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4. A Hybrid Routing Control Mechanism for Dual-Mode Communication of Streetlight Information Acquisition System

Author

Xiang, Min, Zhao, Xudong, Sun, Yongmin, Barbosa, Simone Diniz Junqueira, Series Editor, Filipe, Joaquim, Series Editor, Kotenko, Igor, Series Editor, Sivalingam, Krishna M., Series Editor, Washio, Takashi, Series Editor, Yuan, Junsong, Series Editor, Zhou, Lizhu, Series Editor, Li, Kang, editor, Fei, Minrui, editor, Du, Dajun, editor, Yang, Zhile, editor, and Yang, Dongsheng, editor

Published
2018
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7. Parental Involvement: A Contrast between Rural and Other Communities.

Author

Sun, Yongmin

Abstract

This paper examines rural-urban differences in parent involvement in their children's education, drawing upon such concepts as "community attachment,""community cultural context,""family cultural capital," and "community social capital." As part of the 1992-93 Missouri School Improvement Program, nearly 57,000 parents whose children attended 296 Missouri schools completed a survey that included five items measuring the extent of parent involvement. Schools were grouped into four categories, based on rural or urban school in metropolitan or nonmetropolitan county. Parent involvement was positively related to socioeconomic status (SES) and parent rating of the accessibility of school staff, and was negatively related to minority status, student grade level, number of children in the family, and single-parent status. When these control variables were held constant, parents whose children attended nonmetro rural schools scored significantly higher on parent involvement than parents in any of the other categories of schools. At the same time, independent of control variables and location of residence, parents who had lived longer within the school district participated more than more recently arrived parents. The effect of SES on parent involvement was greatest in nonmetro rural schools. The results indicate that the effects of individual and contextual characteristics on parent participation can be independent and additive to one another. Contains 22 references. (SV)

Published
1994

12. Corrigendum to ‘Co-occurrence network of microbial communities affected by application of anaerobic fermentation residues during phytoremediation of ionic rare earth tailings area’ [Sci. Total Environ. 856 (2023) 159223]

Author

Chen, Liumeng, primary, Chen, Shasha, additional, Zhang, Yi, additional, Long, Yun, additional, Kong, Xiaoying, additional, Wang, Shujia, additional, Li, Lianhua, additional, Wang, Fei, additional, Sun, Yongmin, additional, and Xu, An, additional

Published
2023
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13. Major ozonated autohemotherapy promoted functional recovery following spinal cord injury in adult rats via the inhibition of oxidative stress and inflammation

Author

Xia Liwei, Sun Yongming, Zhou Yue, Yang Qian, Huang Jianhan, and Liu Dong

Subjects
sci, major ozonated autohemotherapy, inflammation, superoxide dismutase, Biology (General), QH301-705.5
Abstract

This study sought to explore the value of major ozonated autohemotherapy (MOA) as a treatment for spinal cord injury (SCI) in a rat model system. In total, 54 female Sprague-Dawley rats were randomized into sham-operated, SCI model, and MOA treatment groups. We found that relative to the SCI model group, rats that underwent MOA treatment exhibited improved locomotor scores on days 14, 21, and 28 after injury (p < 0.05) together with reduced residual urine on days 5, 7, 14, and 21 after injury (p < 0.05). MOA treatment also lowered proinflammatory TNF-α, IL-1α, and C1q levels on day 3 post-injury (p < 0.05), decreased malondialdehyde levels, and enhanced superoxide dismutase activity (p < 0.001). Activated astrocytes in MOA-treated rats exhibited larger soma and higher levels of extracellular matrix secretion, whereas reactive microglia in the MOA group presented with a ramified morphology in contrast to the amoeboid morphology exhibited by these cells in SCI model rats. MOA offers potential value as a means of protecting spinal cord integrity, potentially through anti-inflammatory, antioxidant, and regulatory effects that shape the polarization of astrocytes and microglia.

Published
2024
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16. Effects of Family Structure Type and Stability on Children's Academic Performance Trajectories

Author

Sun, Yongmin and Li, Yuanzhang

Abstract

Using five waves of panel data from 8,008 children in the ECLS-K, the current study compared children's academic performance growth curves from kindergarten through fifth grade among three types of nondisrupted and three types of disrupted families. The analyses found that children in nondisrupted two-biological-parent and nondisrupted stepparent households consistently made greater progress in their math and reading performances over time than their peers in nondisrupted single-parent, disrupted two-biological-parent, and disrupted alternative families with multiple transitions. These trajectory differences were either partially or completely accounted for by family resources in the kindergarten year (Time 1). Overall, our findings provided strong support for the resource-deprivation perspective and partial support for the instability-stress perspective.

