Browsing by Author "Yang, Xiao"

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    Comparison between the Effects of Acute Physical and Psychosocial Stress on Feedback-Based Learning
    Yang, Xiao; Nackley, Brittany; Friedman, Bruce H. (MDPI, 2023-07-26)
    Stress modulates feedback-based learning, a process that has been implicated in declining mental function in aging and mental disorders. While acute physical and psychosocial stressors have been used interchangeably in studies on feedback-based learning, the two types of stressors involve distinct physiological and psychological processes. Whether the two types of stressors differentially influence feedback processing remains unclear. The present study compared the effects of physical and psychosocial stressors on feedback-based learning. Ninety-six subjects (Mage = 19.11 years; 50 female) completed either a cold pressor task (CPT) or mental arithmetic task (MAT), as the physical or psychosocial stressor, while electrocardiography and blood pressure were measured to assess cardiovascular stress reactivity (CVR). Self-ratings on the emotional valence of the stressors were also obtained. A probabilistic learning task was given prior to and after the stressors. Accuracy in selecting positive (Go accuracy) and avoiding negative stimuli (No-go accuracy) were recorded as learning outcomes. Repeated measures ANOVA and multiple regressions were used to compare the effects of two stressors and examine the effects of CVR and valence on the learning outcomes. The results showed that although the effects of CPT and MAT on feedback processing were not different, CVR and valence influenced Go and No-go accuracy, respectively. The results suggest that stress-modulated feedback-based learning involves multiple pathways and underscore the link between CVR and reward sensitivity. The findings have clinical implications and may contribute to a better understanding of human behavioral systems.
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    Differential Usefulness of Nine Commonly Used Genetic Markers for Identifying Phytophthora Species
    Yang, Xiao; Hong, Chuanxue (Frontiers, 2018-10-03)
    The genus Phytophthora is agriculturally and ecologically important. As the number of Phytophthora species continues to grow, identifying isolates in this genus has become increasingly challenging even by DNA sequencing. This study evaluated nine commonly used genetic markers against 154 formally described and 17 provisionally named Phytophthora species. These genetic markers were the cytochrome-c oxidase 1 (cox1), internal transcribed spacer region (ITS), 60S ribosomal protein L10, beta-tubulin (-tub), elongation factor 1 alpha, enolase, heat shock protein 90, 28S ribosomal DNA, and tigA gene fusion protein (tigA). As indicated by species distance, cox1 had the highest genus-wide resolution, followed by ITS, tigA, and -tub. Resolution of these four markers also varied with (sub)clade. -tub alone could readily identify all species in clade 1, cox1 for clade 2, and tigA for clades 7 and 8. Two or more genetic markers were required to identify species in other clades. For PCR consistency, ITS (99% PCR success rate) and -tub (96%) were easier to amplify than cox1 (75%) and tigA (71%). Accordingly, it is recommended to take a two-step approach: classifying unknown Phytophthora isolates to clade by ITS sequences, as this marker is easy to amplify and its signature sequences are readily available, then identifying to species by one or more of the most informative markers for the respective (sub)clade.
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    Differentiation between the Effects of Physical and Psychosocial Stress on a Feedback-based Learning Task
    Yang, Xiao (Virginia Tech, 2017-07-12)
    Feedback-based learning is a process in which decisions are made based on the previous feedback. This learning process is influenced by acute stress. However, different laboratory stressors elicit different physiological response patterns, which may influence feedback processing differently. Moreover, individual differences in stress reactivity may be associated with reward sensitivity. Therefore, the present study investigated the effects of psychosocial and physical stress on feedback-based learning. The relationship between stress reactivity and reward sensitivity was also examined. Ninety-two college-aged subjects were assigned into the mental arithmetic (MA) task or the cold pressor task (CPT) group. All subjects performed a feedback-based learning task prior to and after the stressor. Cardiovascular reactions, stress experiences, and learning outcomes were recorded during tasks. Trait differences in behavioral inhibition and activation (BIS/BAS) were also measured. Results indicated different patterns of cardiovascular reactions to the MA and CPT. Learning outcomes were differentially influenced by the MA and CPT. Moreover, subjective stress scores were negatively correlated with the learning rate in the pre-stress learning task. Additionally, BAS Drive subscale score was related to the processing of positive feedback. The results suggested that physical and psychosocial stress influence learning through distinct neural mechanisms and psychological processes. Motivational processes underlie the relationship between stress reactivity and reward sensitivity. This study extended research on stress and learning, and the findings have applied implications in various areas.
