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A Systems Biology Approach for Studying Heterotopic Ossification： Proteomic Analysis of Clinical Serum and Tissue Samples

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Genomics, Proteomics & Bioinformatics 2018年第3期16卷 212-220页

作者： erin l. Crowgey Jennifer T. Wyffels Patrick M. Osborn thomas T. Wood laura e. edsberg Nemours Biomedical Research Nemours Alfred I. duPont Hospital for Children Wilmington DE 19803 USA Natural and He.lth Sciences Researeh Center Center for Wound Healing Research Daemen College Amherst NY 14226 USA Department of Computer and Information Sciences Center for Bioinformatics and Computational Biology University of Delaware Newark DE 19711 USA San Antonio Military Medical Center San Antonio TX 78219 USA

Heterotopic ossification （HO） refers to the abnormal formation of bone in soft tissue. Although some of the unde.lying processes of HO have been described, there are currently no clinical tests using validated biomarkers for predicting HO formation. As such, the diagnosis is made radiographically after HO has formed. To identify potential and novel biomarkers for HO, we used isobaric tags for relative and absolute quantitation （iTRAQ） and high-throughput antibody arrays to produce a semi-quantitative proteomics survey of serum and tissue from subjects with （HO ＋） and without （HO-） heterotopic ossification. The resulting data were then analyzed using a systems biology approach. We found that serum samples from subjects experiencing traumatic injuries with resulting HO have a different proteomic expression controls. Subsequent quantitative elISA identified profile compared to those from the matched five blood serum proteins that were differentially regulated between the HO-- and HO- groups. Compared to HO- samples, the amount of insulin-like growth factor I （IGF1） was up-regulated in HO＋ samples, whereas a lower amount of osteopontin （OPN）, myeloperoxidase （MPO）, runt-related transcription factor 2 （RUNX2）,and growth differentiation factor 2 or bone morphogenetic protein 9 （BMP-9） was found in HO ＋ samples （Welch two sample t-test; P 〈 0.05）. These proteins, in combination with potential serum biomarkers previously reported, are key candidates for a serum diagnostic panel that may enable early detection of HO prior to radiographic and clinical manifestations.

关键词： Heterotopic ossification Proteomics Runt-related transcriptionfactor 2 extrace.lular matrixorganization Keratinization

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Decreased bioavailability of aminomethylphosphonic acid(AMPA)in genetically modified corn with activated carbon or calcium montmorillonite clay inclusion in soil

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Journal of environmental Sciences 2021年第2期33卷 131-143页

作者： Sara e.Hearon Meichen Wang thomas J.McDonald Timothy D.Phillips Veterinary Integrative Biosciences Department College of Veterinary Medicine and Biomedical Sciences Texas A&M Uniuersity College StationTx 77845USA Department of environmental and Occupational He.lth School of Public He.lth Texas A&M UniversityCollege Station400 Bizzell St College StationTX 77843USA

The widespread use of pesticides has resulted in detectable residues throughout the environment,sometimes at concentrations we.l above regulatory ***,the development of safe,effective,field-practical,and economically feasible strategies to mitigate the effects of pesticides is *** is an organophosphorus herbicide that is degraded to aminomethylphosphonic acid(AMPA),a toxic and persistent metabolite that can accumulate in soil and sediment and translocate to *** this study,we investigated the binding efficacy of activated carbon(AC)and calcium montmorillonite(CM)clay to decrease AMPA bioavailability from soil and AMPA translocation to *** isotherms and thermodynamic studies on AC and CM were conducted and showed tight binding(enthalpy values>-20 k J/mol)for AMPA with high capacities(0.25 mol/kg and 0.38 mol/kg,respectively),based on derivations from the.langmuir model.A hydra assay was utilized to indicate toxicity of AMPA and the inclusion of 1%AC and CM both resulted in 90%protection of the hydra(**p≤0.01).Further studies in glyphosate-contaminated soil showed that AC and CM significantly reduced AMPA bioavailability by 53%and 44%,*** in genetically modified(GM)corn showed a conversion of glyphosate to AMPA in roots and sprouts over a 10-day exposure *** of AC and CM reduced AMPA residues in roots and sprouts by 47%-61%.These studies collectively indicate that AC and CM are effective sorbents for AMPA and could be used to reduce AMPA bioavailability from soil and AMPA residues in GM corn plants.

