Browsing by Author "Chen, Y"

Now showing 1 - 17 of 17
  • Thumbnail Image
    ItemOpen Access
    A jet-like outflow toward the high-mass (proto) stellar object IRAS 18566+0408
    (Astronomy & Astrophysics, 2007-07) Zhang, Q; Sridharan, TK; Hunter, TR; Chen, Y; Beuther, H; Wyrowski, F
  • Thumbnail Image
    ItemOpen Access
    An empirical Bayesian method for multivariate meta-analysis with an application in clinical trials
    (Communication in Statistics-Theory and Methods, 2014) Chen, Y; Luo, S; Chu, H; Su, X; Nie, L
  • Thumbnail Image
    ItemOpen Access
    An Experimental Investigation into the Scope Assignment of Japanese and Chinese Quantifier-Negation Sentences
    (Languages, 2024-03-01) Chen, Y
    Quantifier-Negation sentences such as all teachers did not use Sandy’s car are known to allow an inverse scope interpretation in English. However, there is a lack of experimental evidence to determine whether this interpretation is allowed in equivalent sentences in Japanese and Chinese. To address this issue, this study conducted a sentence–picture matching truth value judgment experiment in both Japanese and Chinese. The data suggested that Japanese Quantifier-Negation sentences do allow inverse scope readings, which suggests that the subject may be interpreted within the scope of negation. In contrast, Chinese Quantifier-Negation sentences prohibit inverse scope readings, which is in accordance with the strong scope rigidity consistently observed in this language. This paper also discussed how to develop a valid experiment for investigating scope ambiguities.
  • Thumbnail Image
    ItemOpen Access
    Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation.
    (PLoS Genet, 2014-04) Janbon, G; Ormerod, KL; Paulet, D; Byrnes, EJ; Yadav, V; Chatterjee, G; Mullapudi, N; Hon, C; Billmyre, RB; Brunel, F; Bahn, Y; Chen, W; Chen, Y; Chow, EWL; Coppée, J; Floyd-Averette, A; Gaillardin, C; Gerik, KJ; Goldberg, J; Gonzalez-Hilarion, S; Gujja, S; Hamlin, JL; Hsueh, Y; Ianiri, G; Jones, S; Kodira, CD; Kozubowski, L; Lam, W; Marra, M; Mesner, LD; Mieczkowski, PA; Moyrand, F; Nielsen, K; Proux, C; Rossignol, T; Schein, JE; Sun, S; Wollschlaeger, C; Wood, IA; Zeng, Q; Neuvéglise, C; Newlon, CS; Perfect, JR; Lodge, JK; Idnurm, A; Stajich, JE; Kronstad, JW; Sanyal, K; Heitman, J; Fraser, JA; Cuomo, CA; Dietrich, FS
    Cryptococcus neoformans is a pathogenic basidiomycetous yeast responsible for more than 600,000 deaths each year. It occurs as two serotypes (A and D) representing two varieties (i.e. grubii and neoformans, respectively). Here, we sequenced the genome and performed an RNA-Seq-based analysis of the C. neoformans var. grubii transcriptome structure. We determined the chromosomal locations, analyzed the sequence/structural features of the centromeres, and identified origins of replication. The genome was annotated based on automated and manual curation. More than 40,000 introns populating more than 99% of the expressed genes were identified. Although most of these introns are located in the coding DNA sequences (CDS), over 2,000 introns in the untranslated regions (UTRs) were also identified. Poly(A)-containing reads were employed to locate the polyadenylation sites of more than 80% of the genes. Examination of the sequences around these sites revealed a new poly(A)-site-associated motif (AUGHAH). In addition, 1,197 miscRNAs were identified. These miscRNAs can be spliced and/or polyadenylated, but do not appear to have obvious coding capacities. Finally, this genome sequence enabled a comparative analysis of strain H99 variants obtained after laboratory passage. The spectrum of mutations identified provides insights into the genetics underlying the micro-evolution of a laboratory strain, and identifies mutations involved in stress responses, mating efficiency, and virulence.
  • Thumbnail Image
    ItemOpen Access
    Bayesian analysis on meta-analysis of case-control studies accounting for within-study correlation
    (Statistical Methods in Medical Research, 2015) Chen, Y; Chu, H; Luo, S; Nie, L; Chen, S
  • Thumbnail Image
    ItemOpen Access
    Bayesian inference on risk differences: an application to multivariate meta-analysis of adverse events in clinical trials
    (Statistics in Biopharmaceutical Research, 2013) Chen, Y; Luo, S; Chu, H; Wei, P
  • Thumbnail Image
    ItemOpen Access
    dbl-1/TGF-β and daf-12/NHR Signaling Mediate Cell-Nonautonomous Effects of daf-16/FOXO on Starvation-Induced Developmental Arrest.
