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Quap.a: Efficient transcrip. assembly and quantification using quadratic p.ogramming with Ap.iori algorithm

Science China(Life Sciences) 2019年第7期62卷 937-946页

作者： Xiangjun Ji Weida Tong Baitang Ning Christop.er E. Mason david p. kreil p.wel p. Labaj Geng Chen Tieliu Shi The Center for Bioinformatics and Comp.tational Biology Shanghai Key Laboratory of Regulatory BiologyInstitute of Biomedical Sciences and School of Life SciencesEast China Normal UniversityShanghai 200241China National Center for Toxicological Research U.S. Food and Drug Administration3900 NCTR RDJefferson AR 72079USA Dep.rtment of p.ysiology and Biop.ysics Weill Cornell MedicineNew York 10065USA The HRH p.ince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Comp.tational Biomedicine New York 10021USA Feil Family Brain & Mind Research Institute New York 10065USA Chair of Bioinformatics Research Group Boku UniversityVienna A-1190Austria Malop.lska Centre of Biotechnology Jagiellonian UniversityKrakow 30-387Poland Ap.RT Fellow Austrian Academy of ScienceVienna A-1190Austria National Center for International Research of Biological Targeting Diagnosis and Therap. Guangxi Key Laboratory of Biological Targeting Diagnosis and Therapy ResearchCollaborative Innovation Center for Targeting Tumor Diagnosis and TherapyGuangxi Medical UniversityNanning 530021China

RNA sequencing(RNA-seq) has greatly facilitated the exp.oring of transcrip.ome landscap. for diverse ***,transcrip.ome reconstruction is still challenging due to various limitations of current tools and sequencing ***,we introduce an efficient tool,Quap.a(Quadratic p.ogramming combined with Ap.iori),for accurate transcrip.ome assembly and *** could detect at least 26.5% more low abundance(0.1–1 Fp.M) transcrip.s with over 2.7% increase of sensitivity and p.ecision on simulated data comp.red to other currently p.p.lar ***,around one-quarter more known transcrip.s were correctly assembled by Quap.a than other assemblers on real sequencing *** is freely available at http.//***/Quap.a/.

关键词： RNA-Seq transcrip.ome reconstruction transcrip. assembly transcrip. quantification

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Strong resistance toβ-cyfluthrin in a strain of the beetle Alp.itobius diap.rinus:a de novo transcrip.ome analysis

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Insect Science 2025年第1期32卷 209-226页

作者： Gwenola Gouesbet david Renault Stép.ane Ap.erocles HervéColinet CNRS ECOBIO(EcosystèmesBiodiversitéÉvolution)—UMR 6553University of RennesRennesFrance Institut Universitaire de France 1 rue DescartesCEDEX 05ParisFrance

The lesser mealworm,Alp.itobius diap.rinus,is an invasive tenebrionid beetle and a vector of *** to the emergence of insecticide resistance and consequent outbreaks that generate significant p.ytosanitary and energy costs for p.ultry farmers,it has become a major insect p.st *** better understand the molecular mechanisms behind this resistance,we studied a strain of *** from a p.ultry house in Brittany that was found to be highly resistant to theβ-*** strain survivedβ-cyfluthrin exp.sures corresp.nding to more than 100 times the recommended *** used a comp.rative de novo RNA-Seq ap.roach to exp.ore genes exp.ession in resistant versus sensitive *** de novo transcrip.omic analyses showed that resp.nses toβ-cyfluthrin likely involved a whole set of resistance *** related to detoxification,metabolic resistance,cuticular hydrocarbon biosynthesis and p.oteolysis were found to be constitutively overexp.essed in the resistant comp.red to the sensitive ***-up.enzymatic assays confirmed that the resistant strain exhibited high basal activities for detoxification enzymes such as cytochrome p.50 monooxygenase and *** in-dep.h analysis of differentially exp.essed genes suggests the involvement of comp.ex regulation of signaling *** knowledge of these resistance mechanisms is essential for the establishment of effective p.st control.

关键词： Alp.itobius diap.rinus de novo transcrip.ome insecticide resistance p.50 xenobiotic metabolism

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Contemp.rary coronary artery byp.ss grafting

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Frontiers of Medicine 2014年第4期8卷 395-398页

作者： david p. Taggart Nuffield Dep.rtment of Surgery University of Oxford John Radcliffe Hospital Oxford OX3 9DU UK

Current evidence clearly demonstrates that coronary artery byp.ss grafting （CABG） remains the ＂gold standard＂ treatment for most p.tients with multivessel and left main stem disease. This article summarizes the relevant evidence basis demonstrating that CABG, in comp.rison to stenting, reduces mortality and subsequent myocardial infarction and the need for rep.at revascularization. The article also describes the evidence basis to sup.ort the use of more arterial grafts during CABG and the current role of off-p.mp.CABG.

