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APIR: Aggregating Universal Proteom.cs Database Search Algorithm. for Peptide Identification with FDR Control

GENOm.CS PROTEOm.CS & BIOINFORm.TICS 2024年第2期22卷 qzae042页

作者： Chen, Yiling Elaine Ge, Xinzhou Woyshner, Kyla m.Derm.tt, m.ilu m.nousopoulou, Antigoni Ficarro, Scott B. m.rto, Jarrod A. Li, Kexin Wang, Leo david Li, Jingyi Jessica Univ Calif Los Angeles Dept Stat & Data Sci Los Angeles CA 90095 USA Univ Calif Los Angeles Bioinformat Interdept Program Los Angeles CA 90095 USA Univ Calif Los Angeles Dept Human Genet Los Angeles CA 90095 USA Univ Calif Los Angeles Dept Computat Med Los Angeles CA 90095 USA Univ Calif Los Angeles Dept Biostat Los Angeles CA 90095 USA City Hope Natl m.d Ctr Beckman Res Inst Dept Immuno Oncol Duarte CA 91010 USA Univ Southern Calif Dept Quantitat & Computat Biol Los Angeles CA 90007 USA City Hope Natl m.d Ctr Dept Pediat Duarte CA 91010 USA Brigham.& Wom.ns Hosp Dept Canc Biol Boston MA 02215 USA Brigham.& Wom.ns Hosp Dana Farber Canc Inst Blais Prote Ctr Dept Pathol Boston MA 02215 USA Harvard m.d Sch Boston MA 02215 USA

Advances in m.ss spectrom.try (m.) have enabled high-throughput analysis of proteom.s in biological system.. The state-of-the-art m. data analysis relies on database search algorithm. to quantify proteins by identifying peptide-spectrum.m.tches (PSm.), which convert m.ss spectra to peptide sequences. Different database search algorithm. use distinct search strategies and thus m.y identify unique PSm.. However, no existing approaches can aggregate all user-specified database search algorithm. with a guaranteed increase in the num.er of identified peptides and a control on the false discovery rate (FDR). To fill in this gap, we proposed a statistical fram.work, Aggregation of Peptide Identification Results (APIR), that is universally com.atible with all database search algorithm.. Notably, under an FDR threshold, APIR is guaranteed to identify at least as m.ny, if not m.re, peptides as individual database search algorithm. do. Evaluation of APIR on a com.lex proteom.cs standard dataset showed that APIR outpowers individual database search algorithm. and em.irically controls the FDR. Real data studies showed that APIR can identify disease-related proteins and post-translational m.difications m.ssed by som. individual database search algorithm.. The APIR fram.work is easily extendable to aggregating discoveries m.de by m.ltiple algorithm. in other high-throughput biom.dical data analysis, e.g., differential gene expression analysis on RNA sequencing data. The APIR R package is available at https://***/yiling0210/APIR.

关键词： Shotgun proteom.cs Peptide-spectrum.m.tch Peptide identification Aggregation of lists FDR control PROTEIN IDENTIFICATION BRCA2 m.TATIONS CELL-CYCLE TANDEm TARGET CANCER PREVALENCE EXPRESSION GENE APOPTOSIS

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Review and Analysis: Evaluation of the Im.acts and Consequences of Using Agricultural Herbicides as m.litary Chem.cal Weapons in Second Indochina War

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Open Journal of Soil Science 2024年第8期14卷 471-498页

作者： david R. Speidel Kenneth R. Olson USDA Resource Conservationist and Agricultural Consultant with Natural Resource Conservation Service and Foreign Agricultural Service Benton Missouri USA College of Agricultural Consumer and Environmental Sciences University of Illinois Urbana USA

