Science topic

Citrus sinensis - Science topic

Citrus sinensis is a plant species of the genus CITRUS, family RUTACEAE that provides the familiar orange fruit which is also a source of orange oil.
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We do not intend to dry the peel as we assume some components might be lost.
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To extract compounds from fresh orange peel, you can use a variety of techniques that will preserve the bioactive components while preventing degradation. Here are some commonly used methods for extracting from fresh orange peel:
1. Cold Pressing (Mechanical Pressing)
Description:Cold pressing is a common technique used for extracting essential oils and juice from citrus peels. In this method, the fresh peel is mechanically pressed or squeezed to extract the volatile compounds (mainly essential oils) and juice.
Steps:
  • Cut the fresh orange peel into small pieces.
  • Use a cold press or hydraulic press to mechanically extract the oil and juice from the peel.
  • This method helps preserve the essential oils and other components without high heat, which can degrade sensitive compounds.
Benefits:
  • Retains a high yield of essential oils.
  • Minimal heat exposure, preserving volatile compounds.
2. Solvent Extraction (Using Non-Polar Solvents)
Description:Solvent extraction involves using a solvent (such as ethanol, hexane, or dichloromethane) to dissolve and extract essential oils and other lipophilic compounds from the fresh peel.
Steps:
  • Cut the fresh peel into small pieces or grate it.
  • Add the peel to a solvent (ethanol or hexane are commonly used).
  • Let it soak for several hours or up to 24 hours in a closed container, shaking occasionally.
  • Filter the mixture to separate the peel from the solvent.
  • Evaporate the solvent under reduced pressure (using a rotary evaporator) to concentrate the extract.
Benefits:
  • Effective for extracting both essential oils and other lipophilic compounds (like flavonoids and alkaloids).
  • Solvents can be chosen to match the polarity of the target compounds.
3. Steam Distillation
Description:Steam distillation is a traditional method for extracting essential oils. In this process, steam is used to separate volatile compounds from the fresh peel.
Steps:
  • Place fresh orange peel into a distillation apparatus (such as a Clevenger or steam distillation apparatus).
  • Introduce steam into the chamber where the peel is contained.
  • The steam causes the essential oils to evaporate and carry with it the volatile compounds.
  • The vapor is condensed into a liquid phase and separated into an essential oil and water phase.
Benefits:
  • Highly effective for extracting volatile essential oils.
  • No need for solvents, which may be beneficial for maintaining the purity of the extract.
4. Soxhlet Extraction
Description:Soxhlet extraction uses a continuous extraction method where the solvent is repeatedly cycled over the fresh peel to extract components over time.
Steps:
  • Cut the fresh orange peel into smaller pieces and place it in the thimble of the Soxhlet apparatus.
  • Use a solvent (such as ethanol or hexane) to extract the target compounds.
  • Heat the solvent to boiling, and it will condense and drip over the peel, repeatedly extracting compounds as it circulates.
  • After several cycles, the solvent is evaporated to concentrate the extract.
Benefits:
  • Suitable for extracting both volatile and non-volatile components.
  • Continuous extraction improves the efficiency of the process.
5. Ultrasonic-Assisted Extraction (UAE)
Description:Ultrasonic extraction utilizes high-frequency sound waves to create cavitation bubbles in the solvent, which increases the mass transfer of compounds from the orange peel to the solvent.
Steps:
  • Place small pieces or ground fresh peel into a solvent (usually ethanol or methanol).
  • Apply ultrasonic waves to the mixture for a set period, typically 20–60 minutes.
  • After the extraction, filter the mixture to separate the solvent from the peel.
  • Evaporate the solvent to obtain the extract.
Benefits:
  • Fast and efficient method for extracting bioactive compounds.
  • Uses lower temperatures than other methods, reducing the risk of thermal degradation.
6. Maceration (Simple Extraction)
Description:Maceration is a simple method where the fresh peel is soaked in a solvent at room temperature, and the compounds are extracted by diffusion over time.
Steps:
  • Cut or grind the fresh orange peel into small pieces.
  • Add the peel to a solvent (e.g., ethanol, methanol, or water).
  • Let the mixture sit for 24–48 hours, shaking occasionally to promote diffusion.
  • Filter and concentrate the solvent to obtain the extract.
Benefits:
  • Simple and cost-effective method.
  • Suitable for extracting both lipophilic and hydrophilic compounds.
Considerations for Fresh Orange Peel Extraction:
  • Freshness of Peel: Use fresh peel to ensure that volatile components, especially essential oils, are not lost due to drying.
  • Solvent Selection: Choose a solvent that matches the polarity of the compounds you're targeting (e.g., ethanol for polar compounds or hexane for non-polar compounds).
  • Temperature Sensitivity: Avoid high temperatures that may degrade volatile compounds or heat-sensitive bioactive molecules.
  • Purity: Ensure that the extraction method does not introduce contaminants or impurities that could interfere with the analysis of the compounds.
Each of these methods has its advantages, depending on the compounds you're looking to extract and the specific application.
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I am showing two curves here, both reaching convergence. Blue (force constant of 250 kJ/mol/nm and velocity 0.01 nm/ps) and orange (force constant of 500 kJ/mol/nm and velocity 0.05 nm/ps). To the best of my knowledge, it is preferable to go for the lowest values because we don't want to perturb the system too much. But with the blue plot, it is not smooth. I do see a small plateau/microstate. I don't know if that's ok.
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The blue curve shows a smoother, more stable transition in the force, indicating better system stability with a lower perturbation. The small plateau or microstate you notice is not uncommon and may not be an issue, but it can be further investigated by refining the force constant or simulation parameters.
The orange curve shows a sharper peak and potentially more disturbance due to the higher force constant and velocity. While it can still be valid, the smoother blue curve is typically preferred to avoid introducing large perturbations.
All of which can we easily done at mdsim360.com, a new platform that lets you run MD simulations entirely online without local installation.
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I need more pdf on this topic
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Although some studies do not agree with the use of citrus fruits due to acidity, my own experience has proven the opposite.
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We are having a big problem of citrus decline problem.
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While no citrus variety is completely resistant to HLB, some mandarin and sweet orange cultivars exhibit a higher level of tolerance to the disease, making them considered "HLB-tolerant germplasm"; notable examples include the 'Sugar Belle' mandarin hybrid ('LB8-9') and certain selections within the sweet orange category, but even these tolerant varieties will still show disease symptoms under heavy HLB pressure.
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I am trying to investigate the thermal stability of a protein I work with using the TSA with SYPRO Orange. However, even though my protein produces a peak at about 43 degrees, it shows very high fluorescence at lower temperatures. What could be the possible reason for this high background? How can I optimize the assay?
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The high fluorescence at low temperatures for your protein could be due to:
1. Increased protein stability
2. Reduced protein denaturation
3. Enhanced fluorophore binding
4. Decreased quenching
5. Changes in protein conformation
Temperature-dependent fluorescence:
At lower temperatures:
- Protein movements slow down, reducing quenching.
- Fluorophores may bind more tightly, increasing fluorescence.
- Protein structure becomes more rigid, enhancing fluorescence.
Possible explanations:
1. Hydrophobic interactions: Low temperatures strengthen hydrophobic interactions, stabilizing protein structur
e.
2. Hydrogen bonding: Low temperatures enhance hydrogen bonding, stabilizing protein-fuorophore complex.
3. Reduced protein aggregation: Low temperatures minimize aggregation, increasing fluorescent protein population.
Consider:
1. Protein purification and quality
2. Buffer composition and pH
3. Fluorophore properties and concentration
4. Instrument settings and calibration
To confirm:
1. Perform temperature-dependent fluorescence titration.
2. Measure protein stability using circular dichroism (CD) or differential scanning fluorimetry (DSF).
3. Test protein-fuorophore interaction using fluorescence lifetime measurements.
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I have a response variable called skin yellowness, which I will measure via a scored color chart, whereby 1 is pale yellow and 15 is orange. I'm not sure if this counts as an ordinal variable, because the scale is numerical and is basically a value for pigmentation (making it a numerical variable) or if it is ordinal, because the score suggests some sort of order. Can anyone help?
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Based on the information provided, the scale can be treated as an ordinal scale for color (Yellowness) but not an interval or linear one for color. Because color is a perception, the degree of "yellowness" differs from mere pigmentation. In addition, there is no consensus definition for what is called "yellowness." Mere pigmentation is physical and linear.
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Hello everyone! I observed in my culture (htert-RPE1 cells) an orange- red particle at the bottom of the dish. It is visible to the naked eye as a very very small red dot. Could it be a contamination (for example mold spores)?
Thank you in advance for your help!
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No it is just some leftover debris on your plate. Might be a manufacturing error but won't really impact your culture. Try to adjust the soft knob to focus on your cells, it'll disappear because it's in a different layer than the cells. If your cells are suddenly misbehaving, report this issue to your supplier.
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First titanium nanoparticles were made through green synthesis.
To perform photocatalysis of methyl orange dye, different light sources were used.
We added 0.05g(50mg) of TiO2 nanoparticles, 0.5 ml hydrogen peroxide to a 50ml solution of methyl orange in a set of two beakers, stirred in the dark for half an hour to achieve the absorption - dis equilibrium.
One beaker was kept under the UV light of biosafety cabinet since we do not have a photoreactor. But after 3 hours of irradiation, it did not degrade the dye.
The other beaker was kept under tungsten bulb as the light source with a distance of 5 cm on a constant stirrer for 3 hours.
But after 3 hours of exposure to light there was no sign of degradation.