Published
2011
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17. Postdivorce Family Stability and Changes in Adolescents' Academic Performance: A Growth-Curve Model

Author

Sun, Yongmin and Li, Yuanzhang

Abstract

Three waves of panel data from 7,897 adolescents in the National Education Longitudinal Studies have been used to investigate whether a stabilized postdivorce family environment benefits adolescents' academic performance trajectories. The analyses indicate that compared with peers who grow up in stable postdivorce families, children of divorce who experience additional family transitions during late adolescence make less progress in their math and social studies performance over time. Furthermore, family resource differences before and during late adolescence either partially or completely account for the less positive performance trajectories in two types of divorced families. Finally, daughters in unstable postdivorce families appear to make less academic progress over time than sons. The study illustrates the importance of incorporating both postdivorce family transitions and repeatedly measured child outcomes in the investigation of divorce effects. (Contains 2 tables and 3 notes.)

Published
2009
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18. Stable Postdivorce Family Structures during Late Adolescence and Socioeconomic Consequences in Adulthood

Author

Sun, Yongmin and Li, Yuanzhang

Abstract

Using four waves of panel data from 6,954 American young adults in the National Education Longitudinal Study, we compare the long-term socioeconomic consequences of growing up in two types of divorced families. Our findings show that the negative socioeconomic consequences of growing up in unstable postdivorce families are at least twice as large as those of staying in a stabilized postdivorce family environment through late adolescence. The study also finds that variations in parental resources during late adolescence partially explain the divorce effects on most attainment indicators. Further, parental divorce appears to affect the socioeconomic attainment of male and female offspring alike. Overall, the study underlines the importance of including postdivorce family dynamics in studying the effect of parental divorce.

Published
2008
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19. Application of titanium clip marking in localization of 37 cases of rectal cancer before radiotherapy

Author

Li Zengjun, Sun Yongmin, Liu Jinqi, Wang Yawei, Hai‐peng Wang, and Chen Ming

Subjects
medicine.medical_specialty, medicine.diagnostic_test, business.industry, Colorectal cancer, medicine.medical_treatment, R895-920, chemistry.chemical_element, Colonoscopy, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, medicine.disease, titanium clip, Radiation therapy, Medical physics. Medical radiology. Nuclear medicine, Oncology, chemistry, colonoscopy, medicine, Radiology, business, rectal cancer, radiotherapy, RC254-282, Titanium
Abstract

Objectives At present, locating radiotherapy targets for rectal cancer is mostly assisted by computed tomography (CT) and/or magnetic resonance (MR) imaging. This article discusses the role of the upper and lower margins of rectal cancer lesions under colonoscopy in accurately delineating target areas of radiotherapy. Methods A total of 37 patients with rectal cancer diagnosed by histopathology at the Shandong Provincial Cancer Hospital, affiliated with Shandong University, from 1 July 2017 to 1 August 2018 were selected before treatment. The upper and lower margins of the lesion were marked by titanium clips under the assistance of ultrasound and a magnifying endoscope in each patient, as well as the lower edge of the titanium clip from the anal margin. In the same position and in a thermal plastic membrane body fixation device, patients underwent CT and MR examinations to outline the gross tumor target area (GTV). The radiation therapy planning system calculated the length of the GTV under CT and MR (GTVCT, GTVMR), and the distance from the lower edge of the GTV to the anal margin. The application value of titanium clip labeling by colonoscopy in radiotherapy localization for rectal cancer was evaluated according to differences of GTV lengths by three methods. Results GTVs measured by endoscopic titanium clip labeling, CT localization, and MR localization were 5.84 ± 2.035 cm,6.97 ± 1.658 cm, and 5.45 ± 2.088 cm, respectively. The length of GTVtitanium clip was not significantly different from the length of GTVMR (P = 0.162). The marked lesion lengths by the endoscopic titanium clips and MR localization were significantly smaller than that measured by CT (GTV titanium clip

Published
2020

20. The Effects of Residence Location on Parental Involvement with the School: A Contrast between Nonmetropolitan Rural and Other Communities.

Author

Sun, Yongmin, Hobbs, Daryl, Elder, William, and Sun, Dongchu

Abstract

Among 57,139 parents surveyed in 296 Missouri schools, parents from dual-parent families and longer-term school district residents participated in school activities more than their respective counterparts. Parent participation in nonmetropolitan-rural areas was greater than in other locations when social and demographic characteristics were controlled but was more affected by parental socioeconomic status. (Contains 31 references.) (SV)

Published
1997

21. Multi-level Analyses of Television Viewing among High School Students: A Contrast between Nonmetropolitan Rural and Other Communities.

Author

Sun, Yongmin

Abstract

A survey of students in 179 Missouri high schools found that rural, male, and minority students watched more television than their counterparts; that rural students' perceptions of environmental safety impacted the length of television watching; and that the difference in viewing time between white and minority students was smaller in rural areas than in urban communities. (LP)

Published
1994

24. Circ_0067835 Knockdown Enhances the Radiosensitivity of Colorectal Cancer by miR-296-5p/IGF1R Axis

Author

Wang,Peng, Sun,Yongmin, Yang,Yang, Chen,Yanzhao, Liu,Hui, Wang,Peng, Sun,Yongmin, Yang,Yang, Chen,Yanzhao, and Liu,Hui

