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Characterization of Binding Sites of Eukaryotic Transcription Factors

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Genomics, Proteomics & Bioinformatics 2006年第2期4卷 67-79页

作者： j.ang Qian jimmy Lin Donald j. Zack The Wilmer Institute Department of Molecular Biology and Genetics Department of Neuroscience McKusick-Nathans Institute of Genetic Medicine Johns Hopkins University School of Medicine Baltimore MD 21287 USA.

To explore the nature of eukaryotic transcription factor （TF） binding sites and determine how they differ from surrounding DNA sequences, we examined four features associated with DNA binding sites： G＋C content, pattern complexity, palindromic structure, and Markov sequence ordering. Our analysis of the regulatory motifs obtained from the TRANSFAC databases using yeast intergenic sequences as background, revealed that these four features show variable enrichment in motif sequences. For example, motif sequences were more likely to have palindromic structure than were background sequences. In addition, these features were tightly localized to the regulatory motifs, indicating that they are a property of the motif sequences themselves and are not shared by the general promoter ＂environment＂ in which the regulatory motifs reside. By breaking down the motif sequences according to the TF classes to which they bind, more specific associations were identified. Finally, we found that some correlations, such as G＋C content enrichment, were species-specific, while others, such as complexity enrichment, were universal across the species examined. The quantitative analysis provided here should increase our understanding of protein-DNA interactions and also help facilitate the discovery of regulatory motifs through bioinformatics.

关键词： transcription factor promoter gene regulation bioinformatics

Modeling of daily pan evaporation using partial least squares regression

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Science China(Technological Sciences) 2011年第1期54卷 163-174页

作者： ABUDU Shalamu CUI ChunLiang j. Phillip KING jimmy MORENO A. Salim BAWAZIR Xinj.ang Water Resources Research Institute Urumqi 830049 China Civil Engineering Department New Mexico State University Las Cruces New Mexico 88001 USA

This study presented the application of partial least squares regression （PLSR） in estimating daily pan evaporation by utilizing the unique feature of PLSR in eliminating collinearity issues in predictor variables. The climate variables and daily pan evaporation data measured at two weather stations located near Elephant Butte Reservoir, New Mexico, USA and a weather station located in Shanshan County, Xinj.ang, China were used in the study. The nonlinear relationship between climate variables and daily pan evaporation was successfully modeled using PLSR approach by solving collinearity that exists in the climate variables. The modeling results were compared to artificial neural networks （ANN） models with the same input variables. The resuits showed that the nonlinear equations developed using PLSR has similar performance with complex ANN approach for the study sites. The modeling process was straightforward and the equations were simpler and more explicit than the ANN black-box models.

关键词： modeling daily pan evaporation partial least squares regression artificial neural networks meteorological data

Leaf morphogenesis:The multifaceted roles of mechanics

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Molecular Plant 2022年第7期15卷 1098-1119页

作者： Kexin Guo Changj.n Huang Yansong Miao Daniel j.Cosgrove K.jimmy Hsia School of Mechanical and Aerospace Engineering Nanyang Technological UniversitySingapore 639798Singapore School of Biological Sciences Nanyang Technological UniversitySingapore 637551Singapore Department of Biology The Pennsylvania State UniversityUniversity ParkPA 16802USA School of Chemical and Biomedical Engineering Nanyang Technological UniversitySingapore 637459Singapore

Plants produce a rich diversity of biological forms,and the diversity of leaves is especially *** of leaf morphogenesis have been studied in the past two decades,with a growing focus on the interactive roles of mechanics in recent *** of plant organs involves feedback by mechanical stress:growth induces stress,and stress affects growth and *** much attention has been given to potential stress-sensing mechanisms and cellular responses,the mechanical principles guiding morphogenesis have not been well *** we synthesize the overarching roles of mechanics and mechanical stress in multilevel and multiple stages of leaf morphogenesis,encompassing leaf primordium initiation,phyllotaxis and venation patterning,and the establishment of complex mature leaf ***,the roles of mechanics at multiscale levels,from subcellular cytoskeletal molecules to single cells to tissues at the organ scale,are *** highlighting the role of mechanical buckling in the formation of three-dimensional leaf shapes,this review integrates the perspectives of mechanics and biology to provide broader insights into the mechanobiology of leaf morphogenesis.

