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Which kind of HPLC column can be used for ethanol detection in LB medium after bacteria growth 24 hours?
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Hi everyone!
So I am trying to concentrate my recombinant proteins in order to make some assays with them, but I need a "considerable" concentration of each. One of my proteins is around 9kDa and the other one 15.8 kDa. They have been tagged with a 6 His and went already through a Nickel column. SDS PAGEs show considerable concentration of certain amount of protein of interest in many, fragments, hence, it was decided to concentrate them using a PES protein concentrator (3,000 MW concentrators) . However, when spinnning them as protocol suggests and collecting every flowthrough (FT) to localize any "lost" proteins, as well as the concentrated sample, rather than seeing a considerable larger band on the SDS , the bands are discrete, not much concentration is found and there is no protein whatsoever in any other FT to suggest protein is being lost through the filter. Am I facing degradation, or why is it that even concentrating it, is not concentrated.
Thank you all! Welcoming any suggestions or corrections!
Best wishes,
Jorge
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The proteins may be sticking to the filter device. Another approach to concentration may be preferable.
One idea is to rebind them to a small nickel column (assuming the imidazole has already been removed by dialysis), and elute them in a single concentrated fraction with a high concentration of imidazole.
Another idea is to concentrate them by freeze-drying. This is best done after removing most of the low-molecular-weight solutes by dialysis, since the solutes will also be concentrated.
A third idea is to place the sample in a low molecular-weight-cutoff dialysis bag and partially dehydrate the sample by immersing the bag in a dry absorbent resin, such as Bio-Gel or Sephadex, replacing the resin occasionally as it swells.
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Hello,
I received some GWAS results. There is a column for SNP, position, REF/ALT allele, p value, SE, which is pretty straightforward. However, I am confused about the column titled 'Effect', they are values ranging from -1.4 to 1.3. Any help would be greatly appreciated, thank you in advance.
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That is the effect size, the "beta" of the regression.
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I am trying to run a method from a column that is 250x4.6 mm, 8 um particle size into a column that is 300x7.8 mm, 9 um particle size. The makeup of the column is pretty much the same. They are each run as isocratic methods. How much more should I load or how should I adjust other parameters to comensate?
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In order to have a similar retention time increase the flow rate by a factor of 3.5
You can increase the load by a factor of 3.
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Recently my pepsin column got some blockage, supposedly because of the precipitation of aggregated protein. Multiple washes with 0.1% FA or pepsin wash (1.5M GuHCl + AcN + FA 95.2/4/0.8), as well as reverse flushing didn't help, the pressure is still too high. It seems like the column cannot be used anymore anyways, so I was wondering if there's any other washing method that I could try?
Even if it's somewhat dangerous to use it on the pepsin column.
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İsmail Emir Akyildiz , thanks a lot for your advice!
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I am trying to simulate a rectangular short column (L/D ratio of 2) for cyclic load under axial compression. I am using the concrete damage plasticity model for concrete. The first problem I am facing is excess lateral stiffness in my ABAQUS model as you can see in the force vs displacement curve. I am trying to match the slope of the red curve generated by the cyclic hysteresis response of the column. The dashed line is the result I got. I have only included the elastic property for concrete for this instance. All the pictures related to the analysis are listed below.
  • The analysis procedure is static/general for
  • C3D8R element used for concrete
  • T3D2 element used for reinforcement
  • Analysis was done in 2 steps axial load and lateral displacement
Can anyone tell me what I am doing wrong?
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If you got it from the Compressometer results attached to your cylinders, it is probably correct. I thought you were trying to verify someone else's article.
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I am looking for the specifications and instructions for use for HPLC column Aqua C18 (3um, 125A, 150 x 4.6 mm, Phenomenex). This is a rather old column, and I could not find this information on Phenomenex web site.
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Thank you very much for your help.
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We used the DNA Clean & Concentrator-100 (D4030) from Zymo Research to clean and concentrate our 100 µg DNA. Unfortunately, our yield was only 8%.
We initially believed that, due to our DNA being over 10 kb, it was not eluted properly from the column. However, upon checking the DNA in the flow-through and wash samples at each step, we discovered that most of our DNA did not bind to the column. Specifically, 90% of our DNA existed in the flow-through. When we applied the flow-through containing this DNA to another company's DNA binding column, most of the DNA bound well to the column. Consequently, we suspect there is a problem with the DNA binding column of the Zymo kit.
Has anyone had a similar experience? If so, how did you resolve the problem?
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I have a similar problem. Obtaining 4% of original midiprep plasmid dna from this kit. Any updates on fixing this issue?
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Dear colleagues, we are now analyzing fecal samples with the MS but some precipitates occur after the SP3 digestion and elution. We are trying to understand the cause and identify ways to remove them as they harm the LC columns. Thank you for your help and your suggestions.
All the best
Giacomo
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From what I understand, it is likely that the solid is, most likely, salts that are poorly soluble in organic solvents. Try to eliminate them from sample preparation processes, if possible, only perform liquid-liquid extractions or do clean-ups of your extracts in ion exchange resins (e.g., XAD). Alternatively, use acidic (non-buffered) aqueous solutions as mobile phases. Do not use organic solvents such as methanol or acetonitrile.
Best Regards.
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I am facing an issue with how chromatograms are recorded. From time to time, on our chromatograms the peak assigned to heptane is integrated as well and this gives us wrong results. Sometimes the value of this peck is less than 0,01 %, but there are situations when it is 20 % . I made no changes for the methods. I don’t know why this problem appears randomly and what can be the cause? Do you think that it could be a bubble of air, the manual injection or may be is the column? On this GC, we have another column with automatic injection, and this problem never arrived on this one.
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thank you for your time in writing such a elaborate and complex answer.
Best regards
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mobile phase: methanol/ACN (90:10, v/v) + 9 μM TEA.
Can I use n-hexane as the injection solvent?
Will this cause column clogging or damage?
I know that acetonitrile and n-hexane are immiscible.
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You did not provide any information about the HPLC column or sample you selected. The column type, name, dimensions, sample and full method info would be needed to understand what you are really doing first.
Your injection solution should be the same as your mobile phase. This is a basic fundamental of chromatography. *The sample and mobile phase solution should be fully miscible (100%). Chromatography is not possible if the sample can not be fully dissolved in the mobile phase. Hexane is NOT miscible with methanol or acetonitrile so would not be used with those solvents alone. Also, running pure ACN and Methanol on a column does not sound like an appropriate mobile phase so you really need to stop what you are doing and speak to a local chromatographer (or your teacher) at your school to obtain help in using the HPLC system. You may damage one of the columns or instrument.
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I have some columns for my Thermo Scientific GC-MS:
1) DB-WAX
2) DB-1
c) DB-17HT
d) VF-1MS
e) TR-FAME
f) TG-5MS
g) TG-WAXMS A
In my opinion, for polyphenols as flavonoid (and their glicosides) and phenolic acids (present in vegetable, grains, food analysis), I would prefere DB-1, VF-1MS and TG-5MS.
Your opinion will be valuable for me...a lot!
I am using TG-5MS. but I expected better results than the ones I am having...
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Any opinions or experiences about the ZB-5MS column?
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Lately, I’ve been encountering issues with the longevity of my Liquid Chromatography tandem Mass Spectrometry (LC-MS/MS) columns. Specifically, I use the ZORBAX Eclipse Plus C18 RRHD (Rapid Resolution HD) 2.1x100 mm 1.8 micron column from Agilent on my Agilent 1290 Infinity II LC/6475LC/TQ Mass Spectrometer. My method involves using 100% Methanol for Mobile phase A and a 5 millimolar Ammonium acetate in a 1% acetic acid solution. Initially, the column pressure remained stable at 326 bar for up to 100 samples. However, after running 200 samples over the course of a month, I’ve noticed a gradual increase in pressure by 10-20 bars daily. I’ve attempted the recommended washing protocol, which starts with a 5-minute wash using 100% water to remove the buffer, followed by a 5-minute wash with 98% water and 2% Methanol. The gradient is then gradually reduced to 50% water and 50% Methanol, eventually reaching 2% water and 98% Methanol at the 45-minute mark of the washing process. Despite these efforts, the pressure continues to rise, and there’s been a shift in my analyte’s retention time (RT). Acquiring a new column will take some time, so I’m seeking a way to restore my column to its original pressure if possible.
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Normally, if the column used has been properly equilibrated and an observed gradual increase of pressure "over-normal" continues run-to-run, this indicates one of two things: (1) That Column fouling is taking place OR (2) you have a clogged HPLC pump OUTLET FRIT. Both of these errors will result in what you observe. More info follows...
Let us take a look at these two problems in a bit more detail.
(1) Column Fouling: Columns ger fouled with sample over time. This may be from overloading the column with sample (use less sample!) or from improper column washing. Make sure you wash the column down with a solution that is stronger than the mobile phase used for the analysis. In your example using MeOH and water ("5 mM Ammonium acetate in a 1% acetic acid solution is basically water) you will need to use a different solvent for this purpose. The wash solvent should be fully soluable with your samples and stronger than MeOH. Perhaps ACN would be best? Remember to separate your Analysis method from your column wash methods. When the analysis method is complete, the solvent composition should NOT be directed back to the starting conditions within the same method (a common newbie mistake). *We used to do this back in the early 1980's, before computers. Professional training today is different and a second 'new method' (known as "The wash method") is programmed to run after the analysis method. Create and save a "Column Wash" method where you change from MeOH in your example to ACN (which is "stronger" and will elute off different material). In this example; Flush the column with acidified water plus a max of 95% ACN. Create and save another method, a third method, that equilibrates the column in your initial analysis mobile phase (this is how the pros do it, using separate methods for each task. Makes it easy to automate the tasks). Now you should have three dedicated methods that can be called on or run sequentially to: equilibrate the column, run the analysis, wash the column, equilibrate the column .... This helps to insure all runs are washed, equilibrated and analyzed the SAME (machines are really good at this).
(2) Obstructed Pump Outlet Filter: As a professional consultant I am asked to troubleshoot many HPLC system issues where the system back-pressure slowly increases over time (days, weeks, months) and while #1 above is often to blame, there is another reason. Inside every HPLC pump is a small filter designed to catch piston seal debris and other larger particulate matter from making its way into the very narrow passages of the HPLC system, especially the injector. These very inexpensive filters are consumable parts which are designed to be replaced on a regular basis to maintain proper function. If they are not replaced, then they fill with debris resulting in a PARTIAL OBSTRUCTION of the flow path. This is observed as a slow increase in system pressure over time. It also may appear as an increase in back-pressure when directed solvent to waste (pump to waste, not to column). When directed to waste only, the expected back-pressure should be very, very low. In fact you should know what the normal pressure should be given a specific solvent and flow rate for your system. If the pressure is higher than normal, then the frit is probably overdue for replacement. Change it.
  • BTW: HPLC Columns are consumable items and do not last forever. With some applications, 200-injections would be perfectly acceptable before disposal (i.e. amino-acid analysis). We do not have enough info to know if this is the case here.
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After completing DNA extraction from whole blood using the QIAamp DNA Mini kit but obtaining no yield, I suspect the DNA might be retained in the column. How can I recover the DNA from the column.
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For my DNA extraction, the last stage of elution is usually done with 70% ethanol, 80% ethanol (washing step), centrifugation, air drying the column and then eluting with hot water into another tube by centrifugation.