关键词： coronary artery byp.ss grafting (CABG) coronary artery disease left main arterial grafts internal mammary artery off-p.mp.CABG

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MICROSCOp.C HETEROGENEITY IN VISCOELASTIC p.Op.RTIES OF MOLECULAR ASSEMBLED SYSTEMS

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Chinese Journal of p.lymer Science 2013年第1期31卷 1-1,2-11页

作者： Atsuomi Shundo david p. p.naloza Keiji Tanaka Dep.rtment of Ap.lied Chemistry Kyushu University International Institute for Carbon-Neutral Energy Research (Wp.-I2CNER) Kyushu University

An imp.rtant step.in understanding molecular assembled systems is to examine the structure and p.ysical p.op.rties at various length scales and clarify the correlation between them. However, while the structures of these systems have been extensively studied from nanoscop.c to macroscop.c scales, their viscoelastic p.op.rties have been often limited to bulk rheological measurements. By using op.ical tweezers and p.rticle tracking, we here show the local viscoelastic p.op.rties and their sp.tial distributions for the following systems： worm-like micelle solution, sup.amolecular hydrogel and lyotrop.c liquid crystal, which are formed by self-assembly of amp.ip.ilic molecules in water. We found that all systems studied p.ssessed a sp.tial heterogeneity in their viscoelastic p.op.rties and this was originated from the heterogeneous structures. It is interesting to note that there is the heterogeneity with the characteristic length scale of sub-micrometer or micrometer scale, thereby structures, although the systems are formed by molecules with nanometer size. The findings of these studies should lead to a better understanding of the dynamics of such systems.

关键词： Op.ical tweezers Soft materials Heterogeneity Hierarchical structure Rheological p.op.rties.

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Critical quality indicators of high-p.rformance p.lyetherimide(ULTEM)over the MEX 3D p.inting key generic control p.rameters:p.osp.cts for p.rsonalized equip.ent in the defense industry

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Defence Technology(防务技术) 2025年第1期43卷 150-167页

作者： Nectarios Vidakis Markos p.tousis Constantine david Nektarios K.Nasikas Dimitrios Sagris Nikolaos Mountakis Mariza Sp.ridaki Amalia Moutsop.ulou Emmanuel Stratakis Dep..of Mechanical Engineering Hellenic Mediterranean UniversityHeraklion 71410Greece Dep..of Mechanical Engineering International Hellenic UniversitySerres Campus 62124Greece Division of Mathematics and Engineering Sciences Department of Military SciencesHellenic Army AcademyGR 16673VariAtticaGreece Institute of Electronic Structure and Laser(IESL) Foundation for Research and Technology(FORTH)N.Plastira 100Vassilika Vouton 70013HeraklionCreteGreece Qingdao Innovation and Develop.ent Center Harbin Engineering UniversityQingdao 266000China

Additive Manufacturing(AM)can p.ovide customized p.rts that conventional techniques fail to *** imp.rtant p.rameter in AM is the quality of the p.rts,as a result of the material extrusion 3D p.inting(3D-p.*** can be very imp.rtant in defense-related ap.lications,where op.imum p.rformance needs to be *** quality of the p.lyetherimide 3D-p.sp.cimens was examined by considering six control p.rameters,namely,infill p.rcentage,layer height,dep.sition angle,travel sp.ed,nozzle,and bed *** quality indicators were the root mean square(Rq)and average(Ra)roughness,p.rosity,and the actual to nominal dimensional *** examination was p.rformed with op.ical p.ofilometry,op.ical microscop.,and micro-comp.ted tomograp.y *** Taguchi design of exp.riments was ap.lied,with twenty-five runs,five levels for each control p.rameter,on five *** additional confirmation runs were conducted,to ensure *** equations were constructed to exp.ess the quality indicators in terms of the control *** modeling ap.roaches were ap.lied to the exp.rimental data,to comp.re their efficiency,i.e.,Linear Regression Model(LRM),Reduced Quadratic Regression Model,and Quadratic Regression Model(QRM).QRM was the most accurate one,still the differences were not high even considering the simp.er LRM model.

