begin with semantic processes. Overall, our current findings indicate that the arousal level of visual images impacts both behavioral and ERP effects of affective priming.
Section
Cognitive and Behavioral Neuroscience
doi:10.1016/j.brainres.2012.07.023
PMCID: PMC3694405  PMID: 22820299
Affective priming; Valence; Arousal; Evaluation decision task
18.  Prediction and Analysis of Post-Translational Pyruvoyl Residue Modification Sites from Internal Serines in Proteins 
PLoS ONE  2013;8(6):e66678.
Most of pyruvoyl-dependent proteins observed in prokaryotes and eukaryotes are critical regulatory enzymes, which are primary targets of inhibitors for anti-cancer and anti-parasitic therapy. These proteins undergo an autocatalytic, intramolecular self-cleavage reaction in which a covalently bound pyruvoyl group is generated on a conserved serine residue. Traditional detections of the modified serine sites are performed by experimental approaches, which are often labor-intensive and time-consuming. In this study, we initiated in an attempt for the computational predictions of such serine sites with Feature Selection based on a Random Forest. Since only a small number of experimentally verified pyruvoyl-modified proteins are collected in the protein database at its current version, we only used a small dataset in this study. After removing proteins with sequence identities >60%, a non-redundant dataset was generated and was used, which contained only 46 proteins, with one pyruvoyl serine site for each protein. Several types of features were considered in our method including PSSM conservation scores, disorders, secondary structures, solvent accessibilities, amino acid factors and amino acid occurrence frequencies. As a result, a pretty good performance was achieved in our dataset. The best 100.00% accuracy and 1.0000 MCC value were obtained from the training dataset, and 93.75% accuracy and 0.8441 MCC value from the testing dataset. The optimal feature set contained 9 features. Analysis of the optimal feature set indicated the important roles of some specific features in determining the pyruvoyl-group-serine sites, which were consistent with several results of earlier experimental studies. These selected features may shed some light on the in-depth understanding of the mechanism of the post-translational self-maturation process, providing guidelines for experimental validation. Future work should be made as more pyruvoyl-modified proteins are found and the method should be evaluated on larger datasets. At last, the predicting software can be downloaded from http://www.nkbiox.com/sub/pyrupred/index.html.
doi:10.1371/journal.pone.0066678
PMCID: PMC3689656  PMID: 23805260
19.  Aging and Repetition Priming for Targets and Distracters in a Working Memory Task 
A combined working memory/repetition priming task was administered to 13 young (mean age 23) and 13 elderly (mean age 69) adults. Each participant memorized a sample target face at the beginning of a trial and then determined whether each of 13 serially presented test faces matched the sample target. In each trial, both the target and one particular distracter face were repeated during the test phase. Within-trial repetition priming effects indicated the contribution of implicit memory to task performance. Response times decreased as items were tested repeatedly within a trial, but this decrement was greater for distracters than for targets. Young and older participants were equally accurate at identifying targets, but elderly were slightly less accurate for distracters. Elderly participants showed repetition priming effects during the working memory task for both targets and distracters, while the young showed such effects only for distracters. The results suggest that active maintenance in working memory, but not inhibition or rejection of distracters, may suppress implicit memory systems.
doi:10.1080/138255890969555
PMCID: PMC3678549  PMID: 16887789
aging; repetition priming; working memory; implicit memory; explicit memory
20.  Woulda, coulda, shoulda: the Evaluation and the Impact of the Alternative Outcome 
Psychophysiology  2011;48(10):1354-1360.
The alternative outcome refers to the outcome of the unselected option in decision-making tasks, which has significant influence on the chosen outcome evaluation. Most paradigms have presented the alternative outcome either after or simultaneous with the chosen outcome, which complicates the observation on the brain activity associated with the alternative outcome. To circumvent this perceived shortcoming, we modified the classic paradigm designed by Yeung & Sanfey (2004) such that the alternative outcome was presented before the chosen outcome in each trial while electroencephalographic (EEG) was recorded. The feedback-related negativity (FRN) elicited by the positive alternative outcome was larger than that elicited by the negative alternative outcome, suggesting that the participants evaluated the positive alternative outcome as negative feedback. Moreover, the FRN and the P3 elicited by the chosen outcome were influenced by the valence of the alternative outcome. The current study reveals that the alternative outcome is treated as important information even though it is economically neutral.
doi:10.1111/j.1469-8986.2011.01215.x
PMCID: PMC3673557  PMID: 21569049
decision making; outcome evaluation; alternative outcome; feedback-related negativity (FRN); logic error; counterfactual thinking
21.  Sensation Seeking Predicts Brain Responses in the Old-New Task: Converging Multimodal Neuroimaging Evidence 
Novel images and message content enhance visual attention and memory for high sensation seekers, but the neural mechanisms associated with this effect are unclear. To investigate the individual differences in brain responses to new and old (studied) visual stimuli, we utilized Event-related Potentials (ERP) and functional Magnetic Resonance Imaging (fMRI) measures to examine brain reactivity among high and low sensation seekers during a classic old-new memory recognition task. Twenty low and 20 high sensation seekers completed separate, but parallel, ERP and fMRI sessions. For each session, participants initially studied drawings of common images, and then performed an old-new recognition task during scanning. High sensation seekers showed greater ERP responses to new objects at the frontal N2 ERP component, compared to low sensation seekers. The ERP Novelty-N2 responses were correlated with fMRI responses in the orbitofrontal gyrus. Sensation seeking status also modulated the FN400 ERP component indexing familiarity and conceptual learning, along with fMRI responses in the caudate nucleus, which correlated with FN400 activity. No group differences were found in the late ERP positive components indexing classic old-new amplitude effects. Our combined ERP & fMRI results suggest that sensation-seeking personality affects the early brain responses to visual processing, but not the later stage of memory recognition.
doi:10.1016/j.ijpsycho.2012.03.003
PMCID: PMC3367102  PMID: 22484516
novelty seeking personality; old-new effect; recognition memory; evoked potentials; brain imaging; ERP; fMRI
22.  Beyond Valence and Magnitude: a Flexible Evaluative Coding System in the Brain 
Neuropsychologia  2011;49(14):3891-3897.
