pdf_HandsOn-Geant4-DNA
plot.C
n ROOT
is already installed on your system n ROOT macro is read to plot histograms from dna.root file
Output of dnaphysics
7
e-_G4DNAElastic e-_G4DNAExcitation e-_G4DNAIonisation e-_G4DNAAttachment e-_G4DNAVibExcitation proton_G4DNAExcitation proton_G4DNAIonisation proton_G4DNAChargeDec. hydrogen_G4DNAExcitation hydrogen_G4DNAIonisation hydrogen_G4DNAChargeInc. alpha_G4DNAExcitation alpha_G4DNAIonisation alpha_G4DNAChargeDec. alpha+_G4DNAExcitation alpha+_G4DNAIonisation alpha+_G4DNAChargeDec. alpha+_G4DNAChargeInc. helium_G4DNAExcitation helium_G4DNAIonisation helium_G4DNAChargeInc. 11 12 13 14 15 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32
n TestEm12
3
dnaphysics
dnaphysics advanced example
4 ¨
Located in $G4INSTALL/examples/advanced/dnaphysics
Gea nt4 9.5 BET A
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This example teaches to Geant4 users how to use the Geant4-DNA physics processes and models in a liquid water volume
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It also explains how to easily change the density of the target material (liquid water) : « variable density material » new feature of Geant4
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Possibility to investigate density change effects
n
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In snavigator, look at the following classes
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Usage of G4EmDNAPhysics builder Recording of particles & processes Positions of pre-step points Energy deposit for each step Change of value of water density Handling of histograms (creation, filling up, saving)
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Tutorials & Teachings Download « Dnaphysics Hands On » Save it on your desktop
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On your Geant4 virtual machine
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Open a terminal mv /mnt/hgfs/Desktop/dnaphysics.tar tar –xvf dnaphysics.tar cd dnaphysics snavigator & gmake
Run dnaphysics
6
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On your terminal
¤ $G4WORKDIR/bin/$G4SYSTEM/DNAPhysics
n The
macro file dna.mac is read n 100 electrons of 1 keV are shot n No visualization by default n Results are saved in dna.root file
PROCESS
G4DNAElastic* theDNAElasticProcess = new G4DNAElastic("e-_G4DNAElastic"); theDNAElasticProcess->SetModel(new G4DNAChampionElasticModel()); // or alternative model //theDNAElasticProcess->SetModel(new G4DNAScreenedRutherfordElasticModel()); ph->RegisterProcess(theDNAElasticProcess, particle);
¤
What is included in the G4EmDNAPhysics builder ?
11 void G4EmDNAPhysics::ConstructParticle() { // bosons G4Gamma::Gamma(); // leptons G4Electron::Electron(); G4Positron::Positron(); // baryons G4Proton::Proton(); G4GenericIon::GenericIonDefinition(); G4DNAGenericIonsManager * genericIonsManager; genericIonsManager=G4DNAGenericIonsManager::Instance(); genericIonsManager->GetIon("alpha++"); genericIonsManager->GetIon("alpha+"); genericIonsManager->GetIon("helium"); genericIonsManager->GetIon("hydrogen"); }
¤ advanced
examples located in $G4INSTALL/examples/advanced
n dnaphysics n microdosimetry
¤ extendes
examples located in $G4INSTALL/examples/extended
1
GEANT4-DNA HANDS ON
KIT Tutorial, October 25-26, 2011, Karlsruhe
3 examples
2
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We are going to try 3 Geant4 examples which make use of Geant4-DNA Physics processes
private: G4double cutForGamma; G4double cutForElectron; G4double cutForPositron; G4double currentDefaultCut; G4VPhysicsConstructor* }; emPhysicsList;
PhysicsList implementation
n
eg. 1.06 g/cm3 average density of cell nucleus (cf. PARTRAC)
Install dnaphysics
5
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For usage with Geant4 9.4, download the example from http://geant4.in2p3.fr
Proton and He2+ nuclei can gain electrons and become H, He+, He0
G4EmDNAPhysics: Physics processes & models for electrons
12
void G4EmDNAPhysics::ConstructProcess() { G4PhysicsListHelper* ph = G4PhysicsListHelper::GetPhysicsListHelper(); theParticleIterator->reset(); while( (*theParticleIterator)() ) { G4ParticleDefinition* particle = theParticleIterator->value(); G4String particleName = particle->GetParticleName();
SteppingAction
n n n
¤ ¤
DetectorConstruction
n
Hale Waihona Puke HistoManagern
PhysicsList header
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#include "G4VModularPhysicsList.hh" #include "globals.hh » class G4VPhysicsConstructor; class PhysicsList: public G4VModularPhysicsList { public: PhysicsList(); ~PhysicsList(); void ConstructParticle(); void ConstructProcess(); void SetCuts(); void SetCutForGamma(G4double); void SetCutForElectron(G4double); void SetCutForPositron(G4double);
4DNA fingerprinting实验4 DNA指纹图谱分析
实验4 DNA 指纹图谱分析4.1 相 关 基 础 知 识1984年英国莱斯特大学的遗传学家Jefferys 及其合作者首次将分离的人源小卫星DNA 用作基因探针，同人体核DNA 的酶切片段杂交，获得了由多个位点上的等位基因组成的长度不等的杂交带图纹，这种图纹极少有两个人完全相同，故称为"DNA 指纹"，意思是它同人的指纹一样是每个人所特有的。
DNA 指纹的图像在X 光胶片中呈一系列条纹，很像商品上的条形码。
DNA 指纹图谱，开创了检测DNA 多态性（生物的不同个体或不同种群在DNA结构上存在着差异）的多种多样的手段，如RFLP （限制性内切酶酶切片段长度多态性）分析、串联重复序列分析、RAPD（随机扩增多态性DNA ）分析等等。
各种分析方法均以DNA 的多态性为基础，产生具有高度个体特异性的DNA 指纹图谱，由于DNA 指纹图谱具有高度的变异性和稳定的遗传性，且仍按简单的孟德尔方式遗传，成为目前最具吸引力的遗传标记。
DNA 指纹具有下述特点：1．高度的特异性：研究表明，两个随机个体具有相同DNA 图形的概率仅3×10－11；如果同时用两种探针进行比较，两个个体完全相同的概率小于5×10－19。
全世界人口约50亿，即5×109。
因此，除非是同卵双生子女，否则几乎不可能有两个人的DNA 指纹的图形完全相同。
2．稳定的遗传性：DNA 是人的遗传物质，其特征是由父母遗传的。
分析发现， DNA 指纹图谱中几乎每一条带纹都能在其双亲之一的图谱中找到，这种带纹符合经典的孟德尔遗传规律，即双方的特征平均传递50％给子代。
3．体细胞稳定性：即同图1. DNA 指纹图谱的孟德尔方式遗传图 2 传统指纹鉴定技术(a)和DNA 指纹图谱鉴定技术(b)一个人的不同组织如血液、肌肉、毛发、精液等产生的DNA指纹图形完全一致。
1985年Jefferys博士首先将DNA指纹技术应用于法医鉴定。
Feng Zhang实验室CRISPR设计工具在iPSCs基因组编辑中的应用说明说明书
Genome editing in iPSCsCrispr designWe used the Feng Zhang lab CRISPR Design tool () to design the guide RNA. The guide RNA should bind as closely as possible to the target nucleotide (ideally between 2-10 bp).To correct a mutation, the mutated DNA sequence should be used for the gRNA design.To introduce a mutation, the wild-type DNA sequence should be used for the gRNA design.For each selected gRNA, order two oligonucleotides - the sense and antisense of the guide sequence. The BbsI restriction site overhangs (depends on the plasmid) are as follows:Fw oligo: 5’-CACC[G]”guide_sense_sequence”-3’Rv oligo: 5’-AAAC”guide_antisense_sequence”[C]-3’Resuspend each oligo in distilled water to 100µM.Note: only add the G and the C in square brackets if the guide doesn't start with a G. This is necessary for optimal transcription initiation from the U6 promoter.Typically, we design two gRNAs and test the cutting efficiency before the HDR experiment.Design of ssDNA Oligo HDR donor templateWe use a mix of up to 4 HDR donor ssDNA Oligos (100nt long) depending on the targeted mutation, the gRNA binding site and the PAM sequence.We will design the donor OligosCloning of guide RNA in the pSpCas9(BB)-2A-GFP vector (Addgene: px458)Step1. Oligo phosphorylation and annealing:To phosphorylate and anneal each pair of oligos, combine the following in a 0.2ml tube:1 µl oligo Fw (100µM in water)1 µl oligo Rv (100µM in water)1 µl 10X T4 Ligation Buffer (NEB)6.5 µl ddH2 O0.5 µl T4 PNK (NEB)Total volume = 10 µl totalIncubate37°C 30 min95°C 5 minRamp down to 25°C at 5°C/minStep 2. Digestion and ligation:1 µl pX330 or other backbone vector pSpCas9(BB)-2A-GFP (100ng/ul)2 µl of diluted oligo duplex from step 1 (diluted 1:250 in water)2 µl 10X FastDigest Buffer1 µl DTT (10mM)1 µl ATP (10mM)1 µl FastDigest BbsI (ThermoFisher)0.5 µl T7 DNA ligase (NEB)11.5 µl ddH2OTotal volume = 20 µlIncubate:37°C 5 min23°C 5 minCycle 6 times (total run time ~1h)Step 3. Transformation:•Add 5µl of ligation mix to 50 µl E.coli strain e.g One Shot competent cells•Incubate on ice for 20 minutes•Heat-shock the cells at 42°C for 45 seconds•Cool on ice for 2 minutes•Add 500µl of SOC media and incubate at 37°C with shaking for 30 minutes•Plate 100µl of the transformed bacteria on LB-agar + 100µg/ml ampicillin plates.•Incubate at 37°C overnight.Step 4. E coli colony screening for gRNAThe next morning, pick 5 colonies and incubate overnight in 5ml LB + 100µg/ml ampicilline at 37°C with shaking. After 8 hours, isolate the DNA with a DNA miniprep kit and send for Sanger sequencing with the hU6_Fw primer (5’-ACTATCATATGCTTACCGTAAC-3’).iPSC cultureReagents:•Essential 8 (Life Technologies, A14666SA)•Matrigel™ hESC-Qualified Matrix (Corning, cat. no. 354277)•Gentle Dissociation Solution (Stem Cell Technologies 07174)•Y-27632-HCl (Biorbyt, cat. no. orb154626)Thawing hiPSC:•hiPSC should be either generated in-house or can be obtained from available depositories e.g Wicell, Coriell or the Stanford CVI iPSC Biobank.•Remove vial from liquid nitrogen, place in 37 °C water bath until only a sliver of ice remains.Transfer the vial content dropwise (~1 mL) to a 15 mL conical tube filled with 4 ml of pre-warmed E8 supplemented with 2.5µM Y-27632 (E8 + iRock)•Centrifuge at 200 g for 4 min. Carefully aspirate the supernatant. Re-suspend the cell pellet in 2 mL of E8 + iRock and transfer to 1 well of a Matrigel-coated 6-well plate •Change media every 24 h with fresh E8. Cells should be 70-80% confluent in 3-4 days Passage of hiPSC:•Ideally cells should have reached 70-80% confluence in 3-4 days (adjust split ratio accordingly, typically 1/6-1/12).•Aspirate the E8 culture medium.•Add 2 mL per well of Gentle Dissociation Solution, incubate for 6-8 min at RT (in hood) •Whilst waiting, aspirate medium from Matrigel-coated plates and replace with 1 mL of E8Y.•Aspirate Gentle Dissociation Solution from each well.•Add 1 mL of E8 + iRock medium to the well. Gently detach the colonies by scraping with a serological pipette or a cell scraper. Add 6 mL of E8 + iRock for a 1:6 split.•Mix gently and transfer 1 mL in each well of the 6-well plate (2ml per well total volume). NOTE: We aim to keep the pluripotent cells in the logarithmic growth phase. Cells should not be allowed to become more than 90% confluent.TransfectionThe day before transfection, split the cells 1:2/1:3. Cell should be 50-60% confluent the next day: •Remove the medium•Wash once with PBS•Add 2.0ml Gentle Dissociation Solution•Incubate 5 min 37°C•Gently pipette up and down to dissociate the cells•Plate in a previously coated new well in E8 + iRock.On the day of transfection:•Replace media with fresh E8 media (1.0 mL/well).•For each well of a 6-well plate, prepare 4 separate reactions•Prepare the reactions by adding the reagents in the order shown:(i)Set up the CRISPR-Cas9-gRNA rxn:Mix A:o200 µL of Opti-MEMo10 µL of Lipofectamine Stem reagentMix B:o200 µL of Opti-MEMo1µg of CRISPR/Cas9 vector (pSpCas9(BB)-2A-GFP)Combine mix A & B – mix well and incubate for 15min @ RT(ii) A separate reaction is set up for the ssDNA donor oligos:Mix C:o200 µL of Opti-MEMo7.5 µL of RNAi max reagentMix D:o200 µL of Opti-MEMo 4 µg of ssDNA donor mix (if using 4 oligos, use 1µg each)Combine mix C & D – mix well and incubate for 15min @ RT•Add 400µl transfection mix of A+B and 400µl transfection mix of C+D to one well•Place the cells back in the incubator•After 4 hours, aspirate the transfection media from each well and replace with 2ml of fresh E8 supplemented with E8 + iRock•16-24h later, check the transfected cells under a fluorescent microscope for GFP+. Typically, the transfection efficiency is 5%-30% depending on the iPSC line. We FACs sort the cells 24-36h post transfection.FACS GFP+ cells•Aspirate the media•Wash once with PBS•Add 2.0 ml TrypLE express•Incubate 5-6 min 37°C until cells have detached – mix gently with a P1000 pipette to break down the cells to single cells•Add 4ml E8 + iRock•Transfer to a 15ml tube•Centrifuge 5 min @200g room temperature•Discard the supernatant and re-suspend the cells in 0.4 ml E8 + iRock•Filter the suspension through a 35-µm mesh Corning™ Falcon™ Test Tube with Cell Strainer Snap Cap•Prepare a 15ml collection tube containing 6ml E8 + iRock•Sort GFP-expressing cells using FACS sorter with a 100-µm nozzle – typically we sort 12,000 cells•Plate sorted cells in 6-well plates at a density of 2000 cells/well in E8 + 2.5µM iRcokIsolation of iPSC ClonesUsually 8-10 days after sorting, single iPSC colonies are large enough to be picked. We usually pick 30-40 clones that are clearly isolated from 3-6 wells of a 6-well plate.