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Are Gene Expression Microarray Analyses Reliable? A Review of Studies of Retinoic Acid Responsive Genes

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Genomics, Proteomics & Bioinformatics 2003年第1期1卷 9-14页

作者： peter j.van der Spek Andreas Kremer Lynn Murry Michael G.Walker janssen Pharmaceutica Beerse BelgiumJanssen Pharmaceutica Beerse BelgiumIncyte Genomics Inc. CA 94087 USAIncyte Genomics Inc. CA 94087 USA

Microarray analyses of gene expression are widely used, but reports of the same analyses by different groups give widely divergent results, and raise questions regarding reproducibility and reliability. We take as an example recent published reports on microarray experiments that were designed to identify retinoic acid responsive genes. These reports show substantial differences in their results. In this article, we review the methodology, results, and potential causes of differences in these applications of microarrays. Finally, we suggest practices to improve the reliability and reproducibility of microarray experiments.

关键词： microarrays retinoic acid response gene reliability case studies

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FtsH4 protease controls biogenesis of the PSII complex by dual regulation of high light-inducible proteins

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Plant Communications 2023年第1期4卷 272-286页

作者： Vendula Krynická Petra Skotnicová Philip j.jackson Samuel Barnett jianfeng Yu Anna Wysocka Radek Kaña Mark j.Dickman peter j.Nixon C.Neil Hunter josef Komenda The Czech Academy of Sciences Institute of MicrobiologyCentre AlgatechNovohradská 23737901 TreboñCzech Republic Plants Photosynthesis and SoilSchool of BiosciencesUniversity of SheffieldSheffield S102TNUK Department of Chemical and Biological Engineering University of SheffieldSheffield S13JDUK Sir Ernst Chain Building-Wolfson Laboratories Department of Life SciencesSouth Kensington CampusImperial College LondonLondon SW72AZUK Faculty of Science University of South Bohemia37005 Ceské BudějoviceCzech Republic

FtsH proteases are membrane-embedded proteolytic complexes important for protein quality control and regulation of various physiological processes in bacteria,mitochondria,and *** most cyanobacteria,the model species Synechocystis *** 6803 contains four FtsH homologs,FtsH1–***1–FtsH3 form two hetero-oligomeric complexes,FtsH1/3 and FtsH2/3,which play a pivotal role in acclimation to nutrient deficiency and photosystem Ⅱ quality control,***4 differs from the other three homologs by the formation of a homo-oligomeric complex,and together with Arabidopsis thaliana AtFtsH7/9 orthologs,it has been assigned to another phylogenetic group of unknown *** results exclude the possibility that Synechocystis FtsH4 structurally or functionally substitutes for the missing or non-functional FtsH2 subunit in the FtsH2/3 ***,we demonstrate that FtsH4 is involved in the biogenesis of photosystem Ⅱ by dual regulation of high light-inducible proteins(Hlips).FtsH4 positively regulates expression of Hlips shortly after high light exposure but is also responsible for Hlip removal under conditions when their elevated levels are no longer *** provide experimental support for Hlips as proteolytic substrates of *** labeling of FtsH4 enabled us to assess its localization using advanced microscopic *** show that FtsH4 complexes are concentrated in well-defined membrane regions at the inner and outer periphery of the thylakoid *** on the identification of proteins that co-purified with the tagged FtsH4,we speculate that FtsH4 concentrates in special compartments in which the biogenesis of photosynthetic complexes takes place.

关键词： thylakoid photosystemⅡbiogenesis FtsH4 high light-inducible protein proteolysis

ON AN EXTENSION OF ABEL-GONTSCHAROFF'S EXPANSION FORMULA

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Analysis in Theory and Applications 2005年第4期21卷 359-369页

作者： Tianxiao He Leetsch C. Hsu peter j. S. Shiue Illinois Wesleyan University USA Dalian University of Technology China University of Nevada Las Vegas USA

We present a constructive generalization of Abel-Gontscharoff＇s series expansion to higher dimensions. A constructive application to a problem of multivariate interpolation is also investigated. In addition, two algo... 详细信息