We had balance the pH also by adding HCL dropwise to make the methyl orange dye solution acidic (4-5 pH).
The experiment does not yield result in either of the above mentioned light sources. What are the factors that need to be changed or are missing for dye degradation to occur.
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I don't doubt the UV light source. I think that the UV light might be absorbed by the glass of the beaker. So, no UV light reaches the inside and the degradation cannot take. But I don't know.
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What are the merits of using Methyl Orange rather than other Dyes in photocatalytic degradation?
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In summary, the ability of methyl orange to absorb visible light, facilitate electron transfer, and provide stable, cost-effective sensitization makes it the preferred choice in many photodegradation studies compared to other dyes that may lack these beneficial properties.
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We´ve been using the Picro Sirius Red staining for several years now (done in out core facility) to show fibrosis development.
However suddenly our stainings, which usually had a yellow background turned orange, which makes the red fibers much harder to adequately quantify.
Our core facility hasn´t strayed from the usual protocol and no solutions were replaced or anything done differently than before, at least according to them.
We´ve done several stainings by hand, all of which have come out orange.
Does anyone have any idea how exactly this might have happened or how to make our background lighter yellowish as it was before?
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Bree Barand do you also include the formalin fixation and then 3 washes in 100% EtOH before staining?
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AAZ
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Extracting formaldehyde from a fruit like a banana or orange would be challenging because formaldehyde is not a natural component of fruits. Formaldehyde is primarily used as a preservative in some foods but not typically found naturally occurring in fruits. However, if you're interested in extracting formaldehyde for some specific purpose, such as analytical testing or research, you would likely need to employ chemical methods rather than extraction from fruits.
One possible method to extract formaldehyde from a food sample involves acid hydrolysis followed by derivatization. Here's a simplified outline of the process:
1. Sample Preparation: Start by preparing your fruit sample. Crush or blend the fruit to a homogenous mixture.
2. Acid Hydrolysis: Add an acidic solution to the fruit sample. This will hydrolyze any formaldehyde-bound compounds, releasing formaldehyde into solution.
3. Derivatization: Formaldehyde is highly reactive and can form adducts with various compounds. Derivatization involves reacting formaldehyde with a suitable reagent to form a stable derivative that can be more easily analyzed or detected.
4. Extraction: Depending on the specific method and derivatization used, you may need to extract the formaldehyde derivative from the solution to separate it from other components.
5. Analysis: Finally, analyze the extracted formaldehyde derivative using analytical techniques such as gas chromatography-mass spectrometry (GC-MS) or high-performance liquid chromatography (HPLC) to quantify the amount of formaldehyde present.
Keep in mind that handling formaldehyde and performing chemical extractions requires proper safety precautions and expertise in laboratory techniques. Additionally, if you're considering this for any practical application, it's crucial to ensure compliance with regulations regarding the use and handling of formaldehyde.
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I want to stain acute brain slices with calcium orange and DAPI, but I am not sure whether these two kinds of dye can be added together or not.
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The DAPI excitation peak is at 359 nm and the emission peak is at 457 nm. The Calcium Orange excitation peak is at 549 nm and the emission peak is at 574 nm. (There needs to be esterase activity present to cleave the AM ester off the calcium orange.) Therefore, the fluorescence ranges can be separated by flow cytometry and fluorescence microscopy optical filters, allowing the two dyes to be used together.
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I have a recipe of loading dye (10 mM EDTA, 1X TBE, pinch of Xylene cynol and Orange G dye which is made upto 10 ml with 100% Formamide) but somehow the bands of the nucleotide product (enzymatically degraded DNA) are not distinct and well defined or fuzzy. I use 1 X TBE buffer (freshly prepared), the volt used to run the gel is 1500-2000 Volt or 25-40 W. Could you please suggest the recipe of loading dye or other factors that could give crisp bands for publication purpose. Any advice would be highly appreciated.
Thank you in advance
Prem
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All enzymes that work on DNA have Mg2+ as a cofactor. So, I think the EDTA you have in your buffer will already do the job, as it complexes the Mg2+. Concerning proteins bound to DNA, an alternative to phenol extraction is to use proteinase K for the deproteinization of the samples.
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What kind of chemical is used as an anti-mold agent in orange wrapping paper?
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Hello Friends 🎄
Season's greetings🎄
I recomend my abstract in the bilmescongress🍄
Effects of gamma radiation and electron beam on samples of the Peanut Candies contaminated with Aspergillus flavus🍞
Gisele Ferreira de Souza1,🇧🇷
Laith Khalil Tawfeeq Al-Ani2m
🇧🇷
1 University of Sao Paulo, Brazil
2 School of Biology Science, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia;
* Corresponding Author (Gisele Ferreira de Souza)🍠
Abstract🍩
Peanuts is known usage in making foods and generation of oil in Brazil like peanut candies and potential contaminated with several mycotoxigenic fungi as Aspergillus flavus. Therefore, it is possible A. flavus secreting some mycotoxins into contamination peanuts.🍬
This study is aimed to determine effects of gamma radiation and electron beam in reduction peanut candies contaminated with A, flavus. The samples of peanut candies were included two types of peanut candy, (A) Diet Peanut Candies, (B) Organic Peanuts Candies that divided treatments divided into two groups First: contaminated groups with A. flavus, and Second: control without contaminated which receive radiation of 0, 5 and 10 kGy dosage of electron beam EB and gamma radiation GR. Some samples of No inoculation were illuminated with a similar dosage to evaluate the sensors. 🍕
The results indicated that 0.80 of the samples had an average water capacity. Illumination or irradiation of gamma radiation and electron beam at a dosage of 5 and 10 kGy were able to eliminate the A. flavus in the samples of Brazil peanuts. Analyzes of Aflatoxin indicated that electron beam doses of 5 and 10 kGy lowers aflatoxins levels by 53.32 and 65.66% correspondingly. Moreover this same dosage of gamma radiation lowered the levels of toxins by 70.61 and 84.15% respectively as compared to the control groups. The irradiation energy could affect A. flavus without change in characterize tastes of peanut candy and potential reduction mycotoxins in this candy. 🍭
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Need this for my research please also indicate which article it was from, thank you.
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You may find the answer here
However, a number of factors can affect the concentration of Methyl Orange dye in textile wastewater, including the type of dye used, the dyeing process, and wastewater treatment efficiency. There are generally a few milligrams per liter (mg/L) to several hundred milligrams per liter (mg/L) of dyes in textile wastewater.
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I am doing comet assay for gills of fish, the fish were exposed to pesticides primarily.The problem i am facing that the cells are not picking stain.Can anyone tell that while using acrydine orange in order to stain DNA of gills.which concentration we should use?
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@all The concentration of acridine orange for staining DNA in a comet assay can vary depending on the specific protocol and the sensitivity required for your experiment. However, a common concentration range for acridine orange staining in comet assays is typically between 1 and 10 μg/mL. Here are some considerations:
  1. Start with a Lower Concentration:Begin with a lower concentration, such as 1-2 μg/mL, and assess the staining efficiency. This allows you to evaluate if the staining is sufficient without saturating the signal.
  2. Optimize Based on Signal Intensity:Evaluate the comet assay slides under a fluorescence microscope. If the signal is weak or the cells are not picking up the stain, consider increasing the acridine orange concentration incrementally.
  3. Avoid High Concentrations:While acridine orange is commonly used in the range mentioned, excessively high concentrations can lead to over-staining and result in a loss of sensitivity or accuracy in detecting DNA damage.
  4. Consider pH of Staining Solution:Ensure that the pH of your staining solution is suitable for acridine orange. The optimal pH for acridine orange is often around 4.5 to 5.5.
  5. Dilution in Buffer:Prepare your acridine orange solution by diluting it in an appropriate buffer (e.g., TBE or TAE). The choice of buffer can also influence staining efficiency.
  6. Time of Staining:Optimize the staining time. Depending on the specific protocol, incubation times with acridine orange typically range from a few minutes to around 15 minutes.
  7. Check for Autofluorescence:Be cautious of potential autofluorescence in the sample, especially if you're working with tissues exposed to pesticides. Autofluorescence can interfere with the signal and may be mistaken for staining.
  8. Positive Control:Include a positive control with known DNA damage to ensure that your assay is sensitive enough to detect the level of damage you expect.
Remember to document the concentrations and conditions you use during optimization, and keep track of any changes made. If you are still facing issues with staining, it may be helpful to consult published protocols, reach out to colleagues with experience in comet assays, or consider contacting the manufacturer of the acridine orange for specific recommendations.
Additionally, consider assessing the overall health and integrity of your gill samples, as exposure to pesticides might affect the structural integrity of cells and impact the results of the comet assay.
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In September this year, I noticed an orange/green coloured scum layer in a slow-running river (see pictures) close to my hometown (Deinze, Belgium) containing green and orange clusters, as can be seen at the close-range picture of the bloom. 
Microscopical analysis revealed a micture of Microcystis-colonies (a bloom-forming cyanobacterium, the green part of the scum layer) and an unknown organism of which I have no clue what it could be. I encountered a similar (mixed) bloom about 10 years ago in a recreative lake in Flanders (see report-snippet in attachment).
It might be some micro-algae, or spores/pollen (but in this season?) infected by an aquatic fungus, or both structures (cells and what looks like hyphae) might concern the same organism (a fungus?). I however doubt it concerns a micro-algae.
Since than, I received more records of such scum layers from the nearby river Scheldt, and I personally saw something quite similar in the river Moldau at Prague three weeks ago. I hope someone familiar with this organism can tell me what it is?