Outcome evaluation is a cognitive process that plays an important role in our daily lives. In most paradigms utilized in the field of experimental psychology, outcome valence and outcome magnitude are the two major features investigated. The classical “independent coding model” suggest that outcome valence and outcome magnitude are evaluated by separate neural mechanisms that may be mapped onto discrete event-related potential (ERP) components: feedback-related negativity (FRN) and the P3, respectively. To examine this model, we presented outcome valence and magnitude sequentially rather than simultaneously. The results reveal that when only outcome valence or magnitude is known, both the FRN and the P3 encode that outcome feature; when both aspects of outcome are known, the cognitive functions of the two components dissociate: the FRN responds to the information available in the current context, while the P3 pattern depends on outcome presentation sequence. The current study indicates that the human evaluative system, indexed in part by the FRN and the P3, is more flexible than previous theories suggested.
doi:10.1016/j.neuropsychologia.2011.10.006
PMCID: PMC3665265  PMID: 22019775
Decision-making; outcome evaluation; outcome valence; outcome magnitude; event-related potential (ERP); feedback-related negativity (FRN); P3
23.  Brain Potentials Distinguish New and Studied Objects during Working Memory 
Human brain mapping  2008;29(4):441-452.
We investigated brain responses to matching versus nonmatching objects in working memory with a modified delayed match-to-sample task using event-related potentials (ERPs). In addition, ERP correlates of new items (new matches/new nonmatches) and previously studied items (studied matches/studied nonmatches) were examined in the working memory task. Half of the common visual objects were initially studied until 95% accuracy was attained and half were new. Each memory trial began with the presentation of a sample object followed by nine test objects. Participants indicated whether each test item was the same as the object held in mind (i.e., match) or a nonmatch. Compared to studied matches, new matches evoked activity that was 50 msec earlier and largest at frontal sites. In contrast, P3 activity associated with studied nonmatches was larger than for new nonmatches at mostly posterior sites, which parallels previously reported old-new ERP effects. The ERP source analysis further confirms that the cortical mechanisms underlying matching objects and rejecting irrelevant objects during the task are both temporally and spatially distinct. Moreover, our current findings suggest that prior learning affects brain responses to matching visual items during a working memory task.
doi:10.1002/hbm.20409
PMCID: PMC3665269  PMID: 17497630
ERPs; visual memory; matching; delayed match-to-sample; stimulus evaluation; common objects; LORETA
24.  Binding 3D Object Perception in Human Visual Cortex 
Journal of cognitive neuroscience  2008;20(4):553-562.
How do visual luminance, shape, motion, and depth bind together in the brain to represent the coherent percept of a 3D object within hundreds of milliseconds (ms)? We provide evidence from simultaneous magneto-encephalographic (MEG) and electro-encephalographic (EEG) data that perception of 3D objects defined by luminance or motion elicits sequential activity in human visual cortices within 500 ms. Following activation of the primary visual cortex around 100 ms, 3D objects elicited sequential activity with only little overlap (dynamic 3D shapes: hMT- LO-vTemp, stationary 3D shapes: LO-vTemp). A delay of 80 ms, both in MEG / EEG responses and in reaction times (RT), was found when additional motion information was processed. We also found significant positive correlations between RT, and MEG and EEG responses in the right temporal location. After about 400 ms, long lasting activity was observed in the parietal cortex and concurrently in previously activated regions. Novel time-frequency analyses indicate that the activity in the Lateral Occipital (LO) complex is associated with an increase of induced power in the gamma band, a hallmark of binding. The close correspondence of an induced gamma response with concurrent sources located in LO in both experimental conditions at different points in time (~200 ms for luminance and ~300 ms for dynamic cues) strongly suggests that LO is the key region for the assembly of object features. The assembly is fed forward to achieve coherent perception of a 3D object within 500 ms.
doi:10.1162/jocn.2008.20050
PMCID: PMC3658156  PMID: 18052779
25.  New Measures to Detect Malingered Neurocognitive Deficit: Applying Reaction Time and Event-Related Potentials 
The ability of the Test of Memory Malingering (TOMM), reaction times (RT) and Event-Related Potentials (ERP) to detect malingered neurocognitive deficit (MNCD) was examined in 32 normal individuals answering under honest (HON; n = 16) or malingering instructions (MAL; n = 16) as well as in 15 patients with Traumatic Brain Injury (TBI) who answered under honest instructions. Overall, the TOMM was the most effective at classifying groups. However, new accuracy, RT, and ERP measures reached promising hit rates in the range of 71%-88%. In particular, the difference in frontal versus posterior ERP obtained during an old-new task was effective at classifying MAL vs. TBI (hit rate = 87%).
doi:10.1080/13803390701754746
PMCID: PMC3649037  PMID: 18608662

Results 1-25 (55)