关键词： Glyphosate AMPA Activated carbon Calcium montmorillonite Sorbent

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Beyond the RPA and GW methods with adiabatic xc-kernels for accurate ground state and quasiparticle energies

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npj Computational Materials 2019年第1期5卷 202-224页

作者： thomas Olsen Christopher e.Patrick Jefferson e.Bates Adrienn Ruzsinszky Kristian S.Thygesen Computational Atomic-Scale Materials Design(CAMD) Department of PhysicsTechnical University of DenmarkKongens LyngbyDenmark Department of Physics University of WarwickCoventry CV47ALUK A.R.Smith Department of Chemistry and Fermentation Sciences Appalachian State UniversityBooneNC 28607USA Department of Physics Temple UniversityPhiladelphiaPA 19122USA Center for Nanostructured Graphene(CNG) Department of PhysicsTechnical University of DenmarkKongens LyngbyDenmark

We review the theory and application of adiabatic exchange–correlation(xc)-kernels for ab initio calculations of ground state energies and quasiparticle excitations within the frameworks of the adiabatic connection fluctuation dissipation theorem and Hedin’s equations,*** different xc-kernels,which are all rooted in the homogeneous electron gas,are introduced but hereafter we focus on the specific class of renormalized adiabatic kernels,in particular the rAlDA and *** kernels drastically improve the description of short-range correlations as compared to the random phase approximation(RPA),resulting in significantly better correlation *** effect greatly reduces the reliance on error cance.lations,which is essential in RPA,and systematically improves covalent bond energies while preserving the good performance of the RPA for dispersive *** quasiparticle energies,the xc-kernels account for vertex corrections that are missing in the GW *** this context,we show that the short-range correlations mainly correct the absolute band positions while the band gap is less affected in agreement with the known good performance of GW for the *** renormalized xc-kernels offer a rigorous extension of the RPA and GW methods with clear improvements in terms of accuracy at little extra computational cost.

关键词： adiabatic kernels quasi

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Femoral impaction grafting

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World Journal of Orthopedics 2013年第1期4卷 7-11页

作者： John A Scane.li thomas e Brown Department of Orthopedic Surgery University of Virginia School of Medicine Charlottesville VA 22908 United States

Femoral impaction grafting is a reconstruction option applicable to both simple and complex femoral component revisions. It is one of the preferred techniques for reconstructing large femoral defects when the isthmus is non-supportive. The available.level of evidence is primarily derived from case series, which shows a mean survivorship of 90.5%, with revision or re-operation as the end-point, with an average follow-up of 11 years. The rate of femoral fracture requiring re-operation or revision of the component varies between several large case series, ranging from 2.5% to 9%, with an average of 5.4%.

关键词： Femoral impaction grafting Femoral revision Bone grafting Revision total hip arthroplasty Bone loss

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Bipolar Membranes for Ion Management in(Photo)electrochemical energy Conversion

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Accounts of Materials Research 2021年第12期2卷 1156-1166页

作者： Zhifei Yan thomas e.Mallouk Department of Chemistry University of PennsylvaniaPhiladelphiaPennsylvania 19104United States Department of Chemistry and Chemical Biology Harvard UniversityCambridgeMA 02138United States

CONSPeCTUS:(Photo)electrochemical energy conversion is important in the development of a carbon-neutral energy economy because it can provide a pathway for mitigating the intermittency of renewable energy sources such as wind and *** order to operate efficiently,these technologies,which include photoelectrochemical ce.ls,water and CO_(2) electrolyzers,fuel ce.ls,and redox flow batteries,require fast charge transfer kinetics at the electrode/electrolyte interface as we.l as robust ion management in the *** conventional electrolyzers and fuel ce.ls,the electrolyte is strongly acidic or basic and ionic current is carried by H^(+)or OH^(−)*** contrast,photoelectrodes and electrocatalysts for water splitting are often studied in buffered *** question of ion balance in these systems led us to analyze the polarization losses due to ion concentration gradients in ce.ls that employed various buffer−membrane *** driving the buffer ions across an ionomer membrane not only lowers the buffer capacity of an aqueous electrolyte but also introduces pH gradients that result in significant energy losses.

