Science topic

Fixatives - Science topic

Fixatives are agents employed in the preparation of histologic or pathologic specimens for the purpose of maintaining the existing form and structure of all of the constituent elements. Great numbers of different agents are used; some are also decalcifying and hardening agents. They must quickly kill and coagulate living tissue.
Questions related to Fixatives
  • asked a question related to Fixatives
Question
1 answer
NOTE 1 [file ions.mdp]:
With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
that with the Verlet scheme, nstlist has no effect on the accuracy of
your simulation.
Setting the LD random seed to -397045813
Generated 100474 of the 100576 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 66298 of the 100576 1-4 parameter combinations
Relevant answer
Answer
The error message you're seeing from `ions.mdp` is a **warning rather than a fatal error**, meaning your simulation can likely still run, but optimizing `nstlist` may improve performance.
Here's what the message indicates and how to fix it:
1. **Understanding `nstlist`**:
- `nstlist` is the frequency (in steps) at which the neighbor list is updated in a molecular dynamics simulation. With the Verlet integration scheme, `nstlist` does not impact accuracy, but a higher value can improve simulation performance by reducing the frequency of neighbor list updates.
- GROMACS recommends setting `nstlist` to `>= 10` for CPU-only runs and `>= 20` for GPU-accelerated runs.
2. **Modifying `nstlist` in `ions.mdp`**:
- Open `ions.mdp` (or your main `.mdp` file if you’re including it differently) and locate the `nstlist` parameter.
- Update the line to reflect a recommended setting. For example:
```plaintext
nstlist = 20
```
This value is recommended for GPU use. For CPU-only runs, you can set `nstlist = 10`.
3. **Explanation of Other Notes**:
- The other lines (random seed, non-bonded and 1-4 interactions) indicate that GROMACS is initializing parameters for your simulation. They’re informational and confirm that certain interaction combinations are generated properly.
After adjusting `nstlist`, re-run the `grompp` command to process your `.mdp` file again:
```bash
gmx grompp -f ions.mdp -c system.gro -p topol.top -o ions.tpr
```
  • asked a question related to Fixatives
Question
3 answers
Do climate changes cause a decrease in the amount of annual rainfall in dry areas, or do they cause a change in the fluctuation of the dates and intensity of rains? as we notice an increase in cases of floods and torrential torrents in those areas? This leads to the question of the rain isolines, whether they are fixed or variable as a result of the severity of climate changes?
Relevant answer
Answer
There are dust clouds which has created deserts from western India to Morocco for the last 2,000-5,500 years, that you can read about at https://www.ecoseeds.com/cool.html
What the dust in the air does, is it changes the dew point, so that moisture cannot form rain clouds. The other thing it does, is forms a wall against rain clouds, so they stall and pour rain on that barrier. This dust cloud is so strong, it can stop Category-5 cyclones like GONU you can see at https://www.ecoseeds.com/GONU.html
However, since 1985, the amount of moisture in the air has increase due to Global Warming, so that is cancelling out the effects of the dust. In the past in Arabia, the torrential rains used to happen every few centuries. Now if is several times a year, that you can read about at https://www.ecoseeds.com/cool2.html
By replanting the local native grasses, wildflowers and trees, that insulates the land and settles the dust, so that the dew point can change and produce gentle rains instead of torrential flood. Also, by cloud seeding on a weekly basis, then the rain clouds and moisture can be dispersed and directed somewhat and keep it moving instead of flooding a particular spot.
We have been having four years of discussions about this issue at https://www.researchgate.net/post/How_we_can_reach_the_food_security_in_country_90_is_desert
Image of the "Pakistan-Arabia Dust Cloud" trapping a cyclone last year.
  • asked a question related to Fixatives
Question
4 answers
Can orthodontic treatment fix black triangles in teeth?
