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Impact of preoperative antibiotics and other variables on integrated microbiome-host transcriptomic data generated from colorectal cancer resections

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World Journal of Gastroenterology 2021年第14期27卷 1465-1482页

作者： Sarah A Malik Chencan Zhu Jinyu Li joseph f lacomb Paula I Denoya Igor Kravets Joshua D Miller Jie Yang Melissa Kramer W Richard McCombie Charles E Robertson Daniel N frank Ellen Li Department of Medicine Renaissance School of MedicineStony Brook UniversityStony BrookNY 11794United States Department of Applied Mathematics and Statistics Stony Brook UniversityStony BrookNY 11794United States Stony Brook Cancer Center Biostatistics and Bioinformatics Shared Resource Stony Brook UniversityStony BrookNY 11794United States Department of Pathology Renaissance School of MedicineStony Brook UniversityStony BrookNY 11794United States Department of Surgery Renaissance School of MedicineStony Brook UniversityStony BrookNY 11794United States Department of family Population and Preventive MedicineStony Brook UniversityStony BrookNY 11794United States Cold Spring Harbor Laboratory Cancer Center Sequencing Technologies and Analysis Shared Resource Cold Spring HarborNY 11724United States Department of Medicine University of Colorado Anschutz Medical CampusAuroraCO 80045United States

BACKGROUND Integrative multi-omic approaches have been increasingly applied to discovery and functional studies of complex human ***-term preoperative antibiotics have been adopted to reduce site infections in colorectal cancer(CRC)*** hypothesize that the antibiotics will impact analysis of multi-omic datasets generated from resection samples to investigate biological CRC risk *** To assess the impact of preoperative antibiotics and other variables on integrated microbiome and human transcriptomic data generated from archived CRC resection *** Genomic DNA(gDNA)and RNA were extracted from prospectively collected 51 pairs of frozen sporadic CRC tumor and adjacent non-tumor mucosal samples from 50 CRC patients archived at a single medical center from *** 16S rRNA gene sequencing(V3V4 region,paired end,300 bp)and confirmatory quantitative polymerase chain reaction(qPCR)assays were conducted on *** sequencing(IPE,125 bp)was performed on parallel tumor and non-tumor RNA samples with RNA Integrity Numbers scores≥*** PERMANOVA detected significant effects of tumor vs nontumor histology(P=0.002)and antibiotics(P=0.001)on microbialβ-diversity,but CRC tumor location(left vs right),diabetes mellitus vs not diabetic and Black/African Ancestry(AA)vs not Black/AA,did not reach *** mixed models detected significant tumor vs nontumor histology*antibiotics interaction terms for 14 genus level *** confirmed increased fusobacterium abundance in tumor vs nontumor groups,and detected significantly reduced bacterial load in the(+)antibiotics *** coordinate analysis of the transcriptomic data showed a clear separation between tumor and nontumor *** expressed genes obtained from separate analyses of tumor and nontumor samples,are presented for the antibiotics,CRC location,diabetes and Black/AA race *** Recent adoption of additional preoperative antibiotics as sta

关键词： Colorectal cancer Antibiotics African Continental Ancestry Group Diabetes mellitus 16S rRNA gene RNA-sequencing

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Merging bound states in the continuum in an open acoustic resonator

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Science China(Physics,Mechanics & Astronomy) 2025年第1期Mechanics & Astronomy) .卷 124-131页

作者： Lujun Huang Bin Jia Artem S.Pilipchuk Sibo Huang Chen Shen Almas f.Sadreev Yong Li Andrey E.Miroshnichenko School of Physics and Electronic Sciences East China Normal University Institute of Acoustics Tongji University L.V.Kirensky Institute of Physics Department of Mechanical Engineering Rowan University School of Engineering and Technology University of New South Wales at Canberra

Bound states in the continuum （BICs） are perfectly localized resonances despite embedding in the continuum ***,an isolated BIC is very sensitive to the structure ***,we report merging acoustic BICs in a single open resonator,robust against the structure *** find that both symmetry-protected BIC and friedrich-Wintgen BIC are sustained in a single coupled waveguide-resonator *** varying the height and length of the resonator,these two BICs move toward each other and merge into a single one at a critical *** to an individual BIC,the merged BIC is robust against fabrication error because its Q-factor is proportional to ΔL-4,whereΔL embodies the structure *** essence of this extraordinary phenomenon is perfectly explained by the two-and three-level approximations of the effective nonHermitian ***,we present direct experimental demonstrations of the moving and merging of BICs in a coupled 3D waveguide-resonator,which are evidenced by the vanishing of the linewidth of fano resonance in the transmission *** results may find exciting applications in designing high-quality acoustic sources,sensors and filters.