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    An expanded phylogeny for the genus Phytophthora
    Yang, Xiao; Tyler, Brett M.; Hong, Chuanxue (2017-11-21)
    A comprehensive phylogeny representing 142 described and 43 provisionally named Phytophthora species is reported here for this rapidly expanding genus. This phylogeny features signature sequences of 114 ex-types and numerous authentic isolates that were designated as representative isolates by the originators of the respective species. Multiple new subclades were assigned in clades 2, 6, 7, and 9. A single species P. lilii was placed basal to clades 1 to 5, and 7. Phytophthora stricta was placed basal to other clade 8 species, P. asparagi to clade 6 and P. intercalaris to clade 10. On the basis of this phylogeny and ancestral state reconstructions, new hypotheses were proposed for the evolutionary history of sporangial papillation of Phytophthora species. Non-papillate ancestral Phytophthora species were inferred to evolve through separate evolutionary paths to either papillate or semi-papillate species.
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    A high-temperature tolerant species in clade 9 of the genus Phytophthora: P-hydrogena sp nov
    Yang, Xiao; Gallegly, Mannon E.; Hong, Chuanxue (Mycological Society of America, 2014-01)
    A previously unknown Phytophthora species was isolated from irrigation water in Virginia, USA. This novel species produces abundant noncaducous and nonpapillate sporangia in soil water extract solution. It sometimes produces chlamydospores and hyphal swellings in aged cultures and in Petri's solution. This species has optimum vegetative growth at 30 C and grows well at 35 C. The lowest and highest temperatures for growth are 5 and 40 C. All isolates examined in this study are compatibility type A1 and produce mostly plerotic oospores when paired with an A2 mating-type tester of P. cinnamomi. Sequence analyses of the rDNA internal transcribed spacer (ITS) regions and the mitochondrially encoded cytochrome c oxidase 1 (cox 1) gene placed this species in clade 9 of the genus Phytophthora. These characteristics support the description of this taxon as a new species for which we propose the name P. hydrogena sp. nov. Further phylogenetic and physiological investigations of clade 9 species revealed a high-temperature tolerant cluster including P. hydrogena, P. aquimorbida, P. hydropathica, P. irrigata, P. chrysanthemi, P. insolita, P. polonica and P. parsiana. These species all grow well at 35 C. The monophyly of the species in this heat-tolerant cluster except P. insolita and P. polonica is highly supported by the maximum-likelihood analyses of the ITS and cox 1 sequences.
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    Inland Water Greenhouse Gas Budgets for RECCAP2: 1. State-Of-The-Art of Global Scale Assessments
    Lauerwald, Ronny; Allen, George H.; Deemer, Bridget R.; Liu, Shaoda; Maavara, Taylor; Raymond, Peter; Alcott, Lewis; Bastviken, David; Hastie, Adam; Holgerson, Meredith A.; Johnson, Matthew S.; Lehner, Bernhard; Lin, Peirong; Marzadri, Alessandra; Ran, Lishan; Tian, Hanqin; Yang, Xiao; Yao, Yuanzhi; Regnier, Pierre (American Geophysical Union, 2023-05-05)
    Inland waters are important emitters of the greenhouse gasses (GHGs) carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) to the atmosphere. In the framework of the 2nd phase of the REgional Carbon Cycle Assessment and Processes (RECCAP-2) initiative, we review the state of the art in estimating inland water GHG budgets at global scale, which has substantially advanced since the first phase of RECCAP nearly 10 years ago. The development of increasingly sophisticated upscaling techniques, including statistical prediction and process-based models, allows for spatially explicit estimates that are needed for regionalized assessments of continental GHG budgets such as those established for RECCAP. A few recent estimates also resolve the seasonal and/or interannual variability in inland water GHG emissions. Nonetheless, the global-scale assessment of inland water emissions remains challenging because of limited spatial and temporal coverage of observations and persisting uncertainties in the abundance and distribution of inland water surface areas. To decrease these uncertainties, more empirical work on the contributions of hot-spots and hot-moments to overall inland water GHG emissions is particularly needed.