关键词： electrolyte driving kinetics

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Morphology-dependent space charge polarization and dielectric relaxation of CdO nanomorphotypes

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Journal of Advanced Dielectrics 2016年第4期6卷 37-44页

作者： Paulose thomas K.e.Abraham Department of Physics St.Berchmans College Changanassery686101KeralaIndia

A versatile approach signifying the morphology-dependent dielectric polarization and relaxation mechanisms of cadmium oxide(CdO)nanosphere,nanoflakes and nanoparallelepiped morphotypes as a function of frequency and temperature is *** of dielectric property is observed due to the changes of space charge/interfacial polarization resulting from the variations of surface to volume ratio of ***,colossal dielectric constant value has been observed in CdO nano-sphere having larger surface to volume *** order of dielectric constant(dc)values observed for the present nanomorphologies is:dc of sphere>dc of flakes>dc of parallelepiped resembles the order of surface to volume ratios of the present morphologies *** experimental data of complex impedance values are numerically fitted using theoretical models which provide the information of role of grain resistance on dielectric polarization and Cole–Cole type mechanism of dielectric relaxation *** activation energies for electron transport are found to be 0.087 eV for spheres,0.074 eV for flakes and 0.067 for parallelepiped nanomorphotypes of *** dielectric and impedance spectroscopic analysis of the present material opens up wide scope for morphology-dependent tuning of nanomaterials for electrical applications.

关键词： CdO nanomorphotype space charge polarization impedance spectroscopy Cole-Cole dielectric relaxation.

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Preliminary evaluation of a decision support tool for biochar amendment

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Biochar 2020年第1期2卷 93-105页

作者： Claire.l.Phillips Sarah e.light Adam lindsley thomas A.Wanzek Kylie M.Meyer Kristin M.Trippe USDA-ARS Forage Seed and Cere.l Research Unit 3450 SW Campus WayCorvallisOR 97331USA University of California Cooperative extension 142A Garden HighwayYuba CityCA 95991USA Department of Crop and Soil Science Oregon State UniversityCorvallisOR 97331USA

Meta-analyses have shown that only about half of biochar addition studies report improved plant *** improve yield response,here we describe a decision support tool(DST)for selecting a biochar type and amendment rate to meet soil and crop management goals,based on soil and biochar tests values and crop requirements as reported by regional extension *** data from a greenhouse wheat trial,we assessed whether this approach could predict changes in soil chemistry and whether it could identify soils in which amendment would stimulate crop *** data indicated that the DST could provide semi-quantitative predictions of biochar amendment rates needed to meet target soil pH levels,with recommended rates averaging 25%higher than were *** DST was better at predicting biochar application rates to provision P and *** six soil types,post-harvest measurements of extractable-K showed an average 104%recovery of the quantities estimated to be provisioned by conifer wood or wheat straw ***-P recovery averaged 101%in two sandy soils with low P-retention but was considerably lower in four soils with higher P-retention ***-house data also showed that wheat growth improved only when biochar alleviated pH that was substantially below critical thresholds for plant growth,and supported the principle of using crop-specific pH requirements as part of an approach for biochar *** field trials that evaluate yield responses in several nutrient-deficient or acidified soils will be needed to provide a robust evaluation of this DST.