Many thanks!
Jeroen
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Kouadri Mohamed El Amine indeed, it seems rust spores and Alnus is a tree growing on the riverbanks of the river where this orange scum layer developed! It seems this rust spore concentration on water is a rare phenomenon. Many thanks for the suggestion and potentially identification!
cheers,
Jeroen
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Anyone knows exact dye name with code and other information. Reactive orange with 418 nm wavelength.?
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Here is the SDS of methyl orange - I have no clue whether it has lambda max 418 nm but if you have a spectrophotometer (dual) then that does not matter
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I have prepared an azo dye with orange colour in polar solvents. As is seen in the absorption spectra, absorption is in the UV region and up to around 400 nm in the visible. However, an orange colour solution typically shows absorbance in the 500-600 nm range. This dye also shows a green specular reflectance in a dry solid form. Could anyone please explain the possible reasons for these two phenomena?
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The peak of the absorption spectrum is at 361 nm, which is in the UV, but there is nonzero absorbance at wavelengths between 400 and 500 nm, which is in the visible. The spectrum is dominated absorbance by the shorter (violet) wavelengths, which gives a yellow color, with just enough of the blue wavelength absorbance to give it an orange color.
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What is the best dye to use for Automated Liquid Handling System dispensing verification? Currently i am using Orange G. but if you have a good data with other dyes, please share it with me. Thank you.
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Sigma and Thermo-Fisher sell it. Certificates of analysis may be available at the vendor's web site once you have the lot number.
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hello evryone,
when a polymer has a narrow( fig below) distribution, the macromolecules don't flow in the same way, so this will impact the polymer's viscosity, which can lead to extrusion distortion.
On the other hand, if the polymer's distribution is wide( fig below), there is consistency in the viscosity, so the orange skin ( fig below) effect is hardly noticeable. is it true ?
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Dear Hakim Bout, melt extrusion defects are the consequences of many processing parameters, MWD is one of them, since diferent lengths chains have differents relaxation responses (times) while recalling at the exist of the dies. My Regards
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jurnal hukum adat mengenai pembagian harta warisan menurut prespektiv islam kelompok saya terdiri dari 2 orang yakni:
raihan ramadhan hayatuddin (2210611085)
rasendrya hendarwin (2210611386)
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How are you
Can you write the question in English?
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I know that both Orange G and Bromophenol blue are negatively charged dyes and that Orange G may migrate faster in an agarose gel.
I found a resource that says Orange G can be used in Native-PAGE and in a DNA PAGE but I cannot find any resources that say whether the two dyes are interchangeable in a protein SDS-PAGE.
Any insight would be greatly appreciated.
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Yes, I use it all the time. Works great for NIR scanning with a LiCor. LiCor sells a pre-made 4X loading solution.
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As the melting point of methyl orange solution is 300-degree cel, I want to use methyl orange solution as a solvent for the synthesis of conducting polymer. Please discuss.
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No, methyl orange will decay at 300‒500 °C. It represents an azo dye: sodium 4-[(4-dimethylamino)phenylazo]benzenesulfonate, and the azo functional group would not survive heating at 300‒500 °C. Methyl orange can break down to mutagenic radicals at various conditions, so be careful when handling solutions of it.
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As the question already implies, i made a mistake during restriction enzyme digestion and added the 6x loading dye to the DNA insert fot checking on the gel. 10ul was added to the gel for checking but the other 60ul that was supposed to be used for ligation later on also has the 6x loading dye added to a concentration of 1x. Will this be a problem later? Will the dye be removed during the GeneJet PCR purifications later? How should i proceed? All input is welcome.
Kind regards.
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Hi there,
As when you perform gel purification, the silica column purification process allows to remove the DNA "staining" molecules...
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This is CD20 staining (orange) in mice spleen,
Plz notice the weak stain in white circle compare with the brighter stain in other area.
what's the reason?
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Airbubbles could be also responsible for such images. Another reason: If you are proceeding your immuno on slides, it could be the case that somtimes the antibody solution gets behind the sections. This explaines the more intensiv staining result in the border area. I recommand the free floating method when you are working with fixed sections of thickness more then 20µm. This technique could help to prevent such fenomena.
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Hi All, I am using cell mask orange dye to label HEK 293 T cells plasma membrane. I am using 5 ug of dye as final concentration and incubating cells for 10 min at 37•C. I am facing issue with dye internalisation. I did staining before fixation as well as after fixation. In both case All dye internalize. So here is the protocol I am using:
1. Growing cells
2. wash with PBS
3. Stained with cell mask orange for 10 min
4. washing 3 time with PBS
5. Fixation with 4% PFA
6. Washing with PBS.
7. Stored in PBS,Same day Imaging.
Note: Some time I pellet down the cells after second step and then stained the cell suspension. At the end step I just mount the sample on slide.
How can I prevent dye internalization in cell? what are the possible reason of this issue? Please let me know.
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Shoyab Ansari I found your email thread with our Tech Support. I am replying to it with some additional thoughts. Please feel free to reply back if you have any questions.
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For my project, I use MG63 cell line. These cells grew well in the first passage. But after the second passage, there were many dead cells and the culture medium became turbid and powdery (The culture medium placed in the incubator alone, its turbidity did not increase). Also, the culture medium was cultured on agar to determine bacterial contamination but did not show any contamination. In the next days, the attached cells also detached and died. Also, after changing the culture medium, the orange color of the medium quickly changes to pink within an hour (fresh complete medium contains 10% serum, 1% NEAA, 1% L-glu and 1% pen/strp). What is the cause of this cell death and change in color and turbidity of the culture media? Thankful
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First of all it might be due to other types of contamination (e.g. fungi) or expired/contaminated materials. If you are using RPMI-1640 powder make sure you add bicarbonate and keep the solution in the dark. Double check the protocol provided by the manufacturer. If none of these works, here is a reliable protocol for MG63 cell culture you can use instead. Good luck.
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I am using sypro orange in thermal melt experiments and am seeing a peak at 52C in the no protein controls, only when I do a full plate assay. I have seen that people mention dye binding to plastic is a problem in DSF – what does this background look like? Is it a peak or just high background? I am using Hepes Buffered Saline pH 7.4 and 20X final Sypro in a BioRad Opus384 qPCR machine and their recommended 384 well pcr plates. I get a really strong peak at 52C – is this something that you have seen?
Thanks, any feedback would be greatly appreciated!
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Thanks, I will try reducing the Sypro. Do you work with sypro in the dark? I keep the solution dark but then set up the plate with light, I am wondering if plate set up needs to be done in the dark?
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Hi all! There is something that always calls my attention when I am working with Eosin Y, an organic dye and a photocatalyst. The color of its solutions depends on the concentration and the solvent. But also, and homogeneous solution in water/tBuOH, for example, is orange within the body but pink on the edge of the solution!
If you have any comments, want to share your experience I would appreciate it.
Thanks in advance!
Leo!
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I am seeing this phenomena in a non-quartz vial.
Thank you for the reference!
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Please somebody tell the absorbance value recorded for all dyes for ppm... Specially for RhB, methyl violet, methylene blue, or methyl orange.. Tell the absorbance value recorded..
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Thanks, please prepare very dilute solution and check absorbance, which should not more than 1
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Recently i made 5 dilute solution of methyl orange in water, then measured their surface tension. results showed that surface tension increased by increasing the concentration. dose any body know the reason?
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Methyl orange can form a Zwitterion ion (both positive and negatively charged groups on the same molecule). It also is a flat planar molecule with two hydrophobic aromatic rings which would like to remain on the water's surface, while the charged regions, would like to be solvated by the water, however these charge regions of the methyl orange molecule can form hydrogen bond with each other producing an interlinked elastic film on the waters surface and increasing the surface tension.
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So our lab cultures about 2L of ExpiCHO a week in varying volumes from 25mL to 100mL. In the last 2 weeks we have had 4 flasks (all 100mL) show this weird growth behavior. Other transfections from the same day appear normal, and used the same media. All cultures were properly given 1st and 2nd feeds.
I personally did not perform the transfection, so issues involving human error are possible, but it supposedly was performed routinely without problems.
I am unsure as to what could even have happened, and what is exactly going on in the flask. It appears to be aggregation, and the culture looks to have grown since transfection date. Indeed while the one was a more brownish color, but have the indicative "orange" color of a viable culture, as to a pale yellow of a dead culture.
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Hi, we had somewhat the same issue and in our hands this was not contamination. ExpiCHO cells have always the tendency to clump a bit and we noticed that when we started production from a culture with too many clumps, the end result looked somewhat what you have there. We 'fixed' the problem by filtering our culture every few weeks. Hope this helps, Lennart.
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I want to clone eGFP gene in PUC19 plasmid using benchling app. I am trying to add my insert but one of its sticky end is not compatible. Can somebody tell me which enzyme will i choose from the highlighted orange enzymes? need help in the clonning steps. can somebody guide me in this. i have attached the images. The insert has to be added between BamHl and Ecor1. I have already added my backbone. Now i have to add insert.
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You can follow two strategies; one is to design a new pair of primers with desired restriction sites on the 5’ end, then run a PCR to amplify the gene of interest, and thereafter the cloning. The second strategy can be reached by making the sticky ends blunt. To remove the 3' overhangs or fill up the 5' overhangs you can use the Klenow fragment. Therefore, you can clone the blunt-ended fragment in any site with blunt ends. Remember to screen colonies to find that the gene has been cloned in the correct direction (5' to 3').
