Browsing by Author "Sun, Min"
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- Cognitive Diagnostic Model, a Simulated-Based Study: Understanding Compensatory Reparameterized Unified Model (CRUM)Galeshi, Roofia (Virginia Tech, 2012-09-24)A recent trend in education has been toward formative assessments to enable teachers, parents, and administrators assist students succeed. Cognitive diagnostic modeling (CDM) has the potential to provide valuable information for stakeholders to assist students identify their skill deficiency in specific academic subjects. Cognitive diagnosis models are mainly viewed as a family of latent class confirmatory probabilistic models. These models allow the mapping of students' skill profiles/academic ability. Using a complex simulation studies, the methodological issues in one of the existing cognitive models, referred to as compensatory reparameterized unified model (CRUM) under the log-linear model family of CDM, was investigated. In order for practitioners to implement these models, their item parameter recovery and examinees' classifications need to be studied in detail. A series of complex simulated data were generated for investigation with the following designs: three attributes with seven items, three attributes with thirty five items, four attributes with fifteen items, and five attributes with thirty one items. Each dataset was generated with observations of: 50, 100, 500, 1,000, 5,000, and 10,000 examinees. The first manuscript is the report of the investigation of how accurately CRUM could recover item parameters and classify examinees under true QMattrix specification and various research designs. The results suggested that the test length with regards to number of attributes and sample size affects the item parameter recovery and examinees classification accuracy. The second manuscript is the report of the investigation of the sensitivity of relative fit indices in detecting misfit for over- and opposite-Q-Matrix misspecifications. The relative fit indices under investigation were Akaike information criterion (AIC), Bayesian information criterion (BIC), and sample size adjusted Bayesian information criterion (ssaBIC). The results suggested that the CRUM can be a robust model given the consideration to the observation number and item/attribute combinations. The findings of this dissertation fill some of the existing gaps in the methodological issues regarding cognitive models' applicability and generalizability. It helps practitioners design tests in CDM framework in order to attain reliable and valid results.
- Comparative transcriptome study of switchgrass (Panicum virgatum L.) homologous autopolyploid and its parental amphidiploid responding to consistent drought stressChen, Peilin; Chen, Jing; Sun, Min; Yan, Haidong; Feng, Guangyan; Wu, Bingchao; Zhang, Xinquan; Wang, Xiaoshan; Huang, Linkai (2020-10-15)Background Newly formed polyploids may experience short-term adaptative changes in their genome that may enhance the resistance of plants to stress. Considering the increasingly serious effects of drought on biofuel plants, whole genome duplication (WGD) may be an efficient way to proceed with drought resistant breeding. However, the molecular mechanism of drought response before/after WGD remains largely unclear. Results We found that autoploid switchgrass (Panicum virgatum L.) 8X Alamo had higher drought tolerance than its parent amphidiploid 4X Alamo using physiological tests. RNA and microRNA sequencing at different time points during drought were then conducted on 8X Alamo and 4X Alamo switchgrass. The specific differentially expressed transcripts (DETs) that related to drought stress (DS) in 8X Alamo were enriched in ribonucleoside and ribonucleotide binding, while the drought-related DETs in 4X Alamo were enriched in structural molecule activity. Ploidy-related DETs were primarily associated with signal transduction mechanisms. Weighted gene co-expression network analysis (WGCNA) detected three significant DS-related modules, and their DETs were primarily enriched in biosynthesis process and photosynthesis. A total of 26 differentially expressed microRNAs (DEmiRs) were detected, and among them, sbi-microRNA 399b was only expressed in 8X Alamo. The targets of microRNAs that were responded to polyploidization and drought stress all contained cytochrome P450 and superoxide dismutase genes. Conclusions This study explored the drought response of 8X and 4X Alamo switchgrass on both physiological and transcriptional levels, and provided experimental and sequencing data basis for a short-term adaptability study and drought-resistant biofuel plant breeding.
