@article{liu_lu_zhang_2013, title={Kernel smoothed profile likelihood estimation in the accelerated failure time frailty model for clustered survival data}, volume={100}, ISSN={["0006-3444"]}, DOI={10.1093/biomet/ast012}, abstractNote={Clustered survival data frequently arise in biomedical applications, where event times of interest are clustered into groups such as families. In this article we consider an accelerated failure time frailty model for clustered survival data and develop nonparametric maximum likelihood estimation for it via a kernel smoother aided EM algorithm. We show that the proposed estimator for the regression coefficients is consistent, asymptotically normal and semiparametric efficient when the kernel bandwidth is properly chosen. An EM-aided numerical differentiation method is derived for estimating its variance. Simulation studies evaluate the finite sample performance of the estimator, and it is applied to the Diabetic Retinopathy data set.}, number={3}, journal={BIOMETRIKA}, author={Liu, Bo and Lu, Wenbin and Zhang, Jiajia}, year={2013}, month={Sep}, pages={741–755} }
 @article{liu_louws_sutton_correll_2012, title={A rapid qualitative molecular method for the identification of Colletotrichum acutatum and C. gloeosporioides}, volume={132}, ISSN={["1573-8469"]}, DOI={10.1007/s10658-011-9904-1}, number={4}, journal={EUROPEAN JOURNAL OF PLANT PATHOLOGY}, author={Liu, Bo and Louws, Frank J. and Sutton, Turner B. and Correll, James C.}, year={2012}, month={Apr}, pages={593–607} }
 @article{liu_munster_johnson_louws_2011, title={First report of anthracnose caused by colletotrichum fragariae on cyclamen in North Carolina}, volume={95}, number={11}, journal={Plant Disease}, author={Liu, B. and Munster, M. and Johnson, C. and Louws, F. J.}, year={2011}, pages={1480–1481} }
 @article{liu_glenn_buckley_2008, title={Trichoderma communities in soils from organic, sustainable, and conventional farms, and their relation with Southern blight of tomato}, volume={40}, ISSN={["0038-0717"]}, DOI={10.1016/j.soilbio.2007.12.005}, abstractNote={The objectives of this research were to investigate the relationship between propagule numbers and genetic diversity of Trichoderma species and Southern blight of tomato caused by soilborne plant pathogen Sclerotium rolfsii in soils with long-term organic, sustainable, and conventional farms. Dilution plating was use to quantify the propagule numbers of Trichoderma, denaturing gradient gel electrophoresis (DGGE) and DNA sequence analysis were used to identify Trichoderma species, and greenhouse assay were conducted for soil suppressiveness to Southern blight. The propagule numbers of Trichoderma tend to be higher in soils from conventional farms. There was no clear separation for the propagule numbers of Trichoderma based on different management systems using canonical correspondence analysis (CCA). However, there was general separation for total microbial communities based on organic and conventional management systems using CCA. That suggests that the difference of soil suppressiveness to disease from organic, sustainable, and conventional farms is due to the difference of the total microbial diversity but not directly due to the Trichoderma populations in each farming system. The propagule numbers of soil Trichoderma did not significantly correlate with the diseases suppressiveness, although individual species of Trichoderma harzianum was shown to be related to disease suppressiveness. Moreover, several Trichoderma species were found in the soil tested based on DGGE and DNA sequence analysis. Trichoderma hamatum, T. harzianum, Trichoderma virens, and Trichoderma erinaecem were the most abundant species in tested soil.}, number={5}, journal={SOIL BIOLOGY & BIOCHEMISTRY}, author={Liu, Bo and Glenn, Deborah and Buckley, Katrina}, year={2008}, month={May}, pages={1124–1136} }
 @article{liu_tu_hu_gumpertz_ristaino_2007, title={Effect of organnic, sustainable, and conventional management strategies in grower fields on soil physical, chemical, and biological factors and the incidence of Southern blight}, volume={37}, ISSN={["1873-0272"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-34748831003&partnerID=MN8TOARS}, DOI={10.1016/j.apsoil.2007.06.007}, abstractNote={The objectives of our research were to evaluate the impact of organic, sustainable, and conventional management strategies in grower fields on soil physical, chemical, and biological factors including soil microbial species and functional diversity and their effect on the Basidiomycete plant pathogen Sclerotium rolfsii, causal agent of Southern blight. Soils from 10 field locations including conventional, organic and sustainable farms were sampled and assayed for disease suppressiveness in greenhouse assays, and soil quality indicators. Soils from organic and sustainable farms were more suppressive to Southern blight than soils from conventional farms. Soils from organic farms had improved soil chemical factors and higher levels of extractable C and N, higher microbial biomass carbon and nitrogen, and net mineralizable N. In addition, soil microbial respiration was higher in soils from organic than sustainable or conventional farms, indicating that microbial activity was greater in these soils. Populations of fungi and thermophiles were significantly higher in soils from organic and sustainable than conventional fields. The diversity of bacterial functional communities was also greater in soils from organic farms, while species diversity was similar. Soils from organic and sustainable farms had improved soil health as indicated by a number of soil physical, chemical and biological factors and reduced disease.