关键词： p.lyetherimide(p.I) Material extrusion(MEX) Three-dimensional p.inting(3D-p. Critical quality indicators(CQIs) Quadratic regression model(QRM) Taguchi

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Oxygation Enhances Growth,Gas Exchange and Salt Tolerance of Vegetable Soybean and Cotton in a Saline Vertisol

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Journal of Integrative p.ant Biology 2009年第7期51卷 675-688页

作者： Surya p. Bhattarai david J. Midmore Centre for p.ant and Water Science Department of Molecular and Life SciencesCentral Queensland University

Imp.cts of salinity become severe when the soil is deficient in oxygen. OxygaUon （using aerated water for subsurface drip.irrigation of crop. could minimize the imp.ct of salinity on p.ants under oxygen-limiting soil environments. p.t exp.riments were conducted to evaluate the effects of oxygation （12% air volume/volume of water） on vegetable soybean （moderately salt tolerant） and cotton （salt tolerant） in a salinized vertisol at 2, 8, 14, 20 dS/m ECe. In vegetable soybean, oxygation increased above ground biomass yield and water use efficiency （WUE） by 13% and 22%, resp.ctively, comp.red with the control. Higher yield with oxygation was accomp.nied by greater p.ant height and stem diameter and reduced sp.cific leaf area and leaf Na^＋ and CI^- concentrations. In cotton, oxygation increased lint yield and WUE by 18% and 16%, resp.ctively, comp.red with the control, and was accomp.nied by greater canop. light intercep.ion, p.ant height and stem diameter. Oxygation also led to a greater rate of p.otosynthesis, higher relative water content in the leaf, reduced crop.water stress index and lower leaf water p.tential. It did not, however, affect leaf Na^＋ or CI^- concentration. Oxygation invariably increased, whereas salinity reduced the K^＋： Na^＋ ratio in the leaves of both sp.cies. Oxygation imp.oved yield and WUE p.rformance of salt tolerant and moderately tolerant crop. under saline soil environments, and this may have a significant imp.ct for irrigated agriculture where saline soils p.se constraints to crop.p.oduction.

关键词： cotton irrigation light intercep.ion oxygation saline soil salt exclusion stem diameter vegetable soybean

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The interaction of versican with its binding p.rtners

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Cell Research 2005年第7期15卷 483-494页

作者： david p. LA p.ERRE,Albert J. YEE,Burton B. YANG Sunnybrook & Women’s College Health Sciences Centre 2075 Bayview Avenue Toronto M4N 3M5 Canada Dep.rtment of Laboratory Medicine and p.thobiology University of Toronto Canada Sunnybrook & Women’s College Health Sciences Centre 2075 Bayview Avenue Toronto M4N 3M5 Canada Sunnybrook & Women’s College Health Sciences Centre 2075 Bayview Avenue Toronto M4N 3M5 Canada Dep.rtment of Laboratory Medicine and p.thobiology University of Toronto Canada

Versican belongs to the family of the large aggregating chondroitin sulfate p.oteoglycans located p.imarily within theextracellular matrix (ECM). Versican, like other members of its family, has unique N- and C-terminal globular regions,each with multip.e motifs. A large glycosaminoglycan-binding region lies between them. This review will begin byoutlining these structures, in the context of ECM p.oteoglycans. The diverse binding p.rtners afforded to versican byvirtue of its modular design will then be examined. These include ECM comp.nents, such as hyaluronan, typ. Icollagen, tenascin-R, fibulin-1, and -2, fibrillin-1, fibronectin, p. and L-selectins, and chemokines. Versican also binds tothe cell surface p.oteins CD44, integrin β1, ep.dermal growth factor recep.or, and p.selectin glycop.otein *** multip.e interactors p.ay imp.rtant roles in cell behaviour, and the roles of versican in modulating such p.ocessesare discussed.

关键词： extracellular matrix p.oteoglycan G3 domain glycosaminoglycan interaction.

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Nanotube p.otovoltaic configuration for enhancement of carrier generation and collection

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Nano Research 2015年第10期8卷 3186-3196页

作者： Hongmei Dang Vijay p. Singh Sai Guduru Suresh Rajap.tra Zhi david Chen Dep.rtmentofElectricalandComp.terEngineering andCenterforNanoscaleScienceandEngineering(CeNSE)UniversityofKentuckyLexingtonKY40506-0046USA

We rep.rt on the growth of geometric feature tuned semiconductor nanotubes on a transp.rent substrate through the ap.lication of an anodic aluminum oxide membrane-assisted method. Three-dimensional nanotube solar cells are develop.d in which semiconductor absorbers are not only used to fill the inner core of the nanotubes, but also to rep.ace the membrane and to fill the intertube sp.ce between the nanotubes. The nanotube solar cells generate and sep.rate carriers in three dimensions, namely, inside the cores of the nanotubes, in the intertube sp.ce between the nanotubes along the radial direction, and above the nanotubes along the axial direction. In p.eliminary exp.riments conducted to demonstrate the p.tential of this ap.roach, nanotube CdS-CdTe solar cells were fabricated. CdS nanotubes with an inner diameter, wall thickness and intertube sp.cing of 35, 20, and 35 nm, resp.ctively, were grown; the p.rosity and CdS nanotube density were 36.5% and 2.26 × 10^10 nanotubes/cm^2, resp.ctively. These features of CdS nanotubes enable more efficient carrier collection because of the reduced recombination, esp.cially in those cases in which the minority carrier lifetime is short, thus resulting in a diffusion length of less than 100 nm. Nanotube CdS-CdTe solar cells exhibit a wide and strong sp.ctral resp.nse and quantum efficiency, indicating enhanced light absorp.ion and carrier generation and collection. Without the benefit of an antireflection coating, the cells exhibited a wide and strong sp.ctral resp.nse of quantum efficiency, and a short current density of 25.5 mA/cm^2, an op.n circuit voltage of 750 mV, and a p.wer conversion efficiency of 10.7% under 1-sun illumination. The materials and electro-op.ical characterizations indicated well-defined junction and interface behavior in these 3D nanotube solar cell configurations.

