User:Paiges8/sandbox

Reflective essay

 * 1) The article that I worked on was entitled "Paper-based microfluidics." This is a new article on Wikipedia. The only existing article on Wikipedia that addresses this topic somewhat is entitled "Lateral flow test." However, this article refers to more specific types of tests in which analytes bind to particles and a test stripe changes color in the presence of the analyte-particle mixture. Paper-based microfluidics is a much broader topic. As an emerging bioanalytical technique, this topic deserves attention on Wikipedia, particularly regarding fabrication, fluid flow, detection, and applications.
 * 2) My overall contribution to this article was on the applications of paper-based microfluidics. I provided a brief overview of the advantages of paper-based microfluidic devices, including low cost, portable size, filtration of contaminants, and simplicity of use, which make them ideal for point-of-care testing in underdeveloped countries. Because glucose levels are indicative of medical ailments such as diabetes and cancer, my second paragraph detailed devices that have been developed for the detection of glucose. Several of these devices are able to isolate plasma from whole blood so that glucose can be quantified in blood plasma. My third paragraph gave a brief overview of 3D devices for glucose detection, and my final paragraph discussed paper-based microfluidic devices that have been developed for environmental monitoring and food safety evaluations.
 * 3) Responses to suggestions from peer reviewers:
 * 4) Zack provided a lot of suggestions for wording/rewording parts of my article. I took almost all of them into account in order to make my article informative but concise.
 * 5) Zack requested that I provide more details/a figure on what a 3D paper-based microfluidic device looks like. I described the device as consisting of multiple paper layers connected by tape (Whitesides' design).
 * 6) AnneClaire suggested that I cite an additional researcher for my glucose detection paragraph since that paragraph mostly focused on Whitesides' work. I ended up writing a second paragraph about 3D devices for glucose detection, and here I cited Dick Crooks from UT Austin like she suggested.
 * 7) Zack suggested that I describe smartphone detection for paper-based microfluidic devices in more detail. I ended up focusing mostly on device operation for the Salmonella and E. coli devices, but I did add that the smartphone application specifically detects Mie scattering of light, which is directly proportional to concentration of Salmonella or E. coli.
 * 8) AnneClaire said she didn't understand the difference between screen-printed electrodes and electrodes directly printed on filter paper. I created a link from my article to a Wikipedia page on screen printing so that interested users can read more about it. I did not want to get bogged down in the details of electrochemistry in my article.
 * 9) AnneClaire suggested that I add more citations for food safety testing using paper-based microfluidic devices. I described my first citation in more depth and found an additional citation.
 * 10) I really enjoyed this assignment. It was time-consuming to find fifteen sources and try to summarize them in a few short paragraphs. However, I think it was very useful work. I learned how to skillfully search the literature, how to identify useful sources, and how to efficiently read papers for the information I need. This assignment also definitely improved my understanding of class material. I did not end up discussing fabrication in my article, but I did read about it in my initial research. This reading improved my understanding of the lecture notes on fabrication, which made Design Project 1 slightly less daunting. I also think that the Wikipedia trainings made the peer-review process easier because I knew what to look for in a good Wikipedia article. The peer-review process was helpful because I took note of things my classmates did well and didn't do well in their articles, and then applied what I learned to my own article. It was interesting to peer review a Wikipedia article because they are much less dense than scientific papers. I do believe that my Wikipedia article will be useful to others because paper-based microfluidics is rapidly gaining popularity. I imagine that scientists interested in incorporating paper-based microfluidics into their own research will turn to Wikipedia for a brief overview of this emerging technique. In the future, I think that this assignment could be improved if there were fewer online trainings and fewer Sandbox requirements, such as to evaluate a different article. These components of the assignment seemed time-consuming and unnecessary. I think it would also be helpful to have a second round of peer reviews before final drafts are submitted. It might be interesting if, as a class activity, students evaluated Wikipedia articles (not ours, but previously published ones) in groups and presented their suggestions for improvement to the class.

