curtiskleier-log

=Curtis Kleier Log= Note: the links provided in the assignment summary link to my personal wiki page however all current editions are kept on this wiki. The text is mirrored on both sides and links are given in order to facilitate easy transitions between the assignments.


 * __Assignment Summary__**

> **[you can put the properties on a separate page just make sure it is on this wiki JCB]** issues has been addressed and properties are mirrored at both sites.
 * Assignment 1** : Find 5 independent sources of 5 properties associated with a molecule of your choice. Provide all references**. Due November 4, 2010 20:50**
 * Assignment 1: 5 Properties, 5 Sources (Carbon Tetrachloride)


 * Assignment 2**: Write a summary of one of the articles you are reading for your project paragraph by paragraph. One or two sentences per paragraph is fine. You must do this in your own words. No significant amount of text can be copied from the abstract or any part of the paper. Either put the summary in bullet form on your research log or on [|AcaWiki]. **Due November 11, 2010 20:50**
 * Assignment 2: Article Summary Review

(included exhibit from policy statement - summarized through text, believed that the exhibit provided a clear and concise method of summary and that through inclusion of any table with simillar intent would not meet the spirit of academic honesty) Any text or thoughts were referenced by footnote and any words that were used in the original document were included in parentheticals.)
 * Assignment 3:** Answer one of the FAQ questions or create and answer an FAQ question relating to a topic relating to chemistry publishing. You must provide at least one relevant reference. You must summarize in your own words - copying text from anywhere verbatim is not allowed. If all the questions have been answered create a reasonable one on some aspect of chemistry publishing not yet asked. **Due November 18, 2010 20:50**
 * Assignment 3 - Answer FAQ

=Carbon Tetrachloride Physical Properties= Chemspider #: [|5730]

Boiling Point

 * 1) 76.72 *C ([|Wikipedia], [|wiki_cc4_props.png])
 * 2) 76.7 *C ([|Merck Index 14e],[|merck_cc4_props.png])
 * 3) 77 *C ([|Oxford MSDS], [|MSDS_Oxford_CC4_props.png])
 * 4) 76.67 *C ([|NIOSH], [|NIOSH_CC4_props.png])
 * 5) 76.65*C ([|NIST Web Book], [|NIST_BP_CC4_props.png]

Melting Point

 * 1) -22.92*C ([|Wikipedia], [|wiki_cc4_props.png])
 * 2) -23*C ([|Merck Index 14e],[|merck_cc4_props.png])
 * 3) -23 *C ([|Oxford MSDS], [|MSDS_Oxford_CC4_props.png])
 * 4) -22.78*C ([|NIOSH], [|NIOSH_CC4_props.png])
 * 5) -23*C([|Santa Cruz Biotechnology], [|CCl4-_MP_.jpg]) [**changed image link - ck 11/11/10]**

Specific Gravity

 * 1) 1.5967 g/cm^3 ([|Wikipedia], [|wiki_cc4_props.png])
 * 2) 1.589 g/cm^3 ([|Merck Index 14e],[|merck_cc4_props.png])
 * 3) 1.59 g/cm^3 ([|Oxford MSDS], [|MSDS_Oxford_CC4_props.png])
 * 4) 1.59 g/cm^3 ([|NIOSH], [|NIOSH_CC4_props.png])
 * 5) 1.59 g/cm^3 (kPa ([|Santa Cruz Biotechnology], [|VP_SCBT_CC4_Props.png])

Index of Refraction

 * 1) 1.4601 ([|Wikipedia], [|wiki_cc4_props.png])
 * 2) 1.4607 ([|Merck Index 14e],[|merck_cc4_props.png])
 * 3) 1.463 (via Google Scholar, J Stone - J. Opt. Soc. Am, 1972 - opticsinfobase.org  ([|pdf] ),[|RI_ccl4.JPG]  )
 * 4) 1.46 (via Google Scholar, [|The Journal of Physical Chemistry 1995 99 (16), 5817-5825][|Index_of_refraction_ccl.JPG])
 * 5) 1.4605 [|via SciFinder Scholar]

