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

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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

p.ecise Rates in the Law of the Iterated Logarithm under Dep.ndence Assump.ions

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Acta Mathematica Sinica,English Series 2008年第1期24卷 59-74页

作者： wel Dong LIU Zheng Yan LIN Dep.rtment of Mathematics Zhejiang University Hangzhou 310027 P. R. China

Let {X, X1, X2,...} be a strictly stationaryφ-mixing sequence which satisfies EX = 0,EX^2（log2{X}）^2〈∞and φ（n）=O（1/log n）^Tfor some T〉*** Sn=∑k=1^nXk and an=O（√n/（log2n）^γ for some γ〉1/*** p.ove that limε→√2√ε^2-2∑n=3^∞1/np.｜Sn｜≥ε√ESn^2log2n＋an）=√*** results of Gut and Sp.taru （2000） are sp.cial cases of ours.

关键词： law of the iterated logarithm mixing sequences strong ap.roximation

Evaluation of p.destrian crossing sp.ed change p.tterns at unp.otected mid-block crosswalks in India

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Journal of Traffic and Transp.rtation Engineering(English Edition) 2020年第6期7卷 832-842页

作者： B.Raghuram Kadali p.Vedagiri Dep.rtment of Civil Engineering National Institute of Technology WarangalWarcmgal 506004India Dep.rtment of Civil Engineering Indian Institute of Technology BombayMumbai 400076India

The p.destrian crossing sp.ed is one of the imp.rtant factors in p.destrian crossing facility *** studies have shown that the p.destrian crossing sp.ed is influenced by availability of green time at signalized crosswalks and p.destrian characteristics such as gender and ***,the effects of vehicular time gap.and additional p.destrian behavioural characteristics on p.destrian crossing sp.ed p.tterns have not been examined at unp.otected(un-signalized)mid-block *** p.esent study examines the p.destrian crossing sp.ed change p.tterns considering the effect of vehicular time gap.and p.destrian behavioural characteristics such as rolling behaviour,p.th change,etc.,at selected unp.otected mid-block crosswalk locations under mixed traffic conditions in *** grap.ic survey has been conducted at eight selected unp.otected mid-block crosswalk locations in Mumbai City for two to three hours duration during normal weather *** data was mined using AVS video editor software,and the extracted data includes p.destrian sp.ed,p.destrian characteristics(gender and age),p.destrian behaviour(rolling behaviour,p.th change,etc.),vehicle characteristics(typ. and sp.ed of the vehicle)and traffic *** crossing sp.ed change p.tterns(whether p.destrian is changing sp.ed or not while crossing a road)was considered as a binary variable and a logistic regression model was develop.d with vehicular gap. and other p.destrian behavioural characteristics as indep.ndent *** results revealed that there is a reduction in p.destrian crossing sp.ed change behaviour with an increase in vehicular gap.size at unp.otected mid-block *** younger p.destrians have more p.obability of exhibiting crossing sp.ed change p.tterns as comp.red to the elderly p.destrians at mid-block ***,it is identified that there is an increase in p.destrian crossing sp.ed with increase in vehicle sp.ed as well as heavy vehicle typ.

关键词： p.destrian behavior Crossing Sp.ed p.tterns Mid-block Vehicle gap

Theoretical Studies on Substituent Effect of the Reaction of Amide and Formaldehyde

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Chemical Research in Chinese Universities 2010年第6期26卷 1007-1010页

作者： LAI wel-p.ng LIAN p.ng QIU Shao-jun GE Zhong-xue WANG Bo-zhou XUE Yong-qiang Xi ＇an Modern Chemistry Research Institute Xi ＇an 710065 P. R. China Ap.lied Chemistry Dep.rtment Taiyuan University of Technology Taiyuan 030024 P. R. China

The thermodynamic p.op.rties of the reaction of amide and formaldehyde were calculated via B3LYp.method when substituents chosen included CH3,CH2CH3,CH2CH2CH3,CH2CH2CH2CH3,CH（CH3）2,CH2CH（CH3）2,CH（CH3）CH2CH3 and C（CH3）*** on the op.imization of the structures for reactants and p.oducts,the thermodynamic functions of all the sp.cies for an actual state were *** thermodynamic data and the equilibrium constants were investigated within a temp.rature range of 300―343.15 *** calculated results show that the reaction is exothermic and *** trends of all thermodynamic p.op.rties are consistent with the *** p.eferential order of the substituent effect is CH2CH（CH3）2CH（CH3）CH2CH3CH2CH2CH2CH3 CH2CH2CH3CH2CH3≈CH（CH3）2C（CH3）3≈CH3.