    (PLoS Genet, 2015-12) Kaplan, RE; Chen, Y; Moore, BT; Jordan, JM; Maxwell, CS; Schindler, AJ; Baugh, LR
    Nutrient availability has profound influence on development. In the nematode C. elegans, nutrient availability governs post-embryonic development. L1-stage larvae remain in a state of developmental arrest after hatching until they feed. This "L1 arrest" (or "L1 diapause") is associated with increased stress resistance, supporting starvation survival. Loss of the transcription factor daf-16/FOXO, an effector of insulin/IGF signaling, results in arrest-defective and starvation-sensitive phenotypes. We show that daf-16/FOXO regulates L1 arrest cell-nonautonomously, suggesting that insulin/IGF signaling regulates at least one additional signaling pathway. We used mRNA-seq to identify candidate signaling molecules affected by daf-16/FOXO during L1 arrest. dbl-1/TGF-β, a ligand for the Sma/Mab pathway, daf-12/NHR and daf-36/oxygenase, an upstream component of the daf-12 steroid hormone signaling pathway, were up-regulated during L1 arrest in a daf-16/FOXO mutant. Using genetic epistasis analysis, we show that dbl-1/TGF-β and daf-12/NHR steroid hormone signaling pathways are required for the daf-16/FOXO arrest-defective phenotype, suggesting that daf-16/FOXO represses dbl-1/TGF-β, daf-12/NHR and daf-36/oxygenase. The dbl-1/TGF-β and daf-12/NHR pathways have not previously been shown to affect L1 development, but we found that disruption of these pathways delayed L1 development in fed larvae, consistent with these pathways promoting development in starved daf-16/FOXO mutants. Though the dbl-1/TGF-β and daf-12/NHR pathways are epistatic to daf-16/FOXO for the arrest-defective phenotype, disruption of these pathways does not suppress starvation sensitivity of daf-16/FOXO mutants. This observation uncouples starvation survival from developmental arrest, indicating that DAF-16/FOXO targets distinct effectors for each phenotype and revealing that inappropriate development during starvation does not cause the early demise of daf-16/FOXO mutants. Overall, this study shows that daf-16/FOXO promotes developmental arrest cell-nonautonomously by repressing pathways that promote larval development.
  • Thumbnail Image
    ItemOpen Access
    Economic incentives to target species and fish size: Prices and fine-scale product attributes in Norwegian fisheries
    (ICES Journal of Marine Science, 2015-08-19) Asche, F; Chen, Y; Smith, MD
    © International Council for the Exploration of the Sea 2014. All rights reserved.Improved fisheries management provides fishers with more opportunities to maximize harvest value by accounting for valuable attributes of the harvest such as species, harvest timing, fish size, product form, and landing location. Harvest values can also vary by vessel and gear type. Moreover, the extent of targeting can influence the ecosystem in which the fishers operate and provide important management challenges.Weutilize a unique dataset containing daily vessel-level fish landings in one region of Norway in 2010 to investigate the value of an array of attributes, including species, product form, product condition, timing, fish size, vessel type, gear type, and landing location for cod and other whitefish species, aswell as king crab. Wealso investigate to what extent landed value differs across different communities, firms, and plants. The results indicate substantial variation for all attributes, highlighting opportunities for fishers aswell as potential management challenges. For whitefish, the species landed accounts for threequarters of the variation in prices. For cod in particular, the fish size accounts for nearly all variation in prices. In these fisheries, market conditions justify management focus on the biological composition of the catch.
  • Thumbnail Image
    ItemOpen Access
    Effects of nocistatin and nocistatin (10-17) on nociceptin in antagonizing endomorphin-1 and endomorphin-2 analgesia in mice
    (Yaoxue Xuebao, 2002-11-01) Chen, LX; Chen, Y; Peng, YL; Wang, ZZ; Chen, Q; Wang, R
    AIM: To investigate the effects of nocistatin and nocistatin (10-17) on nociceptin in antagonizing endomorphin-1 or endomorphin-2 analgesia in mice. METHODS: Nocistatin and nocistatin (10-17) were synthesized by solid-phase peptide synthesis method. The mouse tail-flick test was used to assess the pain threshold of the mice and observe the effects of nocistatin and nocistatin (10-17). RESULTS: Nociceptin was shown to antagonize endomorphin-1 and endomorphin-2 analgesia. Nocistatin or nocistatin (10-17) produced no significant effect on basic pain threshold; however, both of them were found to reverse the effects of nociceptin in antagonizing endomorphin-1 and endomorphin-2 analgesia. CONCLUSION: Nocistatin and nocistatin (10-17) were shown to reverse the effects of nociceptin in antagonizing endomorphin-1 and endomorphin-2 analgesia at supraspinal level.