关键词： leaf morphogenesis cell-wall mechanics phyllotaxis and venation patterning differential and anisotropic growth mechanical buckling

FACEts of mechanical regulation in the morphogenesis of craniofacial structures

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International j.urnal of Oral Science 2021年第1期13卷 1-16页

作者： Wei Du Arshia Bhoj.ani jimmy K.Hu State Key Laboratory of Oral Diseases&National Clinical Research Center for Oral Diseases&Department of Cariology and Endodontics West China Hospital of StomatologySichuan UniversityChengduChina School of Dentistry University of California Los AngelesLos AngelesCAUSA Molecular Biology Institute University of California Los AngelesLos AngelesCAUSA

During embryonic development,organs undergo distinct and programmed morphological changes as they develop into their functional *** genetics and biochemical signals are well recognized regulators of morphogenesis,mechanical forces and the physical properties of tissues are now emerging as integral parts of this process as *** physical factors drive coordinated cell movements and reorganizations,shape and size changes,proliferation and differentiation,as well as gene expression changes,and ultimately sculpt any developing structure by guiding correct cellular architectures and *** this review we focus on several craniofacial structures,including the tooth,the mandible,the palate,and the *** discuss the spatiotemporal regulation of different mechanical cues at both the cellular and tissue scales during craniofacial development and examine how tissue mechanics control various aspects of cell biology and signaling to shape a developing craniofacial organ.

关键词： architectures organs morphogenesis

Coordinated Buckling of Thick Multi-Walled Carbon Nanotubes Under Uniaxial Compression

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Nano Research 2010年第1期3卷 32-42页

作者： Xu Huang Hongyan Yuan K.jimmy Hsia Sulin Zhang Department of Engineering Science and Mechanics The Pennsylvania State UniversityUniversity ParkPA 16802USA Department of Mechanical Science and Engineering University of IllinoisUrbanaIL 61801USA

Using a generalized quasi-continuum method,we characterize the post-buckling morphologies and energetics of thick multi-walled carbon nanotubes(MWCNTs)under uniaxial *** simulations identify for the first time evolving post-buckling morphologies,ranging from asymmetric periodic rippling to a helical diamond *** attribute the evolving morphologies to the coordinated buckling of the constituent *** post-buckling morphologies result in significantly reduced effective moduli that are strongly dependent on the aspect *** simulation results provide fundamental principles to guide the future design of high-performance,MWCNT-based nanodevices.

关键词： Carbon nanotubes buckling uniaxial compression rippling

Striatins and STRIPAK complex partners in clinical outcomes of patients with breast cancer and responses to drug treatment

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中国癌症研究:英文版 2023年第4期35卷 365-385页

作者： Amber Xinyu Li jimmy j.anyuan Zeng Tracey A Martin Lin Ye Fiona Ruge Andrew j.Sanders Elyas Khan QPing Dou Eleri Davies Wen G j.ang Cardiff China Medical Research Collaborative Division of Cancer and GeneticsCardiff University School of MedicineHeath ParkCardiff CF144XNUK School of Natural and Social Science University of GloucestershireFrancis Close HallCheltenham GL504AZUK Karmanos Cancer Institute Department of OncologySchool of MedicineWayne State UniversityDetroit MI 48201USA Wales Breast Center Cardiff and Vales University Health BoardUniversity Llandough HospitalCardiff CF642XXUK