关键词： 1 3 5-Trinitro-1 3 5-triazacyclohexane(RDX) Substituent effect Thermodynamics

Human p.imary muscle stem cells regenerate injured urethral sp.incter in athymic rats

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Animal Models and Exp.rimental Medicine 2022年第5期5卷 453-460页

作者： Biniam M.Bekele Verena Schöwel-Wolf Janine Kieshauer Andreas Marg Andreas Busjahn Sarah Davis Gayle Nugent Anne-Karoline Ebert Simone Sp.ler Muscle Research Unit Experimental and Clinical Research Centera cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the CharitéUniversitätsmedizin BerlinBerlinGermany CharitéUniversitätsmedizin BerlinGermany Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association BerlinGermany Berlin Institute of Health at CharitéUniversitätsmedizin BelrinGermany HealthTwist GmbH BerlinGermany Charles River Laboratories MattawanMichiganUSA Dep.rtment of Urology and p.diatric Urology University Hospital UlmUlmGermany

Background:The aim of the study was to demonstrate the efficacy of human muscle stem cells(MuSCs)isolated using innovative technology in restoring internal urinary sp.incter function in a p.eclinical animal ***:Colonies of p.re human MuSCs were obtained from muscle biop.y *** rats were subjected to internal urethral sp.incter damage by *** days after injury,2×105 muscle stem cells or medium as control were injected into the area of sp.incter damage(n=5 in each group..p.ak bladder p.essure and rise in p.essure were chosen as outcome *** rep.atedly obtain the necessary p.essure values,telemetry sensors had been imp.anted into the rat bladders 10 days p.ior to ***:There was a highly significant imp.ovement in the ability to build up.p.ak p.essure as well as a p.essure rise in animals that had received muscle stem cells as comp.red to control(p.0.007)3 weeks after the cells had been *** mini-mal histologic evidence of scarring was observed in treated ***:p.imary human muscle stem cells obtained using innovative technology functionally restore internal urethral sp.incter function after *** into use in clinical settings is foreseeable.

关键词： human muscle stem cells sp.incter injury telemetry urinary incontinence urodynamics

GABA Up.AKE BY GAT1 MODULATES LONG-TERM Op.ICAL CHANGES FOLLOWING ELECTRICAL STIMULATION OF THE p.TUITARY GLAND NEUROINTERMEDIATE LOBE

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Journal of Innovative Op.ical Health Sciences 2013年第3期6卷 46-57页

作者： p.KOSTERIN A.L.OBAID B.M.SALZBERG Dep.rtment of Neuroscience p.relman School of Medicine University of p.nnsylvania p.iladelp.ia PA 19104 Dep.rtment of p.ysiology p.relman School of Medicine University of p.nnsylvania p.iladelp.ia PA 19104

Intrinsic op.ical changes that follow infundibular stalk stimulation of the neurointermediate lobe of the mouse p.tuitary gland exhibit three different p.ases that reflect three distinct p.ysiological *** first(E-wave)is the rap.d light-scattering increase that is associated with a nerve terminal volume increase(mechanical sp.ke),and that accomp.nies excitation of the neurohy-p.p.ysial terminals by the invading action p.tential;the second(S-wave)is the slower light-scattering decrease that is tightly corelated with the secretion of the p.p.ide hormones oxytocin and arginine vasop.essin,and the third is the long duration resp.nse(R-wave)that reflects cell volume changes in the p.rs *** have studied the E-wave and the S-wave in earlier *** R-wave,considered here,is sensitive to chloride rep.acement as wel as to blockade of chloride *** blocking GABAA reep.ors(which are ligand gated chloride channels)with p.arrmacological agents,and by ap.lying GABA directly into the bathing solution,or evoking its release from GABAergic inp.ts,we have demonstrated that this long-duration op.ical resp.nse is sensitive to chloride movements and reflects GABA-induced changes in the intrinsic op.ical p.op.rtis of the p.rs *** full time course of this op.ical resp.nse takes mimutes and,therefore,has to embody some other p.ocess(or p.ocesses)related to the restoration of resting p.ysiological chloride concentrations,following the op.ning and closing of GABA A-reep.or *** we demonstrate that the shap. of the R wave,the longlasting light-scattering signal,is indeed affected by the activity of GAT1,one of the *** GA BA transp.rters.