  • Thumbnail Image
    ItemOpen Access
    High Multiplicity Infection by HIV-1 in Men Who Have Sex with Men.
    (PLoS pathogens, 2010) Li, H; Bar, KJ; Wang, S; Decker, JM; Chen, Y; Sun, C; Salazar Gonzalez, JF; Salazar, MG; Learn, GH; Morgan, CJ; Schumacher, JE; Hraber, P; Giorgi, EE; Bhattacharya, T; Korber, BT; Perelson, AS; Eron, JJ; Cohen, MS; Hicks, CB; Haynes, BF; Markowitz, M; Keele, BF; Hahn, BH; Shaw, GM
    Elucidating virus-host interactions responsible for HIV-1 transmission is important for advancing HIV-1 prevention strategies. To this end, single genome amplification (SGA) and sequencing of HIV-1 within the context of a model of random virus evolution has made possible for the first time an unambiguous identification of transmitted/founder viruses and a precise estimation of their numbers. Here, we applied this approach to HIV-1 env analyses in a cohort of acutely infected men who have sex with men (MSM) and found that a high proportion (10 of 28; 36%) had been productively infected by more than one virus. In subjects with multivariant transmission, the minimum number of transmitted viruses ranged from 2 to 10 with viral recombination leading to rapid and extensive genetic shuffling among virus lineages. A combined analysis of these results, together with recently published findings based on identical SGA methods in largely heterosexual (HSX) cohorts, revealed a significantly higher frequency of multivariant transmission in MSM than in HSX [19 of 50 subjects (38%) versus 34 of 175 subjects (19%); Fisher's exact p = 0.008]. To further evaluate the SGA strategy for identifying transmitted/founder viruses, we analyzed 239 overlapping 5' and 3' half genome or env-only sequences from plasma viral RNA (vRNA) and blood mononuclear cell DNA in an MSM subject who had a particularly well-documented virus exposure history 3-6 days before symptom onset and 14-17 days before peak plasma viremia (47,600,000 vRNA molecules/ml). All 239 sequences coalesced to a single transmitted/founder virus genome in a time frame consistent with the clinical history, and a molecular clone of this genome encoded replication competent virus in accord with model predictions. Higher multiplicity of HIV-1 infection in MSM compared with HSX is consistent with the demonstrably higher epidemiological risk of virus acquisition in MSM and could indicate a greater challenge for HIV-1 vaccines than previously recognized.
  • Thumbnail Image
    ItemOpen Access
    Impacts of habitat loss on migratory shorebird populations and communities at stopover sites in the Yellow Sea
    (Biological Conservation, 2022-05) Wang, X; Chen, Y; Melville, DS; Choi, CY; Tan, K; Liu, J; Li, J; Zhang, S; Cao, L; Ma, Z
  • Thumbnail Image
    ItemOpen Access
    mmeta: An R package for multivariate meta-analysis
    (Journal of Statistical Software, 2014) Luo, S; Chen, Y; Su, X; Chu, H
  • Thumbnail Image
    ItemOpen Access
    Overlap valence on 2 + 1 flavor domain wall fermion configurations with deflation and low-mode substitution
    (2010-12-01) Li, A; Alexandru, A; Chen, Y; Doi, T; Dong, SJ; Draper, T; Gong, M; Hasenfratz, A; Horváth, I; Lee, FX; Liu, KF; Mathur, N; Streuer, T; Zhang, JB
    The overlap fermion propagator is calculated on 2 þ 1 flavor domain-wall fermion gauge configurations on 163 32, 243 64 and 323 64 lattices. With hyper-cubic (HYP) smearing and low eigenmode deflation, it is shown that the inversion of the overlap operator can be expedited by 20 times for the 163 32 lattice and 80 times for the 323 64 lattice. The overhead cost for calculating eigenmodes ranges from 4.5 to 7.9 propagators for the above lattices. Through the study of hyperfine splitting, we found that the Oðm2a2Þ error is small and these dynamical fermion lattices can adequately accommodate quark mass up to the charm quark. A preliminary calculation of the low-energy constant mix which characterizes the discretization error of the pion made up of a pair of sea and valence quarks in this mixedaction approach is carried out via the scalar correlator with periodic and antiperiodic boundary conditions. It is found to be small which shifts a 300 MeV pion mass by 10 to 19 MeVon these sets of lattices. We have studied the signal-to-noise issue of the noise source for the meson and baryon. We introduce a new algorithm with Z3 grid source and low eigenmode substitution to study the many-to-all meson and baryon correlators. It is found to be efficient in reducing errors for the correlators of both mesons and baryons. With 64-point Z3 grid source and low-mode substitution, it can reduce the statistical errors of the light quark (m 200–300 MeV) meson and nucleon correlators by a factor of 3–4 as compared to the point source. The Z3 grid source itself can reduce the errors of the charmonium correlators by a factor of 3.