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Can I purify large quantities of phycocyanin (current concentration of 30%) using the ÄKTA system equipped with size exclusion or ion exchange columns?
Could I perform multiple injections to isolate 100 mg of phycocyanin?
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Yes, the ÄKTA protein purification system equipped with size exclusion or ion exchange columns is capable of purifying large quantities of proteins. These systems are designed to handle a wide range of sample volumes and can be scaled up to accommodate large quantities of protein.
Size exclusion chromatography (SEC) is ideal for separating proteins based on their size and molecular weight, while ion exchange chromatography (IEX) separates proteins based on their charge characteristics. Both techniques can be highly effective for purifying proteins at a large scale.
The ÄKTA system offers precise control over purification parameters such as flow rate, gradient formation, and fraction collection, ensuring efficient and reproducible purification of proteins.
However, the scale of purification achievable with ÄKTA systems may vary depending on the specific model and configuration. It's important to verify that your ÄKTA system is equipped with columns and accessories suitable for large-scale purification and to optimize your purification protocol accordingly.
Overall, the ÄKTA protein purification system is a powerful tool for purifying large quantities of proteins using size exclusion or ion exchange chromatography techniques. Rodrigo Conceicao
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In my LC-MS experiment, I am utilizing an Agilent Polaris NH2 column to separate a mixture of glucose, fructose, and sucrose. I am using water and acetonitrile as A and B mobile phases respectively, both with 0.1% ammonium hydroxide. I have employed a gradient elution, starting with 90% B, gradually decreasing to 0%, and then increasing back to 90% B over 17 minutes. Initially, I did not face any issues and the separation was satisfactory. However, lately, I have been encountering problems. Upon analyzing a large number of samples, I could only detect the sucrose peaks in a few standards. Additionally, I noticed a white substance on the ESI source, and I had to clean the spray and ion capillary extensively to regain sensitivity. I am now concerned whether my mobile phase condition can damage the HILIC column.
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Hello. My main guess would be that the column phase is degrading/dissolving. The silica packing that carries the modification (NH2) is what's failing. The manufacturer states pH stability of 2.0 - 8.0 at not more than 40oC, which is typical for silica containing HPLC columns unless specifically modified/stabilized. Higher temperature and salt will speed up the deterioration. The pH of your 0.1% ammonium hydroxide would be close to 11.
Reference: Agilent's Column Care Manual
chrome-extension://efaidnbmnnnibpcajpcglclefindmkaj/https://www.agilent.com/cs/library/packageinsert/public/820000-998_LR.pdf
page 7/110
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Hello everyone.
I have a problem with HPLC. A few days ago, to create a calibration curve with HPLC, I injected solutions with known concentrations into the device, which gave good peaks in the expected time. But now I inject the solution with the unknown concentration into the device with the same HPLC conditions as before and the device does not show a peak. The filtered sample contains sodium sulfite, potassium peroxymonosulfate, and chloroquine.
Operating conditions: HPLC Waters with C18 column, PDA detector at a wavelength of 340 nm, water and acetonitrile as solvents with a ratio of 90:10 and isocratic method, flow rate 1 ml/min, and injection volume is 20 microliters.
I have checked all the connections for leaks and flushed the column with water and methanol, the system is free of air, the flow path is completely open and the waste is coming out, but I still did not see the peak in the expected time.
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Hello spike your sample with know concentration of analyte and see the results with the use calibration curve that you made.
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Hi,
I am a graduate student using a Shimadzu HPLC with a PDA detector.
This instrument was newly installed. Only the tech at installation and myself have run samples.
I am using it for research on cannabinoids specifically CBD and THC and only running diluted standards right now to modify the method.
I am using water (0.1% formic acid) as mobile phase A, and acetonitrile (0.1% formic acid) as mobile phase b. The total run time is 10 min. I have a gradient that starts at 70% B for 3 min, then ramps up to 90% B for 2 min, hold for 1 min, then back down to 70% and hold for the rest of the time. The flow rate is 0.2 mL/min. My injection volume is 1 uL.
The column is a Shimadzu C18-120, 3 um 3.0 x 50 mm.
The PDA detector wavelength is from 190 nm to 600 nm and specific wavelengths are 210 nm and 220 nm.
During my first run I ran a CBD sample (CBD 50 ng/mL in acetonitrile). A mistake was made of not running a blank before the CBD sample :(
I ran several blanks after and still continue to see peaks.
I have remade the blanks many times in different vials, new solutions of blank.
I set up a run consisting of 75 blanks on a 2 minute "cleanout method" run where I was using 90% ACN for the full time. All the blanks in this batch had the same peak with a consistent intensity. (The intensity of the peak did not really decrease over the 75 injections).
I have also run Null injections and have gotten the same peak in those injections as well.
I switched mobile phases from ACN to methanol. When running the blanks with the methanol I still got the same peak. After reversing the column, running methanol through, then fixing the column I still got the same peak again.
First we had thought it was CBD that contaminated the instrument, but after switching the phases and running so many blanks we are not sure if this is something with the instrument that we should try to change/clean?
At this point I am not sure where this peak could be coming from and was looking for some advice/direction on what to try next!
I can provide additional information as needed!
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What is the retention time for the peak in acetonitrile? What is the retention time in methanol?
"Ghost" peaks come from contaminants. Null runs without injections showing the peak tends to rule out the injector as a source of the peak. The peak seems very reproducible.
One source of ghost peaks are contaminants in solvents. It could be the formic acid or water, you still saw the peak when you tried methanol which suggests the acetonitrile might not be the source.
If you post a chromatogram, it would be helpful.
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1. Fire 2. Earthquake 3. Flood
But the big bill comes from 4. not maintaining them. How can we maintain the structures if we can't?
Because the buildings will start falling down on their own.
Insulation. We cover everything. We cover everything with external insulation and plasterboard. External walls, ceilings, load-bearing structure made of reinforced concrete, all covered with insulation and plasterboard.
From the inside, plasterboard on ceilings and walls
What a nice coolness, but there goes the visual control.
1.And there's an earthquake. How do I see the crack to repair it? In the next earthquake either the crack will get bigger or the ceiling will come down on our heads. In corner columns you can't see any failure from the inside because the inside of the column is covered by the masonry.
2.And rusting an iron breaks the concrete overlay and the concrete and steel cooperation is lost How do I repair something I don't see; neither in the ceiling nor in the column?
3.Catch a fire We will burn like candles. Do you know how nice styrofoam burns?
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If you use reinforced concrete it will save you from all of these problems.
1. If you use reinforced concrete after a earthquake it shows crack if you can't see any crack that means it is not so bad in condition.
2. we use steel bars as reinforcement in concrete. Concrete is water resistance characteristics so steel bars are safe for a long time.
3. Concrete is fire resisting material. It can't burn so easily
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Often I need to transform several columns of data into rows of aligned values in a matrix, for multivariate analysis. So randomly ordered values in the same sample are arranged/aligned into the corresponding column. How can I conduct this automatically?
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you can do it in Python easily:
import pandas as pd
dic = {'Sample_1': [1,5],'Sample_2': [2,3,4,5],'Sample_3': [1,3,5]}
min_val=min(min(dic.values()))
max_val=max(max(dic.values()))
def f(x,k):
if x in dic[k]:
return x
else:
return 'NaN'
dic_New = {k: [] for k in dic.keys()}
for k in dic.keys():
for j in range(min_val,max_val+1):
dic_New[k].append(f(j,k))
print(dic)
{'Sample_1': [1, 5], 'Sample_2': [2, 3, 4, 5], 'Sample_3': [1, 3, 5]}
print(dic_New)
{'Sample_1': [1, 'NaN', 'NaN', 'NaN', 5], 'Sample_2': ['NaN', 2, 3, 4, 5], 'Sample_3': [1, 'NaN', 3, 'NaN', 5]}
df=pd.DataFrame.from_dict(dic_New,orient="index")
print(df)
0 1 2 3 4 Sample_1 1 NaN NaN NaN 5 Sample_2 NaN 2 3 4 5 Sample_3 1 NaN 3 NaN 5
change 'NaN' with the values you are interested
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I am working on the ns5 protein of JEV. first i cultured it on N-Z amine media. then purify it by his-trap column followed by sephadex colum. everytime my protein is lost in sephadex column. by his-trap column the purified band concentration is only 7uM. plz give me the suggestion
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To improve the purification of viral proteins, especially when facing challenges with the Sephadex column after using the His-Trap column, consider the following suggestions based on the information from the provided sources:
1. Optimize Purification Methods:
  • Avoid Multiple Purification Steps: Reduce the number of purification steps to minimize protein loss.
  • Consider Alternative Methods: Explore different purification techniques like size-exclusion chromatography (SEC) or ion-exchange chromatography (IEC) mentioned in the sources.
2. Enhance Protein Stability:
  • Maintain Optimal Conditions: Ensure proper buffer conditions, pH, and temperature throughout the purification process to prevent protein denaturation.
  • Use Suitable Buffers: Employ buffers that are compatible with the protein of interest to maintain stability.
3. Troubleshooting Protein Loss:
  • Check Protein Concentration: Monitor protein concentration at each purification step to identify where losses occur.
  • Evaluate Column Performance: Assess the efficiency and suitability of the Sephadex column for your specific protein purification needs.
4. Consider Specific Protein Characteristics:
  • Protein Size and Charge: Understand the size and charge properties of the viral protein to select the most appropriate purification method.
  • Protein Interactions: Consider any specific interactions or characteristics of the NS5 protein of JEV that might affect its purification.
Refer these articles:
2. 10.1016/S0166-0934(02)00069-1
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Hello everyone,
In your experience, what's the recommended number of uses for a single BioRad EconoFit Profinity IMAC column, or any similar prepacked Ni2+ columns? The instruction manual doesn't clearly state this information.
I've used a single column 3 times (for the same protein), cleaning it after every use, and gotten similar results.
Thanks for your help.
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Omar Gonzalez-Ortega Thank you very much for your answer!
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Hi everyone.
I'm having some trouble with the peak shape on VancoShell column. The mobile phases used are 5,5 mM ammonium acetate (pH 4,7) and methanol, in the ratio 20:80. Column temperature is 10°C, and flow rate is 0,17 mL/min. I'm trying to develop LC-MS method for chiral separation of venlafaxin. The instrument is Agiletn 1290 UHPC coupled to Agilent QTOF 6550. In the beginning, the peak shape was OK, but at some point, the peaks started to have shoulders. I tried washing the column with pure methanol, as well as tried to regenerate the column as per instructions. It helped a little, but the peak shape is still not that great.
I'm not sure what happened with the column, since the only thing injected onto it was a standard solution. Does anyone have any advice on how to improve the peak shape? Also, I'm wondering can I reverse flush the column since there is nothing in the manual about that.
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Please provide the EXACT column dimensions for your chiral antibiotic HPLC column.
  1. Are you injecting PURE standard? How did you confirm this?
  2. Do you have a UV/VIS diode-array detector ("DAD") inline with the MS detector? You should, as a DAD would make method development far easier to start with as your compound will be easy to detect.
  3. It is necessary to first establish what K prime is for your method before any comments could be made regarding peak shape.