关键词： Wheat liming Phosphorous Potassium Yield response

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Glow in the Dark： Fluorescent Proteins as Ce.l and Tissue-Specific Markers in Plants

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Molecular Plant 2011年第5期4卷 794-804页

作者： Wenzislava Ckurshumova Adriana e. Caragea Roche.le S. Goldstein thomas Be.leth Department of Ce.l and Systems Biology University of Toronto 25 Willcocks St Toronto ON MSS 3B2 Canada

Since the hallmark discovery of Aequorea victoria＇s Green Fluorescent Protein （GFP） and its adaptation for efficient use in plants, fluorescent protein tags marking expression profiles or genuine proteins of interest have been used to recognize plant tissues and ce.l types, to monitor dynamic ce.l fate selection processes, and to obtain ce.l type-specific transcriptomes. Fluorescent tagging enabled visualization in living tissues and the precise recordings of dy- namic expression pattern changes. The resulting accurate recording of ce.l fate acquisition kinetics in space and time has strongly stimulated mathematical modeling of self-organizing feedback mechanisms. In developmental studies, the use of fluorescent proteins has become critical, where morphological markers of tissues, ce.l types, or differentiation stages are either not known or not easily recognizable. In this review, we focus on the use of fluorescent markers to identify and illuminate otherwise invisible ce.l states in plant development.

关键词： Arabidopsis auxin transport enhancer trap FACS fluorescent proteins GFP gene expression markers live imaging mathematical modeling meristem vascular development.

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Development of German-Ukrainian cooperations for education and research in photogrammetry and laser scanning

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Geo-Spatial Information Science 2021年第1期24卷 152-159,I0016页

作者： thomas luhmann Institute for Applied Sciences and Geoinformatics Jade University of Applied Sciences OldenburgOldenburgGermany

Since 2011 an intensive international cooperation has been in place between the Institute for Applied Photogrammetry and Geoinformatics(IAPG)at the Jade University of Applied Sciences in Oldenburg,Germany,and various Ukrainian *** an initial contact by *** Konecny,the first visit was organized,and was followed by many *** subsequent years an intensive cooperation was established particularly with the National University for Construction and Architecture(KNUCA)in *** addition to architects and civil engineers,KNUCA also trains geodesists,geo-information scientists and landscape *** cooperation today includes the reciprocal exchange of scientists and students,research projects,courses and cooperation at many other *** addition,a commercial company has been established,SPM3D llC,which now employs more than 14 engineers in the field of 3D acquisition,point cloud processing and *** article summarizes the history of the cooperation and presents the results of associated student *** addition,results of joint work on the development of a virtual laser scanner are presented,part of a German-Ukrainian initiative to digitize teaching.

关键词： Internationalization technology transfer curricula reform photogrammetry laser scanning e.learning

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primiReference: a reference for analysis of primary-microRNA expression in single-nucleus sequencing data

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Journal of Genetics and Genomics 2023年第2期50卷 108-121页

作者： Amy e.elias thomas A.Nuñez Bianca Kun Jill A.Kre.ling Roche WilmingtonMA 01887USA. Department of Molecular Biology Cell Biology and BiochemistryBrown UniversityProvidenceRI02903USA Public He.lth Genetics University of PittsburghPittsburghPA 15260USA

Single-nucleus RNA-sequencing technology has revolutionized understanding of nuanced changes in gene expression between ce.l types within ***,our understanding of regulatory RNAs,such as microRNAs(miRNAs),is limited through both single-ce.l and single-nucleus techniques due to the short length of miRNAs in the cytoplasm and the incomplete reference of longer primary miRNA(pri-miRNA)transcripts in the *** build a custom reference to align and count pri-miRNA sequences in singlenucleus *** young and aged subventricular zone(SVZ)nuclei,we show differential expression of pri-miRNAs targeting genes involved in neural stem ce.ls(NSC)differentiation in the aged ***,using wild-type and 5XFAD mouse model cortex nuclei,to validate the use of primiReference,we find ce.l-type-specific expression of pri-miRNAs known to be involved in Alzheimer’s disease(AD).pri-miRNAs likely contribute to NSC dysregulation with age and AD *** is paramount in capturing a global profile of gene expression and regulation in single-nucleus data and can provide key insights into ce.l-type-specific expression of pri-miRNAs,paving the way for future studies of regulation and pathway *** looking at pri-miRNA abundance and transcriptional differences,regulation of gene expression by miRNAs in disease and aging can be further explored.

关键词： Primary-microRNA Aging Subventricular zone Alzheimer’s disease Single-nucleus RNA-Seq microRNA Transcriptomics

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