Applications
Overview

The main advantage of paper-based microfluidic devices over traditional microfluidics devices is their potential for use in the field rather than in a laboratory. Filter paper is advantageous in a field setting because it is capable of removing contaminants from the sample and preventing them from moving down the microchannel. This means that particles will not inhibit the accuracy of paper-based assays when they are used outdoors. Paper-based microfluidic devices are also small in size (approximately a few mm to 2 cm in length and width) compared to other microfluidic platforms, such as droplet-based microfluidic devices, which often use glass slides up to 75 mm in length. Because of their small size and relatively durable material, paper-based microfluidic devices are portable. Paper-based devices are also relatively inexpensive. Filter paper is very cheap, and so are most of the patterning agents used in the fabrication of microchannels, including PDMS and wax. Most of the major paper-based fabrication methods also do not require expensive laboratory equipment. These characteristics of paper-based microfluidics make it ideal for point-of-care testing, particularly in countries that lack advanced medical diagnostic tools. Paper-based microfluidics has also been used to conduct environmental and food safety tests.

Point-of-care testing: glucose detection  

Paper-based microfluidic devices have been designed to monitor a wide variety of medical ailments. Glucose plays an important role in diabetes and cancer, and it can be detected through a catalytic cycle involving glucose oxidase, hydrogen peroxide, and horseradish peroxidase that initiates a reaction between glucose and a color indicator, frequently potassium iodide, on a paper-based microfluidic device. This is an example of colorimetric detection. The first paper-based microfluidic device, developed by George Whitesides’ group at Harvard, was able to simultaneously detect protein as well as glucose via color-change reactions (potassium iodide reaction for glucose and tetrabromophenol blue reaction for the protein BSA). The bottom of the paper device is inserted into a sample solution prepared in-lab, and the amount of color change is observed. More recently, a paper-based microfluidic device using colorimetric detection was developed to quantify glucose in blood plasma. Blood plasma is separated from whole blood samples on a wax-printed device, where red blood cells are agglutinated by antibodies and the blood plasma is able to flow to a second compartment for the color-change reaction. Electrochemical detection has also been used in these devices. It provides greater sensitivity in quantification, whereas colorimetric detection is primarily used for qualitative assessments. Screen-printed electrodes and electrodes directly printed on filter paper have been used. One example of a paper-based microfluidic device utilizing electrochemical detection has a dumbbell shape to isolate plasma from whole blood. The current from the hydrogen peroxide produced in the aforementioned catalytic cycle is measured and converted into concentration of glucose.

3D devices for glucose detection  

Whitesides’ group also developed a 3D paper-based microfluidic device for glucose detection that can produce calibration curves on-chip because of the improved fluid flow design. This 3D device consists of layers of paper patterned with microfluidic channels that are connected by layers of double-sided adhesive tape with holes. The holes in the tape permit flow between channels in alternating layers of paper, so this device allows for more complicated flow paths and enables the detection of multiple samples in a large number (up to ~1,000) of detection zones in the last layer of paper. More recently, 3D paper-based microfluidic devices assembled using origami were developed. Unlike Whitesides’ design, these devices utilize a single layer of patterned paper that is then folded into multiple layers before sample solution is injected into the device. Subsequently, the device can be unfolded and each layer of the device can be analyzed for the simultaneous detection of multiple analytes. This device is simpler and less expensive to fabricate than the aforementioned device using multiple layers of paper. Mixing between the channels in the different layers was not an issue in either device, so both devices were successful in quantifying glucose and BSA in multiple samples simultaneously.

Environmental and food safety tests

Paper-based microfluidic devices have several applications outside of the medical field. For example, paper-based microfluidics has been used extensively in environmental monitoring. Two recent devices were developed for the detection of Salmonella and E. coli . The latter device was specifically used to detect E. coli in 7 field water samples from Tucson, Arizona. Antibody-conjugated polystyrene particles were loaded in the middle of the microfluidic channel, after the sample inlet. Immunoagglutination occurs when samples containing Salmonella or E. coli, respectively, come into contact with these particles. The amount of immunoagglutination can be correlated with increased Mie scattering of light, which was detected with a specialized smartphone application under ambient light. Paper-based microfluidics has also been used to detect pesticides in food products, such as apple juice and milk. A recent design used piezoelectric inkjet printing to imprint paper with the enzyme acetylcholinesterase (AChE) and the substrate indophenyl acetate (IPA), and this paper-based microfluidic device was used to detect organophosphate pesticides (AChE inhibitors) via a decrease in blue-purple color. This device is distinguished by its use of bioactive paper instead of compartments with pre-stored reagents, and it was demonstrated to have good long-term stability, making it ideal for field use. A more recent paper-based microfluidic design utilized a sensor, consisting of fluorescently labeled single-stranded DNA (ssDNA) coupled with graphene oxide, on its surface to simultaneously detect heavy metals and antibiotics in food products. Heavy metals increased fluorescence intensity, whereas antibiotics decreased fluorescence intensity.