•Aspirate media and add 3ml of fresh E8 + iROCK media per well at least 2h before picking.•Manually pick individual iPSC clones (we use a P200 pipette set at 100µl) using a stereo-microscope located inside a cell culture hood, and transfer each clone to a 1.5ml tube.•Pipet up and down 2-3 times to partially dissociate the clone and transfer 90 µl of cell suspension into a separate well of a 24-well plate (Matrigel-coated) containing 500µL of E8+iRock. Savethe remaining 10µl of cells suspension for HDR screening by direct PCR (the samples can bestored at -20o C).•Allow the cells to attach for 24–48 h and then add 500µl E8 media. Feed the cells with fresh E8 media every other day.Genomic DNA isolationProtocol adapted from Phire Animal Tissue Direct PCR Kit (Thermo Fisher; Cat#: F140WH).•For each clone, dilute 0.5µl of DNA Release Additive in 19.5µl Dilution Buffer. We make a master mix for all the clones. Add 20µl of the master mix to each tube containing the ~10 µl of residual cell suspension from the clone picking step.•Mix well and incubate at room temperature for 10 minutes.•Then heat the samples at 98°C for 2 minutes.•Add 25µl of molecular grade water and centrifuge at top speed for 1 min at room temperature to allow for cell debris sedimentation. Use 3µl of the resulting solution as a template in the PCRreaction.Direct PCRPerform PCR using PrimeSTAR GXL DNA Polymerase (Clontech) and primers that amplify a region of 500nt around the target nucleotide. For each sample combine the following:13.5µl ddH2O (for 3µl template DNA)5µl PrimeSTAR GXL Buffer 5X2µl dNTP (2.5mM each)0.5 µl 10µM Fw Primer0.5 µl 10µM Rv Primer0.5 µl PrimeSTAR GXL DNA Polymerase3.0 µl of cell sampleTotal volume = 25 µlSet up the following program on the thermocycler:2 min 98°C10 sec 98°C15 sec 62°C20 sec 68°C(repeat X40)2 min 68°Chold 4°CSanger SequencingFirst, run 5µl of the PCR reaction on a 1% agarose gel to verify genomic DNA amplification.Once verified, the unpurified PCR samples (~20 µl) are sent out for sequencing using either the forward or the reverse primer.。
Draft Guidance for Industry and Food and Drug Administration Staff
Draft Guidance for Industry and 1 Food and Drug Administration2 Staff3 45 eCopy Program for Medical Device6 Submissions78 DRAFT GUIDANCE910 This guidance document is being distributed for comment purposes only.11 Document issued on: [use release date of FR Notice]1213 You should submit comments and suggestions regarding this draft document within 30 days of 14 publication in the Federal Register of the notice announcing the availability of the draft guidance. 15 Submit written comments to the Division of Dockets Management (HFA-305), Food and Drug 16 Administration, 5630 Fishers Lane, rm. 1061, Rockville, MD 20852. Submit electronic17 comments to . Identify all comments with the docket number listed in 18 the notice of availability that publishes in the Federal Register . 1920 For questions regarding this document, contact the Premarket Notification (510(k)) Section or 21 the Premarket Approval Section of CDRH at 301-796-5640 or CBER’s Office of 22 Communication, Outreach and Development at 1-800-835-4709 or 301-827-1800. 23 2425262728U.S. Department of Health and Human Services 29 Food and Drug Administration 30 Center for Devices and Radiological Health 31 Center for Biologics Evaluation and Research32Preface3334Additional Copies3536Additional copies are available from the Internet. You may also send an e-mail request to37dsmica@ to receive an electronic copy of the guidance or send a fax request to 301-38827-8149 to receive a hard copy. Please use the document number (1797) to identify the39guidance you are requesting.4041Additional copies of this guidance document are also available from the Center for Biologics42Evaluation and Research (CBER), Office of Communication, Training and Manufacturers43Assistance (HFM-40), 1401 Rockville Pike, Suite 200N, Rockville, MD 20852-1448, or by44calling 1-800-835-4709 or 301-827-1800, or from the Internet at45/BiologicsBloodVaccines/GuidanceComplianceRegulatoryInformation/defau 46lt.htm.4748Table of Contents491.Introduction (1)502.What is an eCopy? (2)513.Are differences between the contents of an eCopy and paper submission acceptable? 2 524.For what submission types would an eCopy be required? (3)535.What submission types would FDA consider exempt from submission of an eCopy? .4 546.What submission types or applicants should be eligible for an eCopy waiver? (4)557.How many copies of a submission would be needed? (4)568.What are the processing steps for an eCopy? (5)57a. What are the standards for an eCopy? (5)58b. How do I know if my eCopy meets FDA’s standards for acceptance?? (6)59c. What if there is another processing party involved? (6)60d. How do you submit an eCopy to FDA? (6)61e. How does FDA process an eCopy? (7)629.What if your device is regulated by CBER? (7)63a. Will the new eCopy Program apply? (7)64b. Can you submit an electronic submission instead? (7)65c. How do you prepare and submit an electronic submission to CBER? (8)66Attachment 1 –Standards for eCopies (7)67A. Cover Letter that accompanies an eCopy (10)68B. Volume versus non-volume structure (11)69C. Folder naming convention for volume-based submissions that house PDF files (13)70D. Adobe Acrobat PDF file format (14)71E. Non-PDF file formats (15)72F. PDF file naming convention (16)73G. PDF file size limit (17)74H. Creating a PDF version from the source document (17)75I. Bookmarks and hypertext links within PDFs (20)76J. PDFs created from scanning paper documents (21)77K. Common mistakes in creating an eCopy (22)7879Guidance for Industry and Food and Drug 80Administration Staff8182eCopy Program for Medical Device83Submissions84851.Introduction86The purpose of this guidance is to explain the new electronic copy (eCopy) Program for medical 87device submissions. At this time, submission of an eCopy of a medical device submission is88voluntary. However, section 745A(b) of the Federal Food, Drug, and Cosmetic Act (FD&C89Act), added by section 1136 of the Food and Drug Administration Safety and Innovation Act90(FDASIA) (Pub. L. 112-144), requires the submission of eCopies after this guidance is finalized.91This draft guidance describes how the Food and Drug Administration (FDA) plans to implement 92the eCopy Program under section 745A(b) of the FD&C Act. The inclusion of an eCopy is93expected to improve the efficiency of the review process by allowing for the immediate94availability of an electronic version for review rather than relying solely on the paper version.9596This draft guidance provides, among other things, the standards for a valid eCopy under section 97745A(b)(2)(A) of the FD&C Act. In accordance with section 745A(b), following the issuance of98a final guidance on this topic, submission types identified in the final guidance must include an99eCopy in accordance with the standards provided by this guidance for the submission to be100processed and accepted for review by FDA. Submissions submitted without an eCopy and101eCopy submissions that do not meet the standards provided in this guidance will be placed on 102hold until a valid eCopy is submitted to FDA and verified to meet the standards, unless a waiver 103or exemption has been granted. While the submission is on hold, the review clock will not104begin.105106In Section 745A(b), Congress granted explicit statutory authorization to FDA to implement the 107statutory eCopy requirement by providing standards, criteria for waivers, and exemptions in108guidance. Accordingly, to the extent that this document provides such requirements under109section 745A(b) of the FD&C Act (i.e., standards, criteria for waivers, and exemptions),110indicated by the use of the words must or required,this document is not subject to the usual111restrictions in FDA’s good guidance practice (GGP) regulations, such as the requirement that 112guidances not establish legally enforceable responsibilities. See 21 CFR 10.115(d).113114However, this document also provides guidance on FDA’s interpretation of the statutory eCopy 115requirement and the Agency’s current thinking on the best means for implementing other aspects 116of the eCopy program. Therefore, to the extent that this document includes provisions that are 117not “standards,” “criteria for waivers,” or “exemptions” under section 745A(b)(2), this document 118does not create or confer any rights for or on any person and does not operate to bind FDA or the 119public, but will represent the Agency’s current thinking on this topic when finalized. The use of 120the word should in such parts of this guidance means that something is suggested or121recommended, but not required. You can use an alternative approach if the approach satisfies 122Draft – Not for Implementationthe requirements of the applicable statutes and regulations. If you want to discuss an alternative 123approach, contact the FDA staff responsible for implementing this guidance. If you cannot124identify the appropriate FDA staff, call the appropriate number listed on the title page of this125guidance.126127To comply with the GGP regulations and make sure that regulated entities and the public128understand that guidance documents are nonbinding, FDA guidances ordinarily contain standard 129language explaining that guidances should be viewed only as recommendations unless specific 130regulatory or statutory requirements are cited. FDA is not including this standard language in 131this draft guidance because it is not an accurate description of all of the effects of this guidance, 132when finalized. This guidance, when finalized, will contain both binding and nonbinding133provisions. Insofar as this guidance, when finalized, provides “standards,” “criteria for waivers,” 134and “exemptions” pursuant to section 745A(b) of the FD&C Act, it will have binding effect. For 135these reasons, FDA is not including the standard guidance language in this draft guidance.136137The eCopy Program is not intended to impact (reduce or increase) the type or amount of data the 138applicant1 includes in a submission to support clearance or approval. Please refer to other FDA 139device or program-specific guidance documents from CDRH140(/MedicalDevices/DeviceRegulationandGuidance/GuidanceDocuments/defau 141lt.htm) and CBER142/BiologicsBloodVaccines/GuidanceComplianceRegulatoryInformation/Guida 143nces/General/ucm214106.htm) for the appropriate contents for submissions.1441452.What is an eCopy?146An electronic copy (eCopy) is defined as an exact duplicate of the paper submission, created and 147submitted on a compact disc (CD), digital video disc (DVD), or in another electronic media148format that FDA has agreed to accept, accompanied by a copy of the signed cover letter and the 149complete original paper submission.21501513.Are differences between the contents of an eCopy and152paper submission acceptable?153While an eCopy is defined as an exact duplicate of the paper copy, there are limited cases in154which differences between the eCopy and the paper copy may be