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Hello everyone, I have been trying to grow ZF4 cells we ordered from ATCC. We are having a really hard time. First of all, it will grow really slowly and after some days they will die. I have been using pre-warmed DMEM: F-12 Medium +10% FBS + Pen/strep. Also, I have to change the media frequently. It will change the color to orange in a day or so. Does anyone have a similar experience? How did you fix it?
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Hello , your cells may be infected with virus, fungus, mycoplasma. Or your cells are old. Did you check with an invert microscope that the cytoplasm of your cell was not vacuoled or that its membrane was not wrinkled and that the nucleus membrane was not granular? Because if these things happened to your cell. Your culture medium turns orange quickly and your cells die sooner .
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I'm working with Trichoderma species that are very close, around 97~98% identity, I wanted to know what exactly the colors indicate and what their implications are for each partition that the program presents.
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The colors are representing p-values (statistical significance). Only red and black means that your results are statistically significant. Orange and yellow means that your results are not significant. I am not sure about ASAP but I would expect that significance here refers to the partitioning.
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I want to use an agricultural production model to simulate the yield of oranges for different scenarios. However, I can't find a model that contains an orange crop file or a perennial crop that can inspire me. Help me please.
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@Ishak, that is a challenge for tree crops modelling. However, simulation of water use efficiency model can provide reliable yield estimate. I have attached below a paper that I found really useful in this regard.
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Calibration curve methodology from APHA
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What is your dependant variable?
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We have to PIT TAG adult Epinephelus coioides for identification purposes.
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Interesting question
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I want the procedure how to isolate probiotic potential lactic acid bacteria from Fruits
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Also check please the following useful RG link:
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I used Alizarin red staining on osteoblasts without a CPC quantification method. Do you think I can quantify the red/orange color with Image J ? How ?
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Hi J. Ramirez-Franco , here is an image, the staining is not very strong..
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I have added 10-15 % KOH to a 80:20 mix of 2-(2-Ethoxyethoxy)ethanol: 2-Butoxyethanol.
However, after a few hours to a day it starts to go from colorless to yellow to light orange to eventually a deep dark brown.
My questions are:
Why does this happen?
How do I prevent this from happening?
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You can substitute BHA as an antioxidant; it eliminates the formation of colored stilbene-like products. BHA is cheap and easier to get than more hindered phenols.
Also, if I didn't mention it before, you should keep your alkaline glycol solutions in plastic containers, not glass. Glass gradually releases iron, which contributes to discoloration as a catalyst for oxidation. You didn't mention the type of container in your reply, and your picture shows glass containers.
If you can spend some $$ then try an idea inspired by the new "non-yellowing" antioxidants for polyurethane foams such as "Omnistab AN 1135" : https://www.partinchem.com/products/omnistab-an-1135/
These were demonstrated to stop a similar yellowing problem in polyurethane foam that was formerly thought unsolvable. The principle is to use a much more hindered aminophenol than BHT. 2,4,6-tri-tert-butyl phenol would be the closest commercially available reagent like this.
Phosphites are another antioxidant used to prevent discoloration. Phosphites are slower to react with oxygen and peroxides, but are complete in the sense that they can lower oxygen levels to below detectable limits. A similar phosphite-based antioxidant from the same source above is omnistab-an-6136. Both of these "omnistab" products have side-chains that consist of branched, high-molecular weight alkanes. You don't need these necessarily, as they are intended to act like plasticizers in the yellowing polymers. Instead, you may want to test something commercially available in small amounts like tri-isopropyl phosphite or di-tert-butylphosphite at a concentration of 0.5% to see if that works better than BHT. If it does, lower the phosphite concentration until you reach the minimum amount of time for which you want the solution to remain colorless. Phosphites scavenge oxygen, becoming phosphates in the process; hindered phosphates and similar hindered phosphite esters are generally non-nucleophilic and being hindered, should have little effect on reactions. Hindered tri-alkyl phosphites are also higher-boiling than ethanol, but can be distilled off at reduced pressure. Some are checked-for as known impurities in pharmaceutical drugs.
Depending on your chemistry, it may be advantageous to know that tri-aryl phosphines also scavenge oxygen; triphenyl phosphine is a commercially-available example. Triphenyl phosphine reacts slowly with air at ambient temperature, so it must be handled quickly in air. Both triphenylphosphine and triphenylphospine oxide can be difficult to remove from reaction products. This makes them disadvantageous with respect to phosphites, which generally can be distilled under reduced pressure or extracted by water washes during workup of a reaction. Triphenylphosphine immobilized on resins might also help scavenge oxygen from your alkaline ethanol solutions, and the resin beads should be easy to remove when exhausted.
I would not recommend tri-alkyl phosphines as antioxidants as these are typically too reactive toward oxygen; they can be pyrophoric (burst into flame in contact with air), even in dilute solutions. They also participate in reactions with ketones and aldehydes to make alkenes (Wittig reaction).
It's little comfort but the best minds in industry and academia also find this problem vexing.
That's all I can contribute on the subject. Hopefully another contributor will have better ideas or more experience.
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Hi All, I have many breast tissue samples and have stained them with two chromogens (Red and Yellow) and there is co-localization areas (orange) that I am interested to quantify as well. What would be the best approach to quantify these three colors intensity in each sample?
Thank you in advance
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Sorry for asking: does IHC mean that you have a brightfield RGB image with one channel or a multichannel image? If the latter is true, I agree with Molly Brady. But for the other case you would need to do color deconvolution instead of splitting the channels.
Fiji has a number of predefined color deconvolution vectors (Image --> Color --> Color deconvolution). Since I don't know your staining, I don't know if there is one working for you.
Alternatively there is the plugin Color Deconvolution 2, which offers some extra features: https://academic.oup.com/bioinformatics/article/37/10/1485/5913390?guestAccessKey=148a8a4b-24f8-4b42-8742-e985535c9410
And there are of course also other programms, such as Qupath, where you manually annotate cells of interest for automated analysis of the whole sample: https://qupath.readthedocs.io/en/stable/docs/tutorials/cell_detection.html
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I was clearing a cabinet and I have found this plate from November 2021.
It is LB Agar with Neb10 competent cells.
The contaminants seem bright orange.
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Totally agreed!
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I transformed E coli JM109 with pMV361 (Kan resistance) and had a negative control (transformed with water) and 10 plates of the bacteria transformed with the plasmid. Those 10 plates have barely 1 or 2 colonies with the phenotype expected for E. coli, but the negaive control has over 7 colonies some of them kind of orange.
I would expect that if the plates were not correctly made, every one of them would be contaminated. But they have what we expected, very little grow, white, round.
Attached the picture of the negative control plate.
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Could the water be contaminated? Have you tried inoculating the plates with just the same water, and other plates without adding anything but pretending to inoculate them (taking off the lid, pipetting air, etc. - all the physical steps of inoculating), i.e., performing a negative control on the water?
Regards,
Tom Cuff
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I have a regression problem with two objective variables or outputs (named E & r). I made a model for every objective separately. I used Gaussian processes regression.
I obtained prediction for both objectives as can be seen in the attached images (error bar shows standard deviation).
Title of the plots shows R2 & RMSE of prediction. There is a categorical variable in dataset (Mixer) which has two values (50L, 2400L), shown by different colors on the plot.
Next, I calculated R2 & RMSE separately for every Mixer (shown in the legend in the attached images).
As you can see, for objective "E", RMSE of Mixer 2400L (blue color) is less than RMSE of Mixer 50L (orange color). But, its R2 is very low which is surprising for me. I expect that when RMSE is lower, R2 should be higher.
And for objective "r", RMSE of both Mixers are almost similar. But, R2 of Mixer 2400L is much lower.
I have only one assumption about this phenomenon. Reason of low R2 is because of lower No. of samples for Mixer 2400L.
No. of Observations:
  • Total : 119
  • Mixer 50L : 106
  • Mixer 2400L : 13
If you have any idea. please let me know.
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Hmmm. About the smaller sample size and the lower R-squared. I said "The smaller sample size made the regression coefficient standard errors larger, which would make a given sigma smaller in comparison." But I think I'm mistaken in thinking that makes R-squared smaller, but instead, just more volatile. (A quick check on the internet and remembering back a little indicates I was wrong about R-squared.)
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I have a multi-objective minimization problem and the final objective function is written as: F = f1 + f2. However, f1 and f2 are the error functions of two different quantities: orientation error (degrees) and position error (meters). I would like to minimize both of them at the same time.
The questions is: how can I properly scale, or make dimensionless, f1 and f2 before computing F in order to make them comparable (not to add oranges with apples)?
The main difficulty is that I do not know a-priori their range of variation (i.e. orientation and position errors). On the contrary, the ranges of variation of the "original" quantities (i.e. orientation and position) are known from the experimental data.
How is this problem commonly solved in the optimization practice?
Thank you,
Marco
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I would like to thought about the solution with you. That is what I said here is just a proposal hoping it will be beneficial to you.
You have to look at the independent parameters of the two error functions.
If the independent parameters of every one is are different for each of them, then you can optimize every error independent from the other.
If there is mixing of the independent parameters and dependent parameters then you can try the minimization process by independent parameters for each one independently till you get an acceptable error.
If you could not reach the acceptable error, then you can study the minimization of the two together by the adjusting the common parameters.
This may be one possible scheme for solving the problem.