  4. Sudden changes to peak shape are often caused by column fouling (e.g. sample overload) and chiral columns of this type are easy to overload with sample as their capacity is VERY LOW compared to a common C18 type phase.
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To quantify the stoichiometric homeostasis index for N (nitrogen).
The formula is as follows:
log (y)= log(c) +(1/HP)log(x) (4)
where y is the N level in the plant tissue (mgkg−1), x is the N level in the water column (µgL−1), and c is a constant.
now my question id how to calculate the C or what is the value of C?
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Hi everyone,
I have never worked with Inclusion Bodies so do not have a method that really works.
My protein is recombinant ß-casein that is produced both in the soluble fractions of the pellet and the insoluble ones. As for the pellet, we did resolubilization with buffer containing 8 M urea and directly load it on the HisTrap columns. The flow rate was 0.5 mL/min (the slowest on ÄKTA Start machine) but still overpressure often happened. I was pretty sure this was not the best method to purify the desired protein from the resolubilized pellet, and some kind of intermerdiate method needs to be done before purifying on the ÄKTA.
Therefore I need advice of either:
1. What I can do after resolubilization to alleviate the pressure before loading the sample to the HisTrap column? (my protein has a His Tag)
or
2. Is there any other method that can be used to purify the ß-casein? Maybe precipitation?
Column chromatography is not a must so other methods are welcome.
This is a trial and error for me so I can try any suggestions.
All suggestions and discussions are welcome.
Thank you in advance.
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Hi a little update:
I tried to do on column refolding like in the literature or as suggested but didn't work it. However I did do pellet wash before loading on the column with Triton X-100, 1 M NaCl, and regular buffer. I had no pressure problem as the lysate looks clear, but the refolding on the column did not really work out as there was no protein during the elution.
Next time I will try to purify it then do the protein refolding.
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Dear colleagues,
We have recently optimized a TDS-GC-MS method for VOCs (SVOCs) analysis. (Gerstel + Agilent).
A high-temperature column with mid-polarity is chosen for a better resolution (similar to DB-624ms but with a higher operating temperature of 300/320 °C).
Although the desired separation is achieved with a programmed-temperature method (final temperature: 290 °C), some analytes with low boiling points, such as dichloromethane, benzene, and heptane, show unacceptable intensity variation. (The RSD of three replicas can be as high as 30%). On the other hand, compounds with higher boiling points (such as naphthalene and pentadecane) are more stable. (RSD < 5%)
We further lower the final temperature of the method (from 280 °C to 260 °C), and the repeatability of benzene and heptane is much better (RSD < 5%), while the dichloromethane is still fluctuating (RSD ~ 15%).
Any explanation for this phenomenon?
p.s. the column pressure can be very high under high-temperature
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Hey there Junlong Huang,
It's great to hear about your progress with the TDS-GC-MS method for VOCs analysis! Now, regarding your question about the final oven temperature and its influence on the repeatability of low boiling point analytes, let's dive into it.
The fluctuations in intensity you're observing, particularly with dichloromethane, benzene, and heptane, can indeed be puzzling. The change in final oven temperature seems to have a significant impact on the stability of these compounds, with lower temperatures showing better repeatability for benzene and heptane but not so much for dichloromethane.
One potential explanation for this could be the volatility and thermal stability of the compounds. Lower boiling point analytes like dichloromethane are more sensitive to temperature changes, and even a slight variation in final oven temperature can lead to fluctuations in their intensity. On the other hand, compounds with higher boiling points like naphthalene and pentadecane are less affected by these temperature changes, hence the more stable RSD.
Additionally, considering the column pressure under high-temperature conditions is crucial. High pressures can exacerbate the volatility of low boiling point analytes, leading to increased intensity variation.
In summary, the interplay between compound volatility, thermal stability, and column pressure under high-temperature conditions likely contributes to the observed phenomenon. Fine-tuning the method parameters, such as oven temperature and column pressure, can potentially mitigate these fluctuations and improve repeatability.
Hope this sheds some light on the issue! Let me know if you Junlong Huang need further clarification or assistance.
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There are 4 items in one variable and in EFA , items loaded in 2 different columns of other variable
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This is quite common in social research (questionnaires with rating-scales).
In this context, you want to discover what variables combine to express the same underlying construct.
The default in most statistics packages is orthogonal rotation (Varimax), producing columns of factor loadings so that all factors are completely uncorrelated. (or, if creating summative scales, then the factors are minimally correlated.)
This is where theory comes into play. Must your factors be orthogonal? Maybe some correlation among the factors is acceptable. If so, then try a non-orthogonal rotation. (Oblimin, Promax)
see "https://hosted.jalt.org/test/PDF/Brown31.pdf" for a useful discussion.
A common mistake is to include all the rating-scale questions from the questionnaire in the same EFA. Think about your theory. Do you expect to find that some constructs are related to other constructs? Or that perhaps some construct "causes" some other construct? If so, then you want to see some factors correlated with other factors.
In such cases, do not include items that are intended to be "dependent" variables in your EFA. Remove "mediating" variables too, for the same reason.
On the other hand, do you really need to do an Exploratory Factor Analysis? If you are using an established set of scale questions, then you already know what items should go together - your theory in this context. Now that you have gathered your data, then you would want to run a Confirmatory Factor Analysis (CFA, not EFA). That is, you want to confirm that the items that should go together do go together.
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Hello,
I am analyzing purified antibodies using a superdex 200 increase 10/300 GL column. Occasionally, I observe tailing at the peak, particularly with antibodies that have high surface concentrations of Lysine and Arginine.
The figure below shows data from size exclusion chromatography analysis conducted under the same conditions, where tailing was observed in antibodies with high positive charge.
I'm wondering if increased positive charge on the surface could enhance interactions with the column.
Are there any references demonstrating this phenomenon?
Thank you!
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I really appreciate your interest. I'll share the information you requested.
1) pH 7.4 PBS
2) 0.75 mL/min
3) Particle size, d50v : ~ 8.6 μm
Bed dimensions (mm) : 10 × 300-310
Approximate bed volume (mL) : 24
4) RT
5) 1mg/mL, 10μg
6) 280nm
7) The void volume was measured by a senior, not by me, but I'm unsure of the exact value.
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I'm trying to synthesise a product through suzuki coupling using 5-bromo-2-thiophenecarboxylic acid and 2-fluoro-4-methoxyphenylboronic acid.
I tried using Cs2CO3, K2CO3, Na2CO3 as base and regarding solvents I used 1,4-dioxane-water ( 10: 1 ) and THF-water ( 10:1 ). I respected inert atmosphere (degassing and Argon bubbling) in organic solvent as well as in aqueous basic carbonate solution. Temperatures tried were 95, 90, 80 degrees Celsius. As workup, I directly, after cooling down the mixture, add HCl 15% and do the rest of the workup to initiate the isolation of carboxylic acid product. I used boronic acid in excess to avoid purification of 2 carboxylic acids(which is almost ridiculously hard, even with AcOH in column).
Catalyst: Pd(PPh3)4
My percentage yields of pure product were : 14% , 18,9%, 22% and 22%.
I really can't think of something that might increase the yield of the reaction since it's the starting point of many synthesis steps.
Can I get some help/opinions/tips/suggestions please? My next try i want to use 1,4-dioxane and increase temperature to 110-120 degrees celsius, maybe temperature is the main reason. I really don't know. I'm looking forward to read anything you can think of.
Thanks a lot ! It's a huuuuge text and I'm sorry for that, but I wanted to include everything so you have all the informations you need to provide any help.
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What kind of palladium catalyst are you using? I have seen great difference between Pd(PPh4)3 vs PdCl2, for example.
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Hi everyone
As I'm new to HPLC so can you help me which this question " If i got an old HPLC C18 GL column so how can i check if the column still work or not ( about the back pressure or something more?) after that how can i regenerate it?
thank you for your help
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I am trying to purify a cell lysate using a 1 mL His-trap column but the viscosity of the lysate is clogging up the column. What are some solutions to this?
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Treat the lysate with DNase + MgCl2 to reduce the viscosity caused by DNA. Centrifuge the lysate before applying it to the column to remove any particulates.
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Hello
Can anybody suggest me good C18 column for the separation of small molecules which has a long life?
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Ace C18 4.6x250mm
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Hi,
quite specific question if somebody has experience with this column because I cannot pull out fritta and pack column with stationary phase.
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it looks like this.
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I encounter the following problem: I want to send viral RNA for further analysis. As the receiver requires, I must process my samples according to a regular RNA extraction protocol and send the filtered spin columns from the RNA extraction kit, without performing the final elution step. But I don't have the original sample preserved, only the RNA already extracted is stored. Can I do a re-extraction using the stored eluate as the starting material?
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I believe that, even if your RNA sample is pure, making its making up its volume to 200 µL will be OK because most columns have high affinity for RNA. No doubt, you will lose some RNA, but I hope it will be enough for you analysis.
Secondly, don’t worry about RNA degradation at 56°C for 15 minutes because we routinely perform proteinase K treatment at 55°C overnight to separate RNA from proteins. Secondly RNA is exposed to 70°C for 10 minutes for melting before cDNA synthesis.
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Hello friends,
I could not find any template for this journal which stated that it should be doubled column. Any help?
Thanks
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And replace the "STIX1COL" with "STIX2COL" in "APA//wileyNJD-APA.tex" file to get two column style, which would make the first codeline:
'''
\documentclass[APA,STIX2COL]{WileyNJD-v2}
'''
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In planning a 19-story building, I want to use varied concrete grades—lower for slabs and beams, higher for columns (e.g., M50 for columns, M25 for beams and slabs). How much can I differ between these grades while ensuring structural strength and avoiding issues like cold joint formations at beam-column joints? I've heard about a maximum difference of 5N/mm^2, but I'd like clarification with references and reasons for this choice.
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Based on analysis results considering selected grades of concrete for column and beam/sab, the compatibility of sizes of column and beam/slab to be work out needs to be check for construction point of view. Also beam-column junction for this much variable grades needs to be look very carefully performance wise.
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Hi all,
I have some calcium imaging data collected from neurons in the mouse cerebral cortex. I wish to compare the effect of two genotypes. Within each genotype, I have several neurons that were recorded for fluorescence changes over 5 mins each.
The data is therefore arranged as follows: Genotypes (main columns), individual neurons (sub-columns under each column), and time (rows).
Can someone share the best statistical method(s) to apply to compare the distributions (blue and gray lines)? I do not wish to select specific frames or perform multiple comparisons for each time frame.
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I would suggest considering comparing summary values from your fluorescence transients, rather than the entire transient. In my lab, we would get an average transient in each cell, and make measurements off it, then group by experimental manipulation and compare. One obvious comparison would be the peak amplitude. To compare timecourse, you can use the width at half height (half-width), or tau by fitting to an exponential decay function. It is also common to measure the time it takes to rise or decay from 10% to 90% of the peak value.
You might get insights into the best thing to measure by scaling all the transients to the same height, and see if your blue and grey groups differ in other ways.
ANOVA sounds useful, but it only tells you two groups are different. To understand what the specific differences are, you would have to do posthoc comparisons, which leads to point by point comparisons.
Just my thoughts.
Matthew
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I use a DNA/RNA synthesizer from LGC (Biosearch), a MerMade6, to make oligos. The machine has operated for around 16 months and produced about 1500 oligos during this period. As you can see, it is not a heavily used machine.