justified because a paper copy 155is not practical or appropriate for analysis purposes (e.g., raw data and statistical analysis156programs,3 data line listings to facilitate a bioresearch monitoring review) or is not feasible (e.g., 157videos, x-rays). The critical attribute of an eCopy is that it must include in electronic form all 1581 For the purposes of this guidance, applicant includes “submitter,” “sponsor,” or “holder.”2 An eCopy is not considered to be an electronic submission. For information on eSubmissions, refer to “FDAeSubmitter” (/ForIndustry/FDAeSubmitter/default.htm) and “Regulatory Submissions inElectronic Format for Biologic Products”(/BiologicsBloodVaccines/DevelopmentApprovalProcess/ucm163685.htm).3 For information on electronically submitted data, refer to “Clinical Data for Premarket Submissions”(/MedicalDevices/DeviceRegulationandGuidance/HowtoMarketYourDevice/PremarketSubmissi ons/ucm136377.htm).Draft – Not for Implementationdata required for that submission type.4 In other words, the eCopy must include all of the159required information for FDA review, whereas the paper copy can include a page cross-160referencing the location of certain information in the eCopy.161162The cover letter must contain the eCopy statement described in Attachment 1 and describe any 163differences between the paper version and the eCopy. The paper version must also have a164placeholder (e.g., a piece of paper printed with the appropriate section title or a divider165appropriately cross-labeled to the table of contents) that cross-references the eCopy to indicate 166that there are additional data/information in the eCopy and where in the eCopy that information 167is located.168169FDA will consider the eCopy loaded into the appropriate Center’s official document repository 170to be the official record. Any undisclosed differences between the eCopy and the paper version 171may need to be rectified and could delay the review of the submission.1721734. For what submission types is an eCopy required?174Once FDA finalizes this guidance, section 745A(b) of the FD&C Act, as added by section 1136 175of FDASIA, will require an eCopy for the following submission types5:176•Premarket notification submissions (510(k)s), including third party 510(k)s;177•Evaluation of automatic class III designation petitions (de novos);178•Premarket approval applications (PMAs)6;179•Modular PMAs;180•Transitional PMAs;181•Product development protocols (PDPs);182•Investigational device exemptions (IDEs);183•Humanitarian device exemptions (HDEs), including Humanitarian Use Device184designation requests (HUDs);185•Certain investigational new drug applications (INDs)7;186•Certain biologics license applications (BLAs)8; and187•Pre-Submissions9.1884 For example, the content requirements for a 510(k) submission are found in 21 CFR 870.87 and 807.92; those fororiginal PMA submissions are found in 21 CFR 814.20.5 Although not subject to the eCopy legislation, FDA accepts and strongly encourages eCopies for Master AccessFiles (“MAF” submissions), 513(g) Requests for Classification (“C” submissions), and Clinical LaboratoryImprovement Act (CLIA) Categorization – Exempt Device submissions (“X” submissions). If you choose to submit an eCopy, it must meet the standards outlined in Attachment 1.6 This includes all PMA submission types, including, but not limited to, original PMAs, panel-track supplements,180-day supplements, manufacturing site change supplements, and post-approval study supplements.7 Applicable only to those devices regulated by CBER that are also biologics under section 351 of the Public HealthService (PHS) Act and that also require submission of an IND prior to submission of a BLA. Such devices aregenerally those intended for use in screening donated blood for transfusion transmissible diseases.8 Applicable only to those devices regulated by CBER that are also biologics under Section 351 of the PHS Act,including those that do not require submission of an IND prior to the submission of the BLA. Such devicesgenerally include those reagents used in determining donor/recipient compatibility in transfusion medicine inaddition to those for use in screening blood for transfusion transmissible diseases.9 Refer to the draft guidance entitled, “Medical Devices: The Pre-Submission Program and Meetings with FDAStaff” (/MedicalDevices/DeviceRegulationandGuidance/GuidanceDocuments/ucm310375.htm).Draft – Not for Implementation189eCopies for all subsequent submissions to an original submission, including amendments,190supplements, and reports10 to the submission types identified above would also be required even 191if the original was submitted to FDA prior to implementation of the eCopy requirement.1921935.What submission types does FDA consider exempt from 194submission of an eCopy?195Due to the potential urgent nature of the following types of submissions, FDA considers these to 196be exempt from the requirement for an eCopy:197•Compassionate use IDE submissions;198•Emergency use IDE submissions11; and199•Emergency Use Authorizations (EUAs)12.200201However, we encourage you to submit eCopies of these submissions, when feasible, in order to 202facilitate the review process. In addition, this exemption would not preclude you from sending 203in pertinent electronic information, such as imaging data, as supporting information for these 204submission types when an eCopy is not submitted.2052066.What submission types or applicants are eligible for an207eCopy waiver?208FDA believes that, given the widespread availability of software to enable the creation of an209acceptable eCopy at little to no cost, all applicants should have the ability to provide an eCopy. 210Therefore, at this time, FDA does not anticipate the need for waivers, except as described in211Section 9.2122137.How many copies of a submission are needed?214The eCopy Program would not change the overall number of copies to submit to FDA. Upon 215finalization of this guidance document, an eCopy (with a signed cover letter) will serve as one of 216the required number of copies for the various submission types. (See Table 1 below.) FDA will 217accept additional eCopies (each with a signed cover letter) in lieu of additional paper copies as 218long as at least one paper copy is submitted along with the eCopy and the total number of219required copies remains the same.22022110 Reports include all reports submitted to an applicable submission type, including annual/periodic and post-approval reports. Section 745A(b) of the FD&C Act does not apply to Medical Device Reports submitted under 21 CFR Part 803 .11 Please refer to CDRH’s device advice page entitled “IDE Early/Expanded Access”(/MedicalDevices/DeviceRegulationandGuidance/HowtoMarketYourDevice/InvestigationalDevi ceExemptionIDE/ucm051345.htm#compassionateuse) and FDA’s “Guidance on IDE Policies and Procedures”(/MedicalDevices/DeviceRegulationandGuidance/GuidanceDocuments/ucm080202.htm) for additional details on compassionate and emergency use IDE submissions.12 Refer to the guidance entitled, “Emergency Use Authorization of Medical Products”(/RegulatoryInformation/Guidances/ucm125127.htm) for more information on EUAs.Draft – Not for ImplementationFor submission types for which only two copies are required to be submitted, one must be an 222eCopy and the other must be a paper copy. For submission types requiring more than two223copies, this policy would allow additional flexibility in how the application is submitted. For 224example, for an original PMA, you would submit: (1) one eCopy and five paper copies; (2) five 225eCopies and one paper copy; or (3) any other combination that results in six total copies as long 226as there is at least one eCopy and one paper copy.227228Table 1, provides the total number of copies to be submitted to FDA. As explained above, you 229must submit at least one eCopy and one paper submission. The format for the remaining copies 230(i.e., eCopy or paper) is your choice.231232Table 1 – Number of Copies for Submission233Submission Type Total Number ofCopies510(k)s 213Third Party 510(k)s 213Original PMAs and Panel-Track Supplements 614Other PMA supplement types 315PMA reports 2Modular PMAs 3HDEs Same as PMAs,16except for HUDdesignationrequests, whichrequire two.17PDPs Same as PMAsIDEs 318INDs 319BLAs 3Pre-Submissions 32348.What are the processing steps for an eCopy?235Below are the processing steps for the submission and acceptance of an eCopy.236237a.What are the standards for an eCopy?238With regard to the standards for an eCopy submitted to FDA, please refer to Attachment 2391. Because an eCopy cannot be accepted by our eCopy loading system if it does not meet 240the standards, you should carefully review this information.24124213 See 21 CFR 807.90(a)(3)(c).14 See 21 CFR 814.20(b)(2).15 See 21 CFR 814.39(c).16 See 21 CFR 814.104(b)(4).17 See 21 CFR 814.102(d).18 See 21 CFR 812.20(a)(3).19 See 21 CFR 312.23(d).b.How do I know before submission whether my eCopy meets FDA’s243standards for acceptance?244To confirm that your eCopy will meet FDA’s standards, we strongly encourage you to 245use the new free eSubmitter-eCopies tool available on FDA’s website at246/ForIndustry/FDAeSubmitter/ucm317334.htm. One of the benefits of 247utilizing the eSubmitter-eCopies tool is that it creates an eCopy in real-time that is248consistent with the standards. Use of the eSubmitter-eCopies tool is intended to prevent 249delays in review of your submission due to the need to resolve technical issues.250Although it is highly encouraged, you will not be required to utilize the eSubmitter-251eCopies tool and may choose to skip the eSubmitter step.252253Should you have any technical questions when generating your eCopy, please contact 254cdrhesub@ prior to submission of the eCopy to FDA.255256c.What if there is another processing party involved?257In the case that another party (e.g., law firm, consultant) submits a submission on behalf 258of an applicant, the eCopy must still meet the standards for an eCopy in order to be259successfully processed whether accomplished by you (the applicant) or the submitting 260party. While the applicant may or may not include their own cover letter as part of the 261eCopy, our standards require that the submitting party include a signed cover letter with 262an eCopy statement, as described in Attachment 1.263264In the case of Third Party 510(k)s, two separate CDs comprise the eCopy. The first CD 265includes the applicant’s submission and should be clearly marked as such. The contents 266of the CD must include a cover letter with an eCopy statement, as described in267Attachment 1, that the applicant has provided. The second CD includes the Accredited 268Person’s review records and should be clearly marked as such. The Accredited Person is 269responsible for ensuring that the CDs meet the standards in Attachment 1 for an eCopy. 