I think there are mathematical tools for multi objective minimization or maximization. Please follow the link:
Best wishes
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below picture is my analysis model. because at corner part, there are many studs inserted, so such partition is needed. however at the orange color part, at first, it is possible to make a sweep mesh, but because of the influence of the previous partitions, it is difficult to make a mesh like picture 2. After do partition After the partition in the corner, a sketch like Picture 2 appeared in the orange part. And it is impossible to delete it using remove redendant entities. how to solve it,, ?
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Dear Lee,
If the number of partitions, which are needed, is too much (as the number of studs are). That would be time consuming to do it for each stud, also the corrections in mesh or partition (if needed) become difficult.
In such cases that would be probably better to make a script (python code) - get a "Macro" from partition command in Abaqus, then make it parametric and run the code for partitioning, in such way edits become much more easier.
Depends on the place you want to partition, you need just to change sum values in your macro instead of do the partition command again and again. Generally for repetitive commands, it's better to use programming rather than UI(user interface). ( File - Macro Manager - Create Macro)
Hope it helps
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Orange G is also a dye which is used in nucleic acid electrophoretic separation can other dyes like bromophenol blue can also be used? if not why? and which dye can be used in place of orange G.
I have attached below the literature for reference
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Yuri Mirgorod thank you sir for responding
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Hi there,
I'm designing an experiment (not necessarily to be conducted) in which the primary source of nitrogen within large monocultures is manipulated, and yield of crop is measured over time. The objective is to determine the feasibility of using peanuts as a primary source of nitrogen on large-scale agricultural operations.
Site: large-scale (~200 ha) orange grove in Florida.
Treatments: one plot (1-ha) with only peanuts, one plot (1-ha) with some peanuts plus strategically applied synthetic fertilizer.
Control: one plot (1-ha) with no change in fertilizer regime.
Data will be collected from 5 subplots (400m2) per plot (15 total).
Recorded from each subplot will be number of trees and number of boxes of oranges yielded per tree. This data will be scaled up to estimate number of trees per hectare and number of boxes of oranges yielded per hectare.
Feasibility would be determined by change in yield over time. Little variation in average monthly, seasonal, and overall yield per plot would indicate potential feasibility of using peanuts as fertilizer. Great variation between experimental plots and control plot may indicate that peanuts are not suitable sources of nitrogen for monoculture oranges.
What would be the appropriate statistical test to analyze this data? I'm thinking a single-factor ANOVA will tell me differences between treatments, but how can I compare data per treatment over time to determine overall change? Repeated measures ANOVA?
Any suggestions/examples would be appreciated.
Thank you.
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For applying the same, you need 12 degree of freedom. You have 3 treatments. 5 subplots can be treated as replication. Then your df is only 8. If you have 4 treatments, it would be good.
Expecting comments from the statisticians.
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need to know the concentration calculation for my test
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I am conduct my final project which is adsorption process of methyl orange using sugarcane bagasse as adsorbent. However, percentage of dye removal that I get was negative value because the final concentration that I get from adsorbance reading is higher than initial concentration. What should I do to get positive value of percentage dye removal ? Is it relate with the concentration of methyl orange or the amount adsorbent?
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The adsorbent may itself contribute to the absorbance. To correct for this, you should prepare two identical samples differing only in that one of them had no methyl orange in it initially. Then subtract the absorbance of this "blank" from the absorbance of the sample that contained methyl orange.
In addition, you should include in the sample solutions a strong pH buffer for the desired pH to prevent a change in the absorbance spectrum of methyl orange due to a change in pH.
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The figure shows the FTIR analysis for Plastic bag sample after three months of incubation with a fungal strain under special conditions. As demonstrated all T% at wave lengths in orange labels refer to standard FTIR polyolefins specifically LDPE as stated by Wiley Spectra Base (2020) in http://spectrabase.com/spectrum/IWxs9GBuNp. The other minor dips appearing in the carbonyl and double bond region blue labeled, and those in the finger-print region labeled in green were confusing, so please I need your help. FTIR of control (untreated Plastic bag) in red curve and that of treated in blue curve.
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Dear Ahmed,
The treated sample FTIR peak and control sample FTIT seem to be the same and the only differences between them is the amount of transmitance%. In this situation there would be no change in chemical structure of the main sample or if there is, it might be negligible. To be sure about it, it is necessary to make a comparision between the ratio of all FTIR peaks of control and treated samples. For example, the ratio of %T of control sample to the treated sample at 2915, 2848, 1467, 876, and 717 must be calculated. If the difference between all of them is meaningful, so it is acceptable to consider change in chemical structure during treating. Otherwise, it is not possible to consider that its chemical structure was changed.
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I need the detail of method such as the type of solvent and the wavelength . I want the steps in detail.
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Choosing the proper method to determine color of fruit juices depends on how you define/express color and what you want/need this value for?
If you are interested in color, as a general concept/value, you need a color meter which reads out color data e.g. by using the Hunter L-a-b- color-scale. This is a three number code that specifies your color. No need to buy an instrument, this article instructs how to do this with a smart phone:
Big advantage of 'color' measurement is that it uses the complete sample so including pulp and other solids which may contribute to color!
If you are interested in dissolved species that give the color, which are mostly anthocyanins, you need to register spectral data using a UV-VIS spectrometer. Downside is you need to remove solids as they generate a lot of background signal. I worked with grape juice and first spun down the juice in a centrifuge at 5000 rpm, next I used the clear liquid to further dilute in buffer (anthocyanins spectral data changes with pH) and record a spectrum from 900 to 300 nm. I recommend to read: which is the most comprehensive article on anthocyanins characterization.
Hoping this helps you further, kind regards, Leo
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With special reference to India and its neighbouring country.
Sweet Orange, mandarin etc.
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I would like some advise from those who have worked doing XRF for metamorphic rocks with large (centimetric-size) garnet samples. I have done XRF analysis to make pseudosections from these (these are meta-volcanic rocks (Amph, Opx,Plag,Grt,Bt,Ti-Fe oxides)), but I have obtained probably abnormal high Fe % values (~19%), and was advised to make again the bead for XRF. I was wondering what special procedure should I do to make powder from my sample. Do I need to make powder out of a large volume of sample? If so, what is specified as a 'large' volume of sample. Also, there is some yellow/orange alteration (oxides?) in some of the crushed sample, do I need to take away the yellow/orange alteration from it? I Would greatly appreciate any advise!
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Hi Carolina,
I have not done a lot of XRF work on samples with large porphyroblasts or phenocrysts so take what I say below with a grain of salt (or crushed garnet hornblende gneiss).
It might help to prepare several aliquots, maybe 7 or 8, from what you believe to be representative subsamples. Then, take equal portions of each and add to an additional aliquot which you you will ultimately fuse. If you want to be extra careful, you can then run each of the 7 or 8 aliquots to see what the range is and how it compares to your "mixed" aliquot sample. While time consuming, I think it is likely that doing this will give you a "representative" sample of the chemistry of the rock.
Ryan
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We are interested in evaluate the nitrate levels in leaves of sweet orange trees. Do you know a method to do it? We are particularly interested in one that demand few leaves.
Thank you
Luciana Marques de Carvalho
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Hi Luciana
The determination of nutrient concentration as described by Mattos Jr. (2000),
You can check this reference:
"Nutrient content of biomass components of Hamlin sweet orange trees"
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Methyl orange in its structure has a ion of Na+. my question is, after dissolving methyl orange in water, what will happen to that ion? Dose it form NaOH in reaction with water ? consequently, dose the H+ make a combination with methyl Orange? Or if not, do you know what will take place?
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This image explains it completely. Thank you so much.
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The solution of PGMs is include Pd,Pt and Ru ions, it is a solution with orange color. I has a problem for determination of chlorine ion in this solution by titration ( with AgNO3 ), the amount of chlorine ions is very low and due to color of solution, I cannot recognize final point of titration. please help me to found better method.
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Maybe a Chloride Ion Selective Electrode?
Or ionic chromatography?
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Recently I have followed a well accepted method to synthesize Cerium (4) alkoxide, The procedure is attached, I have used procedure number 4, but I obtained nothing but some orange small agglomerates stuck to the bottom of RB, Could you please help me with the possible reasons of this problem? and also is it important to follow the amount of precursors? I am thinking to multiply the amount of precursors (considering the stoichiometric relation ) with maintaining the amount of THF, otherwise in one round procedure the yield CeAlkoxide is only approximately 1 g, Does it lead to any problem?
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Dear Mahsa Amiri many thanks indeed for your very interesting technical question. Actually, we have been working in the area of lanthanide and organolanthanide chemistry for more than 30 years, and we have already published a number of papers involving tetravalent cerium compound. The reference by Bill Evans of 1989 which you provided with your original question is quite familiar to me. The problem with the chemistry of tetravalent cerium alkoxide derivatives is that it looks simple but in practice it is not. We even used the compound (tBuO)3Ce(NO3)(THF)2 many years ago as starting material. I would say that the tetra-tert-butoxide complex Ce(OtBu)4(THF)2 is perhaps easier accessible than the mixed-ligand nitrate species. However, in all cases one should take care of a few precautions:
1. It is very important to exactly use the given amounts of starting materials.
2. The quality of the precursor NaOtBu is decisive for the outcome of these reactions.
Thus the question is if you used commercially available NaOtBu or ion it was freshly prepared from tert-butanol and NaH as described in the Evans paper? The problem with commercial samples of NaOtBu is that they are often partially hydrolyzed, which can be the reason for the observed low yield. I suggest that you freshly prepare your NaOtBu from tert-butanol and sodium hydride (or clean pieces of metallic sodium) and then evaporate the solution (which should be completely clear) to dryness. Then make sure that remaining tert-butanol is completely removed under vacuum. For even better results the product NaOtBu can even be sublimed under high vacuum. With this highly pure NaOtBu the synthesis should give much higher yields.