Abstract

Peng Wang,1,* Yongmin Sun,2,* Yang Yang,1 Yanzhao Chen,1 Hui Liu1 1Department of Nuclear Medicine, Henan Provincial People’s Hospital, Zhengzhou, Henan, People’s Republic of China; 2Department of Nuclear Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, People’s Republic of China*These authors contributed equally to this workCorrespondence: Hui LiuDepartment of Nuclear Medicine, Henan Provincial People’s Hospital, No. 7, Weiwu Road, Jinshui District, Zhengzhou City, Henan Province, People’s Republic of ChinaTel +86 371-65580334Email wpsymw@163.comBackground: Colorectal cancer (CRC) is one of the most common malignant cancers globally. Circular RNAs (circRNAs) have been implicated in the development of CRC. In this paper, we set to explore the precise action of circ_0067835 in CRC progression and radioresistance.Methods: Quantitative real-time polymerase chain reaction (qRT-PCR) was used to evaluate the expression of circ_0067835, microRNA-296-5p (miR-296-5p) and insulin-like growth factor 1 receptor (IGF1R). Western blot was used to measure the level of IGF1R protein. Cell proliferation, cell cycle distribution and apoptosis were determined by Cell Counting Kit-8 (CCK-8), colony formation, flow cytometry and caspase-3 activity assays, respectively. The direct relationship between miR-296-5p and circ_0067835 or IGF1R was verified by dual-luciferase reporter assays. Additionally, in vivo assays were applied to confirm the role of circ_0067835 in vivo.Results: Exosomal circ_0067835 was upregulated in the serum of CRC patients after radiotherapy. Exosome-mediated circ_0067835 knockdown repressed cell proliferation, cell cycle progression, and enhanced cell apoptosis and radiosensitivity in vitro. Circ_0067835 sponged miR-296-5p to regulate IGF1R expression in CRC cells. Moreover, the knockdown of circ_0067835 regulated CRC cell behaviors by up-regulating miR-296-5p and down-regulating IG

Published
2021

26. The contextual effects of community social capital on academic performance

Author

Sun, Yongmin

Subjects
Academic achievement -- Measurement, Infrastructure (Economics) -- Psychological aspects, Social sciences
Abstract

Research indicates that community social capital or infrastructure correlate consistently with academic performance. This finding is supported even when controlling for demographic factors and family social capital, and extrapolations and implications are discussed.

Published
1999

27. The impact of more fully implemented guidance programs on the school experiences of high school students: a statewide evaluation study

Author

Lapan, Richard T., Gysbers, Norman C., and Sun, Yongmin

Subjects
Student guidance services -- Evaluation, High school students -- Psychological aspects
Abstract

Relationships between the statewide implementation of comprehensive guidance programs and the school experiences of high school students were explored. Data from 22,964 students attending 236 Missouri high schools were analyzed by using hierarchical linear modeling. Schools with more fully implemented model guidance programs had students who were more likely to report that (a) they had earned higher grades, (b) their education was better preparing them for their future, (c) their school made more career and college information available to them, and (d) their school had a more positive climate. Positive program effects were found after removing differences due to school enrollment size, socioeconomic status, and percentage of minority students in attendance. Results highlight the important roles school counselors play in promoting the central educational goals of their schools and support a comprehensive guidance program focus for university counseling faculty who train school counselors.

Published
1997

28. Redundancy routing mechanism based on hierarchical forwarding tree for IPv6 communication in power line carrier networks

Author

Sun Yongmin, Yu Xiangchun, Xiang Min, and Qu Qinqin

Subjects
business.industry, Computer science, 020209 energy, ComputerSystemsOrganization_COMPUTER-COMMUNICATIONNETWORKS, 020206 networking & telecommunications, 02 engineering and technology, Subnet, Telecommunications network, IPv6, Beacon frame, Power-line communication, Shortest path problem, 0202 electrical engineering, electronic engineering, information engineering, Redundancy (engineering), business, Decision tree model, Computer network
Abstract

For effectively reducing the packet loss rate and time delay when IPv6 is applied to power line communication system, the redundant routing mechanism based on hierarchical forwarding tree is put forward. A redundancy routing mechanism of IPv6 based on hierarchical forwarding tree is designed for power line carrier communication networks. The hierarchical forwarding tree model for power line carrier networks is constructed by designing IPv6 automatic address allocation method. Each node only needs to maintain a few forwarding entries corresponding to the number of child nodes to generate routing information fast in the subnet. The redundancy routing mechanism of backup parent nodes is designed based on the link quality, address space and networks depth of the beacon frame. By using redundancy routing mechanism, the problem of routing loops in Power Line Communication coming with hierarchical forwarding tree, will be solved and the routing will recover through the shortest path. The actual test results show that the redundancy routing mechanism has good performance on transmitting efficiency and fault-resilient, which efficiently improves the timeliness and reliability of power line carrier communication based on IPv6.