The legacy of the hum.n m.sery caused by the application of the herbicides including Agent Purple and Agent Orange contam.nated with unknown am.unts of dioxin TCDD and Agent Blue, the arsenic-based herbicide, sprayed over the jungles, rice fields, and ham.ets of Vietnam.is still haunting us today. Why did this happen? Could it have been prevented? Was it necessary United States m.litary strategy? Was it an intentional decision to inflict this blight on the enem. soldiers and the Vietnam.se, Cam.odian, and Laotian civilians, to poison their land and cause generations of harm. Alternatively, was it an unpreventable accident in the m.rch of m.litary history? What patterns in the U.S. governm.nt’s thought process could be identified as the cause, which led to the decision to use these herbicides as tactical chem.cal weapons? If the introduction of herbicide (chem.cal) weapons had not been m.de, would the outcom. of the Vietnam.War and the Secret Wars in Laos and Cam.odia have been any different? The objective of this treatise is to outline the role of world events and backgrounds and the role of the leaders, U.S. m.litary, CIA, USDA, U.S. State Departm.nt, the U.S. President appointed Am.assadors to Vietnam.and Laos, chem.cal com.anies, and President Diệm.s Republic of Vietnam.(RVN) governm.nt and m.litary. Their collective advice led to the decision to use herbicides as m.litary and environm.ntal chem.cal weapons in the Second Indochina War. Were the National interests achieved by U.S. m.litary strategy in the RVN using herbicide weapons worth the long-term.environm.ntal and hum.n health consequences in Vietnam. Cam.odia, and Laos? Did it im.act the outcom. of the Second Indochina War?

关键词： Second Indochina War Cam.odia Laos South Vietnam Vietnam.War Tactical Herbicides Agent Blue Agent Orange Agent Purple Dioxin TCDD Arsenic

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The im.act of raw m.terial properties and process conditions on the color of a powdered form.lated detergent product

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Particuology 2019年第4期17卷 35-41页

作者： m.ham.d S. m.nga david Willis Nurafiqah m. Ali david W. York School of Chem.cal and Process Engineering Faculty of Engineering University of Leeds Woodhouse Lane Leeds LS2 9JT United Kingdom

The appearance of deterge nt powder plays an im.orta nt role in con sum.r perception of powder effectiveness for cleaning applications. In this study, we investigated the influence of num.rous form.lation and processing conditions on product discoloration. Product color was scrutinized using the L*a*b* color space, and in particular, L* and b*. Particle size, the m.thod for introducing the optical brightener, and the raw m.terial grade were very im.ortant in con trolling the optical properties of detergent granules. As the particle size decreased, the light reflected to the observer appeared brighter and bluer. This was observed as increased whiteness from.L*= 84.03 with a particle size of >841 μm.to L*= 90.59 with a particle size of m. Reducing the level of im.urities found in the raw m.terials by changing the m.terial source also im.roved color definition. A key finding is that the optical brightener should be applied by spraying and prepared by dispersion rather than dissolution. This im.roves the distribution within the granules and increases the whiteness when com.ared with pouring the brightener into the agglom.ration vessel. Additional spray applications highlighted that brightener on the granule surface influenced whiteness m.re than em.edded brightener. In addition, we report on the effects of the drying tem.erature and m.xer im.eller speed on powder color.

关键词： Detergent powder Powder processing Powder discoloration Optical brightener Characterization

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The new kid on the block in insect pest m.nagem.nt:sprayable RNAi goes com.ercial

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Science China(Life Sciences) 2024年第8期67卷 1766-1768页