For some general overview of organometallic cerium(IV) chemistry please have a look at our review article entitled:
Tetravalent Chemistry: Organometallic
This article is freely available as pubic full text on RG.
Good luck with your research! 👍
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I have coded an ML project stock price prediction, but unfortunately my predicted values follows the training data to some extent and then shows a straight line. Why is this so?
I have attached the code and the graph. Kindly guide me.
Orange line shows training data, green shows test data. Y-axis shows closing price and X-axis shows the date
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Might be caused by some kind of transformation into an interval with an upper bound. Divide your training data and set values by two and see what happens.
Regards,
Joachim
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After extraction of the essential oil, I found a high percentage of limonene presenting more than 90%.
Can I separate the pure limonene from the minority that presents less than 10%?
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Use separating funnel and confirm its purity with GCMS.
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what would be the recommended protocol of acridine orange staining on hydrogel seeded cells by looking in Fluorescent microscopy. can someone have an idea about the concentration of a stock solution of AO, How much AO/PI to use, and what Quantity of cells to use for hydrogel?
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Hi Faiza,
To staining cells and observe by fluorescent microscope, we use Calcein AM/PI to distinguish live/dead cells. For cells in hydrogel, mix your dye with culture medium and staining by replace the medium.
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We have used batch mode ultrasonic assisted adsorption experiments were conducted to study the methyl orange dye removal efficiency using some adsorbent. For each experiment, 100 mL of MO dye solution with prefixed concentration and pH were taken into a beaker and a suitable adsorbent dose was mixed with the solution. Thereafter the mixture solution was sonicated for a prefixed time by using an ultrasonic bath reactor (Rivotek, India) operated at an ultrasound frequency of 30 kHz. The ultrasonic bath reactor was having heater power of 130 W and ultrasound power of 50W, respectively. However the heater power was not used in this study as all the experiments were conducted at room temperature. The volume of water in the ultrasonic bath was 1.5 L.
Now we need to measure the intensity of ultrasound in the reaction vessel (i.e. in the beaker itself) during the reaction. Please provide the steps to measure the intensity of ultrasound in the beaker.
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i never used them before but there exist something call Ultrasonic Energy Meter , and i am seeing that maybe you can get one of this devices and introduce the tip in your beaker and measure the intensity of the ultrasound inside of it, here is a link of the equipment:
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after dilute acid hydrolysis of orange peel should I neutralize the hydrolysate before or after dosage of sugar?
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sugars can break down in an acidic environment, disaccharides can become mono, changing their sweetening power
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I am currently working on LAMP. Since the original mastermix volume was for 100 reactions and to prevent continuous freeze thaw of the mastermix we put the mastermix into smaller volumes and store at 20 degree celsius until we are using it. However, the mastermix in the tubes turned orange instead of remaining pink. Is there any reason why it is turning orange or is there any way to prevent it from turning orange.
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Dear Dr. Ang,
Did you resolve it?... I am experiencing the same problem. My water only control is changing from a pink to an orange color.
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Related to data mining/data science, I recently discovered Orange (https://orange.biolab.si/) a high level very powerful free toolkit. Using it is very simple and you can test different models in order to evaluate the best results. However, when writing paper to a Journal, is it plausible to use it instead of R Studio (for instance) or other tools (PyTorch, Weka, TensorFlow)? Or Orange is best indicated just for teaching?
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Dear Alessandro,
The terms Machine learning, data mining and data science are used interchangeable but there is difference between these terms. Basically all the terms revolve around dealing with the rapidly using large amount of data. Data science derives understanding from structed and unstructured data. It is used for qualitative analysis. It consist of data visualizations, data mining, language processing etc. It is a wider area of research which makes use of many algorithms and operations to derive informative insights from both structured and unstructured information. Where as data mining analyzes data sets created from structed data to find the hidden correlations and patterns. It is subset of data science used to extract data and generate prediction models. Data Mining also incorporates data cleaning, pattern prediction, statistical analysis, data conversion, machine learning, and data visualization. Both play key roles in helping organizations recognize opportunities and arrive at worthwhile decisions/conclusions so that they can take easily decisions to grow the businesses. Additionally, the knowledge needed for procedures in both of these fields also varies. Hence, the analysis of the differences in their approach, tools used and steps applied. Data science tools include Python, Apache spark, SAS, Tableau, R, Tensor flow etc. Data mining tools used as weka, rapid Miner, KNime, Oracle Data Mining, Apache Mahout, Teradata, Orange. These tools are not only used to teach/research but also used by industries to do the analysis as per requirements.
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Hi all, I conducted a binary log regression(yes/no) on 2 independent variables (categorical) called 'Color' and 'Income' using SPSS.
For 'Color':value1=blue , value2=orange , value3= green.
My reference category is Value3=green.
My question is how do I find out if a specific Color is sig or not since SPSS will always use one of the value as baseline and the results become a comparison of 'odds of value 2 vs odds of value 3 being a YES'. I will like to know if value2=Orange is significant in affecting the dependent variable result.
Is recoding each value in 'Color' into a binary variable (independent) then performing the test again correct?
This is a rough sketch of the SPSS output ' Variables in the equation' table:
Color
Color(1)
Color(2)
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Math Mystery wrote: "My question is how do I find out if a specific Color is sig or not since SPSS will always use one of the value as baseline and the results become a comparison of 'odds of value 2 vs odds of value 3 being a YES'. I will like to know if value2=Orange is significant in affecting the dependent variable result."
Orange vs what? If all you care about is orange vs not orange, then use a single indicator variable for orange colour (1 = orange, 0 = not orange) in place of your 3-level categorical predictor.
Another possibility is that you want all pair-wise comparisons of the colours. If so, you can get them by using GENLIN (rather than LOGISTIC REGRESSION) to estimate your model. Here is an example showing that you can get exactly the same model using GENLIN. It uses one of the sample data sets that comes with SPSS. You'll need to change the path on the GET FILE command to show where you have those datasets stored. To make it work for your data, replace Male with your dependent variable, Age with salary, and Race with your colour variable.
* --- start of syntax ---.
NEW FILE.
DATASET CLOSE ALL.
* Edit the path on the next line as needed.
GET FILE = "C:\SPSSdata\survey_sample.sav".
* Compute an indicator variable for Male Sex to use as the outcome.
COMPUTE Male = sex EQ 1.
FORMATS Male (F1).
FREQUENCIES race.
LOGISTIC REGRESSION VARIABLES Male
/METHOD=ENTER race age
/CONTRAST (race)=Indicator(1)
/PRINT=CI(95)
/CRITERIA=PIN(0.05) POUT(0.10) ITERATE(20) CUT(0.5).
* Generalized Linear Models.
GENLIN Male (REFERENCE=FIRST) BY race (ORDER=DESCENDING) WITH age
/MODEL race age INTERCEPT=YES
DISTRIBUTION=BINOMIAL LINK=LOGIT
/CRITERIA METHOD=FISHER(1) SCALE=1 COVB=MODEL MAXITERATIONS=100 MAXSTEPHALVING=5
PCONVERGE=1E-006(ABSOLUTE) SINGULAR=1E-012 ANALYSISTYPE=3(WALD) CILEVEL=95 CITYPE=WALD
LIKELIHOOD=FULL
/EMMEANS TABLES=race SCALE=TRANSFORMED COMPARE=race CONTRAST=PAIRWISE PADJUST=LSD
/MISSING CLASSMISSING=EXCLUDE
/PRINT CPS DESCRIPTIVES MODELINFO FIT SUMMARY SOLUTION.
* --- end of syntax ---.
HTH.
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Kindly conduct the papers and mechanism and methods of Extraction of Bioactive Compounds from Orange Processing By-Products
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Application of orange peel waste in the production of solid biofuels and biosorbents
The dry biomass and the biofuel showed moderate levels of carbon (44–62%), high levels of oxygen (30–47%), lower levels of hydrogen (3–6%), nitrogen (1–2.6%), sulfur (0.4–0.8%) and ash with a maximum of 7.8%. The activation energy was calculated using Kissinger method, involving a 3 step process: volatilization of water, biomass degradation and volatilization of the degradation products. The calorific value obtained was 19.3 MJ/kg. The studies of metal biosorption based on the Langmuir model obtained the best possible data fits. The results obtained in this work indicated that the potential use of waste orange peel as a biosorbent and as a solid biofuel are feasible, this product could be used in industrial processes, favoring the world economy.
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So i have data something like this in SPSS at the moment:
case 1: orange, bananas, mangoes
case 2: bananas, oranges, mangoes
So the first respondent ranked orange as best fruit whilst second ranked banana as the best fruit.
  1. The variables i used were strings i.e. o, b and m, should this be a problem?
  2. Secondly, how do i assign rank to a particular column e.g. orange should be ranked 1 as it is in left most column, when the data was imported from sogosurvey ? See ranking.png for the actual data
  3. Also, is there a quick way to add replacement variable e.g. if the case has value "x" transform it to "yes" and if empty convert it to "no"? The empty cells mean not selected (=no OR 0) and M-multivariate course selected (=yes OR 1) in emptycells.png.
Thanks for your help.
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Yes, it is possible to change the variable data using ranks or there is a feature that you work with while you change the names to numbers, for example: A = 1, B = 2 and so on
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How much raw materials are required for producing 1 kg of final products for each of the following?