Vapor Pressure

 * 1) 11.94 kPa ([|Wikipedia], [|wiki_cc4_props.png])
 * 2) 12.1 kPa ([|Oxford MSDS], [|MSDS_Oxford_CC4_props.png])
 * 3) 12.1 kPa ([|NIOSH], [|NIOSH_CC4_props.png])
 * 4) 12.13 kPa ([|Santa Cruz Biotechnology], [|VP_SCBT_CC4_Props.png])
 * 5) 11.99 kPa (via CrossFire Beilstein, [|Valero, Jose; Gracia, Mariano; Perez, Pascual, Journal of Chemical & Engineering Data [JCEAAX, Volume 39, Issue 4, 1994, Pages 789-792)> ]]([])


 * Assignment 2 - [|58_201.pdf]**
 * [You cannot upload a paper PDF to the wiki - you must link using a DOI JCB]**

**Cannabinoid Receptor 1 Binding Activity and Quantitative Analysis of Cannabis sativa L.. Smoke and Vapor** Justin FISCHEDICK, Frank VANDERKOOY,* and Robert VERPOORTE Division of Pharmacognosy, Section of Metabolomics, Institute of Biology, Leiden University; P.O. Box 9502, 2300RA Leiden, the Netherlands. //Received September 9, 2009; accepted November 10, 2009; published online November 24, 2009// [|Chem. Pharm. Bull. 58(2) 201 - 207(Feb 2010)// doi:10.1248/cpb.58.201] **Note: will redo summary as part of final paper.** **Paragraph 1** 400 Chemicals have been identified in Cannabis with 70 falling into the cannabinoid group of psychoactives. ∆ 9 - Tetrahydrocannabinol is the main psychoactive by binding the CB1 and CB2 receptors. CB1 and CB2 Receptors interact with FA Amides and Esters

**Paragraph 2** Cannabis is illegal in most nations however medications are available which are based on cannainoids These are synthetic and processed versions of THC and cannabidiol These are used as treatments for nausea, appetite stimulation, chemotherapy, MS, pain and even Tourette’s

**Paragraph 3** Consumption by smoking, eating, or drinking Heating changes the form of the THCA to THC which is the psychoactive version Vaporization provides an alternative to smoking by reducing the temperature below the plant combustion temperature

**Paragraph 4** Identification of the cannabis smoke has been studied Study of the health effects via vaporization is important as a delivery method Vaporization allows for the suppression of pyrolytic by-products Study of additional compounds within the vapor

**Paragraph 5** Effectiveness of smoking vs vaporization through identification of the components of the smoke Binding activity of the CB1 differential between the cannabis smoke and pure THC.

**Paragraph 6** Experimental methods and plant source. Three cannabis varieties with various levels of THC.

**Paragraph 7** Reference terpenoids were 39 in quantity Reference cannabinoids for THC(8,9), THCA, CBD, CBG CBC and THCV, CBN All solvents were appropriate for procedural methods

**Paragraph 8** Sample preparation via validated method in triplicate 1 gram w/40ml ethanol and centrifuged at 2500 rpm for 5 minutes and transfered to 100ml flask Sample was processed with 25ml, 100ml ethanol

**Paragraph 9** Joints were weighed with 1g/joints and 2 joints per sample One puff every 30s to volume of 35ml and collected over 50ml 1:1 ethanol:hexane 3 Samples for each variety

**Paragraph 10** Vapor Collection via 250mg plant material for 5 total portions per sample and 1.25 g cannabis per sample 3 sets of samples for variety Trapped over 50:50 ethanol:n-hexane, 100ml Sample analyzed via GC-hydrogen FID, GC-MS, HPLC

**Paragraph 11** GC-FID analysis was completed via autosampler with a .25um column Injector temperature was 230C at 4ul with a ramp of 3C starting at 60C and ending at 240C held for 5minutes Samples were run undiluted and reference at 1mg/ml