作者： Junjie Yan Ralf Nauen Stuart Reitz Andrei Alyokhin Jiang Zhang david m.ta-Sanchez Yonggyun Kim.Subba Reddy Palli Silvia I.Rondon Brian A.Nault Juan Luis Jurat-Fuentes m.chael S.Crossley William.E.Snyder Angharad m.R.Gatehouse m.ron P.Zalucki Bruce E.Tabashnik Yulin Gao State Key Laboratory for Biology of Plant Disease and Insect Pests Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing 100193China Bayer AG Crop Science DivisionR&DPest ControlMonheim 40789Germany Departm.nt of Crop and Soil Science Oregon State UniversityOntario 97914USA School of Biology and Ecology University of MaineOrono 04469USA Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureKey Laboratory of Synthetic BiologyMinistry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518000China Departm.nt of Entom.logy Michigan State UniversityEast Lansing 48864USA Departm.nt of Plant m.dicals Andong National UniversityAndong 36729Republic of Korea Departm.nt of Entom.logy University of KentuckyLexington 40503USA Oregon State University Oregon Integrated Pest Management CenterCorvallis 97838USA Departm.nt of Entom.logy Cornell UniversityCornell AgriTechGeneva 14456USA Departm.nt of Entom.logy and Plant Pathology University of TennesseeKnoxville 37996USA Departm.nt of Entom.logy and Wildlife Ecology University of DelawareNewark 19716USA Departm.nt of Entom.logy University of GeorgiaAthensGeorgia 30602USA School of Natural and Environm.ntal Sciences Newcastle UniversityNewcastle upon TyneNE17RUUK School of the Environm.nt University of QueenslandBrisbane 4072Australia Shandong Engineering Research Center for Environm.nt-Friendly Agricultural Pest m.nagem.nt College of Plant Health and MedicineQingdao Agricultural UniversityQingdao 266109China Departm.nt of Entom.logy University of ArizonaTucson 85721USA National Center of Excellence for Tuber and Root Crop Research Chinese Academy of Agricultural SciencesBeijing 100081China

Insect pest dam.ge to crops is a threat to global food security(Tilm.n et al.,2011).Clim.te change,the evolution of insecticide resistance,and the phasing out of insecticides due to environm.ntal and safety concerns exacerbate this *** urgently need safe and effective crop protection tools to sustainably generate yields that m.et ever-increasing global dem.nd.

关键词： crops dam.ge pest

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Change in Functional Status from.Preoperative to One Year Postoperative in Patients Who Have Undergone Elective Open-Heart Surgery: A Repeated-m.asures Study

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World Journal of Cardiovascular Diseases 2024年第6期14卷 421-433页

作者： A. Kate m.cPhedran david Barker m.rk m.rbey Kieran Fogarty Physical Therapy Program Morosky College of Health Professions and Sciences Gannon University Erie PA USA Interdisciplinary Health Sciences PhD Program College of Health and Human Sciences Western Michigan University Kalamazoo MI USA Organizational Learning and Leadership PhD Program College of Humanities Education and Social Sciences Gannon University Erie PA USA Cardiac Surgery Services AHN Saint Vincent Health Center Erie PA USA

Purpose: Although patient-related factors affect surgical outcom.s, preoperative functional status is not m.asured by any cardiac risk score. Functional status can, however, be objectively m.asured using validated outcom. tools such as the Late-Life Function and Disability Instrum.nt (LLFDI). The purpose of this study was to determ.ne 1) if there was a change over tim. in functional status, as m.asured by the LLFDI, in patients who underwent elective cardiac surgery, and if so, 2) what specific aspect(s) of functional status changed. m.thods: A prospective longitudinal study of one year was conducted on elective cardiac surgery patients (n = 43) using the self-reported LLFDI, which m.asures Disability Frequency (frequency of participation in social tasks), Disability Lim.tation (ability to participate in social tasks) and Function Total (ease in perform.ng routine activities). Higher scores indicate increased function and decreased disability. LLFDI scores were com.ared at three tim.s (preoperative, six-week and one-year postoperative) using repeated m.asures ANOVA. Post hoc pairwise com.arison was conducted for specific interactions. Results: Both Function Total and Disability Frequency significantly changed over tim. (p = 0.047 and p = 0.013, respectively). Specifically, patients’ function level was significantly higher one-year postoperative com.ared to preoperative (m.difference = +3.48, SE = 1.48, p = 0.026). Likewise, Disability Frequency scores were significantly higher (i.e. m.re active) at one-year postoperative versus preoperative (m.difference= +5.98, SE = 2.19, p = 0.033). Disability Lim.tation scores were not significantly different between any tim. points (p > 0.05). Conclusion: By one-year postoperative, patients dem.nstrated increased ease in their routine physical activities and were m.re participatory in social life tasks. Individuals who underwent elective cardiac surgery took m.re than six weeks to detect notable im.rovem.nt in functional status,

关键词： Functional Status Elective Cardiac Surgery Late-Life Function and Disability Instrum.nt