Relevant answer
Answer
yes of course
  • asked a question related to Fixatives
Question
4 answers
Human understanding includes different types of thinking, including growth and fixed mindset, analytical cognitions, past or present-oriented observations, and future-thinking notions. In your opinion, what is future-thinking mindset?
Relevant answer
Answer
Dear Doctor
Go To
When the new normal is a no-show: Why future-mindedness is the mindset organizations need now
By Maggie Wooll, MBA
January 24, 2022
BetterUp
[Being future-minded is a mindset that balances optimistic action with thoughtful pragmatism in order to imagine and envision possible futures. It is a form of preparation to ready ourselves for what comes next.
Future-mindedness is optimistic. It isn’t that the world is rosy, that positivity is the answer, or that “everything will just work out.”
Action-oriented optimism includes:
  • Deliberately looking for upside and possibility and orienting toward finding opportunity.
  • Having confidence about our ability to take action and shape outcomes.
Future-mindedness is pragmatic. This means acknowledging that unknown events beyond our control will likely change the situation and thinking through what that might look like.
Thoughtful pragmatism includes:
  • Creating space to reflect and question what could change to upend a plan or invalidate the current goal.
  • Considering how you might respond and what happens next.
The future-minded are flexible to change, skilled at planning, imagining outcomes, setting goals, and executing flexibly. People high in future-mindedness also tend to be high in resilience, self-efficacy, cognitive agility, and optimism.]
  • asked a question related to Fixatives
Question
4 answers
Despite going through available literature and getting a basic understanding of how Kernel Density Estimation works when analysing home ranges, I cannot make my Biotas works. Does anybody know about some more detailed guidelines/manuals/training videos etc., for Biotas? Provided manual on their website says very little about navigating within the software and setting required parameters. For instance, choosing a window with (LSCV), I have no idea what units are represented there. In my case, I have a limited dataset, let's say less than 100 GPS fixes of the Little owl, which moves on a small scale. Moreover, it roosts often on the same spots; therefore, my points are dense and sometimes even overlaid. I would like to avoid manipulating hard data and exclude those overlaying points from analyses because I still think they have important information value. Would it be still possible to make a fixed KDE with LSCV under such conditions?
Any help will be highly appreciated. Thx a lot.
Relevant answer
i just come across to your question which is i also have difficulty in using this software. Have you get your solution? Tomáš Bušina
  • asked a question related to Fixatives
Question
2 answers
Hi!
I plan on doing a JC-10 MMP assay and would like to know if I can add it to my flow cytometry panel. My protocol includes surface and intracellular staining (Fix/Perm Foxp3 eBioscience kit). I know JC-10 only works on live cells. I plan to first incubate the cells with the JC-10 reagents (as recommended by the manufacturer) and then do my regular flow protocol on these cells to ultimately run them on the cytometer.
Would the fix/perm step interfere with the JC-10 assay? Should I run the JC-10 assay separately from my flow panel?
Thanks!
Relevant answer
Answer
I am not an expert in this field, but I am very interested and have researched to find an answer. I received some assistance from tlooto.com for this response. Could you please review the response below to see if it is correct?
The JC-10 MMP assay is designed for live cell analysis and is sensitive to changes in mitochondrial membrane potential. The fixation and permeabilization steps in your flow cytometry protocol could disrupt the mitochondrial membrane potential, leading to inaccurate JC-10 results. Fixation generally causes JC-10 to lose its function, as it relies on intact mitochondrial membranes for accurate readings [1][2]. It is recommended to perform the JC-10 assay separately from your intracellular staining protocol. First, measure mitochondrial membrane potential in live cells using JC-10. Then, in a separate experiment, conduct surface and intracellular staining after fixation and permeabilization to ensure accurate assessments of both mitochondrial function and intracellular markers without interference.