Initial planning for my article
I will be working on an article about Paper microfluidics for Wikipedia. There is currently no article exclusively on this topic on Wikipedia. This is the most closely related article I have found: Lateral flow test. However, the lateral flow test is mostly used for qualitative purposes, such as the standard at-home pregnancy test. Paper microfluidic devices have more quantitative applications and thus deserve their own Wikipedia page. Therefore, Julian and I will be creating an article basically from scratch.

Since this is a new Wikipedia page, we will need to have a pretty solid introduction section going over the basics of paper microfluidics. We will consult a lot of reliable review articles to do so. Here are a few headings I was considering for our article:

- History

- Fabrication (how they're made, comparison of these methods)
 * wax printing
 * photolithography
 * etc.

- Fluid flow in paper microfluidic devices

- Detection methods
 * electrochemical

- Applications
 * glucose detection
 * E. coli/ salmonella detection
 * cardiovascular disease/cancer detection
 * etc.

- 2D versus 3D devices

- Analytical advantages

- Disadvantages/trade-offs

Article Evaluation
Article title: Gas chromatography-mass spectrometry

https://en.wikipedia.org/wiki/Gas_chromatography%E2%80%93mass_spectrometry Reflection paragraph
 * Missing references related to the use of GC-MS in analyzing samples from Mars and in airport security (both in introduction)
 * Definition of nonspecific versus specific tests in the introduction was a little distracting. This probably belongs on a forensics page.
 * Needs a section on 2D GC-MS
 * History section needs more detail
 * No in-text citations in the “Types of mass spectrometer detectors” or “GC-tandem MS” sections!
 * Same for “Chemical Ionization” section – which is vague to begin with
 * “When the amount of information collected about the ions in a given gas chromatographic peak decreases, the sensitivity of the analysis increases. So, SIM analysis allows for a smaller quantity of a compound to be detected and measured, but the degree of certainty about the identity of that compound is reduced.” – This could be worded better.
 * There are only a few references in the applications section, which makes no sense – this section should have plenty of references to papers!
 * Criminal forensics and law enforcement sections could be combined, with more detail added, too
 * Outdated astrochemistry reference – talks about a projected project in 2014
 * The Talk page looks like it has only been active once per year for the past few years now
 * The introduction was recently modified because it included an incorrect historical discussion of mass spectrometers as detectors for GC
 * Also lots of modifications to the references – links fixed and unrelated references noted
 * Clarity of paragraphs has also been fixed
 * What is referenced is good – the links all work and the sources support the statements being made. The problem is that there are not enough citations.
 * lots of peer reviewed journal articles
 * Part of WikiProject Mass Spectrometry – this is a top importance article for that project

Overall, I enjoyed reading this article. There were really good descriptions of the basics of gas chromatography and mass spectrometry. The authors also gave thorough explanations of more complicated mass spectrometry topics, such as types of ionization and full scan mode versus selective ion monitoring (SIM). However, this article falls short in its lack of references. Paragraph-length descriptions are given without a single in-text citation! This needs to be fixed by a team of editors. Some other small issues I noticed were outdated statements, a distracting description of specific and nonspecific tests in forensics, and separate criminal forensics and law enforcement application sections that should be combined. Text I posted to the article's talk page

It seems like this article is lacking citations in several of the major sections. For example, "Types of mass spectrometer detectors," "GC-tandem MS," and the "Analysis" sections have no in-text citations! As a graduate student in chemistry, I really like the information in these sections. But there needs to be citations so people who are less familiar with chemistry can validate the information given. Is anyone willing to take on this task? Any analytical chemistry textbook would probably be a good place to start. Paiges8 (talk) 01:51, 19 January 2018 (UTC)

Add to an article
I added the following sentences to https://en.wikipedia.org/wiki/Gas_chromatography%E2%80%93mass_spectrometry:

"A simple and selective GC-MS method for detecting marijuana usage was recently developed by the Robert Koch-Institute in Germany. It involves identifying an acid metabolite of tetrahyhydrocannabinol (THC), the active ingredient in marijuana, in urine samples by employing derivatization in the sample preparation."

"In drug screening, GC-MS methods frequently utilize liquid-liquid extraction as a part of sample preparation, in which target compounds are extracted from blood plasma."