关键词： acoustic resonances bound state in the continuum high-Q resonances

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Recovery of rare and precious metals from urban mines —— A review

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frontiers of Environmental Science & Engineering 2017年第5期11卷 3-19页

作者： Mengmeng Wang Quanyin Tan joseph f. Chiang Jinhui Li Key Laboratory for Solid Waste Management and Environment Safety (Tsinghua University) Ministry of Education of China School of Environment Tsinghua University Beijing 100084 China Department of Chemistry and Biochemistry State University of New York College at Oneonta Oneonta NY 13820 USA

Urban mining is essential for continued natural resource extraction. The recovery of rare and precious metals （RPMs） from urban mines has attracted increasing attention from both academic and industrial sectors, because of the broad application and high price of RPMs, and their low content in natural ores. This study summarizes the distribution characteristics of various RPMs in urban mines, and the advantages and shortcomings of various technologies for RPM recovery from urban mines, including both conventional （pyrometallurgical, hydrometallurgical, and biometallurgical processing）, and emerging （electrochemical, supereritieal fluid, mechanochemical, and ionic liquids processing） technologies. Mechanical/physical technologies are commonly employed to separate RPMs from nonmetallic components in a pre-treatment process. A pyrometallurgical process is often used tbr RPM recovery, although the expensive equipment required has limited its use in small and medium-sized enterprises. Hydrometallurgical processing is effective and easy to operate, with high selectivity of target metals and high recovery efficiency of RPMs, compared to pyrometallurgy. Biometallurgy, though, has shown the most promise for leaching RPMs from urban mines, because of its low cost and environmental friendliness. Newly developed technologies electrochemical, supercritical fluid, ionic liquid, and mechanochemical have offered new choices and achieved some success in laboratory experiments, especially as efficient and environmentally friendly methods of recycling RPMs. With continuing advances in science and technology, more technologies will no doubt be developed in this field, and be able to contribute to the sustainability of RPM mining.

关键词： Rare and precious metals (RPMs) Distribution characteristics Recycling technology Emerging technology Supercritical fluid

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Compost Input Effect on Dryland Wheat and forage Yields and Soil Quality

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Pedosphere 2018年第3期28卷 451-462页

作者： francisco J. CALDERON Merle f. VIGIL joseph BENJAMIN United States Department of Agriculture-Agricultural Research Service (USDA-ARS) Central Great Plains Research Station Akron80720 CO( USA)

Organic agricultural systems rely on organic amendments to achieve crop fertility requirements, and weed control must be achieved without synthetic herbicides. Our objective was to determine the crop yield and soil quality as affected by a transition from grass to dryland organic agriculture in the Central Great Plains of North America. This study evaluated three beef feedlot compost(BfC)treatments in 2010–2015 following biennial application rates: 0(control), 22.9, and 108.7 t ha^(-1) on two dryland organic cropping systems: a wheat(Triticum aestivum)-fallow(Wf) rotation harvested for grain and a triticale(Triticosecale)/pea(Pisum sativum)-fallow(T/P-f) rotation harvested for forage. The triticale + pea biomass responded positively to the 108.7-t ha^(-1) BfC treatment,but not the 22.9-t ha^(-1) BfC treatment. The wheat biomass was not affected by BfC addition, but biomass N content *** feedlot compost input did not increase wheat grain yields, but had a positive effect on wheat grain Zn content. Soil total C and N contents increased with the rate of 108.7 t ha^(-1) BfC after three applications, but not with 22.9 t ha^(-1) BfC. Soil enzyme activities associated with N and C cycling responded positively to the 108.7-t ha^(-1) BfC treatment. Saturated salts were high in the soil receiving 108.7 t ha^(-1) of BfC, but did not affect crop yields. These results showed that BfC was effective in enhancing forage yields, wheat grain quality, and soil C and N, as well as specific microbial enzymes important for nutrient cycling. However, the large rates of BfC necessary to elicit these positive responses did not increase grain yields, and resulted in an excessive buildup of soil P.

关键词： organic agriculture soil C soil enzyme activity soil N pea triticale

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Towards real-time pilot-in-the-loop CfD simulations of helicopter/ship dynamic interface

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International Journal of Modeling, Simulation, and Scientific Computing 2017年第4期8卷 64-88页

作者： Ilker Oruc joseph f.Horn Jeremy Shipman Susan Polsky Department of Aerospace Engineering The Pennsylvania State University University Park PA 16802USA CRAfT Tech PipersvillePA 18947USA NAVAIR Paxutent RiverMD 20670USA

This study presents the development of computationally efficient coupling of Navier–Stokes Computational fluid Dynamics(CfD)with a helicopter flight dynamics model with the ultimate goal of real-time simulation of airwake effects in the helicopter/ship Dynamic Interface(DI).The flight dynamics model is free to move within a computational domain,where the main rotor forces are converted to source terms in the momentum equations of the CfD solution using an actuator disk ***,the CfD solver calculates induced velocities that are fed back to the simulation and affect the aerodynamic loads in the flight *** CfD solver models the inflow,ground effect and interactional aerodynamics in the flight dynamics simulation,and these calculations can be coupled with the solution of the external flow(e.g.,ship airwake effects).The simulation framework for fully-coupled pilot-in-the-loop(PIL)flight dynamics/CfD is demonstrated for a simplified shedding *** tests were performed with 0.38 million structured grid cells running on 352 processors and showed near-real-time *** to the coupling interface are described that allow the simulation run at near-real-time execution speeds on currently available computing *** in computing hardware are expected to allow real-time simulations.