Reference
[1]
Cossarizza, A., Baccarani-Contri, M., Kalashnikova, G., & Franceschi, C. (1993). A new method for the cytofluorimetric analysis of mitochondrial membrane potential using the J-aggregate forming lipophilic cation 5,5',6,6'-tetrachloro-1,1',3,3'-tetraethylbenzimidazolcarbocyanine iodide (JC-1). Biochemical and Biophysical Research Communications, 197(1), 40-5.
[2]
Marcondes, N., Terra, S., Lasta, C. S., Hlavac, N., Dalmolin, M. L., Lacerda, L., Faulhaber, G., & González, F. (2018). Comparison of JC‐1 and MitoTracker probes for mitochondrial viability assessment in stored canine platelet concentrates: A flow cytometry study. Cytometry Part A, 95.
  • asked a question related to Fixatives
Question
3 answers
Banach's Fixed Point Theorem (also known as Contraction Mapping Theorem) can be applied to prove the existence and uniqueness of solutions to differential equations with boundary conditions by transforming the differential equation into a fixed-point problem in an appropriate function space.
what are the key steps of this process?
Relevant answer
Answer
Fixed point theorems have been a useful tool for proving existence of solutions in differential equations. Below is an example.
This uses the Tychonoff which is more general than the Contraction principle which requires a Banach space.
The key process is to define a mapping that associates with a function y a solution x. This mapping is constructed as such that the fixed point is the solution one seeks.
  • asked a question related to Fixatives
Question
1 answer
Hi everyone
I accidently deleted the cas.h5 file about a simulation of CFD. I recovered file by Recuva and when I opened it this error appeared. How can i fix this error.
Thanks everyone
Relevant answer
Answer
To open a recovered cas.h5 file, you typically need to use a programming language or software that supports HDF5 files, as .h5 is the file extension for HDF5 (Hierarchical Data Format version 5). Here are some common ways to open and work with this file:
Using Python with H5py
  1. Install H5py: If you haven't already, install the h5py library using pip:Copybashpip install h5py
  2. Open the File: You can read the contents of the file using the following Python code:Copypythonimport h5py # Replace 'path/to/cas.h5' with the actual path to your file with h5py.File('path/to/cas.h5', 'r') as file: # List all groups print("Keys: %s" % file.keys()) # Access a dataset dataset = file['your_dataset_name'] # Replace with your actual dataset name data = dataset[:] print(data)
Using HDFView
  1. Download HDFView: You can download
  • asked a question related to Fixatives
Question
1 answer
Relative Permeability (RP): Has anything to do with Darcy’s Law?
RP: Most important and least understood property (we only have a limited number of well-characterized studies on RP)
RP: Manifestation of complicated pore-level displacement physics along with the characteristics of fluid-fluid and fluid-solid interactions
RP: The actual measurement poses a real challenge
(a)By using laboratory-scale experiments using representative rock-fluid systems
(3-phase RP is almost exorbitantly difficult, costly & time-consuming);
(For a given rock-fluid system and under fixed experimental conditions, RPs are not unique functions of phase saturations, but would depend upon saturation history)
(The problem of saturation history in 3-phase flows is more convoluted since there are 2 independent phase saturations, increasing the number of process paths significantly)
(We have more than 2 saturation histories in 3-phase flow, as the saturation of each phase may increase, or, decrease, or, may remain unchanged) OR,
(b) By using Empirical Correlations; OR,
(c) By using Physically-based Pore-Scale Models
(d) (b) & (c) require high-quality experimental data for development and validation
Even if we assume the Reservoir to be Water-Wet, RP of the most wetting-phase remains to be independent of saturation history, however, the RPs of the intermediate-wetting and the most non-wetting phases remain significantly affected by saturation history.
Relevant answer
Answer
Yes, relative permeability (RP) is closely related to Darcy’s Law when describing fluid flow in porous media, particularly in multiphase flow systems (e.g., oil, water, and gas in a reservoir).