All preventive maintenances were ok, and the machine was operating just fine and yielding very good quality oligos......
But then it started to present a misalignment between the cart/columns block and the capilaries, pouring reagents out of the columns.
If you look closely you can see that, when the cart with the columns moves and gets to the position assigned, it doesn't stop completely, but slides juuuust a little bit instead. Such a mess!
Calibration doesn't solve the problem: after a calibration, reagents will be delivered correctly into the columns in the first cycle, but as with every move the cart slides a little bit, the misalignment starts to sum up with every move and, at the 3rd cycle, reagents are being spilled outside the columns already.
We are in Brazil. Remotely, LGC team couldn't help. They couldn't even find the problem. The visit of LGC engineering team will coast a lot, and while we are working in resources an bureaucracies to get them here, tips from other users would be welcome and much appreciated.
This machine works with step motor / step motion, which is similar to printers and a lot of other machines. Have you ever seen this kind of issue?
Alternatively, do you know other MerMade users you can put me in touch with?
Thanks in advance
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Thanks, Andrei!
I certainly did! I took pictures and I have a meeting with them scheduled for tomorrow!
Maybe they won't replace it because the machine is out of warranty... But I'll make some noise anyway, that brought us a lot of trouble!
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I have a 5038 bp DNA fragment I am trying to extract from an agarose gel with little success. I am running a 50 cycle PCR with HF Q5 Polymerase and get a bright band of the expected size. I have tried both the Qaigen and Monarch gel extraction kits. Monarch performs a little better, but my yield is still low (32.5ng/ul).
I have tried the following adjustments:
1. 1% and 0.7% agarose gels
2. TAE and TBE buffers
3. Centrifuge speeds between 2000-13000 rpm
4. 50C elution buffer
5. Recycling eluate up to 3X through the column.
6. 5 minute RT incubation after adding EB to the column membrane
7. Ensuring the gel is completely dissolved
How can I improve yield? Is there another method of extracting DNA from agarose gels (freezing gel)?
Thanks!
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Hey Sajid Alvi I´m currently facing a similar problem , how did you solve it?
Thanks
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We've been using the AdvanceBio SEC column 120A 1.9um 2.1x150mm PEEK with an Agilent LC QTOF but recently we have been problems with this column and we were not able to perform any runs.
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I strongly recommend Waters XBridge Premier Protein SEC Column with MaxPeak Premier Protein SEC Guard as the far best SEC column (couple) in terms of providing resolution, reproducibility, and stability...The main issue with this column is that you should strictly follow the user guide and need to keep your LC system and all tubings sterilized. Any microbial growth leading to detrimental effects on the SEC column (experienced, unfortunately)...I also suggest you use the guard to extend your column lifetime which is a bit expensive to purchase.
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As stated above, one of most popular concepts is a 3-column semi with tower mounted on one of the columns. Since the major wind loadings especially exciting moment on tower base passing on one of the columns, the other two columns don't share 1/3 of the loadings. This arrangement seems inefficient for the other columns and thus it is not a cost-effective solution. In addition, since RNA is located on one of the columns which is away from platform center, it will experience larger acceleration compared to tower is arranged at center of the platform. There are other disadvantages, such as carrying ballast on other two columns in order to have an even keel at quayside which leads to increase draft at quayside to reduce selections of qualified yards for constructions. This issue is more pronouned for large turbine, say 15MW WTG. You may add temporary buoyancy modulars to mitigate this weakness. However, additional costs will be incurred. Please share your thoughts. Thanks,
Jun
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After reading everyone’s answers, I concluded that the three-column and half-tower design is a solution that balances stability, ease of installation and maintenance, and space utilization. But in practical applications, these factors need to be weighed based on specific circumstances and needs to select the most suitable floating wind tower design.
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Hello everyone, I've just realized that I haven't put the RNeasy MinElute spin column I received with the RNA extraction kit (Qiagen) in the fridge... I received them in December and I've just put them in the fridge on January 17. Knowing that it's quite cold in our lab (around 18 degrees). Is this a problem?
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Contact the manufacturer for the best advice regarding the product.
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We are using MS5A column for H2 and O2 detection during photocatalysis experiment. Is this column afraid of water and we should not use manual injection and only use autosampler.
but many researchers using manual injection and take samples from the reactor filled with water?
What is correct as we don't have autosampler?
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Please contact someone knowledgeable and local regarding proper operation of the instrument. You may damage the instrument is used without having someone with training supervise or assist you. * Molecular-sieve coated (or based) columns are highly susceptible to contamination by water (and CO2). They should not be used for water or CO (CO2) analysis. Column deterioration and damage (drifting retention times are often a first sign of trouble) often result from the introduction of water into the gas stream. SAMPLES for analysis MUST BE DRY to use with molesive type columns. If contaminated with water, you can try to dry the column out per the column manufacturer's recommendations (e.g.. 310C for ~8-hours, but as their are many types of molesive columns, please refer to specific manufacturers recommendations).
Note: Unless the injection method or technique used are performed incorrectly, the "mode" of injection (manual vs automated) has absolutely nothing to do with the issue.
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What is the difference between XTerra RP18 and C18 HPLC column?
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The primary distinction between XTerra RP18 and C18 HPLC columns is rooted in the bonding of the C18 ligand and the existence of an embedded polar group at the base of the ligand, specifically within the XTerra RP18 column.
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Good morning, I have two datasets with the exact same columns. I would like to select rows that have a matching ID between the two datasets (Please, see tables below).I tried to merge datasets with the r bind function but all rows were included. Do you have some advice to keep only rows with a matching ID?
Input
df1
ID VAR 1 VAR 2
a ... ...
b ... ...
c ... ...
d ... ...
df2
ID VAR 1 VAR 2
a ... ...
b ... ...
e ... ...
f ... ...
Output
df
ID VAR 1 VAR 2
a ... ...
b ... ...
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I found a solution to this problem.
df2[df2$ID %in% df1$ID,]
df1 includes all identifiers that you want to select matching rows and df2 your dataset including all variables
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Hi there.
I have to use the pET28a-SUMO vector to get my target protein.
However, I can‘t separate it from SUMO tag.
My protein was about 15 Kda big and has a about 5 value of pI.
Due to the process next is about X-ray diffraction.
How I can i get my protein without tag or without 80% tag?
After tag on/off-columns cleavage, my protein will stick on the Ni column if I want to remove the tag only if I introduce buffer with imidazole. But buffer with imidazole will bring the SUMO tag down even you use 10mM imidazole.
How can i get my protein without SUMO tag ??????
I have tried ion exchange chromatography and It was not work.
6His tag only? Inclusion body.
MBP tag?TEV is trash enzyme and same problem when i remove the tag.
GST tag?A little of protein is soluble.
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Try to change another protease cleavage sites, such as ULP1
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Dearest fellow scientists,
I've been trying analyze some ions with ion chromatography using suppressed conductivity detection. One of the ions im trying to measure is tertbutylammonium (TBA). Sadly I saw no elution of TBA and I have no idea why. TBA does not seem to show a peak, or elute at all.
I've tried to find literature as to why TBA does not elute but I couldn't find a lot of information. There was one article that examined the elution of TBA on silica and polymer based columns, and it stated that the elution was only possible on a silica-based column (Source: ).
Sadly the article does not explain why the elution was not possible on polymer-based columns, and I want to know why. I'm also questioning the validity of the information, so I decided to ask the experts at ResearchGate :)
Specs of my instrument:
- Dionex ICS-6000
- Dionex CS18 2x250mm cation exchanger column
- Dionex ICS-6000 Dual pump
- Dionex ICS-6000 Eluent Generator
- Dionex ICS-6000 CS-6_cation conductivity detector
Specs of my method:
- Injection volume: 5 microliters
- Flow: 0.25 mL/min
- Mobile phase: Gradient (shown in the attached figure)
- Column temperature: 30 degrees Celsius
- Amperage of the suppressor: 30 mA
- Runtime: 30 minutes
If there's any additional information required, let me know! Thank you in advance.
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The retention time of hydrophobic tetrabutylammonium cation containing sixteen carbon atoms depends strongly on the hydrophobicity of your chromatographic column/resin, so you need to use acetonitrile in the eluent to get elution or to use very hydrophilic IC column.
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Now we are working on extracting large-sized plasmids(55kbp,70kbp,100kbp) from E.coli EPI300 by traditional DNA ethanol precipitation method without the spin column. But we can't get good results (Gel electrophoresis does not show distinct, singular target bands.) PS: The colony PCR validation results indicated that the plasmid has successfully been transferred into EPI300.
Any suggestion is welcome. (any commercial kit, methods, protocols)
Thanks.
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Hi, for bacmid extraction we proceed as with small plasmid (3ml of preculture/pellet/solution sds NaOH/then acetate de K...phenol/chloroform/EtoH precipitation) exept that we did not vortex (just invert tubes up and down by hand 5-times at each step). However the yield is very small as large plasmids are not in multiple copies in the bacteria (so it is not easy to see them on a gel; they were only used to transfect SF9 cells) If you want to do restriction map for example you will need to start with larger volume. there is kit to extract bacmid (Qiagen, Thermo-fischer....)
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I'm running MQ on some peptide-level enrichment TurboID samples, so I'm interested in quantifying individual peptides. In past versions of Maxquant (v1.6.14 etc), the peptides.txt file contained LFQ intensity columns for each peptide. However, I just ran my data in Maxquant v 2.4.12, and the LFQ intensity columns are missing in the peptides.txt file. I ran it twice to make sure I had selected all the correct parameters. Does anyone know why these columns are missing, and how to recover them?
Thanks!
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Hi Tarabryn,
to be honest, I have never used LFQ quantification on single peptide level, However there are a multitute of settings to define the calculation for LFQ.
Maybe, most important is to set the min peptide ratio for LFQ from 2 (default) to 1.
It also makes sense to disable the fast LFQ function.
Then set the type of peptides which should be considered for LFQ (i.e. Unique, Razor etc. and modified or unmodified only (depending on your experimental question.
I hope you can find the way to recover the LFQ values with the newer MQ versions.
Good luck!
Murat
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Hi all
I’m working with RP HPLC
With injecting the sample from the same vial on a 4.6x250mm column (C18, 5um, 1ml/min) for several injections I get varying peak integrity
Is there a rational explanation for this?
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Hi everyone. I wish you all a Merry Christmas and a Happy New Year ahead! I hope you are doing well.
I have a question. In Opensees, why reinforced concrete beam-column joint is assumed as a parallelogram in modeling in 2D?
Thanks.
Regards,
Kaustav Sengupta
#reinforcedconcrete #RC #rc #reinforcedconcretejoint #reinforcedconcretebeamcolumnjoint #beamcolumnjoint #opensees #Opensees #joint #jointmodelling #parallelogram
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In OpenSees, a reinforced concrete beam-column joint is often modeled using a "parallelogram" analogy to simplify the representation of the joint behavior. This approach is based on the idea that the joint shear deformation can be captured using a simplified truss analogy, where the joint region is represented as a parallelogram.
The decision to model a reinforced concrete joint as a parallelogram is a simplification for computational efficiency and ease of implementation. Here are some reasons why this approximation is commonly used:
  1. Computational Efficiency:A parallelogram analogy simplifies the modeling process and reduces computational complexity. The joint behavior is represented in a way that is computationally efficient, making it easier to analyze structural systems with many joints.