**Paragraph 12** GC-MS Analysis completed by a 3ul ingection and a manifold temp of 60C and trap temp of 220C. Samples run undiluted and references run at concentrations of 1mg/ml

**Paragraph 13** HPLC analysis for acidic and neutral cannabinoids using Methanol and formic acid in various concentration for the mobile phase. Phase change from 70% Solvent A - 100% solvent B over 25 minutes Flow Rate was 1.5ml/min

**Paragraph 14** CB1 Receptor detection via membrane with dilution of 1:200 assay buffer. All solutions were prepared daily. All samples were diluted to 10nm and final concentrations for non-specific binding CP-55940

**Paragraph 15** Radioactive displacement over 1 hour at 30C.

**Paragraph 16** HPLC data table shows THC in the ethanol extracts accounting for molecular weights Granulating the Flower buds removes the cannabinoids THC in vapor and smoke declines with inverse relationship to vaporization efficiency

**Paragraph 17** GC Identification was inconclusive with products not determined with reference. NIST library was used for smoke samples


 * Assignment 3 **

===3. Describe and compare the data management and reporting policies of the NIH and NSF pertaining to chemistry.=== [edited by Curtis Kleier]

Overall data management is broken down into thre areas - Security, Archival, and data certification. Data security issues relate to data access and retrieval through a variety of means. Data archival relates to the storage medium and backup systems thare are required to be in place. The third area of data management is the most important as it relates to how data is inputed, verified and to what level of accuracy must be captured before the data can be considered useful.(1)

__NIH Data management__ NIH Security Protocal is divided between on campus and off campus badging process. These are separated into a variety of different security levels and are issued by two entities which include the NIH PD and the Division of Personnel Security and Access Control. These badges also provide access to all computer termianls and building access via SmartCard or other 'legacy' device. (These locations include the Bethesda Campus, Ft.. Detrick, Biomedical Research Center, Rocky Mountain Labs and Triangle Park). All NIH servers, computers(Laptops & Desktops) must have smartcard access in order to secure any data which would have an adverse effect on operations(2) and will apply to laptops and web accessible programs by May of 2011. Those that are members of outside organizations can utlize the NIH Federated Authentication tools to use their own onsite authentication methods. In the case of off campus research which is funded by the NIH grantees are required to comply with policies designed to prevent the disclosure of sensitive information as goverend by FISMA. .

NIH set requirements for data archival and destruction of the data devices. These services are provided by the Center of Information Technology(CIT) and regulated by the Federal Information Processign Standards Publication(FIPS) 200. These policies require that all drives be sterilized at the end of term in order to keep data secure. NIH also allows individual laboratories to set data managment and reporting policies for deliverables by non-us laboratories(3). This regulations are governed under federal regulations 21 CFR 58 and 42 CLP 493. These define that the data must allow for optimal laboratory operations through annual audits and visits which provide consistent and reproducible results.(3)

There are also polcies that require grantees to secure their data when being funded by NIH grants. NIH Funded programs require that the results be made to the research community and to the public.(4) It provides that some information can be made available through a 'on request' only forum.(5) Most information that is generated from a NIH funded grant is considered to be public in order to foster an environment of collaboration and accountability. This isformation is published at the NIH website located at report.nih.gov. If information is submitted to the NIH that is considered to be proprietary can be kept confidential but it is discouraged by NIH.

__NIH Reporting Polciy__ In regards to specific research data the NIH handles all request for release of the specified data through the FOIA request. According to NIH Grants Policy statement 2.3.11.2.3 allows that only final data be published and allows the following information to be held in confidence: preliminary analyses; drafts of scientific papers; plans for future research; peer reviews; communications with colleagues; physical objects (e.g., laboratory samples, audio or video tapes); trade secrets; commercial information; materials necessary to be held confidential by a researcher until publication in a peer-reviewed journal; information that is protected under the law (e.g., intellectual property); personnel and medical files and similar files, the disclosure of which would constitute an unwarranted invasion of personal privacy; or information that could be used to identify a particular person in a research study.(5)