}, number={3}, journal={APPLIED SOIL ECOLOGY}, author={Liu, Bo and Tu, Cong and Hu, Shuijin and Gumpertz, Marcia and Ristaino, Jean Beagle}, year={2007}, month={Nov}, pages={202–214} }
 @article{ristaino_johnson_blanco-meneses_liu_2007, title={Identification of the tobacco blue mold pathogen, Peronospora tabacina, by polymerase chain reaction}, volume={91}, ISSN={["1943-7692"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-34249085921&partnerID=MN8TOARS}, DOI={10.1094/PDIS-91-6-0685}, abstractNote={ Tobacco blue mold, caused by the oomycete pathogen Peronospora tabacina, is a highly destructive pathogen of tobacco (Nicotiana tabacum) seed beds, transplants, and production fields in the United States. The pathogen also causes systemic infection in transplants. We used polymerase chain reaction (PCR) with the primers ITS4 and ITS5, sequencing, and restriction digestion to differentiate P. tabacina from other important tobacco pathogens, including Alternaria alternata, Cercospora nicotianae, Phytophthora glovera, P. parasitica, Pythium aphanidermatum, P. dissotocum, P. myriotylum, P. ultimum, Rhizoctonia solani, Sclerotinia sclerotiorum, Sclerotium rolfsii, Thielaviopsis basicola, and related Peronospora spp. A specific PCR primer, called PTAB, was developed and used with ITS4 to amplify a 764-bp region of DNA that was diagnostic for P. tabacina. The PTAB/ITS4 primers did not amplify host DNA or the other tobacco pathogens and were specific for P. tabacina on tobacco. DNA was detected to levels of 0.0125 ng. The PTAB primer was useful for detection of the pathogen in fresh, air-dried, and cured tobacco leaves. This primer will be useful for disease diagnosis, epidemiology, and regulatory work to reduce disease spread among fields. }, number={6}, journal={PLANT DISEASE}, author={Ristaino, Jean Beagle and Johnson, Andrea and Blanco-Meneses, Monica and Liu, Bo}, year={2007}, month={Jun}, pages={685–691} }
 @article{liu_gumpertz_hu_ristaino_2007, title={Long-term effects of organic and synthetic soil fertility amendments on soil microbial communities and the development of southern blight}, volume={39}, ISSN={["1879-3428"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-34250215285&partnerID=MN8TOARS}, DOI={10.1016/j.soilbio.2007.04.001}, abstractNote={The effects of tillage and soil fertility amendments on the relationship between the suppressiveness of soils to southern blight and soil physical, chemical and biological factors were examined in experimental station plots in North Carolina. Main plots were either tilled frequently or surface-mulched after one initial tillage. Organic soil amendments including composted cotton gin trash, composted poultry manure, an incorporated rye–vetch green manure, or synthetic fertilizer were applied to subplots in a split-plot design experiment. Incidence of southern blight was lower in surfaced-mulched than tilled soils. Incidence of southern blight was also lower in soils amended with cotton gin trash than those amended with poultry manure, rye–vetch green manure or synthetic fertilizer. Soil water content was negatively correlated with the incidence of disease in both years. Disease incidence was negatively correlated with the level of potassium, calcium, cation exchange capacity (CEC), base saturation (BS) and humic matter in 2002, and net mineralizable nitrogen in 2001. Although, populations of thermophilic organisms were significantly higher in soils amended with cotton gin trash than the other three fertility amendments in each year, there was no significant correlation between the populations of thermophiles and incidence of the disease. Bacterial community diversity indices based on community-level physiological profiling (CLPP) and denaturing gradient gel electrophoresis (DGGE) were significantly higher in soils amended with cotton gin trash than those amended with poultry manure, green manure or synthetic fertilizer. There was a significant negative correlation between the incidence of southern blight, and CLPP and DGGE diversity indices. Greater differences in the richness of bacterial functional groups than genotypes were observed. These results demonstrate that organic soil fertility amendments and cotton gin trash in particular, reduced the development of the disease and affected soil physical, chemical and biological parameters.}, number={9}, journal={SOIL BIOLOGY & BIOCHEMISTRY}, author={Liu, Bo and Gumpertz, Marcia L. and Hu, Shuijin and Ristaino, Jean Beagle}, year={2007}, month={Sep}, pages={2302–2316} }