  2. Ease of Implementation:Modeling a joint as a parallelogram simplifies the implementation of the constitutive models and numerical algorithms within the software. It allows for a straightforward representation of the joint's response under various loading conditions.
  3. Shear Deformation:The parallelogram analogy captures the essential features of shear deformation in the joint region. Shear forces are often the critical components of joint behavior, especially in seismic loading conditions.
  4. Empirical Validation:The parallelogram analogy has been found to provide reasonable results when compared to experimental data for a range of joint configurations. While it is a simplified representation, it has been validated against physical tests to some extent.
It's important to note that this simplification is a compromise between accuracy and computational efficiency. In reality, reinforced concrete joints exhibit complex behavior, including shear, flexure, and axial deformations. For more accurate simulations, researchers may use more sophisticated modeling techniques or advanced constitutive models that capture the intricacies of joint behavior.
When using OpenSees or any other structural analysis software, it's crucial to be aware of the underlying assumptions and limitations of the chosen modeling approach. Engineers should validate their models against experimental data and exercise caution when applying simplified representations to critical structural components.
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Hi! I'm trying to validate a method for the separation and quantification of 5 different organic acids (trans-aconitic, malic, citric, acetic and lactic). I've run some tests but there is a problem: I can se multiple peaks for each acid in my chromatogram. Any suggestions of what could be happening? I'll leave the conditions I've been using:
Mobile fase: 95% H2O pH 2.5 with HCl/ 5% MeCN
Volume of inyection: 10 microL
Flow rate: 0.8 mL/min
Column Temperature: 25°C
Column: Xterra Waters RP18 4.6 x 150 mm with 5 micrometers particle size
Equipment: Perkin Elmer LC 300
Detector: diode array
Wavelenght: 240 nm
Thank you very much for your help!
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I'm not sure switching to gradient elution can address this issue.
Maria Kefalas, based on what we have as an input info about the problem, I would consider these things as potential source of those additional peaks:
1. Impurities - in case the retention times of those additional peaks are repeatable in each run. It could be caused by suboptimal storage conditions of the standards or their age or even (least likely imho) sample preparation procedure;
2. Again impurities, but with the LC column itself as a source of them. Can be checked using the column of similar or the same ligand chemistry;
3. Instrument malfunction - in case the retention times of those additional peaks are not repeatable, the one should consider the contamination of detector flow cell from previous analyses. Usually, user manuals to the instrument provide more detailed information on this aspect.
I hope I didn't miss any other important things on this problem.
Regards,
Denis.
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I modeled the 2D frame with OpenSeesPy in a way that the concrete class is variable, there is a distributed load on the beams and horizontal load on only 2 nodes, I analyzed the statics in this way, but I am getting an error in the analysis part.
My modeling steps are very similar to the OpenSeesPy 2D Portal Frame example:
However, while I was doing the analysis using eigen in the example, I did not use eigen. I would like your comments.
import time
import sys
import os
import openseespy.opensees as ops
import numpy as np
import matplotlib.pyplot as plt
m = 1.0
s = 1.0
cm = m/100
mm = m/1000
m2=m*m
cm2=cm*cm
mm2 = mm*mm
kN = 1.0
N = kN/1000
MPa = N/(mm**2)
pi = 3.14
g = 9.81
GPa = 1000*MPa
ton = kN*(s**2)/m
matTag=1
for i in range(0,8):
# remove existing model
ops.wipe()
# set modelbuilder
ops.model('basic', '-ndm', 2, '-ndf', 3)
L_x = 3.0*m # Span
L_y = 3.0*m # Story Height
b=0.3*m
h=0.3*m
# Node Coordinates Matrix (size : nn x 2)
node_coords = np.array([[0, 0], [L_x, 0],
[0, L_y], [L_x, L_y],
[0, 2*L_y], [L_x, 2*L_y],
[0, L_y], [L_x, L_y],
[0, 2*L_y], [L_x, 2*L_y]])
# Element Connectivity Matrix (size: nel x 2)
connectivity = [[1,3], [2,4],
[3,5], [4,6],
[7,8], [9,10],
[7,3], [8,4],
[9,5], [10,6]
]
# Get Number of elements
nel = len(connectivity)
# Distinguish beams, columns & hinges by their element tag ID
all_the_beams = [5, 6]
all_the_cols = [1, 2, 3, 4]
[ops.node(n+1,*node_coords[n])
for n in range(len(node_coords))];
# Boundary Conditions
## Fixing the Base Nodes
[ops.fix(n, 1, 1, 1)
for n in [1, 2]];
fpc = [30,33,36,39,42,45,48,50]
epsc0 = [0.002,0.002,0.002,0.002,0.002,0.002,0.002,0.002]
fpcu = [33,36,39,42,45,48,51,54]
epsU = [0.008,0.0078,0.0075,0.0073,0.0070,0.0068,0.0065,0.0063]
Ec=(3250*(fpc[i]**0.5)+14000)
A=b*h
I=(b*h**3)/12
ops.uniaxialMaterial('Concrete01', matTag, fpc[i], epsc0[i], fpcu[i], epsU[i])
sections = {'Column':{'b':b, 'h':h,'A':A, 'I':I},
'Beam':{'b':300, 'h':500, 'A':300*300,'I':(300*(300**3)/12) }}
# Transformations
ops.geomTransf('Linear', 1)
# Beams
[ops.element('elasticBeamColumn', e, *connectivity[e-1], sections['Beam']['A'], Ec, sections['Beam']['I'], 1)
for e in all_the_beams];
# Columns
[ops.element('elasticBeamColumn', e, *connectivity[e-1], sections['Column']['A'], Ec, sections['Column']['I'], 1)
for e in all_the_cols];
D_L = 0.27*(kN/m) # Distributed load
C_L = 0.27*(kN) # Concentrated load
# Now, loads & lumped masses will be added to the domain.
loaded_nodes = [3,5]
loaded_elems = [5,6]
ops.timeSeries('Linear',1,'-factor',1.0)
ops.pattern('Plain', 1, 1)
[ops.load(n, *[0,-C_L,0]) for n in loaded_nodes];
ops.eleLoad('-ele', *loaded_elems,'-type', '-beamUniform',-D_L)
# create SOE
ops.system("BandSPD")
# create DOF number
ops.numberer("RCM")
# create constraint handler
ops.constraints("Plain")
# create integrator
ops.integrator("LoadControl", 1.0)
# create algorithm
ops.algorithm("Linear")
# create analysis object
ops.analysis("Static")
# perform the analysis
ops.analyze(1)
# get node displacements
ux = ops.nodeDisp(5, 1)
uy = ops.nodeDisp(3, 1)
print(ux,uy)
print('Model built successfully!')
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I'm glad to be of help.
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We have extracted RNA from our fungal strain, growing in three different carbon source growth conditions. We have received the RNA-Seq data and have carried out different gene expression analysis (DESeq) between either two of the growth conditions.
Now we are interested in the absolute gene expression levels across all the growth conditions apart from DESeq.
I have the raw hit-counts files ready in a table, first column is gene ID, 2-10 columns are the three replicates of condition 1, condition2 and condition3, respectively.
The next step would be normalization of the read counts and generate the absolute gene expression levels. However, I have limited knowledge of R, in this case, can I do it manually or have to use R to do that? Is there any package (including normalization) I can use? How can I generate a table or even a plot such as heatmap of the top 10 genes?
Thank you very much. Any hint or guide will be very much appreciated.
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Hello Tiantian Fu,
DESeq2 can generate such files, usually the best one is VST normalized table, where you plot each gene alone with very little variations among samples.
Regarding the top 10, they are the 10 genes with the lowest FDR values from the DESeq2 results table, then you can go back to the VST normalized table and calculate the Z scores of the top 10 genes. After that you can use GraphPad prism to plot a heatmap.
Hope this helps
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I am currently trying to characterize shortmers of large nucleotides (up to 10k bases) from HPLC fractions and the samples I have available are of very low concentration, especially after fraction collection. Does anyone have experience in this area and have suggestions for how to concentrate the target while removing the mobile phase reagents in the matrix?
I've tried rotovaping followed by purification by silica spin columns with mixed results and concentrations that are still quite low. I've considered TFF spin columns but those are MWC and I need to retain all shortmers and demonstrate that they are indeed nucleotides.
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To add to Guobing Xiang 's answer, I'm assuming you use reverse phase HPLC to purify your samples?
Although this is written for flash chromatography, the same general procedure can be used for solid phase extraction cartridges or a small preparative HPLC column. I recommend an AQ type C18 to avoid phase collapse:
Desalting Samples with RediSep Gold C18Aq Columns (teledyneisco.com)
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I am working with an AKTA Go equipment. And according to their manuals, it is not possible to use reverse flow in this type of equipment. However, to perform deeper or more effective cleaning in some types of columns, it is required to pass the cleaning reagents through the columns by reverse flow. For example, in Histrap HP, Capto Q and DEAE columns, among others. I thought about connecting the columns upside down, but.... Is it safe to connect such columns like that in those equipments? In the opposite direction than usual? Does anyone have some kind of bibliography or infographic to read about the subject and the procedures to do it?
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In hplc we used to connect colums upside down in case of predicted column blockade to clean them opening the other end to waste if correct connector is found it can be connected but , need to be carefully check the column properties , before connecting
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Hi,
I did an exploratory factor analysis. Direct Oblimin and Principal Axis factoring. The 12 variables loaded on 2 factors. The factor loadings on factor 1 (column one in pattern matrix) and factor loadings on factor 2 (column two in pattern matrix) are highly negatively correlated (R2=0.991).
Is this normal or problematic? Thank you!
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I don't think it is common to report the correlation between loadings on different factors. I would report (among other things) the actual loadings (pattern matrix), the structure matrix (correlations between variables and factors), and the correlations between the factors.
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I want to use sma-based reinforcement at the particular face in the beam and column. Moreover, is it possible to use typical steel reinforcement and sma-based reinforcement in the same section of beam/column? I need guidelines on how to model it.
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Hi dear Prince!
Please read this article for a more detailed discussion:
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I have been having troubles with column purification (for DNA) recently. I am assuming that the reason is the residual ethanol. I used to centrifuge at max speed for 2 minutes to remove residual ethanol. Would using a desiccator do a better job at drying the column?
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Hi there,
In general, the alcohol should not be the problem when you centrifuged for 2 min...
A desiccator will not work, since it usually contains substances that absorb water.
Instead, spin the columns once to remove alcohol, add warm elution buffer (half of what you usually use), incubate for about 1 min and spin them again to elute the DNA.
Afterwards, add the second half of your elution buffer, wait and spin again.
That way you will not have any alcohol in the second elution step.
Good luck,
Sebastian
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I found the node of error from result tree. At that node i haven't specifically applied any constraint and it is at the intersection of beam and column
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Tejaswini Chilupuri, In visualization module, check the region where the Incorrect Dof is applied and troubleshoot your model accordingly.
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Dear colleagues, does anyone use COSMOSIL Direct Cartridge Holder (ID 4,6 mm, Product No 19989-71). Should I use wrenches to tighten holder to COSMOSIL analytical column (ID 4,6 mm) or it is hand-tigten only to connect with column?