关键词： Abel-Gontscharoff's Expansion Formula Abel-Gontscharoff-Gould polynomial multivariate Abel-Gontscharoff interpolation higher dimensional dot product annihilation coefficients

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High Speed Rail Learning System(HSRLS)-Taking Advantage of Online Technologies in Railway Education

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International journal of Transportation Science and Technology 2015年第2期4卷 179-196页

作者： Pasi T.Lautala peter j.Haas john L.Velat Michigan Technological University Michigan Tech Transportation Institute Michigan Technological University

The United States has taken initial steps toward developing a high speed rail(HSR)network,but the domestic workforce experience and institutional knowledge necessary for the planning,design,construction,and operations of HSR is *** paper describes and provides preliminary assessment of the High Speed Rail Learning System(HSRLS),a demonstration project that seeks to address gaps in HSR knowledge and skills in the *** HSRLS developers designed an online education system to serve as a clearinghouse for railrelated information and content,connect teachers,trainers,and students at pre-,and postgraduate levels,and to collect demographic and professional information on groups and individuals interested in *** paper explores the technology review,selection process,and content *** visits and demographic information from over 4,000 unique individuals and 600 HSRLS course registrations are analyzed and assessed.

关键词： Higher education Workforce demand High Speed Rail Railroad education On-Line education Web-based teaching and learning

Application of Polynomial Interpolation in the Chinese Remainder Problem

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journal of Mathematical Research with Applications 2017年第1期37卷 90-96页

作者： Tianxiao HE Scott MACDONALD peter j.-S.SHIUE Department of Mathematics Illinois Wesleyan University Math Learning Center University of Nevada Las Vegas Department of Mathematical Sciences University of Nevada

This paper presents an application of polynomial interpolation in the solution of the Chinese Remainder Problem for bother integers and polynomials.

关键词： Chinese Remainder problem Chinese Remainder theorem Lagrange interpolation Newton interpolation

Industry Based ＂Hands-On＂ Undergraduate Vibration Course for Engineering and Engineering Technology Students

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journal of Mechanics Engineering and Automation 2013年第2期3卷 71-77页

作者： Geoffrey j. peter Manufacturing and Mechanical Engineering and Technology Program Oregon Institute of Technology - Wilsonville CampusPortland Oregon 97225 USA

Modem technology and manufacturing methods often require engineers who understand the fundamental principles of vibration theory and who are also skilled in vibration applications. Simply processing, remembering and applying the material learned from lectures and laboratory experiments With artificial criteria are inadequate. Hands-on teaching techniques with real-world problems are needed to complete the engineering students＇ education. This paper demonstrates how hands-on experiments performed in industry support and increase the students＇ understanding of fundamental principles and skill in their applications. Graduates with both knowledge and skill are more competitive in today＇s job market. A one-quarter industry-based vibration course was developed and taught with a hands-on segment at the Manufacturing and Mechanical Engineering and Technology （MMET） program at Oregon Institute of Technology （OIT） - Portland Campus. This novel instructional approach provided students with the opportunity to immediately apply material, learned in class and laboratory, in real-world industry situations with real-world problems. This instructional approach is applicable in many engineering fields and the author found the mechanical vibrations class particularly well suited for this instructional design style. The hands-on approach, grounded in the vibration course curriculum, provided a direct link to the fundamentals of vibration in industry. Student comments are included to demonstrate the value perceived by the students. Although this curriculum experiment involved mechanical engineering technology students, it would benefit mechanical engineering students equally well. In addition, the paper provides a brief description of the industries that participated in this project. Industries were selected because they use vibration based manufacturing, perform extreme testing or design their products to avoid failure due to vibrations.

关键词： Vibrations novel curriculum manufacturing mechanical engineering technology.