Published
2017
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29. Marital Disruption, Parental Investment, and Children's Academic Achievement: A Prospective Analysis

Author

SUN, YONGMIN and LI, YUANZHANG

Subjects
Marital status -- Social aspects, Academic achievement -- Social aspects, Education -- Parent participation, Parent and child -- Social aspects, Family and marriage, Sociology and social work
Abstract

Although previous research has noted the detrimental impact of parents' marital disruption on children's schooling, less is known about whether such detriments are observable prior to the disruption. Based on two waves of a nationally representative longitudinal data set, this study has found that even prior to family dissolution, both boys and girls from families that subsequently dissolve perform less well than their peers whose parents remain married. Families at the predisruption stage are also characterized by a shortage of financial, cultural, human, and social capital, even after demographics are controlled. In addition, some parental investment measures yield a smaller educational return for students whose families subsequently dissolve than for those whose parents remain married. Our results also indicate that the negative postdisruption effects on children's academic achievement can he either largely or completely predicted by performance and investment differences at the predisruption stage.

Published
2001

31. The academic success of East-Asian-American students - an investment model

Author

Sun, Yongmin

Subjects
Students -- Rating of, Academic achievement -- Analysis, Mathematics -- Study and teaching, Science -- Study and teaching, Social sciences
Abstract

A study was conducted to analyze causes of the Asian effect on students' performance in mathematics and science courses using an investment model that supports cultural, human, financial and social capital concepts. Results indicated that variations in investment correlated with the Asian effect. Findings also showed that the investment framework can effectively support studies on the Asian effect.