Thanks in advance for any help!
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Hi,
I have to plot the wave function at the both valence band and conduction band. I have generated the PARCHG file using vasp. There are 10 columns in this file. What actually they represent? Which columns are needed for this purpose? I was not success to plot this file in VESTA. Could anyone please tell me how to plot with details? Thank you.
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The PARCHG file is structured similar to the CHGCAR. The columns do not represent anything in particular, they are just the charge density value at a certain point in the cell, but structured into columns.
Once you have the PARCHG file you should be able to visualize it in VESTA, just make sure the name is only PARCHG or ending with .vasp, otherwise it may not recongnize it.
For plotting the VB and CB, you can follow this link: https://www.vasp.at/wiki/index.php/Band_decomposed_charge_densities. But as a summary, you should use the IBAND key with the band indices of the last occupied band and first unoccupied band (which you can see in the OUTCAR or EIGENVAL files)
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I have a question regarding purification of bisulfite converted DNA. Everytime by Bisulfite converted DNA will stuck inside the column whenever I do the purification. Kindly help me in this regard.
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Asegúrese de que la columna utilizada sea adecuada para manipular ADN convertido con bisulfito. El tamaño de poro de algunas columnas puede no ser adecuado para la purificación de este tipo de ADN.
La capacidad de unión del ADN convertido con bisulfito variará mucho en diferentes valores de pH. Asegúrese de que el pH de la muestra sea adecuado para la adsorción de ADN en la columna.
La concentración de sal tiene un efecto importante sobre la unión del ADN a la columna. Si la concentración de sal es demasiado alta o demasiado baja, es posible que el ADN no se una a la columna ni pase a través de ella de manera efectiva. Compruebe que el tampón utilizado tenga la concentración y el tipo de sal correctos.
Las condiciones de elución (como la composición del tampón de elución y el pH) también tienen un impacto importante en la liberación de ADN de la columna.
Asegúrese de que la muestra sea completamente homogénea y esté limpia antes de cargarla en la columna. Es posible que sea necesario centrifugar para eliminar cualquier sedimento que pueda obstruir la columna.
Los caudales demasiado rápidos pueden dar lugar a que el ADN no tenga tiempo suficiente para unirse al material de la columna.
La temperatura experimental también puede afectar la unión y elución del ADN; intente realizar experimentos a diferentes temperaturas.
Calidad y estado de la columna.
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Hello PCD community,
I am very interested in building collaborations and discussion around post-column derivatisations in HPLC applications.
This is an area of application that provides selective detection for target components, that may, (1) Simplify analysis of the target species in complex samples, (2) provide a means of detection for solutes with limited chromophores, or other aspects of the sample that make it difficult to detect, or (3) provide a method for confirming the nature of the analyte that responds to the PCD reagent.
I'm seeking knowledge on how and why others in the field undertake their assays and I hope we can build informative discussion on this important area of analytical chemistry.
Looking forward to discussion.
Regards
Andrew
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Hi Andrew, I am currently not doing PCD, but I am happy to be part of the discussion.
Regards,
Danijela
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Hello wonderful people out there,
Could anyone please advise why BRIG keeps on generating the following error message while running the analysis:
SYS_ERROR:The following error occurred: org.xml.sax.SAXException: value for 'sequenceLength' attribute in cgview element must be greater than 10 in null at line 1 column 1047
I have latest Java version and BLAST+ installed. Any thoughts please?
Sincerely,
Ravendra
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Thank you Mohammad Imam, for your detailed suggestions! Much appreciated.
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I want to digest sumo/His label when the protein in still hang on the Ni column. I wash the undesired proteins as usual, then balance the column with 3ml enzyme digestion buffer, then add sumo enzyme for digesting the fusion protein at 4℃ for 12h in 4ml sumo digesting buffer. Then catch the flow through liquid, take some sample from flow through liquid and beads after elution for SDS-PAGE, the brand explains the label did not have been cut, it is still on the beads entirely.
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G.Dharmamoorthy First of all, I really appreciate your help. About changing buffer. I already balance the column with sumo cleavage buffer before adding the sumo protease. Unfortunately is still not working.
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Hi everyone,
I'm new in ASPEN, my question is related to the possibility of simulating an adsorption column where on one side you have a stream of pure hydrogen and on the other side you have a stream of a liquid metal. The objective of this column is to solubilize the hydrogen in the liquid metal according to Sieverts' law. Then, as an apposite step, I would like to simulate the stripping of the hydrogen solubilized in the liquid metal by using an inert gas.
My question is twofold: 1) is it possible to add a liquid metal with known thermophysical and transport properties in ASPEN? 2) how do I have to implement the Sieverts' law since only Henry'ss law seems to be implemented in ASPEN?
The absorption column is indeed a packed column.
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Luigi Candido , Hi luigi. Any update on your findings?
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Hello all,
I am currently trying to purify a fragment of the large surface protein of HBV however during purification I notice that a white precipitate form on the Ni-NTA column. (At pH 8.0; pI of protein = 6.97) I'm using a simple lysis buffer (50 mM imidazole, 50 mM NaH2PO4, 300 mM NaCl, (5% glycerol in some cases but no significant difference))
The protein was in solution in the cell lysate, ie before loading onto the column and the precipitate is confirmed to be my protein.
Washing and eluting at pH 8 resulted in a milky, cloudy white eluate.
Washing and eluting at lower pH of below 6 has helped to solubilize protein and the solution is clear.
For subsequent experiments I need to bind my protein to Ni-NTA carrying liposomes but as soon as my protein comes into contact with them it precipitates. The protein also precipitated when adding a bit of NiSO4 solution.
Any ideas as to how I can avoid this issue?
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Do you observe the same precipitation when using IMAC columns with immobilized Cobalt, Copper or Zinc ions? You can basically screen all the first row transition metals for that matter.
Good luck!
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Hello everyone,
I have applied 1D CNN on speech emotion recognition, when I shuffled columns I got diffrent results, for example, using matrix(:,[1 2 3]) gives different classification results than matrix(:,[2 3 1]) which should be the same, I have tried rng("default") but it hasn't resolved the issue. Can someone please assist me with this?
Thank you in advance!
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Hamza Roubhi I appreciate your dedication to applying 1D CNN in the domain of speech emotion recognition and your commitment to addressing the issue concerning the variation in classification results when shuffling columns. As a fellow researcher with a background in signal processing, I understand the significance of consistency and reliability in the outcomes of such analyses.
When encountering discrepancies in results due to column shuffling, it is essential to ensure that the underlying data preprocessing and feature extraction methods remain consistent across different column arrangements. Validating the integrity of the data and confirming that the shuffling process does not introduce unintended variations can help maintain the robustness and reliability of the classification results.
Additionally, verifying the implementation of the CNN architecture, including the configuration of the layers, activation functions, and training parameters, is crucial in ensuring reproducibility and consistency in the classification outcomes. Reviewing the model's initialization procedures and ensuring that the randomization process aligns with the desired standards of consistency can potentially address the issue you are facing.
Furthermore, conducting thorough checks on the data partitioning and validation procedures, such as cross-validation techniques, can help identify any potential sources of variability that may arise due to the shuffled column arrangements. Ensuring that the model training and testing processes maintain consistency and adhere to standardized protocols can contribute to the stability and reliability of the classification results.
I recommend conducting a systematic evaluation of the data preprocessing, model architecture, and training protocols to pinpoint any potential sources of variation that may arise during the column shuffling process. By adhering to rigorous validation practices and ensuring the reproducibility of results across different column permutations, you can enhance the reliability and robustness of your CNN-based classification framework for speech emotion recognition.
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Hello,
I am currently working on a packed column model in SolidWorks. The column comprises a packing material consisting of numerous beads (or other packing types such as Raschig rings) initially positioned outside and above the column. To achieve a random packing configuration, I utilized SolidWorks Motion Study. By defining contacts between parts and enabling gravity forces, the beads descend and fill the column randomly, as depicted in the attached file (including the assembly, parts, and screenshots). Now, I aim to maintain the positions of these beads once I transition from the Motion Study tab to the Model tab. Does anyone have a solution for this?
Thank you.
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I finally found a solution to this question, we have to choose "Make assembly from assembly" from file menu, and then, when a new assembly is created, we have to right click on the Assembly, and choose "Desolve assembly" to break the link with the original one.
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One day my HPLC peaks were nice and tall, narrow, almost perfectly Gaussian, and the next day they were short and fat.
Same sample in the same solvent
Same HPLC method
Measured the mobile phase flow rate and it was correct
So I call the column manufacturer and they suggested:
Smaller sample loop - still short and fat
Lower concentration - still short and fat
Completely different column (C-18) - still short and fat.
Any ideas?
Thank you
Kevin
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I just heard back from the instrument manufacturer; the symptoms indicate a lamp failure.
Kevin
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Ratio between Total protein load, Volume elute and concentration elute.
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"Load" amount (concentration and VOLUME) may change everything. Standard practice is to conduct a formal "Load Study" using your exact method and column to determine and measure, scientifically, the changes that take place. Depending on the desired goal(s), an optimum load can be identified for YOUR specific application. *It will be different for every method as there are no universal ratios or values.
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I was asked to design a benzene production plant via a thermal toluene hydrodealkylation process, and one of the parts was to separate the benzene and toluene via distillation. I am unsure why the thermal separation is taken at 3 bar pressure. The 3 bar was assumed from the Richard Turton book - Analysis, Synthesis, and Design of Chemical Processes, Fourth Edition by Richard Turton.
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Boiling point difference between benzene and toluene increase with pressure and hence relative volatility also increases, that could be the reason of separation at 3 bar.
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This problem is relatively easy solved when stiffeners are identical and obeying rotational Hooke's law, i.e., are linear. The case of different but comparable with each other stiffeness coefficients is very cumbersome and it demands solving a system of transcendental equations to get a critical load even in Euler'sregime.
I've failed in searching the solution of this problem in scientific and educational literature however I don't like "to invent a bike". May be anybody has some references on this problem or even an article or book chapter.
The way I solve this problrm see the paper "Buckling in inelastic regime of a uniform console with symmetrical cross section: computer modeling by the use of Maple 18" on my profile.
Thanx everybody in advance
Best regards
Viktor
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Probably jurisprudence, not so sure.
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Which mobile phase, a wavelenght and a flow rate would be the best?
The column is packed with ODP stationary phase. My sample also contains NaOH, H2O2, therefore I need to avoid interference of these substances.
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Dear Agnė Keselytė,
First of all, I would like to inform you that the best method for DMSO analysis is Gas Chromatograph (GC) because having solvent this technique is best suitable.
Gene@rally, DMSO is not analysis by HPLC because the traces can be remain in system and DMSO will cause corrosion.
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LigaTrap's Human IgA purification column and Cytiva's HiTrap Protein A column do not isolate IgA type 1 and 2 from other immunoglobulins. LigaTrap's technical service informed me that their resin would bind other immunoglobulins, not just IgAs. I tried Cytiva's column with the understanding that it would capture IgA in the column, but it did not. What we are setting out to do is very simple, we want to deplete a commercial CSF of IgAs, so we need a column that will bind IgAs only. I have not been successful in finding a product that does this, and would appreciate any help or advice. Thank you!
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Thank you for sharing this!