Distributed Bio-Hydrogen Refueling Stations

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journal of Earth Science and Engineering 2016年第4期6卷 183-190页

作者： peter j. Schubert Richard G. Lugar Center for Renewable Energy lndiana University-Purdue University Indianapolis Indianapolis 1N 46202 United States

Hydrogen fuel cell cars are now available for lease and for sale. Renewable hydrogen fuel can be produced from water via electrolysis, or from biomass via gasification. Electrolysis is power-hungry with high demand from solar or wind power. Gasification, however, can be energy self-sufficient using a recently-patented thermochemical conversion technology known as I-HPG （indirectly-heated pyrolytic gasification）. I-HPG produces a tar-free syngas from non-food woody biomass. This means the balance of plant can be small, so the overall system is economical at modest sizes. This makes it possible to produce renewable hydrogen from local agricultural residues; sufficient to create distributed refueling stations wherever there is feedstock. This work describes the specifics of a novel bio-hydrogen refueling station whereby the syngas produced has much of the hydrogen extracted with the remainder powering a generator to provide the electric power to the I-HPG system. Thus the system runs continuously. When paired with another new technology, moderate-pressure storage of hydrogen in porous silicon, there is the potential to also power the refueling operation. Such systems can be operated independently. It is even possible to design an energy self-sufficient farm where all electric power, heat, and hydrogen fuel is produced from the non-food residues of agricultural operations. No water is required, and the carbon footprint is negative, or at least neutral.

关键词： Biomass hydrogen distributed generation fuel cell vehicle

Systems psychopharmacology:A network approach to developing novel therapies

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World journal of Psychiatry 2016年第1期6卷 66-83页

作者： peter j Gebicke-Haerter Central Institute of Mental Health Medical Faculty MannheimHeidelberg University

The multifactorial origin of most chronic disorders of the brain, including schizophrenia, has been well accepted. Consequently, pharmacotherapy would require multitargeted strategies. This contrasts to the majority of drug therapies used until now, addressing more or less specifically only one target molecule. Nevertheless, quite some searches for multiple molecular targets specific for mental disorders have been undertaken. For example, genome-wide association studies have been conducted to discover new target genes of disease. Unfortunately, these attempts have not fulfilled the great hopes they have started with. Polypharmacology and network pharmacology approaches of drug treatment endeavor to abandon the one-drug one-target thinking. To this end, most approaches set out to investigate network topologies searching for modules, endowed with "important" nodes, such as "hubs" or "bottlenecks", encompassing features of disease networks, and being useful as tentative targets of drug therapies. This kind of research appears to be very promising. However, blocking or inhibiting "important" targets may easily result in destruction of network integrity. Therefore, it is suggested here to study functions of nodes with lower centrality for more subtle impact on network behavior. Targeting multiple nodes with low impact on network integrity by drugs with multiple activities("dirty drugs") or by several drugs, simultaneously, avoids to disrupt network integrity and may reset deviant dynamics of disease. Natural products typically display multi target functions and therefore could help to identify useful biological targets. Hence, future efforts should consider to combine drug-target networks with target-disease networks using mathematical(graph theoretical) tools, which could help to develop new therapeutic strategies in long-term psychiatric disorders.

关键词： Polypharmacology Drug-target networks Network topology Disease networks Genome-wide association studies Epigenetics Schizophrenia Herbal extracts

RECONSTRUCTING THE ROYAL FAMILY OF RAMESSES Ⅱ AND ITS HIERARCHICAL STRUCTURE

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journal of Ancient Civilizations 2016年第1期31卷 7-44页

作者： peter j. Brand University of Memphis

Introduction： The Great Family of Ramesses II 2Among his many achievements that have marked Ramesses II as one of Egypt＇s greatest pharaohs, his multiple wives and his stupendous progeny of approximately 100 children stands as one of the most remarkable.3 By comparison with all other pharaohs, he appears unique, from the surviving evidence at least. In fact, we know of more royal sons of Ramesses II than of all the kings of Egypt＇s Eighteenth Dynasty.4 Indeed, the numbers of royal children that appear in the unprecedented monumental processional lists of his sons and daughters on several of his Egyptian and Nubian temples prompted Marjorie Fisher in her recent study of his sons to suggest that many of these princes may have been his grandchildren instead.5

关键词：层次结构 Fisher 法老王埃及儿子大惯性孩子

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