Academia Sinica

About: Academia Sinica is a facility organization based out in Taipei, Taiwan. It is known for research contribution in the topics: Population & Galaxy. The organization has 52086 authors who have published 65998 publications receiving 1728114 citations. The organization is also known as: Central Research Academy.

Adsorption and diffusion of Li on pristine and defective graphene.

Abstract: With first-principles DFT calculations, the interaction between Li and carbon in graphene-based nanostructures is investigated as Li is adsorbed on graphene. It is found that the Li/C ratio of less than 1/6 for the single-layer graphene is favorable energetically, which can explain what has been observed in Raman spectrum reported recently. In addition, it is also found that the pristine graphene cannot enhance the diffusion energetics of Li ion. However, the presence of vacancy defects can increase the ratio of Li/C largely. With double-vacancy and higher-order defects, Li ion can diffuse freely in the direction perpendicular to the graphene sheets and hence boost the diffusion energetics to some extent.

KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns.

Abstract: Due to the importance of protein phosphorylation in cellular control, many researches are undertaken to predict the kinase-specific phosphorylation sites. Referred to our previous work, KinasePhos 1.0, incorporated profile hidden Markov model (HMM) with flanking residues of the kinase-specific phosphorylation sites. Herein, a new web server, KinasePhos 2.0, incorporates support vector machines (SVM) with the protein sequence profile and protein coupling pattern, which is a novel feature used for identifying phosphorylation sites. The coupling pattern [XdZ] denotes the amino acid coupling-pattern of amino acid types X and Z that are separated by d amino acids. The differences or quotients of coupling strength C(XdZ) between the positive set of phosphorylation sites and the background set of whole protein sequences from Swiss-Prot are computed to determine the number of coupling patterns for training SVM models. After the evaluation based on k-fold cross-validation and Jackknife cross-validation, the average predictive accuracy of phosphorylated serine, threonine, tyrosine and histidine are 90, 93, 88 and 93%, respectively. KinasePhos 2.0 performs better than other tools previously developed. The proposed web server is freely available at http://KinasePhos2.mbc.nctu.edu.tw/.

EGFR modulates microRNA maturation in response to hypoxia through phosphorylation of AGO2

Abstract: MicroRNAs (miRNAs) are generated by two-step processing to yield small RNAs that negatively regulate target gene expression at the post-transcriptional level. Deregulation of miRNAs has been linked to diverse pathological processes, including cancer. Recent studies have also implicated miRNAs in the regulation of cellular response to a spectrum of stresses, such as hypoxia, which is frequently encountered in the poorly angiogenic core of a solid tumour. However, the upstream regulators of miRNA biogenesis machineries remain obscure, raising the question of how tumour cells efficiently coordinate and impose specificity on miRNA expression and function in response to stresses. Here we show that epidermal growth factor receptor (EGFR), which is the product of a well-characterized oncogene in human cancers, suppresses the maturation of specific tumour-suppressor-like miRNAs in response to hypoxic stress through phosphorylation of argonaute 2 (AGO2) at Tyr 393. The association between EGFR and AGO2 is enhanced by hypoxia, leading to elevated AGO2-Y393 phosphorylation, which in turn reduces the binding of Dicer to AGO2 and inhibits miRNA processing from precursor miRNAs to mature miRNAs. We also identify a long-loop structure in precursor miRNAs as a critical regulatory element in phospho-Y393-AGO2-mediated miRNA maturation. Furthermore, AGO2-Y393 phosphorylation mediates EGFR-enhanced cell survival and invasiveness under hypoxia, and correlates with poorer overall survival in breast cancer patients. Our study reveals a previously unrecognized function of EGFR in miRNA maturation and demonstrates how EGFR is likely to function as a regulator of AGO2 through novel post-translational modification. These findings suggest that modulation of miRNA biogenesis is important for stress response in tumour cells and has potential clinical implications.