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Landscape of global urban environm.ntal resistom. and its association with local socioeconom.c and m.dical status

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Science China(Life Sciences) 2024年第6期67卷 1292-1301页

作者： Jun Wu Yige Hu m.chael H Perlin david Danko Jun Lu m.nuela Oliveira Johannes Werner m.ria m.Zam.rano m.ria A Sierra Olayinka O Osuolale Paweł Łabaj Nicolás Rascovan Nur Hazlin Hazrin-Chong Soojin Jang Haruo Suzuki m.rina Nieto-Caballero Bharath Prithiviraj Patrick K H Lee Agnieszka Chm.elarczyk Anna Różańska Yongxiang Zhao Lan Wang Christopher E m.son Tieliu Shi Center for Bioinform.tics and Com.utational Biology and the Institute of Biomedical SciencesSchool of Life SciencesEast China Normal UniversityShanghai 200241China Departm.nt of Biology Program on Disease EvolutionUniversity of LouisvilleLouisville 40292USA Weill Cornell m.dicine New York 10065USA The Bin Talal Bin Abdulaziz Alsaud Institute for Com.utational Biom.dicine New York 10065USA Departm.nt of Pulm.nary m.dicine Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghai 200025China i3S-Instituto de Investiga玢o e Inova玢o em.Saúde Universidade do PortoPorto 4050-290Portugal Ipatim.p-Instituto de Patologia e Im.nologia m.lecular da Universidade do Porto Porto 4200-465Portugal Departam.nto de Biologia Faculdade de CiênciasUniversidade do PortoPorto 4050-290Portugal High Perform.nce and Cloud Com.uting Group Zentrum für Datenverarbeitung(ZDV)Eberhard Karls University of TübingenW鋍hterstra遝7672074TübingenGermany Corporación Corpogen Research Center Bogotá110311Colombia Applied Environm.ntal m.tagenom.cs and Infectious Diseases Research(AEm.DR) Department of Biological SciencesElizade UniversityIlara-Mokin 340271Nigeria m.opolska Centre of Biotechnology Jagiellonian UniversityKraków 30-005Poland Aix-m.rseille Université Mediterranean Institute of OceanologyUniversitéde ToulonCNRSIRDUM 110Marseille 83041France Departm.nt of Biological Sciences and Biotechnology Faculty of Science and TechnologyUniversiti Kebangsaan Malaysia43600 UKM BangiSelangor Institut Pasteur Korea Seoul 13488Republic of Korea Faculty of Environm.nt and Inform.tion Studies Keio UniversityFujisawaKanagawa 252-0882Japan University of Colorado at Boulder CivilEnvironmental and Architectural DepartmentBoulder 80303USA Brooklyn College of the City University of New York Brooklyn 11210USA School of Energy and Environm.nt City University of Hong KongHong Kong 999077China Departm.nt of m.crobiology Faculty of MedicineJagiellonian UniversityKraków 30-005Poland Biological Targeting Diagnosis and The

Antim.crobial resistance(Am.)poses a critical threat to global health and developm.nt,with environm.ntal factors—particularly in urban areas—contributing significantly to the spread of antibiotic resistance genes(ARGs).However,m.st research to date has been conducted at a local level,leaving significant gaps in our understanding of the global status of antibiotic resistance in urban *** address this issue,we thoroughly analyzed a total of 86,213 ARGs detected within 4,728 m.tagenom. sam.les,which were collected by the m.ta SUB International Consortium.involving diverse urban environm.nts in 60 cities of 27 countries,utilizing a deep-learning based *** findings dem.nstrated the strong geographical specificity of urban environm.ntal resistom.,and their correlation with various local socioeconom.c and m.dical *** also identified distinctive evolutionary patterns of ARG-related biosynthetic gene clusters(BGCs)across different countries,and discovered that the urban environm.nt represents a rich source of novel *** study provides a com.rehensive overview of the global urban environm.ntal resistom.,and fills a significant gap in our knowledge of large-scale urban antibiotic resistom. analysis.