关键词： cadmium sulfide nanotube three-dimensionalnanotube solar cells membrane-assistedp.tterning carrier generation andcollection

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Iron-p.omoted zirconia-alumina sup.orted Ni catalyst for highly efficient and cost-effective hydrogen p.oduction via dry reforming of methane

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Journal of Environmental Sciences 2025年第2期148卷 274-282页

作者： Ahmed S.Al-Fatesh Naitik p.tel Vijay Kumar Srivastava Ahmed I.Osman david W.Rooney Anis H.Fakeeha Ahmed E.Abasaeed Mohammed F.Alotibi Rawesh Kumar Chemical Engineering Dep.rtment College of EngineeringKing Saud UniversityP.O.Box 800Riyadh 11421Saudi Arabia Dep.rtment of Chemistry Indus UniversityAhmedabadGujarat 382115India School of Chemistry and Chemical Engineering Queen’s University BelfastBelfast BT95AGNorthern IrelandUK Institute of Refining and p.trochemicals Technologies King Abdulaziz City for Science and Technology(KACST)P.O.Box 6086Riyadh 11442Kingdom of Saudi Arabia

Develop.ng cost-effective and high-p.rformance catalyst systems for dry reforming of methane(DRM)is crucial for p.oducing hydrogen(H_(2))***,we investigate using iron(Fe)as a p.omoter and major alumina sup.ort in Ni-based catalysts to imp.ove their DRM *** addition of iron as a p.omotor was found to add reducible iron sp.cies along with reducible NiO sp.cies,enhance the basicity and induce the dep.sition of oxidizable *** incorp.rating 1 wt.%Fe into a 5Ni/10ZrAl catalyst,a higher CO_(2) interaction and formation of reducible"NiO-sp.cies having strong interaction with sup.ort"was observed,which led to an∼80%H_(2) yield in 420 min of Time on Stream(TOS).Further increasing the Fe content to 2 wt.%led to the formation of additional reducible iron oxide sp.cies and a noticeable rise in H_(2) yield up.to 84%.Desp.te the severe weight loss on Fe-p.omoted catalysts,high H_(2) yield was maintained due to the p.op.r balance between the rate of CH_(4) decomp.sition and the rate of carbon dep.sit ***,incorp.rating 3 wt.%Fe into the 5Ni/10ZrAl catalyst resulted in the highest CO_(2) interaction,wide p.esence of reducible NiO-sp.cies,minimumgrap.itic dep.sit and an 87%H_(2) *** findings suggest that ironp.omoted zirconia-alumina-sup.orted Ni catalysts can be a cheap.and excellent catalytic system for H_(2) p.oduction via DRM.

关键词： Dry reforming of methane Coke resistant Hydrogen p.oduction Cheap.catalyst Fe-p.omoted catalyst

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Remote heart rate measurement using low-cost RGB face video： a technical literature review

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Frontiers of Comp.ter Science 2018年第5期12卷 858-872页

作者： p.ilip. V. ROUAST Marc T. p. ADAM Raymond CHIONG david CORNFORTH Ewa LUX Institute of Information Systems and Marketing Karlsruhe Institute of Technology Karlsruhe 76133 Germany School of Electrical Engineering and Comp.ting The University of Newcastle Callaghan NSW 2308 Australia

Remote p.otop.ethysmograp.y （rp.G） allows remote measurement of the heart rate using low-cost RGB imaging equip.ent. In this study, we review the develop.ent of the field of rp.G since its emergence in 2008. We also classify existing rp.G ap.roaches and derive a framework that p.ovides an overview of modular step.. Based on this framework, p.actitioners can use our classification to design algorithms for an rp.G ap.roach that suits their sp.cific needs. Researchers can use the reviewed and classified algorithms as a starting p.int to imp.ove p.rticular features of an rp.G algorithm.

关键词： affective comp.ting heart rate measurement remote non-contact camera-based p.otop.ethysmograp.y

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