  • asked a question related to Fixatives
Question
2 answers
Hello everyone, I am using overset mesh for a FSI case, and since the simulation takes a long time, I occasionally have to cancel and restart it from the latest time step. However, when I restart, the airfoil's center of mass reverts to its initial position rather than continuing from the last position before stopping. Has anyone encountered a similar issue or know of a solution? I have attached the vertical movement of the airfoil for both the uninterrupted case and the situation where the simulation was restarted.
Relevant answer
Answer
Dear Ahmed Raafat, Thank you for your response. I tried using 'correctPhi yes;' but the moving mesh still returns to its original location and restarts the simulation from there. I came across this post "https://www.cfd-online.com/Forums/openfoam-solving/253014-restart-overset-simulation-latest-time.html" on CFD-Online: Restarting an Overset Simulation from the Latest Time, which seems to provide the only solution to this issue. However, it involves multiple steps to properly restart the Overset mesh.
  • asked a question related to Fixatives
Question
2 answers
Hello everyone,
I am planning to apply a two-stage DEA model to assess the efficiency of banks. For Stage 1, the input variables include number of employees, total fixed assets, and total operating expenses. The output of Stage 1 and input of Stage 2 are total deposits and total loans. Finally, the outputs of Stage 2 are interest income, non-interest income, and non-performing loans.
I am aware that there are several approaches to selecting variables for a DEA model, such as the intermediation approach, production approach, and profitability approach... among others. However, I am unsure which approach best fits the way I have chosen the variables for the two stages of my DEA model. Could anyone suggest which approach I am following with this variable selection and how I should frame it in my research?
I would greatly appreciate any help or suggestions. Thank you!
Relevant answer
Answer
Samira Akter Tumpa Thank you for your recommendation :)
  • asked a question related to Fixatives
Question
1 answer
The Problems with Layering Anterior Composites and How to Fix Them ?
Relevant answer
Answer
When I first implemented layered anterior composites into my practice, I would frequently finish a case and think to myself, “Oh gawd, this looks terrible.” It took me a while before I figured out why my restorations were not turning out like I had planned. As I practiced, I noticed a few common themes with my technique and eventually learned how to correct my mistakes.
In this article, I share the lessons I learned with the hope to save you a lot of time and heartache. I've found that layering anterior composites make me happy. And isn't life just better when your schedule is stacked with the procedures that make you happy?
From choosing the wrong shade to trying to get too fancy, let's review the most common reasons anterior composites don't turn out quite right, what happened clinically, and how to fix them. The best part is you don't have to start over completely.
Problem No. 1: There's a visible line,Problem No. 2: It's too opaque,Problem No. 3: It's too dark,Problem No. 4: Too much or too little characterization,Problem No. 5: It still looks fake,Problem No. 6: Too grey,Problem No. 7: There's a *&%$! void.
Layering composite in the esthetic zone is an advanced clinical skill that takes practice. Take it easy on yourself and try to have fun learning from your mistakes. Hope this helps
  • asked a question related to Fixatives
Question
2 answers
Hello. When trying to record CV, after the voltage transitions to the negative region, a sharp jump in current is observed. Increasing the concentration of electrolyte, analyte, or electrode area does not help. Sweep speed 100 mV/s, electrolyte concentration 0.1 M. What could be causing this phenomenon and how can I fix it?
Relevant answer
Answer
Igor Lavrentev What solvent and electrodes do you use? Are you bubbling the solution with argon?
  • asked a question related to Fixatives
Question
1 answer
The last author on my recent publication (intra-arterial verapamil vs. nicardipine) is wrong? Can you please update/change this? The author is listed correctly in pubmed, thanks!
Keshav Patel
Relevant answer
Answer
Go to the article page here on ResearchGate platform, and then edit the author's list. Here is a procedure regarding adding, editing, and removing co-author information:
  • asked a question related to Fixatives
Question
2 answers
To induce polarization and study of drain current.