- Examining Relationships of Collegiate Experiences, Gender, and Academic Area with Undergraduate Students' Collaborative Learning SkillsSahbaz, Sumeyra (Virginia Tech, 2015-01-15)Collaborative learning skills are one of the essential learning outcomes for a college education in 21st century. College students are expected to possess the ability to collaborate with others in order to succeed in their career after graduating from college. However, the effects of collegiate experiences on collaborative learning for different gender and academic areas are almost unexplored. In addition, researchers highlight the need for more research on interaction effects to explore whether different types of students respond differently to various collegiate experiences. The researcher examined the relationship of student-student interactions and student-faculty interactions with graduating seniors' perceived collaborative learning skills. Furthermore, the researcher explored whether this relationship was moderated by students' gender, academic area, and retrospective perception of their collaborative learning skills. Social-cognitive learning theory and Astin's involvement theory were used as conceptual frameworks to guide this study. Astin's input-environment-output college impact model served as a theoretical guide. Using an institutional cross-sectional data set, multiple regression analysis was utilized to examine these relationships. According to the results, the relationship between student-student interactions and graduating seniors' perceived collaborative learning skills was positive after controlling for the other independent variables in the study. Further results revealed that the relationship of student-student interactions and student-faculty interactions with the outcome variable was moderated by students' gender, academic area, and retrospective perception of their collaborative learning skill. The relationship between student-faculty interactions and the outcome variable was significantly weaker for male students, whereas the relationship between student-student interactions and the outcome variable was weaker for female student. The relationship between student-faculty interactions and the outcome variable was weaker for students in hard pure academic areas when compared to students in soft applied academic areas, while the opposite was observed for the relationship between student-student interactions and the outcome variable. The findings of the present study can be used to shape students' interactions with faculty and their peers with the awareness that these impact different types of students in different ways.
- Factors that Affect Retention of Novice Teachers in Hard-to-Staff High Schools in VirginiaBlunt, Mechelle Savedge (Virginia Tech, 2013-12-12)The mobility rates within the Kindergarten--Grade 12 teacher workforce are distressing, and the teaching profession has a relatively high turnover rate compared to other occupations. The Commonwealth of Virginia encounters many challenges when attempting to retain highly qualified teachers in schools. Despite the state's efforts to staff all schools, high teacher turnover rates persist. Novice teacher attrition is more prevalent in schools identified as hard-to-staff. Turnover affects not only the composition of faculties at individual schools and the stability of these schools but the quality of the teacher workforce as well. The factors that affect the retention of novice teachers in hard-to-staff high schools in Virginia were examined in this study. Similar to Giacometti's (2005) study, compensation, pre-service preparation, external forces, school culture, in-service training support, motivation to teach, and emotional factors were variables used in this investigation. Demographics, principal leadership actions, and economic conditions were added to Giacometti's original theory of novice teacher retention, and some of Giacometti's variables were refined to improve the theory and the quality of the measurements. Following descriptive and exploratory bivariate analyses, binary logistic regression was applied to predict teacher retention with two levels: planning to leave the school and planning to stay in the school. Results indicate that teachers who planned to leave were more likely to be minorities, to perceive less school cultural support, and to perceive less parental support than those who planned to stay. The results of the study have significant practical implications for school leaders, especially those who serve hard-to-staff high schools, in developing retention plans to keep their highly qualified novice teachers.
- Middle Level Schools in an Era of Standards and Accountability: Adaptations of the Features of the Middle School ConceptNicely, Kenneth Edward (Virginia Tech, 2012-03-16)The literature related to the development of education in the middle grades and to the features associated with the implementation of the middle school concept provides a theoretical grounding for the development and testing of an Innovation Configuration map for the middle school concept. The description provided of the historical development of middle-grades education presents the context for recent research studies and ongoing policy debate. In addition, features of the middle school concept as described within the literature are identified and an overview of salient research findings related to these features is given. A synthesis and critical review of previous research methodologies and findings reveal the need for further research. The purpose of the instrument development and testing process was to identify critical features of the middle school concept implemented in the context of standards and accountability. The instrument development and testing process investigated the nature of the implementation of middle school concept features, recognizing that actual practices in schools may vary somewhat without the schools losing their identity as middle level schools. The principle product of the process was the development of a diagnostic tool that may be used in future research to identify acceptable forms of implementation of the middle level philosophy of education. The instrument development and testing process employed research methodology based on the Concerns-Based Adoption Model (CBAM) of Hall and Hord (2006). Specifically, an Innovation Configuration map was developed identifying components of the middle level philosophy of education and describing variations in implementation of the components.