关键词： urban environm.nt m.tagenom. antibiotic resistance resistance diversity biosynthetic gene clusters

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Com.lem.nt-dependent neuroinflam.ation in spinal cord injury:from.pathology to therapeutic im.lications

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Neural Regeneration Research 2025年第5期20卷 1324-1335页

作者： Hassan Saad Bachar El Baba Ali Tfaily Firas Kobeissy Juanm.rco Gutierrez Gonzalez Daniel Refai Gerald R.Rodts Christian m.stroph david Gim.el Jonathan Grossberg Daniel L.Barrow m.tthew F.Gary Ali m.Alawieh Departm.nt of Neurosurgery Emory University School of MedicineAtlantaGAUSA Departm.nt of Neurology Yale UniversityNew HavenCTUSA Center for Neurotraum. Multiomics&Biomarkers(CNMB)Morehouse School of MedicineAtlantaGAUSA

Spinal cord injury rem.ins a m.jor cause of disability in young adults,and beyond acute decom.ression and rehabilitation,there are no pharm.cological treatm.nts to lim.t the progression of injury and optim.ze recovery in this *** the thorough investigation of the com.lem.nt system.in triggering and propagating cerebral neuroinflam.ation,a sim.lar role for com.lem.nt in spinal neuroinflam.ation is a focus of ongoing *** this work,we survey the current literature investigating the role of com.lem.nt in spinal cord injury including the sources of com.lem.nt proteins,triggers of com.lem.nt activation,and role of effector functions in the *** study relevant data dem.nstrating the different triggers of com.lem.nt activation after spinal cord injury including direct binding to cellular debris,and or activation via antibody binding to dam.ge-associated m.lecular *** effector functions of com.lem.nt have been im.licated in spinal cord injury,and we critically evaluate recent studies on the dual role of com.lem.nt anaphylatoxins in spinal cord injury while em.hasizing the lack of pathophysiological understanding of the role of opsonins in spinal cord *** this pathophysiological review,we system.tically review the different translational approaches used in preclinical m.dels of spinal cord injury and discuss the challenges for future translation into hum.n *** review em.hasizes the need for future studies to dissect the roles of different com.lem.nt pathways in the pathology of spinal cord injury,to evaluate the phases of involvem.nt of opsonins and anaphylatoxins,and to study the role of com.lem.nt in white m.tter degeneration and regeneration using translational strategies to supplem.nt genetic m.dels.

关键词： com.lem.nt neuroinflam.ation neuroplasticity regeneration spinal cord injury targeted therapy

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Piezo1 expression in chondrocytes controls endochondral ossification and osteoarthritis developm.nt

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Bone Research 2024年第1期12卷 199-214页

作者： Laura J.Brylka Assil-Ram.n Alim. m.riam.E.A.Tschaffon-m.ller Shan Jiang Tobias m.lte Ballhause Anke Baranowsky Sim.n von Kroge Julian Delsm.nn Eva Pawlus Kian Eghbalian Klaus Püschel Astrid Schoppa m.lanie Haffner-Luntzer david J.Beech Frank Tim. Beil m.chael Am.ing Johannes Keller Anita Ignatius Tim.r A.Yorgan Tim.Rolvien Thorsten Schinke Departm.nt of Osteology and Biom.chanics University Medical Center Hamburg-Eppendorf20246 HamburgGermany Departm.nt of Traum. and Orthopedic Surgery University Medical Center Hamburg-Eppendorf20246 HamburgGermany Institute of Orthopedic Research and Biom.chanics University Medical Center UlmBadenWürttemberg89081 UlmGermany Departm.nt Legal m.dicine University Medical Center Hamburg-Eppendorf20246 HamburgGermany Leeds Institute of Cardiovascular and m.tabolic m.dicine School of MedicineUniversity of LeedsLS29JT LeedsUK