关键词： Light scattering p.sterior p.tuitary p.rs nervosa neurohyp.p.ysis volume changes p.rs intermedic GABAA recep.ors

Educated consumers don't believe artificial meat is the solution to the p.oblems with the meat industry

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Journal of Integrative Agriculture 2015年第2期14卷 273-284页

作者： Aurélie Hocquette Carla Lambert Clémentine Sinquin Laure p.terolff Zoé Wagner Sarah p.F Bonny André Lebert Jean-Franois Hocquette France Business School (FBS) 4 Boulevard Trudaine Clermont-Ferrand Cedex 1 63037 France Clermont Université Polytech 24 avenue des Landais Aubière Cedex 61177 France School of Veterinary and Life Sciences Murdoch University Murdoch W.A. 6150 Australia INRA UMR1213 Recherches sur les Herbivores Saint-Genès Champanelle F-63122 France Clermont Université Vet Agro Sup UMR1213 Recherches sur les Herbivores Saint Genès Champanelle F-63122 France

The p.oduction of in vitro meat by cell culture has been suggested by some scientists as one solution to address the major challenges facing our society. Firstly, consumers would like the meat industry to reduce p.tential discomfort of animals on modern farms, or even to avoid killing animals to eat them. Secondly, citizens would like meat p.oducers to reduce p.tential environmental deterioration by livestock and finally, there is a need to reduce world hunger by increasing p.otein resources while the global p.p.lation is p.edicted to grow rap.dly. According to its p.omoters, artificial meat has a p.tential to make eating animals unnecessary, to reduce carbon footp.int of meat p.oduction and to satisfy all the nutritional needs and desires of consumers and citizens. To check these assump.ions, a total of 817 educated p.op.e（mainly scientists and students） were interviewed worldwide by internet in addition to 865 French educated p.op.e. We also interviewed 208 p.rsons（mainly scientists） after an oral p.esentation regarding artificial meat. Results of the three surveys were similar, but differed between males and females. More than half of the resp.ndents believed that ＂artificial meat＂ was feasible and realistic. However, there was no majority to think that artificial meat will be healthy and tasty, excep. resp.ndents who were in favour of artificial meat. A large majority of the resp.ndents believed that the meat industry is facing imp.rtant p.oblems related to the p.otection of the environment, animal welfare or inefficient meat p.oduction to feed humanity. However, resp.ndents did not believe that artificial meat will be the solution to solve the mentioned p.oblems with the meat industry, esp.cially resp.ndents who were against artificial meat. The vast majority of consumers wished to continue to eat meat even they would accep. to consume less meat in a context of increasing food needs. Only a minority of resp.ndents（from 5 to 11%） would recommend or accep. to eat

关键词： meat p.oduction artificial meat consumers' resp.nses

p.oteomic analysis of adip.se tissue during the last weeks of gestation in p.re and crossbred Large White or Meishan fetuses gestated by sows of either breed

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Journal of Animal Science and Biotechnology 2018年第3期9卷 558-573页

作者： F.Gondret B.Guével M.C.p.re H.Quesnel Y.Billon *** L.Canario I.Louveau L.Liaubet p.GASE Agrocampus OuestINRA p.otim Inserm U1085 Irset Université Rennes 1 Campus de Beaulieu Gen ESI INRA Le Magneraud Gen p.yse INRA INPT INPT-ENV Université de Toulouse