This is the source I used for both citations (information on different pages in book, 735 and 731, respectively):

Bschmann, Hans-Joachim (22 April 2015). Handbook of GC-MS : Fundamentals and Applications (3 ed.). John Wiley & Sons, Incorporated. pp 731, 735. ISBN 9783527674336. Retrieved 22 January 2018.

Initial drafting of my article
I have narrowed my topic down to the following sections:
 * overview of the major applications of paper microfluidics - why use paper?
 * low cost
 * no expensive lab equipment
 * environmental contaminants will be filtered out, good for field use
 * The major areas of application: point-of-care testing
 * focus on glucose detection (colorimetric devices mostly, also electrochemical ones)
 * Martinez et al.
 * include other forms if there is room (non-communicable disease paper by Warren et al.)
 * ***Might do an entire paragraph on 3D devices, or will just mention one in the glucose section. What do you all think?
 * Another application: environmental and food safety tests
 * E.coli and salmonella detection using smartphones

Article I emailed for peer review
Title: Paper-based Microfluidics

Applications

Overview

The main advantage of paper-based microfluidic devices over traditional microfluidics devices is their potential to be used in a field-setting rather than a laboratory.1,2  Filter paper is advantageous in a field setting because it is capable of removing contaminants, including dirt, from the sample and preventing them from moving down the microchannel. This means that particles will not inhibit the accuracy of paper-based assays when they are used outdoors.2 Paper-microfluidic devices are also small in size (approximately a few mm to 2 cm in length and width)2–4 compared to other microfluidic platforms, such as droplet-based microfluidic devices, which often use glass slides up to 75 mm in length.5,6 Because of their small size, paper-based microfluidic devices are portable.1,2 Paper-based devices are also relatively inexpensive. Filter paper is a very cheap, and so are most of the patterning agents used in the fabrication of microchannels, including PDMS and wax. Most of the major paper-based fabrication methods also do not need expensive laboratory equipment.1 These characteristics of paper-based microfluidics make it ideal for point-of-care testing, particularly in countries that lack advanced medical diagnostic tools.2 Paper-based microfluidics has also been used to conduct environmental and food safety tests.7–9

Point-of-care testing: glucose detection  

Paper microfluidic devices have been designed to test a wide variety of medical ailments. An analyte of great interest in the paper microfluidics world is glucose, which is involved in diseases such as diabetes and cancer.10 Most commonly, these devices utilize colorimetric detection. Colorimetric devices often utilize a catalytic cycle involving glucose oxidase, hydrogen peroxide, and horseradish peroxidase to initiate a reaction between glucose and a color indicator, frequently potassium iodide.10 The first paper microfluidic device, developed by George Whitesides’ group at Harvard, is able to simultaneously detect glucose and protein via color-change reactions (potassium iodide reaction for glucose and tetrabromophenol blue reaction for the protein BSA).2 The bottom of the paper device is inserted into a solution prepared in-lab, and the amount of color change is observed.2 More recently, a paper-based microfluidic device using colorimetric detection was developed to quantify glucose in blood plasma. Blood plasma is separated from whole blood samples on a wax-printed device, where red blood cells are agglutinated by antibodies and the blood plasma is able to flow to a second compartment for the color-change reaction.3 Whitesides’ group also developed a 3D paper-based microfluidic device for glucose detection that can produce calibration curves on-chip because of the improved fluid flow design.11

Electrochemical detection has also been used in these devices. It provides greater sensitivity in quantification, whereas colorimetric detection is primarily used for qualitative assessments.1,10 Screen-printed electrodes12 and electrodes directly printed on filter paper13 have been used. One example of a paper-based microfluidic device utilizing electrochemical detection has a dumbbell shape to isolate plasma from whole blood.13 The current of the hydrogen peroxide produced in the aforementioned catalytic cycle is measured and converted into concentration of glucose.13

Environmental and Food Safety Tests

Paper-based microfluidic devices have several applications outside of the medical field. For example, paper-based microfluidics has been used extensively in environmental monitoring.7–9  Two recent devices used a smartphone detection system for the detection of Salmonella8 and E. coli7 after separation on a paper microfluidic device. Paper-based microfluidics has also been used to detect pesticides in food products. A recent design used bioactive paper containing enzyme and substrate instead of compartments with pre-stored reagents to detect organophosphate pesticides.9