Obj.ctive: Striatins(STRNs) family, which contains three multi-domain scaffolding proteins, are cornerstones of the striatins interacting phosphatase and kinase(STRIPAK) complex. Although the role of the STRIPAK complex in cancer has become recognized in recent years, its clinical significance in breast cancer has not been fully ***: Using a freshly frozen breast cancer tissue cohort containing both cancerous and adj.cent normal mammary tissues, we quantitatively evaluated the transcript-level expression of all members within the STRIPAK complex along with some key interacting and regulatory proteins of STRNs. The expression profile of each molecule and the integrated pattern of the complex members were assessed against the clinical-pathological factors of the patients. The Cancer Genome Atlas(TCGA) dataset was used to evaluate the breast cancer patients’ response to chemotherapies. Four human breast cancer cell lines, MDA-MB-231, MDA-MB-361, MCF-7, and SKBR-3, were subsequently adopted for in vitro ***: Here we found that high-level expressions of STRIP2, calmodulin, CCM3, MINK1 and SLMAP were respectively associated with shorter overall survival(OS) of patients. Although the similar pattern observed for STRN3, STRN4 and a contrary pattern observed for PPP2CA, PPP2CB and PPPR1A were not significant, the integrated expression profile of STRNs group and PPP2 group members constitutes a highly significant prognostic indicator for OS [P<0.001, hazard ratio(HR)=2.04, 95% confidence interval(95% CI), 1.36-3.07] and disease-free survival(DFS)(P=0.003, HR=1.40, 95% CI, 1.12-1.75). Reduced expression of STRN3 has an influence on the biological functions including adhesiveness and migration. In line with our clinical findings, the breast cancer cells responded to STRN3 knockdown with changes in their chemo-sensitivity, of which the response is also breast cancer subtype ***: Our results suggest a possible role of the STRIPAK complex

关键词： Striatins STRN3 STRIPAK breast cancer prognosis chemo-resistance

Hallux rigidus: How do I approach it?

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World j.urnal of Orthopedics 2017年第5期8卷 364-371页

作者： Aaron Lam jimmy j.Chan Michele F Surace Ettore Vulcano Albert Einstein College of Medicine Leni and Peter W. May De-partment of Orthopaedic Surgery Icahn School of Medicine at Mount Sinai Department of Orthopedics University of Insubria

Hallux rigidus is a degenerative disease of the first metatarsalphalangeal(MTP) j.int and affects 2.5% of people over age 50. Dorsal osteophytes and narrowed j.int space leads to debilitating pain and limited range of motion. Altered gait mechanics often ensued as 119% of the body force transmit through the 1^(st) MTP j.int during gait cycle. Precise etiology remains under debate with trauma being often cited in the literature. Hallux valgus interphalangeus, female gender, inflammatory and metabolic conditions have all been identified as associative factors. Clinical symptoms, physical exam and radiographic evidence are important in assessing and grading the disease. Non-operative managements including nonsteroidal antiinflammatory drugs, intraarticular inj.ctions, shoe modification, activity modification and physical therapy, should always be attempted for all hallux rigidus patients. The goal of surgery is to relieve pain, maintain stability of the first MTP j.int, and improve function and quality of life. Operative treatments can be divided into j.int-sparing vs j.int-sacrificing. Cheilectomy and moberg osteotomy are examples of j.int-sparing techniques that have demonstrated great success in early stages of hallux rigidus. Arthrodesis is a j.int-sacrificing procedure that has been the gold standard for advanced hallux rigidus. Other newer procedures such as implant arthroplasty, interpositional arthroplasty and arthroscopy, have demonstrated promising early patient outcomes. However, future studies are still needed to validate its long-term efficacy and safety. The choice of procedure should be based on the condition of the j.int, patient's goal and expectations, and surgeon's experience with the technique.