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Hi
I have problem importing thesaurus file to vosviewer. the error is ".... is not valid column header". whatever the first line is, the error repeat as the same. should I make changes to file and then import it?
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Mitra Zarei When encountering issues with importing a thesaurus file into VOSviewer and receiving an error message indicating that a specific column header is not valid, there are several steps you can take to troubleshoot and resolve the problem. Here's a step-by-step guide to help you address this issue:
  1. Review the Thesaurus File Format Requirements:Check the specific format requirements for the thesaurus file in VOSviewer. Ensure that the file follows the designated structure and formatting guidelines, including the required column headers and data organization.
  2. Validate the Column Headers:Open the thesaurus file in a text editor or spreadsheet software such as Microsoft Excel. Verify that the column headers are accurately labeled and correspond to the predefined categories specified by VOSviewer. Ensure that there are no formatting inconsistencies or typographical errors in the column headers.
  3. Confirm the Data Structure and Content:Review the content of the thesaurus file to ensure that it contains relevant and appropriately categorized data. Check that the data entries under each column align with the corresponding header labels and are formatted correctly without any irregularities or data discrepancies.
  4. Adjust the File Structure if Necessary:If the error persists, consider modifying the thesaurus file by adjusting the column headers or reorganizing the data structure to adhere to the required format. Make the necessary changes to ensure that the file is compliant with VOSviewer's import specifications.
  5. Save the File in a Compatible Format:Save the modified thesaurus file in a compatible file format supported by VOSviewer, such as TXT, CSV, or TSV. Ensure that the file is saved with the appropriate encoding and delimiter settings to facilitate seamless importation into VOSviewer without any data parsing errors.
  6. Import the Modified Thesaurus File into VOSviewer:Open VOSviewer and attempt to import the modified thesaurus file. Navigate to the import function, select the appropriate file, and follow the on-screen instructions to complete the import process. Monitor the import procedure to verify that the file is successfully loaded without encountering any column header validation errors.
By following these steps, you can effectively address the issue of the thesaurus file containing invalid column headers and ensure a smooth and error-free importation process in VOSviewer. Making necessary adjustments to the file structure and adhering to the specified formatting requirements will help you successfully utilize the thesaurus file for further analysis and visualization within VOSviewer.
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Do you know what are the cheapest houses made entirely of reinforced concrete on which my patent has a performance? The prefabricated ones.
The acceleration of the earth on which the structure rests imposes a displacement in one direction on the building which reacts with another force in the opposite direction which we call inertia.
These two forces with different heights impose a overturning moment on the structure.
This overturning moment acts as follows.
If we have a rigid and elevated dynamic building made entirely of reinforced concrete, then the building will overturn entirely in a large earthquake. That is, its entire base will become a wall and the wall will become a base.
If the building has beams and columns then neither the columns are simply bent over, nor do the beams have the strength to rotate the building around itself, nor will the base of the building leave the ground. The reason is that neither the beams nor the columns have such strong cross-sections that they are able to rotate the structure and overturn it.
If we have walls and beams then the weaker cross sections of the beams will break, and the structure will be left on the ground without rotating and overturning.
The ceiling, however, will come down on our heads.
Here we see three different structures reacting differently. But not all of them react the way we want them to.
We don't want the columns to break, we don't want the beams to break, and we don't want it to tip over.
If we take the dynamic version of the structure that is made entirely of reinforced concrete that only topples but does not break, and embed it in the ground with strong anchors, then I ask any would-be denier of my method what damage can be done?
The structure will suffer no damage.
Do you know any more are the cheapest houses made entirely of reinforced concrete on which my patent has performed? The prefabricated ones. .... It doesn't pay off...the system and cheap and seismically sound.
The all reinforced concrete building has two main levers.
That of height and that of width.
That of height contrasts with that of width.
The one of height multiplies the moments that descend to the base and overturn the structure, and the one of width resists this overturning. So the force of inertia along with the height multiplies the overturning moments, while the building's footing on the other end of the width lever arm along with the distance from the pivot point stops the building from overturning.
The farther the anchorage is from the pivot point of the rigid building, the lower the overturning force it receives.
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When there is prestressing in the walls and simultaneous compaction in the ground what happens in the video would not happen.
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I have a question from the literature: How does an irrigation rate of (96 mL/hr.) equal (8.5 L/m2.h) if I have a column of 125 mm in diameter and 2m long?
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To convert the irrigation rate from milliliters per hour (mL/hr) to liters per square meter per hour (L/m².h), we need to consider the area of the column.
First, let's calculate the cross-sectional area of the column. The diameter of 125 mm gives a radius of 62.5 mm (or 0.0625 m). Using the formula for the area of a circle (A = πr²), we find:
A = π(0.0625)^2 = 0.01227 m²
Next, we can convert the irrigation rate from mL/hr to L/m².h. Since 1 liter is equal to 1000 milliliters, the conversion factor is:
1 L = 1000 mL
Therefore, to convert 96 mL/hr to L/m².h, we can use the following calculation:
(96 mL/hr) x (1 L/1000 mL) x (1/0.01227 m²) = 7.82 L/m².h
So, the irrigation rate of 96 mL/hr is approximately equal to 7.82 L/m².h for a column with a diameter of 125 mm and a length of 2 m.
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i am optimizing a reactive distillation column. I have simulated a base case in Aspen Plus and now want to calculate its total annual cost in Matlab. while linking aspen Plus and Matlab i need path to node for column diameter from variable explorer in aspen plus i guess the path to node should be " reactive_distillation.Tree.FindNode("\Data\Blocks\RDC\Subobjects\Column Internals\INT-1\Subobjects\Sections\CS-1\Output\CA_DIAM1"). But this path gives zero value for diameter while column diameter is 2.43 can you help in this? what path should i use for this in aspen version 10.
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I want to connect aspen properties with MATLAB. like this:
AspenProperties.Application.Tree.FindNode("\Data\Properties\Analysis\BINRY-1\Output\Prop Data\PROPTAB\VAPOR MOLEFRAC BENZENE 2").value
But its showing an error: Dot indexing is not supported for variables of this type.
Please help me out
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The previous column was C8 column. Now I am using Chiral AMY1 column. The same HPLC device. The same lamp and wavelength.
I read before that changing flow rate affects peak area. Are there any other factors that affect the area significantly?
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No its should not change significantly like 2-3 fold.
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Can anyone tell me please what difference will i have in results between activating or deactivating NLGeom in steps , knowing that i use plasticity values for steel material in property module, the model consists of a beam to column steel joint, i use static loading.
the job is converging only when i desactivate it.. what is the reason ?
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Instead of using the pines ans normal steel, use the magnetic materials, all structures will be stable
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I have a large sparse matrix A which is column rank-defficient. Typical size of A is over 100000x100000. In my computation, I need the matrix W whose columns span the null space of A. But I do not know how to fastly compute all the columns of W.
If A is small-scale, I know there are several numerical methods based on matrix factorization, such as LU, QR, SVD. But for large-scale matrices, I can not find an efficient iterative method to do this.
Could you please give me some help?
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If the matrix is sparse then a sparse LU will enable you to compute the null space. (Row &/or column swaps (= pivoting) may be necessary or useful to keep memory and time costs low.) But otherwise this will become very expensive. Even just storing such a matrix would take (in double precision floating point) over 80GB. Any solver would be an out-of-core type of solver, but would be extremely expensive.
An alternative, if the matrix is real symmetric, is to use the Lanczos method or a variant such as the Lehoucq & Sorensen ARPACK method. More precisely, ARPACK is a restarted Arnoldi method. Then you look for when you have the zero eigenvalue (or simply a very small eigenvalue). The corresponding eigenvector(s) gives a basis for the null space. ARPACK is a semi-iterative method, and so there is a trade-off between the accuracy of the eigenvalues (and eigenvectors) and the number of iterations performed.
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I need to calculate the saturated vapour pressures so I can find the relative volatilities for the shortcut method for the design of a distillation column.
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Just take the Parameters A, B and C of the Basic Antoine Equation from your textbook (like Reid Prausnitz and Poling) or database and compute C1, C2 and C3 for Aspenplus Extended Antoine Equation by multiplying the natural log of 10 (= 2.302...) to C1 and -2.302 to C2.
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Hi Everyone,
I have difficulties with my current work analyzing S-Methylmethionine(SMM).
According to several reports, the analysis of SMM can be done by HPLC with a UV detector (338nm) and OPA reagent. Meanwhile, there is another report showing SMM still can be analyzed without OPA. Later on, I tried to follow the report but I failed to obtain the SMM peak chromatogram.
FYI, the system that I used in my lab:
- HPLC (THermo vanquish)
- UV-DAD detector
- Zorbax AAA column
- 40mM NaH2PO4 (mobile phase A)
- MeOH:ACN:Water (45%:45%:10% mobile phase B)
Please let me know If you guys have any information or experience about analyzing SMM without OPA.
Thank you
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Since my lab have no OPA and the order is still in process, thus, I came up with the idea to find another possibility to analyze SMM without OPA.
I found several references that analyzed SMM without OPA, I followed those papers but I'm still failed.
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I have a large sparse matrix A which is column rank-defficient. Typical size of A is over 100000x100000. In my computation, I need the matrix W whose columns span the null space of A. But I do not know how to fastly compute all the columns of W.
If A is small-scale, I know there are several numerical methods based on matrix factorization, such as LU, QR, SVD. But for large-scale matrices, I can not find an efficient iterative method to do this.
Could you please give me some help?
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This paper: http://cedric.cnam.fr/~bentzc/INITREC/Files/DW10.pdf might be a good starting point.
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Hello everyone,
I'm simulating the axial compressive behavior of both circular and rectangular CFSST stub columns. Things went fine with the circular section but the opposite applied to the rectangular section as the solution didn't converge and not even reach at least my desired applied load (displacement control)
I used both C3D8R element for both steel tube and core concrete with contact property as follows:
Tangential direction: Penalty method with 0.6 coefficient
Normal direction: Hard contact (allows for separation after in contact)
The effect of corner region of the steel tube is also considered by partitioning the steel tube into multiple parts (See figures below). I tried both static general and static riks but none of them converge with the step time increment of:
initial increment: 0.001, minimum: 1E-20, max: 0.05 (or even smaller such as 0.025)
Please help me out guys. I'm really desperate for this problem.
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Dear
Samy Elhadi Oussadou
,
Thank you for your details explanation and the possible procedure that could solve my problem.
The thing is, I'm also working on the simulation of circular CFSST columns and it converges fine and very quick to solve as well. But when I applied the setting of the circular section to the rectangular section, this problem arises as I stated earlier.
I try changing the initial time step, but I don't want to modify the contact properties as it was what many researchers employed in their research work which I cited. Plus, I don't think the contact properties could be what causing this problem, but I'll try adjusting them to see if it helps in anyway.
I could send you my CAE file too if you want to investigate in details about my boundary or loading conditions as well as other material properties.
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Hi all,
So I have been doing high-throughput RNA extractions on xylem from Eucalyptus hybrids (urophylla x grandis). My extraction combines a custom CTAB protocol with silica column binding and purification of the RNA. In a single column format this protocol works great (>50ng/ul, 260/230 between 1.8 and 2.0 etc), but it isn't going great in a 96-well plate, so I am busy optimizing. Generally my yield is a bit low due to the nature of the samples, but I have never had this banding phenomenon circled in blue. The nanodrop readings of these samples aren't fantastic either (below 10ng/ul and 260/230 below 1.00). I have worked with samples before that have organic contamination, but have never seen this banding on a gel before. Any suggestions as to what might be causing this? For context this is a normal 1% agarose gel stained with ethidium bromide and I also treat the gel with bleach beforehand to get rid of any RNases in the agarose.