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    New Species and Phylogeny of the Genus Phytophthora
    Yang, Xiao (Virginia Tech, 2015-01-13)
    The genus Phytophthora includes many agriculturally and ecologically important plant pathogens. Characterization of new Phytophthora species is the first and a most critical step to understanding their biology, ecology and economic importance. Six novel Phytophthora species recovered from irrigation systems at ornamental plant nurseries in Mississippi and Virginia were described based on morphological, physiological and molecular characters: 1. Phytophthora mississippiae sp. nov. produces a mix of non-papillate and semi-papillate sporangia, and catenulate hyphal swellings. It is a heterothallic species. All examined isolates of P. mississippiae are A1. When paired with A2 mating type testers, P. mississippiae produces ornamented oogonia and amphigynous antheridia. It is phylogenetically grouped in Phytophthora subclade 6b based on sequences of the rRNA internal transcribed spacer (ITS) region and the mitochondrially encoded cytochrome c oxidase 1 (cox 1) gene. 2. Phytophthora hydrogena sp. nov. is heterothallic. It produces non-caducous and non-papillate sporangia. It is characterized by frequently producing widening at the pedicel tip of sporangiophores or tapered sporangial based toward the point of attachment. This species is phylogenetically placed in a high-temperature tolerant cluster in Phytophthora clade 9. All members in this cluster grow well at 35 C. 3. Phytophthora virginiana sp. nov. is a self-sterile species. All examined isolates are silent A1. It produces non-caducous and non-papillate sporangia and is also placed in the high-temperature tolerant cluster in clade 9. Morphologically, it is characterized by producing abundant thin-walled, lateral chlamydospores in carrot agar and clarified V8 juice agar. 4. Phytophthora macilentosa sp. nov. is a heterothallic species. Only A1 isolates have been found. It produces characteristic elongated, non-papillate sporangia. It is also a member of the high-temperature cluster in clade 9. 5. Phytophthora stricta sp. nov. is a heterothallic species. It produces unique non-papillate and slightly caducous sporangia with one to three constrictions on its sporangiophore. Phylogenetically, P. stricta represents a new ITS clade within the genus. 6. Phytophthora Xstagnum nothosp. nov. is a novel hybrid species with P. taxon PgChlamydo as its paternal parent and a P. mississippiae-like species as its maternal parent. This new hybrid produces intercalary chlamydospores and catenulate hyphal swellings, which are morphological characters of P. taxon. PgChlamydo and P. mississippiae, respectively. It also produces both smooth-walled and ornamented oogonia, which may be indicative of oogonial characters of its paternal and maternal parents, respectively. By incorporating new Phytophthora species, clusters and clades, phylogenies including approximately 128 Phytophthora taxa were constructed based on sequences of five genetic markers. Among the selected genetic markers, the beta-tubulin (B-tub) gene provided the highest phylogenetic resolution. General phylogenetic structure of the B-tub phylogeny was similar to that in previous multi-locus phylogenies, except that P. cinnamomi, P. parvispora, P. quercina, P. stricta, and a provisional species, P. sp. e1, were not clustered in any of the 10 known Phytophthora clades and represented new clades. The B-tub phylogeny was also used to study the correlations between phylogeny and morphological characteristics including sporangial papillation, caducity, homothallism, and antheridial configuration, as well as maximum growth temperature. The results indicated that the character of sporangial papillation was mostly consistent among species within individual subclades. Maximum growth temperature was also generally correlated with phylogenetic positions. Consistency in caducity, homothallism or antheridial configuration was not found. A new multi-locus phylogeny based on sequences of 11 genetic markers of more than 146 Phytophthora species was proposed to validate new clades and clusters, as well as investigate detailed phylogenetic relations among species in this quickly expanding, taxonomically complex group of plant pathogens.
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    Optimal Design of Single Factor cDNA Microarray experiments and Mixed Models for Gene Expression Data
    Yang, Xiao (Virginia Tech, 2003-02-25)
    Microarray experiments are used to perform gene expression profiling on a large scale. E- and A-optimality of mixed designs was established for experiments with up to 26 different varieties and with the restriction that the number of arrays available is equal to the number of varieties. Because the IBD setting only allows for a single blocking factor (arrays), the search for optimal designs was extended to the Row-Column Design (RCD) setting with blocking factors dye (row) and array (column). Relative efficiencies of these designs were further compared under analysis of variance (ANOVA) models. We also compared the performance of classification analysis for the interwoven loop and the replicated reference designs under four scenarios. The replicated reference design was favored when gene-specific sample variation was large, but the interwoven loop design was preferred for large variation among biological replicates. We applied mixed model methodology to detection and estimation of gene differential expression. For identification of differential gene expression, we favor contrasts which include both variety main effects and variety by gene interactions. In terms of t-statistics for these contrasts, we examined the equivalence between the one- and two-step analyses under both fixed and mixed effects models. We analytically established conditions for equivalence under fixed and mixed models. We investigated the difference of approximation with the two-step analysis in situations where equivalence does not hold. The significant difference between the one- and two-step mixed effects model was further illustrated through Monte Carlo simulation and three case studies. We implemented the one-step analysis for mixed models with the ASREML software.