270In addition, the Accredited Person is responsible for providing a signed cover letter that 271includes an eCopy statement, as described in Attachment 1, that speaks to both: (1) the 272Accredited Person’s portion of the eCopy and (2) the presence of the eCopy statement 273provided by the applicant. It is not sufficient for the Accredited Person to address only 274one of these two eCopy statement issues in their cover letter.275276d.How do you submit an eCopy to FDA?277An eCopy is submitted simultaneously with the paper submission(s). First, attach the 278signed cover letter with the eCopy statement to your eCopy. Then attach this eCopy279package to the paper submission(s) and send them to CDRH’s or CBER’s Document280Control Center20 (DCC). An eCopy that is sent to the DCC without a cover letter and 281accompanying paper submission(s) will be placed on hold.282283If more than one eCopy is to be submitted, then you must attach a signed cover letter as 284described above to each additional eCopy.28528620 Refer to 21 CFR 807.90 for the DCC addresses for CDRH and CBER.e.How does FDA process an eCopy?287If an eCopy passes the validation check, the cover letter and eCopy contents will be288loaded into the appropriate Center’s official submission repository.289290If an eCopy fails the validation check (i.e., is rejected), we will notify you in writing291(e.g., by email or fax) of the reason(s). The notification will describe the logistics for 292submitting a replacement eCopy, including how to properly mark it as a replacement293eCopy, the address to which to send it, and the submission number to write on it. It is 294important that you follow these directions to avoid delays in processing the replacement 295eCopy. The submission will be placed on hold until a valid replacement eCopy is296submitted to FDA and verified to meet the standards.2972989.What if your device is regulated by CBER?299a.Will the new eCopy Requirement apply?300Yes, unless your submission is an entirely electronic submission exempted under this 301guidance, as described below. Upon implementation of the statutory requirement, all 302medical device submission types listed in Section 4 must be accompanied by an eCopy 303regardless of the Center in FDA in which the submission will be reviewed unless the304requirement is waived or exempted. Accordingly, submissions for devices subject to 305review under the FD&C Act and submitted by filing paper copies with CBER’s DCC 306must be accompanied by an eCopy, except where exempted as described below.307308While many submissions made to CBER are still in paper format and require submission 309of multiple copies, CBER is also currently able to receive and manage submissions that 310are entirely electronic.311312Submissions for devices that are subject to licensure under the Public Health Service313(PHS) Act, including biologics license applications and supplements, investigational new 314drug applications, and EUAs and pre-submissions for these devices, may be submitted as 315entirely electronic submissions as detailed in sections 9b and 9c below. FDA will316exempt such entirely electronic submissions from the eCopy requirement.317318FDA additionally waives the eCopy requirement to submit paper copies of any entirely 319electronic submission made to CBER. Accordingly, entirely electronic submissions that 320comply with CBER guidance identified in Section 9.c. below do not need to be321accompanied by paper copies.322323b.Can you submit an electronic submission instead?324Yes, and there are several advantages for both industry and for CBER staff when you 325choose to make submissions electronically.326327The main advantage to you is in the financial savings that will likely result. The costs 328associated with printing, binding, labeling, and shipping multiple paper copies can be 329significant, especially for submissions that contain a great deal of supporting330Draft – Not for Implementationdocumentation. Likewise, we anticipate that FDA will recognize financial savings in that 331FDA avoids the costs associated with tracking, routing, and storing large amounts of332paper when you choose to submit electronically.333334Another advantage with the use of the electronic submission process is that all parties 335involved in the submission and review are referencing the same document – the336electronic one. There is no question about whether the paper copy is an exact copy of the 337eCopy. Electronic submissions may also reduce the need for reviewers to request re-338submission of previously submitted information due to an inability to read or interpret the 339information on the paper copy, as sometimes occurs when documents are photocopied. 340341c.How do you prepare and submit an electronic submission to CBER?342CBER has several resources available to applicants who choose to submit electronic343submissions as outlined in the document “Regulatory Submissions in Electronic Format 344for Biologic Products.”345(/BiologicsBloodVaccines/DevelopmentApprovalProcess/ucm163685 346.htm). Thus, specific details are available in the cited references and will not be repeated 347in this guidance.348349For devices that are regulated under the PHS Act and require the submission of a BLA, 350consult the guidance document entitled “Providing Regulatory Submissions to the Center 351for Biologics Evaluation and Research (CBER) in Electronic Format - Biologics352Marketing Applications”353(/downloads/BiologicsBloodVaccines/GuidanceComplianceRegulator 354yInformation/Guidances/General/UCM192413.pdf) for details on preparing your355electronic submission. Note that certain sections of this guidance, for example, those on 356pharmacology and toxicology, are generally not pertinent to licensed devices.357358For guidance on preparing electronic submissions for other device submissions (e.g.,359510(k)s, PMAs) sent to CBER, please see “Guidance for Industry: Providing Regulatory 360Submissions in Electronic Format - General Considerations”361(/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Guidances 362/UCM072390.pdf) and “CBER SOPP 8110: Submission of Paper Regulatory363Applications to CBER”364(/BiologicsBloodVaccines/GuidanceComplianceRegulatoryInformati 365on/ProceduresSOPPs/ucm079467.htm), which includes information about providing366electronic copies to CBER.367368We are currently developing additional, updated guidance for other electronic369submissions sent to CBER and have issued a revised, updated draft guidance document 370for comment entitled, “Draft Guidance for Industry: Providing Regulatory Submissions 371in Electronic Format-General Considerations”372(/RegulatoryInformation/Guidances/ucm124737.htm). When373finalized, this document will provide an additional resource for applicants preparing374electronic submissions.375376。
生命新诠释：重新编码细菌基因组
62019 7 世界科学生命新诠释：重新编码细菌基因组敦郊外贾森·秦（Jason Chin）的实验室里，一些细菌在撒有营养液体培养基的塑料小盘子里欢快地吃着、繁殖着、呼吸着，看上去很普通，但它们与地球上的其他任何生物——从真菌、鳄梨到郁金香、知更鸟和大象——都有着本质的不同，它们是用不同的遗传密码人工合成的微生物。
事实上，这些大肠杆菌拥有有史以来最广泛的“重新编码”基因组，秦和他在英国医学研究委员会分子生物学实验室的同事最近在《自然》杂志上报道称。
“这是一个重大的里程碑。
”哈佛大学生物学家乔治·丘奇（George Church）说，虽然他没有参与这项新研究。
以下是丘奇和其他几位科学家对合成生物学领域内所取得的这一里程碑式成就的解读。
这个基因组“合成”了什么？所有一切。
科学家把从供应商那里订购的DNA 构建块结合在一起合成了有史以来最大的基因组。
这一过程被称为“编写”基因组，这是基因组编写计划项目（Genome Project-write project，简称“GP-write”）科学家正在做的事情。
(“读取”基因组是人类基因组计划所要做的——确定其数百万或数十亿个DNA 字母或碱基的序列。
)2010年，遗传学先驱克雷格·文特尔和他的同事们用这种方法组装了支原体分枝杆菌的整个基因组，科学家使用GP-write 已经合成了构成面包酵母单一菌株基因组16条染色体中的2条。
但支原体基因组只有108万对碱基，酵母染色体不到100万对。
大肠杆菌有400万对，秦的团队将其切成37个片段并合成了它们，这个过程他很理所当然地称之为“创世起源”。
什么是基因重新编码？本质上来说，基因重新编码改变了基因字典。
地球上的每一种生物都使用相同的64个密码子（由DNA 的A、编译 秦雪F E A T U R E专稿伦Syn61是在琼脂平板上培养的一种“重新编码”基因组的大肠杆菌Copyright©博看网 . All Rights Reserved.72019 7 世界科学T、C 和G 组成的三字母组合）来指定构成蛋白质的氨基酸。
DNA折纸技术
——DNA折纸技术
2013-11-14
2006年美国加州理工学院计算机生物工程师Paul Rothemund开发了一种“DNA折纸术”（ DNA origami technique），像折叠一条长带子那样，把一条DNA长链反 复折叠，形成需要的图形，就像用一根单线条绘制出整幅图画。 折叠后的DNA长链，通过一些“钉子”对适当位置上的DNA 短链加以固定，从而构建出了一张二维结构的精美图谱。
Compared to many other nanoscale systems designed for drug delivery such as polymer micelles and inorganic particles, DNA origami based construction has several advantages: (i) same size, shape, and charge for each particle instead of the size distribution often seen for self-assembled nanostructures; (ii) perfect control of the placement of functionalities on the structure using specific oligos.
DNA折纸技术可以将DNA折叠为二维或三维的纳米级形状。 这种技术是由美国加州理工学院的Paul Rothemund博士发 明的，在诊断设备的新型分子传感器、分子药物容器、药物 递送系统的开发，以及确定酶的级联反应中，DNA折纸技术 都将具有重要的应用。在许多的实验室中， DNA支架，或者 更为精巧的DNA结构正在被用于各种新颖的应用上。
IDEXX 4Dx
Screening for vector-borne disease IDEXX 4Dx® Plus Test clinical reference guideWith the IDEXX 4Dx ® Plus T est, a positive result can also be an indication of ticks and and the pathogens they carry. Know more with every resultdetect antibodies to these pathogens When you use the IDEXX 4Dx Plus T est as a screening tool, you maycarried by these ticks Anaplasmaphagocytophilum Borrelia burgdorferi (Lyme disease)Ehrlichia ewingiiEhrlichia canis Anaplasma platysBabesia spp.Rocky Mountain spotted feverEhrlichia chaffeensis TularemiaRocky Mountain spotted fever STARIBartonella spp.Babesia spp.Ehrlichia canis Brown dog tickRhipicephalus sanguineusAmerican dog tickDermacentor variabilisBlack-legged tick (deer tick)Ixodes scapularis Ixodes pacificusLone star tickAmblyomma americanumRocky Mountain spotted fever TularemiaGeographic tickdistribution as of 20213that may also transmit other pathogens and infections to dogs and peopleLyme diseasebacterium Borrelia burgdorferi cases that have mild to severe disease.* S erology is typically used to diagnose Lyme disease. B. burgdorferi Did you know?•D ogs testing positive for antibodies to the C 6 peptide had 43% increased risk of having chronic kidney disease (CKD) compared to seronegative dogs.4• T he C 6 peptide used in the IDEXX 4Dx ® Plus Test and Lyme Quant C 6® Antibody Test does not cross-react with the antibody response to commercially available Lyme vaccines.5 • D ogs with seroreactivity to both B. burgdorferi and Anaplasma phagocytophilum may have two times the risk of developing clinical illness than singularly infected dogs.2Borrelia burgdorferiPrimary vectorsIxodes scapularis or Ixodes pacificus Black-legged tick (deer tick)Pathology• Localizes in tissues of infected dogs • Synovitis (may be subclinical) • Lyme nephritisClinical presentationChronic infection with clinical signs that may present acutely:• Fever, anorexia• Polyarthritis, lameness• Rapidly progressive renal failure • Neurologic syndromesLaboratory abnormalities• Elevated C 6 antibody level ≥ 30 U/mL • May have proteinuria• M ay have IDEXX SDMA ® T est result > 14 µg/dLCKD monitoring• Chemistry panel with SDMA – R ecommended to evaluate forthe development of protein-losing kidney disease• Urinalysis with Reflex UPC – R ecommended to evaluate forproteinuria • CBC with blood film evaluation – R ecommended as part of aminimum databaseHeartworm diseaseDirofilaria immitis, the causative agent of heartworm disease, is transmitted when mosquitoes infected with D. immitis larvae feed on (or bite) a healthy dog. Heartworm disease has subtle or mild clinical signs in the early stages, making preventive measures so much more important—especially as advanced infection may result in death.Did you know?•D espite availability of monthly preventives, prevalence rates of canine heartworm have remained consistent nationwide.7•T he American Heartworm Society (AHS) and the Companion Animal Parasite Council (CAPC) recommend testing all dogs for both antigen and microfilariae annually.7,8•F or more information and current recommendations on treating canine heartworm disease, goto or . Dirofilaria immitisPrimary vectorMosquitoPathologyInfective larvae (L3) mature to adult worms in the heart and pulmonary arteriesClinical presentation Asymptomatic at first, later developing:• Mild, persistent cough• Lethargy• Exercise intolerance• Reduced appetite• Weight lossLaboratory abnormalities that may be seen • Eosinophilia• Azotemia• Increased liver enzymes• ProteinuriaAnaplasmaphagocytophilumAnaplasma platysPrimary vectorsIxodes scapularis Ixodes pacificusBlack-legged tick (deer tick)Rhipicephalus sanguineus (brown dog tick)PathologyInfects neutrophilsInfects plateletsClinical presentationCan present acutely:• F ever • Anorexia • Lethargy• Polyarthritis, lameness • Neurologic signsUsually minimal clinical signs, but some dogs may have:• F ever • Uveitis• Petechiae and ecchymoses • EpistaxisLaboratory abnormalities• Thrombocytopenia• Anemia• Lymphopenia• Increased liver enzymesOther findings may be seen:• Decreased albumin • Increased globulin• Increased ALP and ALT • Proteinuria• Decreased Urine SG • Increased UPC NotePrevious infection may not prevent reinfection and persistent infections are possible.9,10Canine anaplasmosisCanine granulocytic anaplasmosis is caused by the bacterium Anaplasma phagocytophilum (transmitted by the black-legged tick [deer tick]). Anaplasma platys (transmitted by the brown dog tick) is the cause of infectious cyclic thrombocytopenia.Did you know?