Characterization of the sources and processes of organic and inorganic aerosols in New York city with a high-resolution time-of-flight aerosol mass apectrometer

Abstract: Submicron aerosol particles (PM1) were measured in-situ using a High-Resolution Time-of-Flight Aerosol Mass Spectrometer during the summer 2009 Field Intensive Study at Queens College in New York, NY Organic aerosol (OA) and sulfate are the two dominant species, accounting for 54% and 24%, respectively, of the total PM1 mass The average mass-based size distribution of OA presents a small mode peaking at ~150 nm (Dva) and an accumulation mode (~550 nm) that is internally mixed with sulfate, nitrate, and ammonium The diurnal cycles of both sulfate and OA peak between 01:00–02:00 pm EST due to photochemical production The average (±σ) oxygen-to-carbon (O/C), hydrogen-to-carbon (H/C), and nitrogen-to-carbon (N/C) ratios of OA in NYC are 036 (±009), 149 (±008), and 0012 (±0005), respectively, corresponding to an average organic mass-to-carbon (OM/OC) ratio of 162 (±011) Positive matrix factorization (PMF) of the high resolution mass spectra identified two primary OA (POA) sources, traffic and cooking, and three secondary OA (SOA) components including a highly oxidized, regional low-volatility oxygenated OA (LV-OOA; O/C = 063), a less oxidized, semi-volatile SV-OOA (O/C = 038) and a unique nitrogen-enriched OA (NOA; N/C = 0053) characterized with prominent CxH2x + 2N+ peaks likely from amino compounds Our results indicate that cooking and traffic are two distinct and mass-equivalent POA sources in NYC, together contributing ~30% of the total OA mass during this study The OA composition is dominated by secondary species, especially during high PM events SV-OOA and LV-OOA on average account for 34% and 30%, respectively, of the total OA mass The chemical evolution of SOA in NYC appears to progress with a continuous oxidation from SV-OOA to LV-OOA, which is further supported by a gradual increase of O/C ratio and a simultaneous decrease of H/C ratio in total OOA Detailed analysis of NOA (58% of OA) presents evidence that organic nitrogen species such as amines might have played an important role in the atmospheric processing of OA in NYC, likely involving both acid-base chemistry and photochemistry In addition, analysis of air mass trajectories and satellite imagery of aerosol optical depth (AOD) indicates that the high potential source regions of secondary sulfate and aged OA are mainly located in regions to the west and southwest of the city

Planck intermediate results: V. Pressure profiles of galaxy clusters from the Sunyaev-Zeldovich effect

Abstract: Taking advantage of the all-sky coverage and broad frequency range of the Planck satellite, we study the Sunyaev-Zeldovich (SZ) and pressure profiles of 62 nearby massive clusters detected at high significance in the 14-month nominal survey. Careful reconstruction of the SZ signal indicates that most clusters are individually detected at least out to R500. By stacking the radial profiles, we have statistically detected the radial SZ signal out to 3R500, i.e., at a density contrast of about 50-100, though the dispersion about the mean profile dominates the statistical errors across the whole radial range. Our measurement is fully consistent with previous Planck results on integrated SZ fluxes, further strengthening the agreement between SZ and X-ray measurements inside R500. Correcting for the effects of the Planck beam, we have calculated the corresponding pressure profiles. This new constraint from SZ measurements is consistent with the X-ray constraints from xmm in the region in which the profiles overlap (i.e., [0.1-1] R500), and is in fairly good agreement with theoretical predictions within the expected dispersion. At larger radii the average pressure profile is shallower than the predictions. Combining the SZ and X-ray observed profiles into a joint fit to a generalised pressure profile gives best-fit parameters [P0, c500, gamma, alpha, beta] = [6.41, 1.81, 0.31, 1.33, 4.13]. Using a reasonable hypothesis for the gas temperature in the cluster outskirts we reconstruct from our stacked pressure profile the gas mass fraction profile out to 3R500. Within the temperature driven uncertainties, our Planck constraints are compatible with the cosmic baryon fraction and expected gas fraction in halos.