  • Thumbnail Image
    ItemOpen Access
    Small molecule dual-inhibitors of TRPV4 and TRPA1 for attenuation of inflammation and pain.
    (Sci Rep, 2016-06-01) Kanju, P; Chen, Y; Lee, W; Yeo, M; Lee, SH; Romac, J; Shahid, R; Fan, P; Gooden, DM; Simon, SA; Spasojevic, I; Mook, RA; Liddle, RA; Guilak, F; Liedtke, WB
    TRPV4 ion channels represent osmo-mechano-TRP channels with pleiotropic function and wide-spread expression. One of the critical functions of TRPV4 in this spectrum is its involvement in pain and inflammation. However, few small-molecule inhibitors of TRPV4 are available. Here we developed TRPV4-inhibitory molecules based on modifications of a known TRPV4-selective tool-compound, GSK205. We not only increased TRPV4-inhibitory potency, but surprisingly also generated two compounds that potently co-inhibit TRPA1, known to function as chemical sensor of noxious and irritant signaling. We demonstrate TRPV4 inhibition by these compounds in primary cells with known TRPV4 expression - articular chondrocytes and astrocytes. Importantly, our novel compounds attenuate pain behavior in a trigeminal irritant pain model that is known to rely on TRPV4 and TRPA1. Furthermore, our novel dual-channel blocker inhibited inflammation and pain-associated behavior in a model of acute pancreatitis - known to also rely on TRPV4 and TRPA1. Our results illustrate proof of a novel concept inherent in our prototype compounds of a drug that targets two functionally-related TRP channels, and thus can be used to combat isoforms of pain and inflammation in-vivo that involve more than one TRP channel. This approach could provide a novel paradigm for treating other relevant health conditions.
  • No Thumbnail Available
    ItemOpen Access
    Streamlined quasispecies and subtype analysis of HIV-1 sequences generated by high-throughput sequencing using the high-performance integrated virtual environment (HIVE)
    (JOURNAL OF THE INTERNATIONAL AIDS SOCIETY, 2016-07) Hora, B; Gulzar, N; Chen, Y; Cai, F; Su, C; Karagiannis, K; Smith, K; Simonyan, V; Shah, SA; Ahmed, M; Sanchez, AM; Stone, M; Cohen, MS; Haynes, BF; Busch, MP; Mazumder, R; Denny, TN; Gao, F
  • Thumbnail Image
    ItemOpen Access
    The effects of the synthetic nocistatin on blood vessel activities
    (Chinese Science Bulletin, 2001-01-01) Chen, Q; Chen, Y; Chen, L; Yang, D; Dong, S; Wang, R
    Nocistatin was synthesized by the solid-phase peptide synthesis method. Its effects on rat systemic arterial pressure; rat hindquarter vascular bed resistance; tension of rabbit pectoral, abdominal, femoral aorta muscle strips without endothelium; and nociceptin induced decreases of rat systemic arterial pressure were determined. The results showed that nocistatin can increase the systemic arterial pressure, increase the hindquarter vascular bed resistance and induce the contraction significantly of abdominal, femoral aorta muscle strips without endothelium; it has no significant effect on tension of pectoral aorta muscle strips, it cannot antagonize significantly the decrease of rat systemic arterial pressure induced by nociceptin. These results suggest that nocistatin has some important effects on blood vessel activities.
  • Thumbnail Image
    ItemOpen Access
    Vanilloid receptor TRPV1-mediated phosphorylation of ERK in murine adjuvant arthritis
    (Osteoarthritis and Cartilage, 2009-02) Chen, Y; Willcockson, HH; Valtschanoff, JG