•M any mammalian species, including humans, are susceptible to A. phagocytophilum infection. •D ogs coinfected with Anaplasma and other bacterial pathogens may have more complex disease presentations and respond more slowly to therapy.• A .platys infects canine platelets and is frequently seen as a coinfection with Ehrlichia canis .Canine ehrlichiosisCanine ehrlichiosis is caused by the bacteria Ehrlichia canis (transmitted by the brown dog tick) and Ehrlichia ewingii (transmitted by the lone star tick). Canine Ehrlichia infections may progress to the subclinical phase or may become chronic infections.Ehrlichia canisEhrlichia ewingiiPrimary vectorRhipicephalus sanguineus (Brown dog tick)Amblyomma americanum (Lone star tick)PathologyInfects monocytes Infects granulocytesClinical presentation• Fever, anorexia, lethargy • Bleeding disorders • Polyarthritis, lameness • Lymphadenomegaly • Neurologic signs• Fever, anorexia, lethargy • Polyarthritis, lameness • Neurologic signsLaboratory abnormalitiesNotePrevious infection may not prevent reinfection, and persistent infections are possible.12,14Did you know?• D ogs coinfected with E. canis and A. platys were found to have more severe anemia and thrombocytopenia than dogs with either single infection.11• I n a study of healthy dogs with antibodies to E. canis , 39% were thrombocytopenic.12• C hronic E. canis infections, if left untreated, can lead to bone marrow dysfunction or kidney disease.• D ogs with Ehrlichia antibodies in E. canis endemic areas had a 112% increased risk of developing chronic kidney disease (CKD).13CKD monitoring• Chemistry panel with SDMA - R ecommended to evaluate forsecondary kidney disease.• Urinalysis with UPC - R ecommended to evaluatefor proteinuria • CBC with blood film - R ecommended as part of aminimum database• Anemia• Thrombocytopenia • Hyperglobulinemia • ProteinuriaOther clinical findings may include:• Decreased albumin • Increased globulin• Mild increased ALT and ALP • Increased SDMA • Creatinine• Decreased urine specific gravity, proteinuria • Increased urine protein:creatinine (UPC) ratio.Serology and PCR for sick patients For dogs presenting with clinical signs consistent with a vector-borne disease, usingserology and PCR together improves your ability to make an accurate diagnosis.Serology Polymerase chain reaction (PCR)Measures Antibody response of host Nucleic acid (DNA) from pathogenBenefits Useful for screening as well as diagnosisof infection Specifically identifies pathogens indicating active infectionLimitations Clinical signs may precede a measurableantibody response A negative PCR result does not necessarily rule out infectionDogs with ehrlichiosis and anaplasmosis may present with clinical signs at different times after infection. Which sick dog are you dealing with? Benefits and limitations of each diagnostic methodrecrudescence presents presents presentsWhen to use the IDEXX vector-borne disease RealPCR™ panels• S ick patients with clinical signsand/or laboratory abnormalitiesconsistent with a vector-borne illness• P atients with subclinical infectionsbased on history, physicalexamination, serology, and clinicallaboratory findings“No single test is sufficientfor diagnosing an infectious disease in a sick patient.”Edward Breitschwerdt, DVM, DACVIM*Professor, Internal MedicineCollege of Veterinary Medicine,North Carolina State University* D r. Breitschwerdt has a business relationship with IDEXX pursuant to which he receives compensation from IDEXX from time to time. The views expressed in this guide are solely those of Dr. Breitschwerdt.References1. G eneral guidelines: Parasite testing and protection guided by veterinarians [dog].Companion Animal Parasite Council website. /guidelines /general-guidelines. Updated July 29, 2020. Accessed November 17. 2021. 2. B eall MJ, Chandrashekar R, Eberts MD, et al. Serological and molecular prevalenceof Borrelia burgdorferi , Anaplasma phagocytophilum , and Ehrlichia species in dogs from Minnesota. Vector-Borne Zoonotic Dis . 2008;8(4):455–464. doi:10.1089/vbz.2007.0236 3. R egions where ticks live [maps]. Centers for Disease Control and Prevention website./ticks/geographic_distribution.html. November 17, 2021. 4. D rake C, Coyne M, McCrann DJ, Buch J, Mack R. Risk of development of chronickidney disease after exposure to Borrelia burgdorferi and Anaplasma spp. T op Companion Anim Med. 2020;42:100491. doi:10.1016/j.tcam.2020.100491 5. O ’Connor TP , Esty KJ, Hanscom JL, Shields P , Philipp MT . Dogs vaccinatedwith common Lyme disease vaccines do not respond to IR 6, the conserved immunodominant region of the VlsE surface protein of Borrelia burgdorferi.Clin Diagn Lab Immunol. 2004;11(3):458–462. doi:10.1128/CDLI.11.3.458-462.2004 6. S traubinger RK. PCR-based quantification of Borrelia burgdorferi organisms in caninetissues over a 500-day postinfection period. J Clin Microbiol. 2000;38(6):2191–2199. doi:10.1128/JCM.38.6.2191-2199.2000 7. C APC prevalence maps: heartworm [dog]. Companion Animal Parasite Councilwebsite. /maps/#/2021/all-year/heartworm-canine/dog/united-states. Accessed November 17, 2021.8. A merican Heartworm Society. Current canine guidelines for the prevention, diagnosis,and management of heartworm infection in dogs . 2020. Accessed November 17, 2021. https:///images/pdf/AHS_Canine_Guidelines_11_ 13_20.pdf?1605556516 9. E genvall A, Lilliehöök I, Bjöersdorff A, et al. Detection of granulocytic Ehrlichia speciesDNA by PCR in persistently infected dogs. Vet Rec . 2000;146(7):186–190. doi:10.1136/vr.146.7.186 10. B reitschwerdt EB, Hegarty BC, Qurollo BA, et al. Intravascular persistence ofAnaplasma platys , Ehrlichia chaffeensis , and Ehrlichia ewingii DNA in the blood of a dog and two family members. Parasit Vectors . 2014;7:298. doi:10.1186/1756-3305-7-298 11. G aunt S, Beall M, Stillman B, et al. Experimental infection and co-infection of dogs withAnaplasma platys and Ehrlichia canis : hematologic, serologic and molecular findings. Parasit Vectors . 2010;3(1):33. doi:10.1186/1756-3305-3-33 12. H egarty BC, de Paiva Diniz PP , Bradley JM, Lorentzen L, Breitschwerdt E. Clinicalrelevance of annual screening using a commercial enzyme-linked immunosorbentassay (SNAP 3Dx) for canine ehrlichiosis. J Am Anim Hosp Assoc. 2009;45(3):118–124. doi:10.5326/0450118 13. B urton W, Drake C, Ogeer J, et al. Association between exposure to Ehrlichia spp.and risk of developing chronic kidney disease in dogs. J Am Anim Hosp Assoc . 2020;56(3):159–164. doi:10.5326/JAAHA-MS-7012 14. S tarkey LA, Barrett AW, Beall MJ, et al. Persistent Ehrlichia ewingii infection indogs after natural tick infestation. J Vet Intern Med . 2015;29(2):552–555. doi:10.1111/jvim.12567 15. S nellgrove AN, Krapiunaya I, Ford SL, et al. Vector competence of Rhipicephalussanguineus sensu stricto for Anaplasma platys . Ticks Tick Borne Dis. 2020;11(6):101517. doi:10.1016/j.ttbdis.2020.101517Depend on the most accurate and comprehensive screenSNAP 4Dx Plus T estReference-laboratory quality in the palm of your hand, for superior diagnostic accuracy at the pointof care.Lab 4Dx Plus T estAvailable from IDEXX Reference Laboratories as a stand-alone test or as part of a more comprehensiveparasite screen with the Fecal Dx Antigen Panel with Lab 4Dx Plus Test-Canine.SNAP ® technology uses a proprietary three-step process to deliver dependable sensitivity and specificity.Available in-clinic or from IDEXX Reference LaboratoriesStrengthen the bonds.IDEXX Laboratories, Inc.One IDEXX DriveWestbrook, Maine 04092United StatesAmerican dog tick (Dermacentor variabilis) photographer: Susan E. Ellis, USDA-APHIS-PPQ. Black-legged tick (Ixodes scapularis), lone star tick (Amblyomma americanum), and brown dog tick (Rhipicephalus sanguineus) photographer: James L. Occi.© 2022 IDEXX Laboratories, Inc. All rights reserved. • 09-69074-13All ®/TM marks are owned by IDEXX Laboratories, Inc. or its affiliates in the United States and/or other countries. The IDEXX Privacy Policy is available at .。
PFU PaperStream IP扫描驱动程序说明书
Advanced software for maximized efficiency Bypass the inconvenience of making fineadjustments to OCR settings with the Paper-Stream IP scanner driver, supporting both TWAIN and ISIS. The software automatically converts scanned images into exceptionally clean images, supporting OCR accuracy even when scanning documents with background patterns or wrinkled and soiled documents. Seamlessly linked to PaperStream IP, Paper-Stream Capture effectively and efficiently feeds information into your organization workflow with its various batch scanning capture features. Automatically utilizing data extracted from barcodes and patch codes, the software also determines your preferred saving destinations and eliminates timeallocated to routine tasks.*Smallest out of scanners that read A3 sized documents, scan A4landscape at over 40 ppm, and all ADF type scanners (based on the investigation by PFU Limited as of March 1st, 2017).Boosted workflow with various functions The scanner is capable of scanning a wide variation of documents: A8 to A3 documents and plastic cards as well as thick folded A2 documents, drawings folded in half, multi-layered receipts, and envelopes by switching between Manual/Single mode. Load documents with ease and reduce your workload before and after scanning, with the scanner’s independent side guides helping you align edges of variously sized documents. Keep track of scanner operations and scan up to 50 previously registered jobs, using the LCD operation panels. The Stacking Control function, a key stable paper feeding mecha-nism, also assists in controlling paper output speed and makes sure that documents are ejected neatly . Operation of all these functions is fairly simple and ensures users with efficient workflow assistance.As the smallest scanner of its class*, the fi-7480 scans A4 landscape documents at 80 ppm/160 ipm (200/300 dpi). Assistance for safe and reliable scanningThe fi-7480 possesses diverse stable paper feeding mechanisms, with its brake rollers functioning as its fundamental mechanism to separate each scanned document. Minimize risk of document damage with stable paper feeding that Paper Protection function provides through its detection of anomalies in sound and monitoring of paper feed distance. And bid farewell to missing edges with the scanner’s Skew Reducer mechanism. Potential information loss, resulting from multiple sheets being fed through the scanner at once, is also no longer an issue with UltrasonicMulti-feed detection.The most compact A3 scanner that reliably handles mixed batches and large sizesDatasheetFUJITSU Image Scanner fi-7480ContactTrademarksABBYY™ FineReader™ Engine © ABBYY. OCR by ABBYY. ABBYY and FineReader are trademarks of ABBYY Software, Ltd. which may be registered in some jurisdictions. ISIS is a trademark of Open Text. Microsoft, Windows, and Windows Server are either registered trademarks or trademarks of Microsoft Corporation in the United States and/or other countries. Linux is the registered trademark of Linus Torvalds in the U.S. and other countries. Any other products or company names appearing in this document are the trademarks or registered trademarks of the respective companies.Safety PrecautionsBe sure to carefully read all safety precautions prior to using this product and use this device as instructed. Do not place this device in wet, moist, steamy, dusty or oily areas. Using this product under such conditions may result in electrical shock, fire or damage to this product. Be sure to limit the use of this product to listed power ratings.ENERGY STAR®PFU Limited, a Fujitsu company, has determined that this product meets the ENERGY STAR® guidelines for energy efficiency. ENERGY STAR® is a registered trademark of the United States.Specifications are subject to change without notice. Visit your local Fujitsu website for more information.