Published
1998

33. Special Reviewers

Author

Abma, Joyce, primary, Acock, Alan, additional, Acs, Gregory, additional, Adams, Michele, additional, Adams, Ryan, additional, Adler, Marina A., additional, Adler‐Baeder, Francesca, additional, Ainsworth, James W., additional, Amin, Sajeda, additional, Anderson, Kathryn, additional, Anderson, Kristin, additional, Anderson, Peter, additional, Anderson, Siwan, additional, Angel, Jacqueline, additional, Arrighi, Barbara, additional, Atkinson, Alice M., additional, Avellar, Sarah, additional, Babcock, Renee, additional, Baber, Kristine, additional, Bachman, Heather, additional, Badgett, M. V. Lee, additional, Bahr, Kathleen S., additional, Bahr, Stephen, additional, Baker, Paul, additional, Banerjee, Leena, additional, Barber, Jennifer, additional, Barker, Judith C., additional, Barnes, Grace M., additional, Barnett, Rosalind C., additional, Barnett, Rosemary, additional, Bartell, Denise S., additional, Bartfeld, Judi, additional, Bartkowski, John, additional, Bartle‐Haring, Suzanne, additional, Bass, Brenda L., additional, Batson, Christie D., additional, Baum II, Charles L., additional, Bauman, Karl E., additional, Beach, Steven, additional, Beattie, Irenee R., additional, Beets, Gijs, additional, Belcastro, Philip, additional, Benda, Brent B., additional, Benin, Mary, additional, Benson, Mark, additional, Berardo, Felix M., additional, Berger, Lawrence M., additional, Berger, Roni, additional, Berke, Debra L., additional, Berry, Brent, additional, Beutel, Ann M., additional, Biddlecom, Ann, additional, Bielby, Denise D., additional, Binstock, Georgina, additional, Bjarnason, Thoroddur, additional, Blair, Clancy, additional, Blaisure, Karen R., additional, Blieszner, Rosemary, additional, Blume, Libby, additional, Bõgin, Catherine, additional, Bokker, Lon, additional, Bornstein, Marc, additional, Borsella, Angela, additional, Boss, Pauline, additional, Bouchard, Genevieve, additional, Bouchey, Heather, additional, Bould, Sally, additional, Boxer, Paul, additional, Boyce Rodgers, Kathleen, additional, Bozick, Robert, additional, Bradbury, Thomas N., additional, Bradley, Robert H., additional, Brady‐Smith, Christy, additional, Bratter, Jenifer, additional, Braun, Bonnie, additional, Brayfield, April A., additional, Brennom, Jennifer M., additional, Britto, Pia, additional, Brown, B. Bradford, additional, Brown, J. Brian, additional, Brown, Susan L., additional, Jane Brubaker, Sarah, additional, Bryson, Alex, additional, Buchanan, Christy, additional, Budescu, David V., additional, Bufford, Rodger, additional, Bulanda, Jennifer, additional, Bulanda, Ronald, additional, Bumpass, Larry L., additional, Bumpus, Matt, additional, Burdette, Amy M., additional, Burgoyne, Carole, additional, Burr, Jeffrey A., additional, Butler, Amy C., additional, Butler, Sarah M., additional, Bygren, Magnus, additional, Campbell, Lori, additional, Capaldi, Deborah, additional, Carbone‐Lopez, Kristin, additional, Carder, Paula, additional, Carini, Robert M., additional, Carlson, Elwood, additional, Carlson, Marcy J., additional, Carney, Dana R., additional, Caron, Sandra, additional, Carpenter, Brian, additional, Carrere, Sybil, additional, Cassidy, Margaret L., additional, Castle, Kathryn, additional, Cate, Rodney M., additional, Chan, Willaim, additional, Charles, Maria, additional, Cheal, David, additional, Hee Chee, Kyong, additional, Chen, Zeng‐yin, additional, Cheng, Simon, additional, Chesley, Noelle, additional, Chito Childs, Erica, additional, Christensen, Andrew, additional, Christopher, Karen L., additional, Christopher, F. Scott, additional, Ciabattari, Teresa, additional, Clements, Andrea D., additional, Clements, Mari, additional, Coatsworth, Doug, additional, Cody, Susan, additional, Cody‐Rydzewski, Susan R., additional, Cognard‐Black, Andrew, additional, Cohan, Catherine, additional, Coles, Roberta L., additional, Levine Coley, Rebekah, additional, Coltrane, Scott, additional, Conley, Terri, additional, Arnet Connidis, Ingrid, additional, Cook, Cynthia T., additional, Cookston, Jeff, additional, Cordova, James V., additional, Cornelius, Tara, additional, Crawford, Duane, additional, Cready, Cynthia M., additional, Crosnoe, Robert, additional, Crowder, Kyle D., additional, Cui, Ming, additional, Curran, Sara, additional, Daly, Martin, additional, David, Kevin M., additional, Davies, Lorraine, additional, Davis, Kelly, additional, Davis, Shannon N., additional, Davis‐Kean, Pamela, additional, De Oliveira, Ebenezer, additional, De St. Aubin, Ed, additional, De Valk, Helga, additional, De Vos, Susan, additional, Deater‐Deckard, Kirby, additional, DeGarmo, David, additional, DeKeseredy, Walter, additional, DeLeire, Thomas, additional, DeLuccie, Mary, additional, Demo, David H., additional, Dempster‐McClain, Donna, additional, Denham, Susanne, additional, Denton, Wayne, additional, DeRose, Laurie, additional, Derscheid, Linda E., additional, Desai, Sonalde, additional, Descartes, Lara, additional, Dew, Jeffrey, additional, Dilworth‐Anderson, Peggye, additional, Dodoo, Francis, additional, Dodson, Lisa, additional, Doll, Kevin, additional, Dollahite, David