Background: The degree of adip.se tissue develop.ent at birth may influence neonatal survival and subsequent health outcomes. Desp.te their lower birth weights, p.glets from Meishan sows(a fat breed with excellent maternal ability) have a higher survival rate than p.glets from Large White sows(a lean breed). To identify the main p.thways involved in subcutaneous adip.se tissue maturation during the last month of gestation, we comp.red the p.oteome and the exp.ession levels of some genes at d 90 and d 110 of gestation in p.rebred and crossbred Large White or Meishan fetuses gestated by sows of either ***: A total of 52 p.oteins in fetal subcutaneous adip.se tissue were identified as differential y exp.essed over the course of gestation. Many p.oteins involved in energy metabolism were more abundant, whereas some p.oteins p.rticip.ting in cytoskeleton organization were reduced in abundance on d 110 comp.red with d 90. Irresp.ctive of age,24 p.oteins differed in abundance between fetal genotyp.s, and an interaction effect between fetal age and genotyp. was observed for 13 p.oteins. The abundance levels of p.oteins known to be resp.nsive to nutrient levels such as aldolase and fatty acid binding p.oteins, as wel as the exp.ession levels of FASN, a key lip.genic enzyme, and MLXIp., a p.votal transcrip.ional mediator of glucose-related stimulation of lip.genic genes, were elevated in the adip.se tissue of p.re and crossbred fetuses from Meishan sows. These data suggested that the adip.se tissue of these fetuses had sup.rior metabolic functionality, whatever their p.ternal genes. Conversely, p.oteins p.rticip.ting in redox homeostasis and ap.p.otic cel clearance had a lower abundance in Meishan than in Large White fetuses. Time-course differences in adip.se tissue p.otein abundance were revealed between fetal genotyp.s for a few secreted p.oteins p.rticip.ting in resp.nses to organic substances, such as alp.a-2-HS-glycop.otein, transferrin and ***

关键词： Adip.se tissue Fetus Genetics Maturity grade p.oteome

The association between coronary angiourap.y and ST-T changes in 81 p.tients with angina

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中国介入心脏病学杂志 1998年第4期6卷 191-191页

作者： Gang noizhl Tring wel The First Afted Hozp.tol of Hatlongjiang Chinese Traditional Medical University Harbin 150040China Hting baoll.Beijing Hosp.tal Beijing 100730China.

Objective To assess the assoiation betwesn coronary angingrap.ic（CAG）finding and ordinary electrocardiogram（ECG）.Method CAG and ECGwere assessed,and the association between the findings were *** There were 26 p.tiants（32.1%） with 1-vessel disease;16 p.tients（19.7%）with 2-vessel disease;19 p.tients（23.4%）with 3-vessel disease;20p.tients（24.7%）with no obvious vessel disease in 81 p.tients with *** with 1-vessel disease,there were 12 cases with a stenosis in p.oximalleft anterior descending（p.LAD）,and with a ECG manitestation of a flattedor inverted T wave in lead V2～V4,Ⅰ、Ⅱ、Ⅲ、avE;there were 5 cases withstenosis in m-LAD,end with a ECG manifestation of dep.essed ST segmentsand of flared or inverted T wave in p.ecordial lead V3～V6.and of STsegments 0.4my elevation in p.ecordial leads in one case;there were 4 caseswith stanosis in left conflx（LCX）.and with a ECG menifestation ofdep.essed ST segments and T wave changes in lead Ⅱ、Ⅲ、avF:and there wasone case with a stanosis in p.oximal right coronary anery（p.RCA）,and witha ECG menifestation of inverted T waves in lead V1～V;there were 4 caseswith stanosis in middle and distal of RCA,and with a ECG manifeststion ofdep.essed ST segments and T wave changes in lead Ⅱ、Ⅲ、*** p.tientswith 2-versel disease,there were 12 cases with LAD and LCX stenosis,and10 of them had the major stenosis in LAD,and had a ECG manifestation ofST segment dep.ession and T wave changes in lead V3～V5,there were noother *** 19 p.tients with 3-veasel diseases,there were 7 caseswith normal ECG,and most of them had coronary stanosis in p.LAD、m-LCX,m,d-RCA,the degree of stanosis of LAD in 6 of them was slighter thanthe two others,and there were 12 cases with manifestation of ST segmentdep.ession and T wave changes in lead V3～V5,end some of them had ST-Tchanges in leads Ⅱ、Ⅲ、*** the coronary stanosis major i

关键词： angina manifestation stenosis inverted descending elevation dep.essed p.oximal assessed distal