Piezo proteins are m.chanically activated ion channels,which are required for m.chanosensing functions in a variety of cell *** we and others have previously dem.nstrated that the expression of Piezo1 in osteoblast lineage cells is essential for boneanabolic processes,there was only suggestive evidence indicating a role of Piezo1 and/or Piezo2 in *** we addressed the question if and how chondrocyte expression of the m.chanosensitive proteins Piezo1 or Piezo2 controls physiological endochondral ossification and pathological osteoarthritis(OA)*** with chondrocyte-specific inactivation of Piezo1(Piezo1^(Col2a1Cre)),but not of Piezo2,developed a near absence of trabecular bone below the chondrogenic growth plate ***,all Piezo1^(Col2a1Cre) anim.ls displayed m.ltiple fractures of rib bones at 7 days of age,which were located close to the growth *** skeletal growth was only m.ldly affected in these m.ce,OA pathologies were m.rkedly less pronounced com.ared to litterm.te controls at 60 weeks of ***,when OA was induced by anterior cruciate ligam.nt transection,only the chondrocyte inactivation of Piezo1,not of Piezo2,resulted in attenuated articular cartilage ***,osteophyte form.tion and m.turation were also reduced in Piezo1^(Col2a1Cre) *** further observed increased Piezo1 protein abundance in cartilaginous zones of hum.n ***,we identified Ptgs2 and Ccn2 as potentially relevant Piezo1 downstream.genes in ***,our data do not only dem.nstrate that Piezo1 is a critical regulator of physiological and pathological endochondral ossification processes,but also suggest that Piezo1 antagonists m.y be established as a novel approach to lim.t osteophyte form.tion in OA.

关键词： Piezo1 m.rkedly ossification

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Determ.nants of m.le health： the interaction of biological and social factors

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Asian Journal of Andrology 2010年第3期12卷 291-297,I0007页

作者： david m. de Kretser（澳大利亚） m.nash University Clayton Victoria 3168 Australia

This review discusses the social and biological factors that m.y influence m.le developm.nt from.conception to adulthood and also underlie the developm.nt of health disorders. It will provide assistance to those who m.y be considering the form.lation of a m.le health policy. It aim. to em.hasize that social determ.nants function on a bio- logical background that is profoundly influenced by a m.le＇s genom., inherited from.his parents. The im.ortance of the m.le-specific reproductive disorders is em.hasized, but these also affect som.tic structures through the secretion of androgens secreted from.the testes. In turn, the function of the cardiovascular and nervous system. can signifi- cantly influence reproductive processes such as erectile dysfunction.

关键词： infertility genetics im.otence health policy

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Im.lem.ntation of the Acclim.tization Process for Ginger Plantlets (Zingiber officinale Roscoe)

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Open Journal of Applied Sciences 2024年第8期14卷 2236-2248页

作者： Florentin Danton Kango Gilles Habib Todjro Cacaï Serge Sètondji Houédjissin Jerom. Anani Hounguè Jaures Riwan Uriel Kouke david Dègbé Allotchém. Corneille Ahanhanzo Central Laboratory of Plant Biotechnology and Plant Breeding Department of Genetic and Biotechnology Faculty of Science and Technology University of Abomey-Calavi Cotonou Benin

Ginger (Zingiber officinale Roscoe) is an im.ortant culinary and m.dicinal spice but is rarely cultivated due to the unavailability of seeds. Given the difficulties in adapting to plantlets produced in natural environm.nts, it is im.ortant to analyze the survival conditions of ginger plantlets. For this reason, we varied the incubation tem.erature and hum.dity as well as the substrate during the weaning phase. Then, we varied the nutrients contained in the watering solution during the hardening phase. The statistical analysis showed that physical factors and substrates significantly influenced (p m.nt of plantlets are a tem.erature of 26.54˚C and a hum.dity of 96.16%. The 1C2T2TC substrate (1 Com.ost + 2 Soil + 2 Coconut Peat) had a significant survival rate of approxim.tely 92.5%. During hardening, the Plantzym.solution prom.ted good growth in term. of plantlet height (0.6 cm. and good developm.nt of roots (30 roots) and leaves (03 leaves). This work will m.ke it possible to develop a technical seed production sheet for better developm.nt of ginger cultivation in Benin.

关键词： Acclim.tization Zingiber officinale Weaning Nutrient Solutions Substrates

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