The release of the data is governed under the NIH GPS 8.2.1 regulation which provides that hte grantee own the rights of the data and can be extended to gropus of people whose primary purpose is education without NIH approval.(6) When the research is published or declared through a media release the NIH grant must be recognized through the specific program number with the caveat that releases any assumed NIH endorsement of the findings.(6) If there are any publications the url or the identifiying document nubmer must be provided in the final report. The published results will also be housed at PubMed as an electronic version of the final, peer reviewed manuascript(NIH GPS 8.2.2) within a year of publication. In order to clarify the reporting process the NIH has issued a table of compliance responsibilities Exhibit 8. Extramural Invention Reporting Compliance Responsibilities (6)||~ Invention Reporting Requirement ||~ Action Required ||~ When Action Must Be Taken ||~ Discussion ||~ 37 CFR part 401 Reference || 401.14(c)(1) || 401.14(g)(2) || 401.14(c)(2) 401.14(f)(1) || 401.2(n) 401.14(f)(4) || PHS 2590 ||
 * **Employee Agreement to Disclose All Inventions** || Grantee employees working under the funding award (e.g., PD/PI) must sign an agreement to abide by the terms of the Bayh-Dole Act and the NIHGPS as they relate to intellectual property rights. || At time of employment-term of employment. || Grantee organizations and consortium participants must have policies in place regarding ownership of intellectual property, including conflict of interest issues. || 401.14(f)(2) ||
 * **Invention Report and “Disclosure”** || The grantee organization must submit to NIH a report of any subject invention. This includes a written description (the so-called “invention disclosure”) of the invention that is complete in technical detail. || Within 2 months of the inventor’s initial report of the invention to the grantee organization. || There is no single format for disclosing the invention to the Federal government. The report must identify inventor(s), NIH grant number, and date of any public disclosure. || 401.14(a)(2)
 * **Rights to Consortium Participant Inventions** || Consortium participants under NIH grants retain rights to any subject inventions they make. || Within 2 months of the inventor’s initial report of the invention to the consortium participant. (The consortium participant has the same invention reporting obligations as the grantee.) || The grantee cannot require ownership of a consortium participant’s subject inventions as a term of the consortium agreement. || 401.14(g)(1)
 * **Election of Title to Invention** || The grantee must notify NIH of its decision to retain or waive title to invention and patent rights. || Within 2 years of the initial reporting of the invention to NIH. ||  || 401.14(b)
 * **Confirmatory License** || For each invention, the grantee must provide a user license to NIH for each invention. || When the initial non-provisional patent application is filed. ||  || 401.14(f)(1) ||
 * **Patent Application** || The grantee must inform NIH of the filing of any non-provisional patent application. The patent application must include a Federal government support clause. || Within 1 year after election of title, unless there is an extension. || Initial patent application is defined as a non-provisional application. The patent application number and filing date must be provided. The following language is to be used on patent application: “This invention was made with government support under (identify the funding award) awarded by (identify the IC and Federal Agency). The government has certain rights in the invention. All communications for such requests must be sent to OER.” || 401.14(c)(3)
 * **Assignment of Rights to Third Party** || If the grantee is a non-profit organization, it must ask NIH approval to assign invention or U.S. patent rights to any third party, including the inventor(s). || As needed. All communication for such requests must be sent to OER. The NIH Office of Technology Transfer serves in an advisory capacity to OER for the processing of such assignment requests. || Grantees that are for-profit entities (including small businesses) do not need to ask approval, but ongoing reporting remains a requirement for each invention. || 401.14(k) ||
 * **Issued Patent** || The grantee must notify NIH that a patent has been issued. || When the patent is issued. || The patent issue date, number, and evidence of Federal government support clause must be provided. || 401.5(f)(2) ||
 * **Extension of Time to Elect Title or File Patent** || The grantee may request an extension of up to 2 years for election of title, or an extension of up to 1 year for filing a patent application. || As needed. || Request for extension of time must be made. Such requests are preapproved. || 401.14(c)(4) ||
 * **Change in Patent Application Status** || The grantee must notify NIH of changes in patent status. || At least 30 days before any pending patent office deadline. || This notification allows NIH to consider continuing the patent action. || 401.14(f)(3) ||
 * **Invention Utilization Report** || The grantee must submit information about the status of commercialization of any invention for which title has been elected. || Annually. || This report gives an indication of whether the objectives of the law are being met. Specific reporting requirements can be found in iEdison ([|http://iEdison.gov]). || 401.14(h) ||
 * **Annual Invention Statement** || The grantee must indicate any inventions made during the previous budget period on all grant awards. || Part of all competing applications and non-competing continuation progress reports. || The information is requested as a checklist item on the PHS 398 application and on the non-competing continuation progress report. || PHS 398 and
 * **Final Invention Statement and Certification** || The grantee must submit to the NIH awarding IC GMO a summary of all inventions made during the entire term of each grant award. || Within 90 days after the project period (competitive segment) ends. || Required information is specified on the HHS 568 form. If no inventions occurred during the project period, a negative report must be submitted. || 401.14(f)(5) ||