关键词： Real-time pilot-in-the-loop computational fluid dynamics(CfD) flight dynamics simulation ship airwake dynamic interface helicopter flight dynamics simulation fully-coupled helicopter/ship

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Comparisons of oxbow lake fish assemblages in relation to bigheaded carp establishment in the lower White River, Arkansas

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Ecological Processes 2024年第1期13卷 188-205页

作者： Michael A.Eggleton Cody J.Salzmann joseph E.Kaiser Shannon C.f.Smith Department of Aquaculture and fisheries University of Arkansas at Pine Bluff Arkansas Game and fish Commission Virginia Institute of Marine Science

Background Since the late 1990s, bigheaded carps(largely silver carp [Hypophthalmichthys molitrix] but also bighead carp [H. nobilis]) have established throughout the lower Mississippi River basin. Using previously studied oxbow lakes in the lower White River basin, Arkansas, we compared current(2017, “post-carp” establishment) fish assemblages to historical(2002, “pre-carp” establishment) fish assemblages. fish assemblages were comprehensively assessed using multiple gears, including boat electrofishing, mini-fyke nets, and experimental small-mesh gill *** T-tests suggested that fish assemblage indices of richness, diversity, evenness, and dominance were often greater(P flected by boat electrofishing and experimental gill nets. However, all indices were generally similar(P > 0.05) between the pre-carp and post-carp period with fish assemblages depicted using mini-fyke nets. Nonmetric multidimensional scaling analyses indicated that fish assemblages differed structurally between pre-carp and post-carp periods. Assemblage differences were linked to both small and large abundance changes for more than 20 species. Abundances of gizzard shad(Dorosoma cepedianum), emerald shiner(Notropis atherinoides), pugnose minnow(Opsopoeodus emiliae), crappies(Pomoxis spp.), bluegill(Lepomis macrochirus), orangespotted sunfish(L. humilis), and yellow bass(Morone mississippiensis) declined between the pre-carp and postcarp periods. Conversely, abundances of weed shiner(N. texanus), pallid shiner(Hybopsis amnis), longear sunfish(L. megalotis), buffalofishes(Ictiobus spp.), and gars(Lepisosteus spp.) generally increased during the same *** Although not possible to conclude assemblage shifts were entirely related to bigheaded carps due to the absence of an appropriate reference system where carps did not establish, the wide establishment of these carps is one of the most pervasive changes to have occurred in the lower White

关键词： Bigheaded carp Silver carp Aquatic nuisance species fish assemblage Oxbow lake Large river

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Influence of surface modified mixed metal oxide nanoparticles on the electrochemical and mechanical properties of polyurethane matrix

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frontiers of Chemical Science and Engineering 2023年第1期17卷 1-14页

作者： joseph Raj Xavier Department of Chemistry Saveetha School of EngineeringSaveetha Institute of Medical and Technical SciencesChennai-602105India

Newly synthesized functional nanoparticles,3-amino-1,2,4-triazole(ATA)/SiO_(2)—TiO_(2)were introduced to the polyurethane(PU)*** techniques were used to investigate the barrier properties of the synthesized PU—ATA/SiO_(2)—TiO_(2)nanocomposite coated steel *** natural seawater,electrochemical impedance spectroscopy experiments indicated outstanding protective behaviour for the PU—ATA/SiO_(2)—TiO_(2)coated *** coating resistance(Rcoat)of PU—ATA/SiO_(2)—TiO_(2)was determined to be 2956.90 kΩ·cm^(−2).The Rcoat of the PU—ATA/SiO_(2)—TiO_(2)nanocomposite coating was found to be over 50%higher than the PU *** current measured along the scratched surface of the PU—ATA/SiO_(2)—TiO_(2)coating was found to be very low(1.65 nA).The enhanced ATA/SiO_(2)—TiO_(2)nanoparticles inhibited the entry of electrolytes into the coating interface,as revealed by scanning electron microscopy/energy dispersive X-ray spectroscopy and X-ray diffraction analysis of the degradation *** contact angle testing validated the hydrophobic nature of the PU—ATA/SiO_(2)—TiO_(2)coating(θ=115.4°).When the concentration of ATA/SiO_(2)—TiO_(2)nanoparticles was 2 wt%,dynamic mechanical analysis revealed better mechanical ***,the newly synthesised PU—ATA/SiO_(2)—TiO_(2)nanocomposite provided excellent barrier and mechanical properties due to the addition of ATA/SiO_(2)—TiO_(2)nanoparticles to the polyurethane,which inhibited material degradation and aided in the prolongation of the coated steel’s life.