1. Orange jam 2. Orange Jelly 3. Orange Marmalade 4. Tomato sauce 5. green Chilli Sauce 6. Tomato puree 7. Ginger paste 8. Canned pineapple
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Hi there sadhan
search the product you wish and it will give you its composition.
good luck
isaac
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I am mixing sodium hydroxide with a stabilizing agent PVP and the solution turns a brown orange. Does that mean that a reaction is taking place? Is there a formation of some sort of gel? The pH is very basic (11-12).
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Phosphate ester may get hydrolyzed.
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Hi
I wondering about how to interpret results in model view (after double cliking) on results, when paireswise chart with orange color of pairs, and the table after with some values with orange too (Adj. sig)
I have a dependent variable called: Organizational loyalty
I have also categorical variable called: job category (1. execustion, 2 maitrise, 3 cadre, 4 cadre superieur, 5 Hors categorie) in english (1 execution, 2 mastery, 3 manager, 4 senior manager, 5 post category manager)
I hope I was clear in my question
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thanks alot Samantha Curle you have save me
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Two new postings:
16. Can Orange County, CA Begin Opening this Week? This was a high profile article in the Orange County Business Journal and explains that CA and OC have not (yet) been hit that hard, but still very vulnerable particularly as LA is now hitting epidemic proportions
17. Weekly Update: Kudos to NY and NJ Discusses new updates with U.S. lagging the rest of the world, but at least NY and NJ make real progress toward recovery.
#covidresearch #covidmodeling #coronavirusupdate
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Interesting idea. Will be interesting to see how well it forecasted in retrospective analysis.
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We use 200 W tungsten lamp as source of light for degradation 20 mL methyl orange solution (10 ppm). How can calculate the irradiation intensity at the catalyst surface (mW/cm2)?
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just a remark:
apart from correct calculation, in the paper you should restrict the result to maximum 2 significant digits and mention that this result is a rough estimation of intensity due to crude point source approximation.
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Does anyone have advice on how to quantify the cells of the anterior pituitary from normal PAS and Orange Staining? I am aware that this is outdated because we have immunohistochemistry, but I am searching to see if there are any publications with the use of Image J or any other software for counting cells.
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These are the examples of slides I did. Sun Yung
Sorry for the late response.
I am writing a paper to compare the results. But I need a reference to compare it. Please note that this is regular histology with PAS stain. It is not immunohistochemistry.
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My boss is using MMSE to test schizophrenia patients' cognitive function. However, the version has a total score of 39. He hopes me to find the origin of the version, but all I found is the version with a 30 maximum score.
The version we are using includes questions like: can you tell me the similarities between oranges and apples? can you tell me the differences between tables and chairs?
Has anyone seen or heard about this version? That would be super helpful!!!!!
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Never heard about this kind of MMSE, sorry
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Given a time series with Events (chart patterns), I want to assess whether events (chart patterns) occur systematic or randomly in a time series.
My idea is to
  1. identify patterns in a given time series
  2. simulate multiple new time series
  3. identify patterns in the simulated time series
  4. compare the results
The key question is how to compare the results. The events (chart patterns) have a specific length and can be overlapping (as illustrated in the image).
I could easily just use the number of events in the original time series and compare them to the count/number of events in the simulated time series by simulating enough time series to construct a confidence interval.
But this would not account for clustering, overlapping and the size of events. Hence, it is not enough to just compare the count/number of events (patterns) but also if there is clustering (margin between events) or differences in the size of the patterns.
I could do the same test for different statistics. But I am wondering if there is a more elegant way.
The image is an example with orange lines being events of different size/length in time. They are overlapping but do not seem to be clustered. If they would be clustered they might only appear in the beginning and end of the time series.
My question is:
How to test if events (with different size, overlapping, and maybe clustered) occur systematic in a time series or randomly?
Are there any similar problems in other disciplines?
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I am working on research to apply six sigma in controlling the quality of the products of an industrial company, I did a case study
The supervisor asked me to use machine learning in the search (eg orange tool)
Do you have ideas or suggestions
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Look at the following link, may give you some idea
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Why are concrete and red-brick buildings cyan in infrared false color (IRFC) images?
Most building materials are made of soil (e.g. red tile roofs or concrete), thus most urban areas have the spectral signature of a soil.
Nevertheless, in IRFC satellite images we usually see bright urban areas in Bright Cyan instead of Dark Brown/LightBrown to Orange or Whitish. why is that?
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Hi @Matteo Biondi
This is because the buildings exhibit shorter wavelength that corresponds to red colour indication
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I was looking for methods for the carotenoids analysis in the urchins' gonads, however, I found that all methods lacked important information such as the initial sample weight, the ratio of sample to solvent, the time for the sample to settle after adding solvents such as n-hexane or Petroleum Ether. Moreover, there is a wide variety of solvents or mixture of solvents used for the same species and each give different results. Also, as mentioned in Chandrika Liyana-Pathirana et al. (2002), after separation of the carotenoid extract in the hexane layer, the reference says to transfer the hexane to 50 ml volumetric flask and make up the volume with hexane, but my extract was already 65 ml, so when I calculate the total carotenoid with the equation, should I use 50 ml or 65 ml?
I have another question, when I have a treatment of triplicate, to measure carotenoid, should I mix samples from all triplicates or should I measure one individual from each replica and then calculate the mean?
My feeding experiment yielded many variation in the color of gonads within the same treatment. So should I discard the very odd color, for example the red, as it occurred in 2 individuals only who appeared diseased and loosing spines, while the remaining samples fluctuated between medium orange roe to dull orange?
I would much appreciate your help with the above specific details in order to be able to run an accurate analysis.
Thank you in advance.
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Thank you for your kind help. I have this reference, however, it misses the details I am asking for.
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its colorimetric detection after interacting a analye with nanoparticles color rapidly change from yellow to orange. after 15 min of interaction take of a absorption spectra only quenching (decrease in absorption intensity) was observed large nanoaggregates was formed which confrmed by DLS. after 45 min visible aggregates are seen in solution. why shift not appear ?
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Dear Ayesha Urooj,
Given that chemical and physical structural changes in light absorbing entities under observation may either cause the absorption maxima of observed spectral absorption bands to move up or down the visible spectrum, or alter their spectral bandwidth, I reason as follows.
The term SPR {Spectral Plasmon Resonance) refers to the mode of vibrational displacement of free (un-bonded) electrons either within a given molecule’s chemical structure, or within a more loosely bonded molecular aggregation.
Three rules now follow: (1) the larger the free path of the electron within the structure the lower the oscillation frequency and therefore, the longer the mean wavelength of light absorption maximum. (2) If more than one resonating entity (each with a distinct frequency) is present peak broadening is observed. (3) Any given resonance mode may easily be inhibited or even quashed by introducing additional resonation modes.
I suggest firstly that in terms of colour and at the low molecular count associated with nano-particles, they behave as ‘super molecules’. Thus, in the initial change from yellow to orange small two and three molecule aggregations are generated which exhibit slightly longer electron resonance path. As aggregation proceeds the subsequent quenching and peak broadening indicate that there is a rapid rise in both quantity and variety of contributing vibrational modes and frequencies.
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I am trying to prepare CuN(CN)2 (=Cu[dca] = Copper(I) dicyanamide) by reducing an aqueous Cu(II) solution to Cu(I) with K2[S2O5] then adding stoichiometric amounts of Na[dca]. However upon addition of the reducing agent I form an orange/brown precipitate in a green solution, I believe this is as a result of the disproportionation of newly formed Cu(I) to Cu (orange/brown precipitate) and Cu(II).
The overall reaction for the reduction is as follows:
Cu2+ + 2HSO3- + 2H2O --> Cu+ + 2HSO4- + 4H+
And the disproportionation:
2Cu+(aq) --> Cu(s) + Cu2+
Are there any other reducing agents which may work better or any ways to stabilise the Cu(I) formed in solution to prevent the disproportionation and allow further reaction with Na[dca]?
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Are you sure that your precipitate is Cu metal rather than Cu2O, which is also reddish in colour?
You could try ascorbic acid as reducing agent - I've used it to make CuCl (very easy method, much nicer than any other I've tried!). To get rid of excess ascorbic acid with less risk of oxidation than if you use water, use methanol: ascorbic acid is significantly soluble in methanol, much less soluble in ethanol.
hth!
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Hi everyone!
I need to study the interaction between a protein and a drug. However, the ligand binds to the hydrophobic regions of the protein, just as SYPRO Orange. Thus, I do not know if the compound and the dye will compete for the same binding sites. Is it possible to characterize the protein-ligand interaction in this conditions?
Thank you all in advance!
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You do not need to use SYPRO Orange and the thermal shift assay to study the interaction of your ligand with the protein. Remember that the thermal shift provides an indirect evidence for interaction, and that the estimation of the binding affinity from changes in Tm is not straightforward. There are dozens of techniques to study molecular interactions.
But, in case you use the thermal shift assay, very likely your ligand will compete with SYPRO Orange for the binding site. A priori is difficult to estimate how strong would be the competition effect. The only way to assess that competition would be performing the binding assay with and without SYPRO Orange (obviously, not with the thermal shift assay).
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I use Qubit to quantify my DNA material, and I have never had quantification problems. However a few weeks ago my lab bought a new Qubit reactive which has a different color (slightly pink) in comparison to the first one (orange), and since that, we realized that there is a big difference in the quantification lectures between both kits.