C., additional, Donnelly, Brenda W., additional, Donnelly, Denise A., additional, Doss, Brian, additional, Drigotas, Stephen, additional, Duncan, Greg J., additional, Duncan, Karen A., additional, Dunham, Charlotte, additional, Dunifon, Rachel, additional, Dunsmore, Julie, additional, Durden, T. Elizabeth, additional, Duxbury, Linda, additional, Dykstra, Pearl, additional, Edin, Kathryn, additional, Edwards, Mark, additional, Ehrenberg, Marion, additional, Ehrle Macomber, Jennifer L., additional, Elliott Wilson, Melanie E., additional, Elman, Cheryl, additional, Epstein, Norman, additional, Eriksen, Shelly, additional, Erlin, Carrie S., additional, Evertsson, Marie, additional, Feinberg, Mark, additional, Felson, Richard B., additional, Feltey, Kathryn, additional, Fenwick, Rudy, additional, Fernando, Rajulton, additional, Ferrick, Margaret, additional, Few, April, additional, Field, Carolyn, additional, Fingerman, Karen L., additional, Fischer, Tamar, additional, Fisher, Terri, additional, Fletcher, Anne C., additional, Fleury‐Steiner, Ruth E., additional, Floyd, Kory, additional, Formoso, Diana, additional, Foster, E. Michael, additional, Franks, Melissa, additional, Frazier, Leslie D., additional, Fruhauf, Christine A., additional, Fruth, Abbey, additional, Kang Fu, Vincent, additional, Fu, Xuanning, additional, Fulcher, Megan, additional, Gage, Anastasia, additional, Gager, Constance T., additional, Gano‐Phillips, Susan, additional, Gao, Ge, additional, Gareis, Karen, additional, Garfinkel, Irwin, additional, Gartner, Rosemary, additional, Gartstein, Maria, additional, Gassanov, Margaret, additional, Gaughan, Monica M., additional, Gavazzi, Stephen M., additional, Ge, Xiaojia, additional, Gennetian, Lisa A., additional, Gerard, Jean, additional, Gerris, Jan, additional, Thompson Gershoff, Elizabeth, additional, Gerteisen Marks, Jennifer P., additional, Giarrusso, Roseann, additional, Gibson‐Davis, Christina, additional, Gierveld, Jenny, additional, Gils, Wouter, additional, Gladstone, Jim, additional, Glaser, Karen, additional, Glenn, Norval, additional, Goldberg, Abbie, additional, Goldberg, Wendy, additional, Golden, Lonnie, additional, Goldscheider, Calvin, additional, Gonzaga, Gian, additional, Good, Marie, additional, Goodnow, Jacqueline, additional, Goodwin, Paula Y., additional, Gordon, Kristina C., additional, Gordon, Rachel, additional, Goyette, Kim A., additional, Gracia, Enrique, additional, Graefe, Deborah, additional, Grant, Darlene, additional, Grasmick, Harold, additional, Green, Kerry, additional, Stevens Greenberg, Jan, additional, Greenfield, Emily A., additional, Greenhaus, Jeffrey H., additional, Greenstein, Theodore, additional, Greve, Arent, additional, Guilamo‐Ramos, Vincent, additional, Guo, Shenyang, additional, Guzzo, Karen, additional, Haas, Linda, additional, Haddock, Shelley A., additional, Hall, Scott, additional, Hamby, Sherry, additional, Hango, Darcy W., additional, Hans, Jason D., additional, Hardesty, Constance, additional, Harknett, Kristen, additional, Harpel, Tammy, additional, Harris, Shanette M., additional, Harwood, Jake, additional, Hawkins, Daniel, additional, Haworth‐Hoeppner, Susan, additional, Heard, Holly, additional, Heaton, Tim B., additional, Helms, Heather, additional, Hendrix, Lewellyn, additional, Henly, Julia R., additional, Henry, Carolyn, additional, Herrick, Susan C., additional, Herting, Jerald, additional, Hertlein, Katherine, additional, Heyman, Richard, additional, Hill, E. Jeffrey, additional, Hiller, Harry H., additional, Hirschl, Thomas, additional, Hoekstra‐Weebers, Josette, additional, Hoelter, Lynette F., additional, Hoffmann, John P., additional, Hofsetter, C. Richard, additional, Hogan, Dennis, additional, Hohmann‐Marriott, Bryndl, additional, Holman, Thomas, additional, Holtzworth‐Munroe, Amy, additional, Honeycutt, James M., additional, Hook, Jennifer, additional, Horwitz, Allan V., additional, Hosley, Cheryl A., additional, Houseknecht, Sharon, additional, Huang, Chien‐Chung, additional, Huber, Joan, additional, Humble, Aine M., additional, Hunter, Andrea, additional, Jo Hunts, Holly, additional, Hwang, Sean‐Shong, additional, Shibley Hyde, Janet, additional, Iacovou, Maria, additional, Iceland, John, additional, Impett, Emily A., additional, Ispa, Jean, additional, Jansen, Miranda, additional, Janson, Gregory R., additional, Jasinski, Jana, additional, Jekielek, Susan, additional, Jeng, Wei‐Shiuan, additional, Jewkes, Rachel, additional, Joesch, Jutta M., additional, Johnson, Matthew, additional, Johnson, Michael P., additional, Johnson, Rosalind B., additional, Jones, Deborah, additional, Jorgensen, Stephen, additional, Joshi, Pamela, additional, Joyner, Kara, additional, Jung, Tony, additional, Kalil, Ariel, additional, Kamo, Yoshinori, additional, Kamp Dush, Claire M., additional, Karremans, Johan, additional, Kasturirangan, Aarati, additional, Kaufman, Gayle, additional, Kaukinen, Catherine, additional, Kazura, Kerry, additional, Kelley, Michelle