*1 Actual scanning speeds are affected by data transmission and software processing times. *2 Indicated speeds are from using JPEG compression. *3 Indicated speeds are from using TIFF CCITT Group 4 compression.*4 Selectable maximum density may vary depending on the length of the scanned document. *5 Limitations may apply to the size of documents that can be scanned, depending on system environment, when scanning at high resolution (over 600 dpi). *6 Capable of scanning documents longer than A3 (297 x 420 mm / 11.7 x 16.5 in.) sizes. When using PaperStream IP (TWAIN/ISIS) to scan at 200 dpi, the maximum scanning length is 5,588 mm (220 in.). *7 Capable of scanning up to 3 cards at a time. (Note: does not set more than one embossed card at a time.) *8 Maximum capacity depends on paper weight and may vary. *9 Numbers are calculated using scanning speeds and typical hours of scanner use, and are not meant to guarantee daily volume or unit durability. *10 Intelligent Sonic Paper Protection. *11 Excludes the ADF paper chute and Stacker. *12 Requires PaperStream IP 1.60.0 or earlier and PaperStream Capture 2.8.2 or earlier. *13 Functions equivalent to those offered by PaperStream IP may not be available with the Image Scanner Driver for Linux or WIA Driver. *14 Refer to the fi Series Support Site for driver/software downloads and full lineup of all supported operating system versions.4,000,000 printed characters or 6 months after opening the bagPrint Cartridge CA00050-0262Brake Roller PA03710-0001 Every 200,000 sheets or one year Pick RollerPA03670-0002Every 200,000 sheets or one yearConsumablesPA43404-A675 PaperStream Capture Pro optional license PaperStream Capture Pro Scan Station (DP)Post Imprinter (FI-748PRB) PA03710-D401 Back-side printing on document OptionsADF paper chute, AC cable, AC adapter, USB cable, Setup DVD-ROMIncluded ItemsMulti image output, Automatic color detection, Blank page detection, Dynamic threshold (iDTC), Advanced DTC, SDTC,Error diffusion, Dither, De-Screen, Emphasis, Dropout color (None/Red/Green/Blue/White/Saturation/Custom), sRGBoutput, Hole punch removal, Index tab cropping, Split image,De-Skew, Edge correction, Vertical streaks reduction, Cropping, Static thresholdImage Processing FunctionsPaperStream IP driver (TWAIN/TWAIN x64/ISIS), WIA Driver *¹³,Image Scanner Driver for Linux (SANE)*¹³*¹⁴, PaperStream Capture, PaperStream ClickScan *¹⁴, Software Operation Panel, Error Recovery Guide, ABBYY FineReader for ScanSnap™*¹⁴, Scanner Central Admin, 2D Barcode for PaperStream *¹⁴Included Software / DriversWindows® 10, Windows® 8.1, Windows® 7, Windows Server® 2019, Windows Server® 2016, Windows Server® 2012 R2, Windows Server® 2012, Windows Server® 2008 R2, Windows Server® 2008*¹², Linux (Ubuntu)Supported Operating System7.6 kg (16 lb)Weight380 x 209 x 168 mm (15.0 x 8.2 x 6.6 in.)Dimensions *¹¹(Width x Depth x Height)ENERGY STAR®, RoHSEnvironmental Compliance 20 to 80% (non-condensing)Relative Humidity 5 to 35 °C (41 to 95 °F)Temperature Operating Environment Less than 0.35 WAuto Standby (Off) Mode1.4 W or less Sleep Mode43 W or less Operating Mode Power Consumption AC 100 to 240 V ±10 %Power Requirements USB 3.0 / USB 2.0 / USB 1.1InterfaceLag detection, Sound detection (iSOP)*¹⁰Paper Protection Overlap detection (Ultrasonic sensor),Length detectionMultifeed Detection 24,000 sheetsExpected Daily Volume *⁹100 sheets (A4 80 g/m² or Letter 20 lb)ADF Capacity *⁸27 to 413 g/m² (7.2 to 110 lb)A8 size: 127 to 209 g/m² (34 to 56 lb)Plastic Card Up to 1.4 mm *⁷Paper Paper Weight (Thickness)5,588 mm (220 in.)Long Page Scanning *⁶50.8 x 69 mm (2 x 2.7 in.) (Portrait)Minimum304.8 x 431.8 mm (12 x 17 in.)Maximum Document Size White / Black (selectable)Background Colors Color: 24-bit, Grayscale: 8-bit, Monochrome: 1-bit Output Format 50 to 600 dpi (adjustable by 1 dpi increments)1,200 dpi (driver)*⁵Output Resolution *⁴(Color / Grayscale / Monochrome)600 dpiOptical ResolutionWhite LED Array x 4 (front x 2, back x 2)Light Source Color CCD x 2 (front x 1, back x 1)Image Sensor Type Scanning Speed *¹ (A4 Portrait)(Color *²/Grayscale *²/Monochrome *³)Simplex: 80 ppm (200/300 dpi)Duplex: 160 ipm (200/300 dpi)Simplex: 65 ppm (200/300 dpi)Duplex: 130 ipm (200/300 dpi)Scanning Speed *¹ (A4 Landscape)(Color *²/Grayscale *²/Monochrome *³)ADF (Automatic Document Feeder) / Manual Feed, DuplexScanner TypeTechnical InformationIndonesiaPT Fujitsu Indonesia Tel: +62 21 570 9330 *********************.com/id/scannersMalaysiaFujitsu (Malaysia) Sdn Bhd Tel: +603 8230 4188askfujitsu .my@/my/scannersPhilippinesFujitsu Philippines, Inc. Tel: +63 2 841 8488 ***************.com/ph/scannersSingaporeFujitsu Asia Pte Ltd Tel: +65 6512 7555 *******************/sg/scannersThailandFujitsu (Thailand) Co., Ltd. Tel: +66 2 302 1500 *******************/th/en/scannersVietnamFujitsu Vietnam Limited Tel: + 84 4 2220 3113 ****************.com/vn/en/scanners。
CRISPR基因编辑技术
TALEN原理
TALEN的特异性打靶的原理：
一对可以特异性识别靶基因的TALE，定位到需要编辑的基因组区域； 然后非特异性核酸内切酶 FokI切断双链DNA从而造成DNA双链断裂（doublestrand break，DSB）； 再通过DNA的自我修复，引起碱基的缺失或突变，从而引起基因突变。 FokI只有在形成二聚体的时候才有内切酶活性。
palindromic repeat /Cas-based RNA-guided DNA endonucleases）
特异性 DNA识别域
+
非特异性 核酸内切酶
ZFN原理
ZFN=蛋白的DNA识别域+核酸内切酶
DNA识别域： 由一系列 Cys2-His2锌指蛋白（zinc-fingers）串联组成（一般3~4个），每
2007 年，Barrangou 等首次发现细菌可能利用CRSPR 系统抵抗噬菌体入 侵；2008 年，Marraffini 等发现细菌CRISPR 系统能阻止外源质粒的转 移，首次利用实验验证了CRISPR 系统的功能
2013 年初，MIT 的研究组首次利用CRISPR/Cas9 系统对人293T 细胞 EMX1 和PVALB 基因以及小鼠Nero2A 细胞Th 基因实现了定点突变。同 年Mali 利用CRISPR/ Cas9 在人293T 细胞和K652 细胞基因的靶位点形成 双链或单链的切口，从而激活细胞的DNA 修复机制高效介导外源基因定 点插入。
CRISPR-Cas系统简介
CRISPR-Cas系统的研究历史
1987 年，日本课题组在K12 大肠杆菌的碱性磷酸酶基因附近发现串联间 隔重复序列，随后发现其广泛存在于细菌和古细菌的基因组中。2002 年， 正式将其命名为成簇的规律间隔的短回文重复序列
2023年高二下半期期中生物试卷带参考答案和解析(江苏省徐州市)
选择题下列不是基因工程理论依据的是（）A.细胞结构相同B.DNA双螺旋结构相同C.遵循中心法则D.共用一套密码子【答案】A【解析】1、基因工程又叫DNA重组技术，是指按照人们的意愿，进行严格的设计，并通过体外DNA重组和转基因等技术，赋予生物以新的遗传特性，从而创造出更符合人们需要的新的生物类型和生物产品。
2、一种生物的基因能与另一种生物基因重组的原因是不同生物的DNA具有相同的结构和化学组成。
3、一种生物的基因能在另一种生物体内表达的原因是生物共用一套遗传密码子。
A、不同的细胞结构不一定相同，如真核细胞和原核细胞的结构相差较大，原核细胞没有成形的细胞核，且细胞的结构与基因工程没有直接的关系，A错误；B、不同生物的DNA分子的结构相同，都具有独特的双螺旋结构，可以相互连接起来，B正确；C、不同的生物都遵循中心法则，C正确；D、不同的生物翻译过程中共用一套遗传密码，因此目的基因在受体细胞可以表达出相同的蛋白质，D正确。
故选A。
选择题判断下列有关基因工程和酶的相关叙述，正确的是()A. 限制酶不能切割烟草花叶病毒的核酸B. 载体的化学本质与载体蛋白相同C. 同种限制酶既可以切割目的基因又可以切割质粒，因此不具备专一性D. DNA连接酶可催化脱氧核苷酸链间形成氢键【答案】A【解析】本题考查基因工程的工具的知识，意在考查考生的识记能力和理解所学知识要点，把握知识间内在联系的能力.限制酶是DNA内切酶，烟草花叶病毒是RNA病毒，酶有专一性，因此不能切割，A正确.基因工程的载体有质粒、噬菌体和动植物病毒，细胞膜运输载体是蛋白，不相同，B错误.同种限制酶既可以切割目的基因又可以切割质粒，但识别的都是相同的核苷酸序列并且在相同的切点作用，仍然体现了酶的专一性，C错误.DNA连接酶可催化DNA片段间形成磷酸二酯键，D错误.选择题现代生物科学技术中涉及的一些生物学概念，不符合集合图所示关系的是（）A.①动物细胞核移植②动物细胞工程③细胞工程B.①cDNA文库②部分基因文库③基因组文库C.①植物组织培养②植物细胞工程③细胞工程D.①质粒②载体蛋白③DNA【答案】D【解析】1、基因工程常用的运载体：质粒、噬菌体的衍生物、动植物病毒。
Geant4 Installation Guide
Geant4 Installation Guide For setting up Geant4 in your computing environmentVersion: geant4 9.4Publication date 17 December, 2010Geant4 CollaborationGeant4 Installation Guide : For setting up Geant4 in your computing environmentby Geant4 CollaborationVersion: geant4 9.4Publication date 17 December, 2010Table of Contents1. Installation Introduction (1)1.1. Supported Computers and Operating Systems (1)1.2. Required Software (1)1.3. Visualization Software (1)1.4. Software for Analysis and Histogramming (2)2. Installation Procedures (3)2.1. Using the Configure Script for installation (3)2.2. Configuring the Environment to Use Geant4 (4)2.3. Installing Geant4 Manually (4)2.3.1. Required Environment Variables (4)2.3.2. Optional Environment Variables (4)2.4. Integrating Geant4 into a Generic Framework (6)3. Tips for Installing on Windows (7)3.1. Windows with the Cygwin Toolset and Microsoft Visual C++ (7)3.2. Building Kernel Libraries DLLs (9)4. Using CMake to Build and Install Geant4 (10)4.1. Prerequisite Software (10)4.2. Building and Installing Geant4 with CMake (10)4.2.1. Running CMake (11)4.2.2. Enabling Optional Components (12)4.2.3. Building Geant4 from CMake Generated Buildscripts (13)4.3. Using Geant4 (13)4.4. Known Issues (14)Chapter 1. Installation IntroductionThis section describes the global computing environment required for installing the Geant4 toolkit. To set up your specific computing environment for Geant4, refer to Section 2 of this Guide.A shell script (Configure) is provided to facilitate the installation procedure, and to help the user set up the environment correctly.1.1. Supported Computers and Operating Systems Geant4 is supported under the following operating systems:•Linux on PC with g++ (gcc compiler)•MacOSX with g++ (gcc compiler)•Windows/XP with MicroSoft Visual C++Currently, this is the set of flavors which can be associated with the environment variable $G4SYSTEM to identify the system architecture and compiler used:Linux - Scientific Linux CERN, SLC5g++ gcc 4.1.2 G4SYSTEM: Linux-g++MacOSX - MacOSX Darwin 10.6g++ gcc 4.2.1 G4SYSTEM: Darwin-g++Windows - Windows XP and Cygwin32MSVC++ 9.0, Visual Studio 2008 G4SYSTEM: WIN32-VCFor a more detailed description of supported platforms/compilers and versions of third party software, please refer to the release notes available with the current release you're using in geant4/ReleaseNotes (also accessible from the web distribution page ).1.2. Required SoftwareTo run Geant4, the following software must be properly installed in your computing environment:• A C++ compiler(compiler from your Unix vendor, g++ or Visual C++ for Windows systems)•The CLHEP library(see the CLHEP reference guide .)•GNU Make (note: g++ preprocessing is used to build file dependencies) is also used and a UNIX shell •The Geant4 toolkit source code1.3. Visualization SoftwareThe above list of software is the minimum required for a non-graphical setup of Geant4. To build and use visualization graphics in Geant4 and/or a graphical user interface (GUI), at least one of the following graphic systems or packages is required in your computing environment:•X Windows.•OpenGL or MesaGL (free software compatible with OpenGL).•DAWN , a PostScript renderer.•Qt , a cross platform application and UI framework (version 4 preferred).•Open Inventor (free software from SGI).•Open Scientist (Interactive environment, including GUI).•HepRApp Browser ( HepRep Browser).Installation Introduction•WIRED4 JAS Plug-In ( HepRep Browser).•Momo (a Java -based GUI environment, GGE, GPE, ...).•VRML browser.Alternatively, you can produce an ascii file for VRML or DAWN.More information is available in Section 8.6, Visualization Drivers, of the User's Guide for Application Developers.1.4. Software for Analysis and Histogramming Histogramming facilities are provided through the AIDA abstract interface. AIDA is not required to build Geant4 itself, but if you wish to use it in your applications, it should be installed following the guide at:•AIDA (Abstract Interfaces for Data Analysis)External, AIDA-compliant packages which provide the necessary functionalities for doing histogramming (and therefore should be installed if you require this functionality in your applications) are:•iAIDA (iAIDA, an implementation of AIDA in C++)•JAS (Java Analysis Studio)•Open Scientist (Interactive Analysis Environment).