关键词： SiO_(2)/TiO_(2)nanoparticle nanocomposite coatings dynamic mechanical analysis electrochemical techniques corrosion colloids and interfaces

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On Two Classes of finite Inseparable p-Groups

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Acta Mathematica Sinica,English Series 2015年第7期31卷 1203-1214页

作者： joseph KIRTL Department of Mathematics Marist College

A finite group is inseparable, it does not split over any proper nontrivial normal subgroup; that is, if it has no nontrivial semidirect product decompositions. This paper investigates two classes of finite inseparabl... 详细信息

关键词： p-group inseparable splitting

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Mitotic phosphorylation of PRC1 at Thr470 is required for PRC1 oligomerization and proper central spindle organization

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Cell Research 2007年第5期17卷 449-457页

作者： joseph Whittaker Department of Anatomy & Neurobiology Morehouse School of Medicine Atlanta GA 30310 USA

During cell division, chromosome segregation is orchestrated by the interaction of spindle microtubules with thecentromere. A dramatic remodeling of interpolar microtubules into an organized central spindle between the separatingchromatids is required for the initiation and execution of cytokinesis. Central spindle organization requires mitotic kine-sins, the chromosomal passenger protein complex, and microtubule bundling protein PRC1. PRC1 is phosphorylated byCdc2 at Thr470 and Thr481 during mitosis. However, the functional relevance of PRC1 phosphorylation at Thr470 hasremained elusive. Here we show that expression of the non-phosphorylatable mutant PRC1but not the phospho-mimi-cking mutant PRC1causes aberrant organization of the central spindle. Immunoprecipitation experiment indicatesthat both PRC1and PRC1mutant proteins associate with wild-type PRC1, suggesting that phosphorylationof Thr470 does not alter PRC1 self-association. In addition, in vitro co-sedimentation experiment showed that PRC1binds to microtubule independent of the phosphorylation state of Thr470. Gel-filtration experiment suggested that phos-phorylation of Thr470 promotes oligomerization of PRC1. Given the fact that prevention of the Thr470 phosphorylationinhibits PRC1 oligomerization in vitro and causes an aberrant organization of central spindle in vivo, we propose thatthis phosphorylation-dependent PRC1 oligomerization ensures that central spindle assembly occurs at the appropriatetime in the cell cycle.

关键词： central spindle microtubule oligomerization PRC1 phosphorylation

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Toll-like receptor signaling in hematopoietic homeostasis and the pathogenesis of hematologic diseases

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frontiers of Medicine 2015年第3期9卷 288-303页

作者： joseph Cannova Biochemistry and Molecular Biology Program Loyola University Chicago Maywood IL 60153 USA Stritch School of Medicine Loyo& University Chicago Maywood IL 60153 USA Oncology Institute Loyola University Chicago Maywood IL 60153 USA Department of Pathology Loyola University Chicago Maywood IL 60153 USA Department of Biology Loyola University Chicago Chicago IL 60660 USA Department of Molecular and Cellular Physiology Loyola University Chicago Maywood IL 60153 USA

Toll-like receptors （TLRs）, which are found in innate immune cells, are essential mediators of rapid inflammatory responses and appropriate T-cell activation in response to infection and tissue damage. Accumulating evidence suggests that TLR signaling is involved in normal hematopoiesis and specific hematologic pathologies. Particular TLRs and their downstream signaling mediators are expressed not only in terminally differentiated innate immune cells but also in early hematopoietic progenitors. Sterile activation of TLR signaling is required to generate early embryonic hematopoietic progenitor cells. In adult animals, TLR signaling directly or indirectly promotes differentiation of myeloid cells at the expense of that of lymphoid cells and the self renewal of hematopoietic stem cells during infection and tissue damage. Activating mutations of the MyD88 gene, which codes for a key adaptor involved in TLR signaling, are commonly detected in B-cell lymphomas and other B-cell hematopathologies. Dysregulated TLR signaling contributes to the pathogenesis of many hematopoietic disorders, including bone marrow failure, myelodysplastic syndrome, and acute myeloid leukemia. Complete elucidation of the molecular mechanisms by which TLR signaling mediates the regulation of both normal and pathogenic hematopoiesis will prove valuable to the development of targeted therapies and strategies for improved treatment of hematopoietic disorders.

关键词： TLR MyD88 hematopoiesis bone marrow failure leukemia myelodysplastic syndrome

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