L., additional, Kemp, Candace, additional, Kerpelman, Jennifer, additional, Kiecolt, K. Jill, additional, Killian, Tim, additional, Kim, Hyoun, additional, Kim, Irene J., additional, Kim, Julia, additional, Kirby, James, additional, Kirkpatrick Johnson, Monica, additional, Kiter Edwards, Margie, additional, Klein, David, additional, Klein, Renate, additional, Klumb, Petra, additional, Knapp, Stan, additional, Knight, Bob, additional, Knoester, Chris, additional, Kohn, Melvin L., additional, Kolburn, Amanda, additional, Korinek, Kim, additional, Koropeckyj‐Cox, Tanya, additional, Kosterman, Rick, additional, Kowal, Amanda, additional, Krampe, Edythe, additional, Kroska, Amy, additional, Krueger, Patrick M., additional, Kurz, Demie, additional, Lambert‐Shute, Jennifer, additional, Lampard, Richard, additional, Lancaster, Sandra, additional, Langenkamp, Amy, additional, Langhinrich‐Rohling, Jennifer, additional, Lansford, Jennifer E., additional, Lareau, Annette, additional, Laughlin, Lynda L., additional, Laurenceau, Jean‐Philippe, additional, Lauster, Nathanael, additional, Lavee, Yoav, additional, Lawton, Leora, additional, Lee, Gary R., additional, Lee, Kristen, additional, Lefkowitz, Eva, additional, Lein, Laura, additional, Leite, Randy, additional, Lempers, Jacques D., additional, Leon, Kim, additional, Leone, Janel, additional, Letiecq, Bethany L., additional, Li, Fuzhong, additional, Lichter, Daniel T., additional, Liefbroer, Aart C., additional, Lim, Soh‐Leong, additional, Lin, I‐Fen, additional, Lincoln, Karen, additional, Linver, Miriam, additional, Linville, Deanna C., additional, Lloyd, Kim, additional, London, Andrew S., additional, Longmore, Monica, additional, Lopoo, Lenard M., additional, Lorenz, Frederick O., additional, Ludwick, Ruth, additional, Lundquist, Jennifer, additional, Luo, Ye, additional, Lyness, Kevin, additional, Lyons, Karen S., additional, Maccoby, Eleanor, additional, MacDermid, Shelley, additional, MacDonald, William L., additional, Yagla Mack, Kristin, additional, Macmillan, Ross, additional, Macomber, Jennifer, additional, MacPhee, David, additional, MacTavish, Katherine, additional, Madise, Nyovani J., additional, Malik, Neena, additional, Manning, Wendy D., additional, Mansfield, DeeAnn, additional, Manzi, Claudia, additional, Margolin, Gayla, additional, Marks, Gary, additional, Marks, Jennifer, additional, Marks, Loren, additional, Marks, Nadine, additional, Marshall, Sheila, additional, Marsiglio, William, additional, Marteleto, Leticia, additional, Martin, Molly A., additional, Martin, Steven P., additional, Mattingly, Marybeth J., additional, Maume, David, additional, McBride, Brent A., additional, McElroy, Mary, additional, McGraw, Lori, additional, McGroder, Sharon M., additional, McHale, Susan M., additional, McPherson, Mervyl J., additional, McQuillan, Julia, additional, Mederer, Helen J., additional, Meekers, Dominique A., additional, Meinhold, Jana, additional, Melby, Janet N., additional, Mellott, Leanna, additional, Menjivar, Cecilia, additional, Messner, Steven, additional, Michaels, Marcia, additional, Milkie, Melissa A., additional, Mirsky, Julia, additional, Mollen, Debra, additional, Monden, Christiaan, additional, Moore, David, additional, Morgan, David, additional, Morgan, S. Phillip, additional, Mosack, Katie E., additional, Muraco, Anna, additional, Murray, Colleen I., additional, Murray, Susan, additional, Mustillo, Sarah, additional, Myers, Barbara J., additional, Myers, Scott M., additional, Myers‐Walls, Judith A., additional, Najarian, Cheryl, additional, Nelson, Margaret, additional, Ngee, Tick, additional, Nievar, Angela, additional, Nock, Steven L., additional, Nomaguchi, Kei, additional, O'Brien, Marion, additional, Okun, Barbara S., additional, Olson, Loreen N., additional, Openshaw, D. Kim, additional, Oppenheimer, Valerie K., additional, Oropesa, Ralph S., additional, Ortiz, Steven, additional, Osborne, Cynthia, additional, Oswald, Ramona, additional, Oyserman, Daphna, additional, Ozer, Elizabeth M., additional, Pahl, Jan, additional, Parcel, Toby L., additional, Parker, Jennifer, additional, Pavalko, Eliza, additional, Pearce, Lisa, additional, Perren, Sonja, additional, Perry, Yvette V., additional, Perry‐Jenkins, Maureen, additional, Peters, Cheryl L., additional, Peterson, Brennan, additional, Philaretou, Andreas, additional, Phua, VooChin, additional, Piercy, Kathy, additional, Pillemer, Karl, additional, Poehlmann, Julie, additional, Pollard, Michael, additional, Porterfield, Shirley L., additional, Powell, Brian, additional, Ann Powell, Mary, additional, Prazak, Miroslava, additional, Proulx, Christine M., additional, Pruchno, Rachel, additional, Pungello, Elizabeth, additional, Punyanunt‐Carter, Narissra, additional, Putnam, Samuel P., additional, Baolian Qin, Desiree, additional, Honn Qualls, Sara, additional, Radina, M. 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Published
2005
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39. The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies

Author

Su Zhenqiang, Shippy Richard, Puri Raj K, Peterson Ron L, Mei Nan, Ma Yunqing, Luo Yuling, Li Quan-Zhen, Kawasaki Ernest S, Hong Huixiao, Herman Damir, Han Jing, Guo Xu, Fuscoe James C, Frueh Felix W, Fan Xiao-hui, Collins Patrick J, Chu Tzu-Ming, Bertholet Vincent, Cao Xiaoxi, Bao Wenjun, Barbacioru Catalin C, Amur Shashi, Qian Feng, Fang Hong, Boysen Cecilie, Croner Lisa J, Guo Lei, Goodsaid Federico M, Perkins Roger G, Harris Stephen C, Jensen Roderick V, Jones Wendell D, Shi Leming, Sun Yongming, Sun Hongmei, Thorn Brett, Turpaz Yaron, Wang Charles, Wang Sue, Warrington Janet A, Willey James C, Wu Jie, Xie Qian, Zhang Liang, Zhang Lu, Zhong Sheng, Wolfinger Russell D, and Tong Weida

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background Reproducibility is a fundamental requirement in scientific experiments. Some recent publications have claimed that microarrays are unreliable because lists of differentially expressed genes (DEGs) are not reproducible in similar experiments. Meanwhile, new statistical methods for identifying DEGs continue to appear in the scientific literature. The resultant variety of existing and emerging methods exacerbates confusion and continuing debate in the microarray community on the appropriate choice of methods for identifying reliable DEG lists. Results Using the data sets generated by the MicroArray Quality Control (MAQC) project, we investigated the impact on the reproducibility of DEG lists of a few widely used gene selection procedures. We present comprehensive results from inter-site comparisons using the same microarray platform, cross-platform comparisons using multiple microarray platforms, and comparisons between microarray results and those from TaqMan – the widely regarded "standard" gene expression platform. Our results demonstrate that (1) previously reported discordance between DEG lists could simply result from ranking and selecting DEGs solely by statistical significance (P) derived from widely used simple t-tests; (2) when fold change (FC) is used as the ranking criterion with a non-stringent P-value cutoff filtering, the DEG lists become much more reproducible, especially when fewer genes are selected as differentially expressed, as is the case in most microarray studies; and (3) the instability of short DEG lists solely based on P-value ranking is an expected mathematical consequence of the high variability of the t-values; the more stringent the P-value threshold, the less reproducible the DEG list is. These observations are also consistent with results from extensive simulation calculations. Conclusion We recommend the use of FC-ranking plus a non-stringent P cutoff as a straightforward and baseline practice in order to generate more reproducible DEG lists. Specifically, the P-value cutoff should not be stringent (too small) and FC should be as large as possible. Our results provide practical guidance to choose the appropriate FC and P-value cutoffs when selecting a given number of DEGs. The FC criterion enhances reproducibility, whereas the P criterion balances sensitivity and specificity.

Published
2008
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40. Analysis of gene expression changes in relation to toxicity and tumorigenesis in the livers of Big Blue transgenic rats fed comfrey (Symphytum officinale)

Author

Mei Nan, Guo Lei, Zhang Lu, Shi Leming, Sun Yongming, Fung Chris, Moland Carrie L, Dial Stacey L, Fuscoe James C, and Chen Tao

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background Comfrey is consumed by humans as a vegetable and a tea, and has been used as an herbal medicine for more than 2000 years. Comfrey, however, is hepatotoxic in livestock and humans and carcinogenic in experimental animals. Our previous study suggested that comfrey induces liver tumors by a genotoxic mechanism and that the pyrrolizidine alkaloids in the plant are responsible for mutation induction and tumor initiation in rat liver. Results In this study, we identified comfrey-induced gene expression profile in the livers of rats. Groups of 6 male transgenic Big Blue rats were fed a basal diet and a diet containing 8% comfrey roots, a dose that resulted in liver tumors in a previous carcinogenicity bioassay. The animals were treated for 12 weeks and sacrificed one day after the final treatment. We used a rat microarray containing 26,857 genes to perform genome-wide gene expression studies. Dietary comfrey resulted in marked changes in liver gene expression, as well as in significant decreases in the body weight and increases in liver mutant frequency. When a two-fold cutoff value and a P-value less than 0.01 were selected, 2,726 genes were identified as differentially expressed in comfrey-fed rats compared to control animals. Among these genes, there were 1,617 genes associated by Ingenuity Pathway Analysis with particular functions, and the differentially expressed genes in comfrey-fed rat livers were involved in metabolism, injury of endothelial cells, and liver injury and abnormalities, including liver fibrosis and cancer development. Conclusion The gene expression profile provides us a better understanding of underlying mechanisms for comfrey-induced hepatic toxicity. Integration of gene expression changes with known pathological changes can be used to formulate a mechanistic scheme for comfrey-induced liver toxicity and tumorigenesis.

Published
2006
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41. Effect of various normalization methods on Applied Biosystems expression array system data

Author

Keys David N, Sun Yongming A, Canales Roger D, Wang Yulei, Barbacioru Catalin C, Chan Frances, Poulter Karen A, and Samaha Raymond R

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background DNA microarray technology provides a powerful tool for characterizing gene expression on a genome scale. While the technology has been widely used in discovery-based medical and basic biological research, its direct application in clinical practice and regulatory decision-making has been questioned. A few key issues, including the reproducibility, reliability, compatibility and standardization of microarray analysis and results, must be critically addressed before any routine usage of microarrays in clinical laboratory and regulated areas can occur. In this study we investigate some of these issues for the Applied Biosystems Human Genome Survey Microarrays. Results We analyzed the gene expression profiles of two samples: brain and universal human reference (UHR), a mixture of RNAs from 10 cancer cell lines, using the Applied Biosystems Human Genome Survey Microarrays. Five technical replicates in three different sites were performed on the same total RNA samples according to manufacturer's standard protocols. Five different methods, quantile, median, scale, VSN and cyclic loess were used to normalize AB microarray data within each site. 1,000 genes spanning a wide dynamic range in gene expression levels were selected for real-time PCR validation. Using the TaqMan® assays data set as the reference set, the performance of the five normalization methods was evaluated focusing on the following criteria: (1) Sensitivity and reproducibility in detection of expression; (2) Fold change correlation with real-time PCR data; (3) Sensitivity and specificity in detection of differential expression; (4) Reproducibility of differentially expressed gene lists. Conclusion Our results showed a high level of concordance between these normalization methods. This is true, regardless of whether signal, detection, variation, fold change measurements and reproducibility were interrogated. Furthermore, we used TaqMan® assays as a reference, to generate TPR and FDR plots for the various normalization methods across the assay range. Little impact is observed on the TP and FP rates in detection of differentially expressed genes. Additionally, little effect was observed by the various normalization methods on the statistical approaches analyzed which indicates a certain robustness of the analysis methods currently in use in the field, particularly when used in conjunction with the Applied Biosystems Gene Expression System.

Published
2006
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