•rAIDA (rAIDA, a Root implementation of AIDA)Chapter 2. Installation ProceduresBefore installing Geant4, the required software listed in Section 1.2 (and Section 1.3 in the case of graphics drivers) of this Installation Guide must already be installed on your system.In this section, a short tutorial on how to install the toolkit's kernel libraries is given. The installation of the Geant4 kernel libraries and the proper configuration of the environment can be achieved either manually (by setting the proper environment variables) or through the Configure shell script, which will allow the installation of just the necessary source code and libraries in a specified installation area.Step-by-Step guides for the installation are also available. See Appendix - Step-by-Step Installation Guides of Geant4 User's Guide - For Application Developers.2.1. Using the Configure Script for installationA shell script is provided for building the libraries and to allow easy installation in a specified area. The Configure shell script is placed in the top directory tree of the distribution (geant4/Configure) and allows the user or system administrator to install the Geant4 toolkit in a semi-automatic way. Some knowledge of the system is required for the installation, such as:•the compiler to be used•the path where the Geant4 toolkit is to be installed ($G4INSTALL)•definition of installation directory paths (optional)•kind of graphics/analysis system(s) installed in the system, and paths to the installation of each graphics/analysis package•the kind of library to be generated: static/shared, compound/granular.To run the installer script for building the libraries of the Geant4 toolkit, one must type the following from the top directory geant4:> ./Configure -buildand follow the on-screen instructions. No system administrator privileges are required at this stage. The script will ask for the path in the system where the Geant4 libraries should be installed later on. The script provides default settings for most of the environment variables to be set. By pressing -RETURN-, the default values will be selected; otherwise the proper selection (or path, in case a path is requested) must be typed in.In case the installation procedure fails for some reason, or you realise the selected options were not correct at the time the installation started, you can repeat the whole process by manually removing the current installation with: > cd geant4/source> make cleanwhere the $G4SYSTEM environment variable (specifying the kind of architecture and compiler used) is manually set in your environment (according to the flavors listed in Section 1.1).In case new modules must be added to an existing build (for example a module for visualization), this can be done manually by re-running Configure and providing the new settings.Once the process of building the libraries has been completed successfully, the Geant4 toolkit can be installed in the specified (already existing) installation area by typing:> ./Configure -installLibraries and necessary source code will be installed in lib/geant4, include/geant4 (if selected to install all headers in a single directory), src/geant4, respectively. System administrator privileges may be required for the installation stage, depending upon where in the system the installation should happen.$G4INSTALL will be set to [INSTALLATION_AREA]/src/geant4.2.2. Configuring the Environment to Use Geant4Once libraries have been installed, the user's environment must be correctly set up for the usage of the Geant4 toolkit. The Configure script provides a way to check the existing installation and provide the correct configuration for the user's environment. Configuration scripts env[.sh.csh] can be generated, and should be sourced by the final users in order to configure their environment according to the performed installation.To generate the configuration scripts, the user should run Configure placed in the installation area, as follows:> $G4INSTALL/ConfigureThis will generate the shell script env.csh (env.sh for bash shell) to be sourced or integrated into the shell login script (.tcshrc or .bashrc). The shell script will be generated in the user's current directory ($PWD). The user can customize it to specify for example her/his proper working directory through the variable $G4WORKDIR. Once the generated script is sourced, the user will be ready to start building a Geant4 application.Refer to section the section Getting Started with Geant4 - How to Make an Executable Program of the Geant4 User's Guide for Application Developers for information on how to build an executable in Geant4.2.3. Installing Geant4 ManuallyBefore proceeding with the installation, some key environment variables must be defined in your user environment in order to specify where all software components are to be placed and to set some compilation options. A complete reference to all environment variables in Geant4 is available in section Appendix - Makefiles and Environment Variables of the Geant4 User's Guide for Application Developers .2.3.1. Required Environment VariablesG4SYSTEM:set to one of the flavors listed in section 1.1 to specify the kind of architecture and compiler usedG4INSTALL:path where the Geant4 toolkit tree is installed (ex. $HOME/geant4)CLHEP_BASE_DIR:path to the CLHEP installation2.3.2. Optional Environment VariablesG4WORKDIR:path of the user's working directory (default in $G4INSTALL)G4LIB:path where the kernel libraries should be installed (default in $G4INSTALL/lib)G4TMP:path where temporary files (object files, dependency files) are placed (default in $G4WORKDIR/tmp)G4BIN:path where final executable files are placed (default in $G4WORKDIR/bin).G4INCLUDE:path where source header files may be mirrored at installation by issuing make includes (default in $G4INSTALL/include)G4DEBUG:flag specifying that libraries be built with debug symbols (requires a lot of disk space). The default is optimised-modeG4LIB_BUILD_SHARED:flag specifying that kernel libraries be built as shared libraries (libraries will then be used by default). If not set, static archive libraries are built by defaultG4LIB_BUILD_STATIC:flag specifying that kernel libraries be built as static archive libraries. Note that you may specify this flag in addition to G4LIB_BUILD_SHARED to build shared and static libraries simultaneously.G4LIB_BUILD_G3TOG4:flag specifying that the library for the g3tog4 module be built. By default the library will not be built.G4LIB_BUILD_ZLIB:flag specifying that an additional library for file compression should be built (not required on Linux/Unix systems, required on Windows if choosing OpenGL or OpenInventor visualization). By default the library will not be built.G4_NO_VERBOSE:defining this flag prevents the compilation of verbosity code (for better performance). The default is with verbosity on.The list of all additional flags (also requiring third-party packages installed) can be found in Section 5.2 of the Geant4 User's Guide for Application Developers .The Geant4 installation requires native STL (the Standard Template Library) as the base foundation class library. This also implies strict ISO-ANSI language compliance. In addition to the above, you might want to set the proper environment for visualization, such as:•the kind of graphics driver(s) installed in the system•the path to the installation of each graphics driverin case you want to build the Geant4 kernel libraries with the graphics drivers built-in. See Visualization - The Visualization Drivers of the Geant4 User's Guide for Application Developers .At this point, you may choose one of two ways to compile and install the kernel libraries, depending on your needs and system resources. From $G4INSTALL/source:1.makeThis will make one library for each "leaf" category (maximum library granularity) and automatically producea map of library use and dependencies.2.make globalThis will make global libraries, one for each major category.The main advantage of the first approach is the speed of building the libraries and of the application, which in some cases can be improved by a factor of two or three compared to the "global library" approach.Using the "granular library" approach a fairly large number (roughly 90) of "leaf" libraries is produced. However, the dependencies and linking list are evaluated and generated automatically on the fly. The top-level GNUmakefile in $G4INSTALL/source parses the dependency files of Geant4 and produces a file libname.map in $G4LIB. libname.map is produced by the tool liblist, whose source code is in $G4INSTALL/config.When building a binary application the script binmake.gmk in $G4INSTALL/config will parse the user's dependency files and use libname.map to determine through liblist the required libraries to add to the linking list. Only the required libraries will be loaded in the link command.The command make libmap issued from $G4INSTALL/source, allows manual rebuilding of the dependency map. The command is issued by default in the normal build process for granular libraries.It is possible to install both "granular" and "compound" libraries, by typing "make" and "make global" in sequence. In this case, to choose usage of granular libraries at link time one should set the flag G4LIB_USE_GRANULAR in the environment; otherwise compound libraries will be adopted by default.2.4. Integrating Geant4 into a Generic FrameworkAs part of the Geant4 kernel libraries installation, it is also possible to put the entire set of header files in a single place, which is determined by the environment variable G4INCLUDE specifying the directory path. Therefore, it's rather straightforward to integrate Geant4 into a generic external framework, by simply knowing the path where header files are located in the system (G4INCLUDE) and where installed libraries are placed (G4LIB).In Section 5.2. (Appendix - Makefiles and Environment Variables) of the Geant4 User's Guide for Application Developers , you can find a list of all the environment variables. In Section 5.3 it is also explained how to integrate external libraries which may or may not use the Geant4 kernel libraries, using the GNUmake build system of Geant4.Chapter 3. Tips for Installing on Windows3.1. Windows with the Cygwin Toolset and Microsoft Visual C++To compile and run Geant4 under Windows systems, some additional information and tools are required, although the installation produre is similar to that required on a UNIX based system. On Windows, the Cygwin toolset and the Microsoft Visual C++ compiler are used.Cygwin32 is a UNIX development environment available for Microsoft Windows. You can freely obtain Cygwin32 from Cygwin or Cygwin/X .We do not support direct use of Visual Studio; i.e. we do not provide Visual Studio workspace (.dsw) or project (.dsp) files, nor we do provide makefiles for the nmake application of MS Visual C++.We use several of the tools provided by the Cygwin toolset:•make.exe as a make tool•g++.exe as a tool to analyse source file dependencies and create dependency (.d) files•several other unix tools like cp, mv, rm, touch, etc.At the installation of the Cygwin toolset it is therefore required to explicitely select some packages (i.e. gmake, gcc, binutils and tcsh from the "devel" category) in addition to those which are part of the default installation.For more details on the toolset, please see the documentation available on the Cygwin pages . The User's Guide has quick start