Any suggestions would be highly appreciated!
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What is your loading dye made of? looks like its concentration is too high.
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adsorption isotherms
kinetics models
BOD
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which software are usefull to Curve fitting ?
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A simple pin-pin column , and the Euler buckling load is Pi^2/L^2*EI. If I have a uniform lateral load, then the deformation of column as a bow, what will be the new Elastic Buckling load, is it going to be same ?
I understand that any axial load, increase the bow deflection by 1/(1-P/PE) , where P is axial load and PE is Euler buckling load (straight case). so the buckling in case of lateral load is still at P=PE, then deformation tends to infinite ?
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Buckling and post-buckling of a compressible slab under combined axial compression and lateral load
Fan-Fan Wang, Yuanbin Wang
ZAMM - Journal of Applied Mathematics and Mechanics / Zeitschrift für Angewandte Mathematik und MechanikVolume 97, Issue 6
First published: 09 January 2017
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Dear all,
I am trying to model the contact between the BEAM elements in my model for collapse analysis. I start off with a simple analysis where I have modelled a beam hitting a column, as shown in the picture below. The beam experienced some stress as it approached the column however no stress was experienced by the column. At the end of the analysis, the beam just passed through the column. How is this possible? Am I doing something wrong?
Any help will be greatly appreciated! Many thanks!
Kind regards,
HEng
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It seems that you have not defined a proper contact between the beam and the column elements. You need to specify a contact pair that includes the surfaces of the beam and the column that are expected to interact. You also need to choose a suitable contact behavior, such as frictionless, rough or frictional, depending on how you want to model the sliding between the beam and the column. You can use the CONTACT_AUTOMATIC_GENERAL option to automatically detect and create contact pairs between beam elements. However, this option assumes that the beams have a cylindrical shape for the contact algorithm, regardless of their actual cross section. You can adjust the contact thickness (offset) by using the parameters SST and SFST in the CONTACT card. Alternatively, you can use the Mortar contact option, which is a segment-to-segment penalty-based contact that assumes a faceted representation of the beam lateral surface. This option is recommended for implicit analysis, but it is also supported in explicit analysis. You can find more information about how to model contact between beam elements in this web page1. I hope this helps you with your analysis.
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I would like to know the minimum and maximum percentage of steel as per international codes.
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The minimum and maximum percentage of steel in concrete elements depends on the type of element, the design code and the loading conditions. Different codes may have different criteria for determining the optimal amount of reinforcement to ensure adequate strength, ductility and serviceability of the structure. Here are some examples of the minimum and maximum percentage of steel as per some international codes:
  • According to IS 456:2000, an Indian standard for plain and reinforced concrete, the minimum percentage of steel in beams is 1%, the maximum is 2%, the minimum in columns is 1%, the maximum is 6%, the minimum in slabs is 0.7%, the maximum is 1%, and the minimum in foundations is 0.7%, the maximum is 0.8%1.
  • According to ACI 318-19, an American standard for building code requirements for structural concrete, the minimum percentage of steel in beams and one-way slabs is 0.75% for Grade 60 (420 MPa) bars or 0.5% for Grade 40 (280 MPa) bars, the maximum is limited by the spacing requirements and the strain compatibility, the minimum in columns is 1% for spiral reinforcement or 0.8% for tied reinforcement, the maximum is 8% for spiral reinforcement or 6% for tied reinforcement, and the minimum in foundations is not specified, but it should be sufficient to resist cracking and provide adequate anchorage2.
  • According to BS EN 1992-1-1:2004, a British standard for design of concrete structures, the minimum percentage of steel in beams and slabs is determined by the crack control requirements, which depend on the exposure class, the concrete cover, the bar diameter and the stress level, the maximum is limited by the ultimate limit state design and the serviceability limit state design, the minimum in columns is 0.8% for normal conditions or 4% for fire conditions, the maximum is limited by the confinement requirements and the buckling resistance, and the minimum in foundations is not specified, but it should be adequate to resist punching shear and bending.
These are just some examples of international codes that provide guidance on the percentage of steel in concrete elements. There may be other codes that have different specifications and requirements. It is important to consult the relevant code and design standards for each project and follow the best practices of structural engineering.
for more information :
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Is there a source for a geocell-reinforced embankment relying on a controlled modulus column?
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Yes, there is a source for a geocell-reinforced embankment relying on a controlled modulus column. The source is a technical paper published in the journal Transportation Infrastructure Geotechnology, titled “Analysis of Geocell-Reinforced Stone Column-Supported Embankment Considering Soil-Structure Interaction” by M. P. Vibhoosha, Anjana Bhasi, and Sitaram Nayak1. The paper presents a three-dimensional coupled analysis of a geocell-reinforced stone column-supported embankment, considering the interactions between the geocell, the infill material, and the surrounding soil. The paper also compares the performance of the geocell-reinforced stone column-supported embankment with that of an ordinary stone column-supported embankment and a geosynthetic-reinforced stone column-supported embankment. The paper can be accessed online from the SpringerLink website2 or downloaded as a PDF file3.
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Specifically, what is the difference between
A) POPDATA=1, LOCPRIOR=1, LOCDATA=0, LOCISPOP=1 and
B) POPDATA=0, LOCPRIOR=1, LOCDATA=1, LOCISPOP=0 ?
For the clustering algorithm and calculating Q, I think it is the same. In both cases, the Locprior model uses the sampling location information, only from formally different sources (POPDATA or LOCDATA column). The further difference is that the A settings generate Q values not only for individuals but also for pre-defined populations.
Am I right?
Thank you.
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Thank you. As mentioned in the question, I am using Structure (version 2.3).
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I can not able to figure out which orbital(px,py,pz etc) corresponds to each column in VASP output file DOSCAR
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The labeling is s p_y p_z p_x d_{xy} d_{yz} d_{z2-r2} d_{xz} d_{x2-y2}, with eventually more columns if the spin and/or the spin-orbit effects are taken into account. These kind of questions can be easily answered by taking a look at the VASP wiki: https://www.vasp.at/wiki/index.php/DOSCAR
Note that the orbital populations are not rotational invariants, i.e., the population of a particular orbital will depend on the orientation of the system within the unit cell defined in the POSCAR, so be careful about the interpretation of these values.
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how to model bulkling of longitudinal rebar in reinforced concrete stub column?
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Using advanced analytical tools like finite element analysis (FEA) and drawing from existing research, We can create accurate models that enhance the safety and longevity of concrete structures. Modeling the buckling of longitudinal rebar in reinforced concrete stub columns is a multifaceted effort that requires a deep understanding of material properties, load conditions, and geometric configurations.
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I have trouble interpreting the chromatogram because of some peaks with a long tail, I think that there is a problem with the column. Can you explain the temperatures you use to clean the column? Did you compare any temperatures to clean it effectively?
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You could try to slowly hire up your chromatograph and then leave it all the night at the maximum temperature allowed (10ºC lower than the max one tolerated by the column).
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total Dna extraction from poultry tissue, kidney, liver, heart using spin column.
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Upper gel:
In samples 3 & 4 there is obviously no or very little DNA.
In my opinion all other DNAs are not properly dissolved and the gel is overloaded; and you might have RNA contamination.
Ensure your DNAs are completely dissolved and as suggested by others determine the concentration and reload equal amounts.
And, as also suggested by others, you should always seek advice from your supervisor or a senior lab member.
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i have an abaqus model which consists of beam to column steel joints with six bolts, and an imposed displacement of 200mm in the beam end.
I want to extract the tension forces in bolts in order to draw (bolt force-moment) curve
for the preloaded and non preloaded bolts.
Can anyone show me the procedure please?
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Engr. Tufail it's in turkish, i couldn't understand what he is explaining...
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Preliminary simulation and numerical investigation was carried out at the National Technical University of Athens in order to draw useful conclusions regarding the usefulness of the new seismic technology. The results were encouraging, as it significantly increased the load-bearing capacity and the shear strength of the cross section near the base by 31%, although the simulation was not performed correctly, resulting in insufficient calculation of the actual benefits. The method applies compression to the cross-section of the wall or shaft using tensioned tendons on all their sides, which are firmly anchored to the ground with expanding pile and anchor mechanisms. The method of compressing the sides of the cross-sections and the mechanism of the anchoring have the following purpose. The prestressing plus the anchoring of the wall sides from their highest level with the foundation ground ensures slight deformation and eliminates the right forces (N), torques (M) and shear (Q). It deflects the inertia intensities in the ground, increases the active cross-section of the wall, ensures a strong foundation ground, corrects the oblique tensile arrows, restores the construction to its original position even after inelastic leakage. Provides less ground displacement, at which point less acceleration. What they did not do in the attachment simulation and the results were altered are the following.
1) The title of the simulation states that it will be placed in a bearing of the carrier while in the simulation it was placed in all 9 pillars of the three-storey construction. The method is effective when you place on all sides of the wells or in elongated walls due to the double lever they have, that of the height and width which helps to reduce the moments of overturning of the walls.
2) In the simulation the anchoring to the ground was not applied because what they did was to apply only loads to the nodes of the highest level. This increases the stiffness of the columns as well as increases the strength of the cross-sections towards the intersection of the base, but it does not deflect the forces in the ground, since there is no anchoring, with the result that the torques inevitably lead to the cross-sections of the joints and break them.
3) The walls, because they are anchored from all their sides to the ground, have more anchoring mechanisms than the columns, which have a small square cross-section and accept only one tendon in the center of their cross-section, so they do not have the required performance in simulation, due to the reduced number of anchorages. On the other hand the walls are more rigid by nature so the deformation is less than with the columns. Also the resistance of the walls to the shear force of the base is by nature greater than that of the small cross section of the column. All of these coefficients that are absent from the simulation distort the results. Another serious comparison factor between my method and the trampled method which was ignored in the simulation, is the high tensile strength of the steel and the low shear strength of the concrete which contribute to the premature rupture of the concrete overlap and the , which destroys the cooperation of concrete and steel in the mechanism of relevance. In the pre-tensioning of my method there is no relevance so neither is this problem. Of course, the increase in the capacity of the foundation soil was completely ignored.
My research is multidimensional. It consists of three different fields of research. For this reason you need a lot of money, time, knowledge of science and above all a lot of patience. Nobody finances my research because they can not assess the risk of investing without having this knowledge that I have gained from my 14 years of research and of course they must be rich. Many times money and knowledge do not go together, although in research it is a necessary condition to have both in order to have results. Conduct.. 1) Research on the response of the structure to seismic shifts with and without my method. 2) I investigate..The response of the foundation ground to static and seismic loads, with and without the anchoring mechanism. 3) I investigate The design of the appropriate anchoring mechanism so that it can withstand the calculated traction loads, and has the ability to improve by compacting different quality soils They are three different researches ... (Civil engineering research, Geological engineering research, Mechanical engineering research) ... with one purpose. To make the constructions in the earthquake cheaper and stronger.
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