关键词： Hallux rigidus Cheilectomy Arthrodiastasis Moberg osteotomy Arthodesis Interpositional arthroplasty Arthroplasty

A Large Scale GIS Geodatabase of Soil Parameters Supporting the Modeling of Conservation Practice Alternatives in the United States

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j.urnal of Geographic Information System 2017年第3期9卷 267-278页

作者： Mauro Di Luzio Mike j. White j.ffrey G. Arnold jimmy R. Williams j.mes R. Kiniry Blackland Research Center Texas A&M AgriLife Research Temple Texas USA Grassland Research Center Agriculture Research Service United States Department of Agriculture Temple Texas USA

Water quality modeling requires across-scale support of combined digital soil elements and simulation parameters. This paper presents the unprecedented development of a large spatial scale (1:250,000) ArcGIS geodatabase coverage designed as a functional repository of soil-parameters for modeling and comparison of water quality outcomes in the United States. The set of target models include: SWAT (Soil and Water Assessment Tool), APEX (Agricultural Policy Environmental Extender), and ALMANAC (Agricultural Land Management Alternatives with Numerical Assessment Criteria). This development relies on the Digital General Soil Map (DGSM) as the source of soil information, and leverages on architectural design and associated tools created for a companion product at higher resolution from which also was extended a procedure for refilling a large number of missing derived parameters. Outlined by regional watershed layouts and supported by GIS land use layers, the core product is developed using the File Geodatabase (FGDB) data structure, which brings, via customized Python-based tools, the data directly into geoprocessing workflows. The FGDB implement efficiently stores spatial soil features, tabular model elements and linked relationships, while seamlessly providing the environment for the extraction, spatial analysis, and mapping of the models’ parameters. As an alternative, the composing spatial elements, polygons and multi-resolution rasters, and the models’ elements are offered as a file-folder system of data with completely Open Source formats. Finally, this geographic database coverage provides support for the traditional large-scale and harmonized application of the models as well as an alternative to the higher resolution companion for areas where this information is still under development.

关键词： Geodatabase Soil SWAT APEX ALMANAC

Bio-Efficacy of Plant-Derived Pesticides against Fall Armyworm (Spodoptera frugiperda) and Their Interactive Effects on Maize Agronomic Performance under Field Conditions

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Agricultural Sciences 2023年第11期14卷 1535-1546页

作者： j.nias Sogra Lux jimmy Kenndy Kamik Alex Galus Department of Agriculture Papua New Guinea University of Technology Lae Papua New Guinea Department of Agriculture Sonoma Adventist College Kokopo Papua New Guinea Coconut Product Limited Rabaul Papua New Guinea National Agricultural Research Institute Kokopo Papua New Guinea

Maize is widely cultivated in Papua New Guinea (PNG) and provides farmers with nutrition and income. However, the fall armyworm (FAW) (Spodoptera frugiperda) (j.E. Smith) (Lepidoptera: Noctuidae) invasion is a threat to its production and supply. Hence, this field experiment was conducted to assess the bio-efficacy of plant-derived pesticides (PDPs) against FAW and their interactive effects on maize agronomic performance under field conditions. The treatments studied were turmeric rhizome extract (TRE), neem leaf ash solution (NLAS), neem bark extract (NBE), and untreated plots (control) and were replicated 5 times using the randomized complete block design. The data were subj.cted to analysis of variance and means were separated by Fisher’s protected least significant difference test. The result showed that the application of PDPs significantly reduced FAW infestation during the period of peak infestation. At 33 DAS, NBE significantly had the lowest number of FAW larvae (0.6) [F (4, 15) = 5.11, p = 0.02] and FAW attack intensity (29.8%) [F (4, 15) = 8.69, p F (4, 15) = 3.58, p = 0.04] and had the highest number of harvested ears (5.0) [F (4, 15) = 3.72, p = 0.04] and fresh ear weights (447 g) [F (4, 15) = 4.65, p = 0.02] compared to NLAS. The TRE and NLAS had performed poorly relative to the control. Hence, NBE can be used to control FAW infestation at a period of high attack intensity (33 DAS). Moreover, this study will provide basic information for future studies on biopesticidal plant extracts as a control of FAW infestation under field conditions in PNG.

关键词： FAW Larvae Attack Intensity Plant Height Harvested Ear Ear Fresh Weight