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I just checked here that dsDNA BR is darker than dsDNA HS. The quantitation range for BR kit is 2-1000 ng and for HS is 0.2-100 ng. Maybe you need to adjust samples before quantifying.
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I am performing in vitro anti-inflammatory assay: inhibiton of albumin denaturation by organic extract and purified fractions from natural material. Since my samples are colored (red, orange, yellow), I keep getting negative vaules, thus indicating pro-inflammatory rather than anti-inflammatory effect of extract/fractions. Concentration range of samples is 1 mg/ml to 62 ug/ml and the turbidity (absorbance at 660 nm) is higher with the increase of concentration. The results are the same even when I subtract the absorbance of blank (pure extract/fractions which almost do not absorb at wavelength mentioned above).
I am calculating the inhibition according to formula:
% Denaturation inhibition = (1−D/C)×100%
Where D is the absorbance reading of the test sample, and C is the absorbance reading without test sample (negative control).
I am measurng turbidity in 96-well plate; the solvent is methanol.
I was wondering if I am doing something wrong with my experiment setup or do you have any ideas how to avoid this problem?
According to the literature, there should be compounds in my extract/fractions that have already showed anti-inflammtory effects.
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I only show our data as for OVA Adsorption Bio Assay by using "Inorganic Particles". In this system, albumin alternation were not observed and Inflammatory materials suppression data were very clearly shown.
I am very doubtful for using organic substance for reducing inflammatory materials because interaction between test samples may be caused and also
solvent's damages.
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I used FITC Isomer I and ethanol and APTES under argon. The precipitate is bright orange. I want to use this for synthesis of nanoparticles (dye conjugated) and the precipitate will not help in this case.
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Amine reactive probes are typically dissolved in anhydrous dimethylformamide (DMF) and may not be stable in alcohols for very long.They are considered unstable once in solution even in DMF. APTES is also very reactive with water, which is required for the ethoxysilane to react, but can form precipitates in just a few hours depending on the water concentration. Because EtOH is somewhat hygroscopic and hard to keep anhydrous, it may not be the best solvent if you want to make a stable solution. Since the eothoxysilane reaction is both a hydrolysis and a condensation reaction, the water content remains the same and the reaction continues until all of the silanes are reacted.
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I previously dispersed anhydrous FeCl3 in chloroform and turned gray to black and used it for thiophene polymerization. Now that I repeat the same method, the color of iron chloride in chloroform is orange and thiophene polymerization is not done either.
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I think the reagents are contaminated or expired. Always use your own new reagents and don't allow other people to use them
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I am doing some simulations with the dyes dispersed in a PMMA and I want to test the device with different dye concentration (ppm). In order to do so, I need the molar absorptivity/molar extinction coefficient so that I can relate it to the transmittance and absorbance. I have the absorption and emission spectra of these Dyes, but I do not know their molar absorptivity/molar extinction coefficient, thus I can not compute the concentration (ppm) that I am using in the sample for the simulations. Does anyone know where can I found this data? I tried searching on the internet, but I did not find anything.
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Hi,
The molar attenuation coefficient is a measurement of how strongly a chemical species ... Different disciplines have different conventions as to whether absorbance is decadic (10-based) or Napierian (e-based).. is a measure of how well a chemical species absorbs a given wavelength of light. It allows you to make comparisons about the probability of electrons transition between levels for different compounds without taking into account differences in concentration or solution length during measurements..
Best Wishes..
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We use one probe with orange (Alexa555) dye to bind to the centromere of one chromosome and another probe with green (Alexa488) dye to bind to a gene. But in some nuclei we can see 5-10 spots that show both colours. However, in other nuclei in the same slide, there are only 2 orange and 2 green spot separately, as we expect it. What could cause this result?
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Hi Rita,
Where do you see the signal? If you see the 5-10 costained spots at the nuclear rim, it would likely be a permeability issue. The probes lack access to the nucleus and stick to the periphery instead.
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Dear all,
I would like to know if the inner part of an immerged object is cleaned by an ultrasonic bath cleaner ?
In my schme, is the green part cleaned ? (orange and blue are two liquids.)
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Hi,
The Ultrasonic bath Process: When excited the transducer increases in size and causes the tank bottom or side to move. This creates a compression wave in the liquid of the tank. ... There are millions of these bubbles created and collapsing every second in an ultrasonic tank.
Best Wishes..
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A while ago during a project I stumbled upon something interesting what happened when I left an aqueous solution of sodium salicylate (pH 14) in sunlight for an extended amount of time. The solution started the turn orange and eventually a dark red colour. I was curious to what this was so I decided replicate the conditions and try to isolate the formed product. The colour of the formed product seems to be dependent on the pH of the solution it is in, being red in basic solutions while yellow in acidic environments, the transition between the two seems to be around a pH of 7. The component itself also fluoresces in UV light. I found a articles describing observations on that the reaction took place under the influence of ultraviolet light, in a basic environment and that the reaction consumed oxygen from the air.
After isolating the component I was left with a off white powder, with possibly some NaCl (which can be seen in the spectrum later on) left in there from the neutralization steps and the removal of the salicylate (precipitating it out as salicylic acid by lowering the pH), most of that had been removed. A TLC, done a few days ago suggests that this is one single component and that no more salicylate is present in the sample. I took an FTIR spectrum of the sample, see the attached files.
While I can do interpretation, I am not that great at it. From what I can see here the arene is still there while both the hydroxyl and the carboxyl group are not present anymore. There does seem to be an aldehyde in the structure. (If my interpretation is correct, of course.)
Does anyone here know what reaction could be going on in this case?
Thanks in advance,
Dagomar Schreuder
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After looking through a few papers I found out it might be disodiumhydroxyquinone.
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I am trying to conduct a heterogeneous Fenton reagent using a natural iron oxide with Methyl orange as my contaminant of choice.
I have not seen any Methyl orange degradation even after 7 hours of reaction time. Does it matter when I add the hydrogen peroxide, should I rather let the solution equilibrate for an hour before adding the hydrogen peroxide. Should I rather use H2SO4 to adjust the pH?
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Hello Dear Alicia
for a solution of ferrous sulphate (FeSO4) in the solution you wish to oxidize with the Fenton's reagent. Slowly add hydrogen peroxide (H2O2) to the solution. Check the pH and adjust the rate of the hydrogen peroxide in order to keep the solution pH between 3 and 6;
the laboratory condion present an effect on analysis
Bests Regard
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When pbi2 is dissolved in dmf, it does not get 100% clear and there is some slight cloudiness. Also, when I create a one-step mapbi3 with these precursors, I'm getting orange cloudiness instead of clear yellow. Where is the problem? Do I have problems with precursors or solvent ?What can I do?
#perovskite #PbI2
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Dear Mohammad,
I would propose to filter out the particulates in the solution to get only the dissolved part of the solution. This may be a possible way to use your chemicals.
Best wishes
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I have tried several solvents such as DMF, THF, chloroform, and m-cresol. Out of these solvents, I think m-cresol mixed better with the polypyrrole powder where the solution changes from dark orange to black. Polypyrrole did not mix or dissolve with DMF, THF, and chloroform. The amount of polypyrrole mixed with m-cresol is actually very less where a considerable amount of polypyrrole powder left after filtration. For electrospinning, I use PU as a carrier for polypyrrole, but to no avail, I could not obtain polypyrrole electrospun fibers.
Thank you for your suggestion and opinion.
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Dear Wong
to prepare a soluble ppy, you must synthesize polymer nanoparticles in special method. we had synthesized soluble NPs in the presence of an anionic surfactant and used them to coat homogeneous films of PPy on the surface of copper electrode via electrospinning method. The presence of an anionic surfactant attached to the surface of polymer NPs leads to the formation of charged polymer NPs, which subsequently stabilizes thenanoparticles and protects them from aggregation through the electrostatic repulsion concept.
Please see: "Sensors and Actuators B 236 (2016) 99–108"
in the mentioned work, we had used Chloroform as solvent in the electrospinning procedure.
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Hello! I am currently culturing SH-SY5Y cells and I have noticed change in the cells cultures over the last few weeks. Can someone please me identify what these are and if they are normal in SH-SY5Y cells?
Yellow and blue arrow image:
- Blue arrow: Is that an S-type cell? Is that normal to find in a SH-SY5Y cell culture?
- Yellow arrow: What is that?
Orange, Black, green arrow image:
- Orange arrow: little dots scattered all over the floor of the plate. What could it be?
- black arrow: finding a lot of circular dots. What are these?
- Green arrow: What is that? Is it normal?
Last question: Is it normal to have both S and N-type cells in a SH-SY5Y culture? Is there a way to separate the two?
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Yes, it is normal for SH-SY5Y. It's neuroblastoma, and the population is not uniform, some will be much more spread than the others, and some will be very loosely attached. You have a good culture, I'd be careful to keep it that way.
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I have an older bottle of formamide that has been maintained at 4C in amber glass, but which is contaminated with a denser orange liquid. This contaminant, while it's certainly liquid, doesn't seem to want to separate out into a discrete phase, but instead rolls around as a mass of individual droplets of ~1-3mm diameter. Does anybody have any ideas what this could be?
Thanks!
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The denser liquid might perhaps be constituted by formic acid (1.22 g/cm3; 20 ºC), ammonium formate, and possibly, a minor amount of water; if the combined effect of low temperature and salting -out might explain phase separation , or at least, a density gradient effect, for the mixture with formamide (1.13 g/cm3). Formic acid could perhaps lixiviate ferrous iron from amber glass container, which should then tend to oxidize to ferric iron, particularly upon air exposure.