__NSF Data Managment Policy__ According to a recent NSF press release the NSF will be instituting a formal data managment plan.(7) In another document the NSF specifies data sharing and access in order to 'promote scientific research ...to replicate results."(8) Over the course of their spring meetings the NSB addressed specific data policy issues in the areas of 'complete data', data storage and retention, timeframe for data release and inclusion of meta data requirements. (9) In the areas of specific access and security the NSF fall under the same umbrella of the the NIH. They are rquired to comply with the FOIA and unlike the NIH they are not expressely allowed to deny access to incomplete data.(9)

The NSF is currently revising their data storage and managment polcies which should go into effect in January. As part of this they have created a program called DataNet which will allow for collaboration between various partners. The program will allow for the preservation of research materials and will become the hub for such programs.(10) This program has the specific goal of developming a collective of organizations that bring archival services, data analysis, information distribuiton skills to the table in the hopes of bringing down the traditional barriers of research.

__NSF Data Reporting Policy__ This is governed under the 45 CFR 650.4(a) in regards to patents, inventions and address intellectual property rights. In this case the NSF requires that a PI disclose intent to patent or invention within 2 months and identification of specific publications which may be linked.(11) In most cases the NSF grants the rights of the intellectual property to the grantee however it reserves the right to retract if it is deemed that by doing so would violate international treaty, NSF statute or agreement.

The NSF governs that the PI be responsible to promply submit the findings of the work within a reasonable amound of time. (10) A difference that was fround form the NIH is that the NSF requires that annual project reports be submitted via the FastLane system and at least 3 months before the end of a budget period.(12) The final report must be submitted within 90 days of the end of the grant and must include; (11) These records must be kept for 3 years by the grantee. These alsoo can be goverend by the data managment plan that is required to be submitted with each grant. This plan will address confidentiality, provisions for re-use and publication.(13) The plan will also be influenced by the specific office which the grant came from if so required. The NSF has specified a data management plan specific to the areas of math, physical science through the division of Chemistry. These requirements will be in effect for the new year (2011). (14). This policy addresses the requirements associated to publication, sharing of data and the findings of all research. The division of Chemistry recognizes that data is published in peer journals and that the chemistry community maintains databases that meet the requirements of open access that does not require grantee intervention. These databases include PubChem and Chemistry WebBook. __Comparison between NSF and NIH Data requirements__ Require Specific areas of publication (NIH yes, NSF No) Specific Time Frame on publications (NIH yes, NSF yes) Storage Timeframe Requirements (NIH no, NSF yes)
 * 1) abstracts of theses;
 * 2) publication citations and reprints of articles;
 * 3) data on scientific collaborations;
 * 4) information on inventions;
 * 5) technical description of the project and results;
 * 6) other materials either required in the grant or considered to be useful to NSF; and
 * 7) Universal Resource Locator numbers of electronic publications generated by the project.

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