- Pangenomic analysis identifies structural variation associated with heat tolerance in pearl milletYan, Haidong; Sun, Min; Zhang, Zhongren; Jin, Yarong; Zhang, Ailing; Lin, Chuang; Wu, Bingchao; He, Min; Xu, Bin; Wang, Jing; Qin, Peng; Mendieta, John Pablo; Nie, Gang; Wang, Jianping; Jones, Chris S. S.; Feng, Guangyan; Srivastava, Rakesh K. K.; Zhang, Xinquan; Bombarely, Aureliano; Luo, Dan; Jin, Long; Peng, Yuanying; Wang, Xiaoshan; Ji, Yang; Tian, Shilin; Huang, Linkai (Nature Portfolio, 2023-03)Pearl millet is an important cereal crop worldwide and shows superior heat tolerance. Here, we developed a graph-based pan-genome by assembling ten chromosomal genomes with one existing assembly adapted to different climates worldwide and captured 424,085 genomic structural variations (SVs). Comparative genomics and transcriptomics analyses revealed the expansion of the RWP-RK transcription factor family and the involvement of endoplasmic reticulum (ER)-related genes in heat tolerance. The overexpression of one RWP-RK gene led to enhanced plant heat tolerance and transactivated ER-related genes quickly, supporting the important roles of RWP-RK transcription factors and ER system in heat tolerance. Furthermore, we found that some SVs affected the gene expression associated with heat tolerance and SVs surrounding ER-related genes shaped adaptation to heat tolerance during domestication in the population. Our study provides a comprehensive genomic resource revealing insights into heat tolerance and laying a foundation for generating more robust crops under the changing climate. A graph-based pan-genome constructed using de novo genome assemblies of ten pearl millet accessions adapted to different climates worldwide identifies structural variations and their contribution to heat tolerance in pearl millet.
- Transcriptional Changes in Pearl Millet Leaves under Heat StressHuang, Dejun; Sun, Min; Zhang, Ailing; Chen, Jishan; Zhang, Jian; Lin, Chuang; Zhang, Huan; Lu, Xiaowen; Wang, Xiaoshan; Yan, Haidong; Tang, Jianan; Huang, Linkai (MDPI, 2021-10-28)High-temperature stress negatively affects the growth and development of plants, and therefore threatens global agricultural safety. Cultivating stress-tolerant plants is the current objective of plant breeding programs. Pearl millet is a multi-purpose plant, commonly used as a forage but also an important food staple. This crop is very heat-resistant and has a higher net assimilation rate than corn under high-temperature stress. However, the response of heat resistant pearl millet has so far not been studied at the transcriptional level. In this study, transcriptome sequencing of pearl millet leaves exposed to different lengths of heat treatment (1 h, 48 h and 96 h) was conducted in order to investigate the molecular mechanisms of the heat stress response and to identify key genes related to heat stress. The results showed that the amount of heat stress-induced DEGs in leaves differs with the length of exposure to high temperatures. The highest value of DEGs (8286) was observed for the group exposed to heat stress for 96 h, while the other two treatments showed lower DEGs values of 4659 DEGs after 1 h exposure and 3981 DEGs after 48 h exposure to heat stress. The DEGs were mainly synthesized in protein folding pathways under high-temperature stress after 1 h exposure. Moreover, a large number of genes encoding ROS scavenging enzymes were activated under heat stress for 1 h and 48 h treatments. The flavonoid synthesis pathway of pearl millet was enriched after heat stress for 96 h. This study analyzed the transcription dynamics under short to long-term heat stress to provide a theoretical basis for the heat resistance response of pearl millet.
- Transcriptome analysis of heat stress and drought stress in pearl millet based on Pacbio full-length transcriptome sequencingSun, Min; Huang, Dejun; Zhang, Ailing; Khan, Imran; Yan, Haidong; Wang, Xiaoshan; Zhang, Xinquan; Zhang, Jian; Huang, Linkai (2020-07-08)Background Heat and drought are serious threats for crop growth and development. As the sixth largest cereal crop in the world, pearl millet can not only be used for food and forage but also as a source of bioenergy. Pearl millet is highly tolerant to heat and drought. Given this, it is considered an ideal crop to study plant stress tolerance and can be used to identify heat-resistant genes. Results In this study, we used Pacbio sequencing data as a reference sequence to analyze the Illumina data of pearl millet that had been subjected to heat and drought stress for 48 h. By summarizing previous studies, we found 26,299 new genes and 63,090 new transcripts, and the number of gene annotations increased by 20.18%. We identified 2792 transcription factors and 1223 transcriptional regulators. There were 318 TFs and 149 TRs differentially expressed under heat stress, and 315 TFs and 128 TRs were differentially expressed under drought stress. We used RNA sequencing to identify 6920 genes and 6484 genes differentially expressed under heat stress and drought stress, respectively. Conclusions Through Pacbio sequencing, we have identified more new genes and new transcripts. On the other hand, comparing the differentially expressed genes under heat tolerance with the DEGs under drought stress, we found that even in the same pathway, pearl millet responds with a different protein.