guides and help with setting up Cygwin with setup.exe.Links to some installation tips for the Cygwin toolset and also "step by step" installation guides can be found in the section Appendix - Step-by-Step Installation Guides - Build for MS Visual C++ of Geant4 User's Guide -For Application Developers.The usage of Cygwin32 for the build environment results in a build procedure similar to that on a UNIX system.The following steps are required to install geant4:1.Install Cygwin (see also notes above and additional installation notes for known issues related to the mostcurrent version):We do not depend on any specific feature of the version of Cygwin, so newer versions (or slightly older) are expected to work.2.Set the environment for MS Visual C++, i.e. set the paths to libraries, include files, and executables for MSVisual C++. This can be done by modifying the start-up batch file cygwin.bat of Cygwin32 to include all the MSDOS commands found in the file vcvars32.bat provided in MS Visual C++ (in the VC++ .NET compiler installation directory, and usually located inside the Common7/Tools directory). This modification should be done after the installation of the Cygwin toolset, so that the environment gets properly set at the time of the invocation of the shell.3.Unpack the source code into a directory of your choice.4.Start the Cygwin shell from the start menu.5.At this point you're ready to install Geant4. If manual installation is chosen, you must set the necessaryenvironment variables. There are various ways to do so; for example through a command file for the Cygwin bash shell. This command file could be named geant4-setup.sh, and you must execute it with. geant4-setup.shincluding the leading dot and blank space. You could also have this as your .bashrc file. The commands in the command file should be:# Set G4SYSTEMexport G4SYSTEM=WIN32-VC## Set Path to CLHEPexport CLHEP_BASE_DIR=C:/usr/local## --- Other optional settings#Turn on verbose to show command used for compilation#export CPPVERBOSE=1#Note, in the example above, CLHEP was installed in C:/usr/local, therefore include/CLHEP and lib/CLHEP.lib must be included therein.6.Once the environment is correctly set, the libraries are built using make from the geant4/source directorytyping make from the Cygwin bash shell prompt.Examples can be built in the same way as the libraries from examples/novice/N01, for instance: type make from the shell prompt.Note that, depending on which external software is used, there may be some warnings in linking about conflictings libraries. This often seems to be caused by an external library compiled for a different run time environment. The binary of the example is placed by default into the geant4/bin/WIN32-VC directory. You may run it either from this directory or from the examples/novice/N01 directory; sample input and output files are placed in each of the examples/novice directories. Some of the examples will need to read data files, and the place has to be given in environment variables again similar to the following example:## Environment variables needed to find geant4 data files:## Data for neutron scattering processes,# distributed in a separate tar file, then placed under dataexport G4NEUTRONHPDATA=c:/usr/local/geant4/data/G4NDL## Data for evaluated neutron cross-sections on natural composition of elements,# distributed in a separate tar file, then placed under dataexport G4NEUTRONXSDATA=c:/usr/local/geant4/data/G4NEUTRONXS## Nuclear Photon evaporation data,# distributed with the source files under dataexport G4LEVELGAMMADATA=c:/usr/local/geant4/data/PhotonEvaporation## Data for radio-active decay hadronic processes under data,# distributed in a separate tar fileexport G4RADIOACTIVEDATA=c:/usr/local/geant4/data/RadiativeDecay## Data for low energy electromagnetic processes,# distributed in a separate tar file, then placed under dataexport G4LEDATA=c:/usr/local/geant4/data/G4EMLOW## Data for shell ionisation cross-sections,# distributed in a separate tar file, then placed under dataexport G4PIIDATA=c:/usr/local/geant4/data/G4PII## Data for nuclear shell effects for INCL/ABLA hadronic model,# distributed in a separate tar file, then placed under dataexport G4ABLADATA=c:/usr/local/geant4/data/G4ABLA## Data for measured optical surface reflectance in optical processes,# distributed in a separate tar file, then placed under dataexport G4REALSURFACEDATA=c:/usr/local/geant4/data/RealSurface#All compiler and linker options are set in config/sys/WIN32-VC.gmk. If you require options different from our choice, you can modify this file.3.2. Building Kernel Libraries DLLsDLLs (Dynamic Link Libraries) on Windows are supported for MS-VC++ and can be built for the compound kernel libraries of Geant4 (see Section 2.3.2 of the Installation Procedure of this Guide for a dissertation on global/compound libraries).The libraries can be built either manually, issuing the command:make dllfrom the directory $G4INSTALL/source or by specifying it through the Configure script used for the installation.Then, to build any application making use of the installed DLLs, the environment variable G4LIB_USE_DLL must be set in the environment.Once the application is built, it is required to specify to the system the path where the DLLs are installed. To do so, add the absolute path (in Cygwin format) of the DLLs installation directory to the PATH variable; for example: export PATH=$PATH:/usr/local/geant4/lib/$G4SYSTEMYou may then be able to run successfully your application.Chapter 4. Using CMake to Build and Install Geant4In release 9.4, a new beta build system for Geant4 using the CMake build system is available. CMake has been chosen as an easy to use and maintain, cross-platform tool that addresses several shortcomings of the existing Configure/Make buildsystem. As a beta, not all of the UI and Visualization drivers available in Geant4 and supported by the current Configure/make build system are available. Also, only the following systems are currently supported in this beta version:•Linux on PC with g++ (GNU compiler) and CMake Makefile generation•MacOSX with g++ (GNU compiler) and CMake Makefile generationIt is expected that the CMake generated buildscripts for Eclipse, KDevelop and Xcode will be functional, but have not been tested yet. Windows builds on XP using the MSVC++ compiler through CygWin have not yet been tested. Native Windows builds using Visual Studio are not yet fullyfunctional. We welcome feedback and problem reports, which should be logged on the Geant4 bug tracking system.4.1. Prerequisite SoftwareTo use the CMake build system, the software listed in Section 1.2 and optionally the Qt4, OpenGL, DAWN and VRML packages listed in Section 1.3 should be installed on your system.In addition, a recent CMake version, specifically one of• 2.6.4• 2.8.*should be installed on your system. Binary packages for CMake of the required versions are generally available on most mainline Linux distributions, and should be preferred if available. Otherwise, source and binary packages for Linux, MacOSX and Windows are available from the Kitware download page.4.2. Building and Installing Geant4 with CMakeCMake processes simple input scripts to generate output buildscripts for a native build tool such as makefiles on UNIX. The build process for Geant4 using CMake is thus to run CMake first to generate the native buildscripts and then to run the native tool using these buildscripts as input to build and install.You should have obtained all the prerequisite software described above, and should have unpacked the Geant4 sources to a location of your choice, for instance/path/to/geant4.9.4We call this directory the source tree. The CMake build enforces an out of source build so that the buildscripts generated by CMake do not mix with the actual Geant4 sources. This is particularly important for developers using a working copy from the geant4 repository, and also means you can build multiple configurations of Geant4 against one single source tree.You therefore need to build Geant4 in a separate directory which we call the build tree. This directory can be created wherever you like, though we strongly recommend it is outside the source tree. In addition, if you wish to use an IDE such as Eclipse, there may be limitations on the location of the build tree relative to the source tree. For these reasons, we recommmend creating your build tree directory alongside the source tree, e.g. using our location from above/path/to/geant4.9.4/path/to/geant4.9.4-buildYou are of course free to experiment here, but the above is the recommended way. You may have as many build trees as you like.4.2.1. Running CMakeCMake generates buildscripts (e.g. Makefiles, Xcode projects) for the build tool (e.g. make, Xcode) of your choice. The first step after setting up the source and build trees is therefore to run CMake in the build tree to generate the needed scripts. We shall assume in the following that we are on *NIX, where CMake defaults to generating Makefiles, and we shall use the CMake command line interface. CMake has other interfaces such as the Curses based ccmake, and if you wish to use these, you should consult the documentation supplied with CMake.If you wish to generate, e.g. Xcode projects, consult the CMake documentation for the -G option which allows you to select another tool. The GUI interface to CMake available on some platforms also has a switch to choose the build tool.Our first step is to move into the build tree directory and then run CMake, pointing it to the source tree, and setting the CMAKE_INSTALL_PREFIX variable to set where geant4 will be installed. Using our example source and build trees from above, and assuming you want to install Geant4 under /install/location (NB $ denotes the prompt, not a literal '$')$ cd /path/to/geant4.9.4-build$ cmake -DCMAKE_INSTALL_PREFIX=/install/location ../geant4.9.4The cmake command is the basic command line interface to CMake. All being well, you will see some platform dependent output (not complete)$ cmake -DCMAKE_INSTALL_PREFIX=/install/location ../geant4.9.4-- The C compiler identification is GNU-- The CXX compiler identification is GNU-- Check for working C compiler: /usr/bin/gcc-- Check for working C compiler: /usr/bin/gcc -- works-- Detecting C compiler ABI info-- Detecting C compiler ABI info - done-- setting default compiler flags for CXX-- Check for working CXX compiler: /usr/bin/c++-- Check for working CXX compiler: /usr/bin/c++ -- works-- Detecting CXX compiler ABI info-- Detecting CXX compiler ABI info - doneCMake will then proceed to check for needed external packages. Assuming these are all installed correctly, then it should continue, giving the output (on Linux with GNU compiler)-- Found CLHEP version: CLHEP 2.1.0.1-- Found CLHEP: TRUE-- Geant4 backwards compatible system name: Linux-- Geant4 backwards compatible compiler name: g++-- Geant4 backwards compatible variable G4SYSTEM : Linux-g++-- Geant4 backwards compatible variable G4INSTALL: /install/location/share/geant4-9.4.0 -- Geant4 backwards compatible variable G4INCLUDE: /install/location/include/geant4-- Geant4 backwards compatible variable G4LIB : /install/location/lib/geant4-9.4.0-- The following Geant4 features are enabled:-- Configuring done-- Generating done-- Build files have been written to: /path/to/geant4.9.4-buildDepending on the speed of your computer and/or filesystem, there may be pauses at the Configuring and Generating stages as CMake actually writes out files.The detection of CLHEP relies on having the clhep-config script in the PATH, and if this is not the case on your system, you may see an error。