Relevant answer
Answer
Hello Lakhmikanta Mishra
You can add interface charge density at the junction of two region.Must define x and y region. you can use following syntax in SILVACO TCAD
interface qf=1e13 x.min=3 x.max=4 y.min=0.057 y.max=0.057
  • asked a question related to Fixatives
Question
2 answers
What causes some stars to appear fixed while others seem to move across the night sky and stars appear very bright in the sky?
Relevant answer
Answer
Dr Himanshu Tiwari thank you for your contribution to the discussion
  • asked a question related to Fixatives
Question
2 answers
Can anyone lease tell me what is the best way to attach agarose beads on a cover glass so that it doesn't move from it's place? Is there any coating material that can hold the beads in it's place?
Relevant answer
Answer
Fixing protein-coated agarose beads on a cover glass is a technique used in various cell biology and biochemistry applications, such as imaging or interaction studies. Here's a step-by-step protocol to help you with this process:
### **Materials Needed:**
1. **Protein-coated agarose beads**
2. **Cover glasses**
3. **Microscope slides**
4. **Fixative solution** (e.g., 0.5% glutaraldehyde or 4% paraformaldehyde in PBS)
5. **Blocking solution** (optional, such as 1-5% BSA in PBS)
6. **PBS (Phosphate-Buffered Saline)**
7. **Mounting medium** (if necessary, depending on your subsequent applications)
8. **Clean pipette tips and tools**
### **Procedure:**
**1. Preparation:**
- **Clean the cover glasses** thoroughly to ensure they are free of dust or contaminants. You can wash them with soap and water, rinse with distilled water, and then sterilize them if needed (e.g., autoclaving or using ethanol).
**2. Prepare the Fixative:**
- If you are using a fixative like **glutaraldehyde** or **paraformaldehyde**, prepare a fresh solution according to your experimental requirements. Typically, a fixative concentration of 0.5% glutaraldehyde or 4% paraformaldehyde in PBS is used.
**3. Coat the Cover Glasses:**
- Place the clean cover glasses on a clean, flat surface (e.g., a sterile Petri dish or a microscope slide).
**4. Apply Beads:**
- Pipette a small volume of the **protein-coated agarose beads** solution directly onto the cover glass. Spread the beads evenly to ensure they form a monolayer or a suitable pattern, depending on your experimental needs.
**5. Fix the Beads:**
- Carefully add enough of the **fixative solution** to cover the beads on the cover glass. Incubate for **10-20 minutes** at room temperature or according to your experimental protocol.
- **Note:** The fixation time might vary depending on the type of fixative and the beads’ surface coating. Check the beads' stability and the fixation's effectiveness.
**6. Wash:**
- After fixation, gently rinse the cover glasses with **PBS** to remove excess fixative. This step helps to reduce background and ensures that the fixative does not interfere with subsequent applications.
**7. Block (if necessary):**
- If you need to block non-specific binding sites, apply a **blocking solution** (e.g., 1-5% BSA in PBS) to the cover glasses and incubate for **30 minutes** at room temperature. This step is optional and depends on the nature of your experiment.
**8. Mount (if applicable):**
- If you need to mount the cover glasses for microscopy or other analyses, you can use a suitable **mounting medium**. Ensure that the medium does not affect the beads or their coating.
**9. Proceed with Analysis:**
- Once the beads are fixed and, if applicable, blocked and mounted, proceed with your imaging or other experimental procedures.
### **Troubleshooting:**
- **Bead Detachment:** If beads are not sticking properly, consider increasing the concentration of fixative or optimizing the fixation time. Ensure that the beads are thoroughly coated and prepared before application.
- **Background Issues:** If you encounter high background or non-specific signals, optimize your blocking conditions or use more stringent washing steps.
- **Bead Aggregation:** To avoid bead aggregation, ensure they are well-dispersed in the solution before applying them to the cover glass. Gentle pipetting or mixing can help achieve a uniform distribution.
By following this protocol, you should be able to successfully fix protein-coated agarose beads onto cover glasses for subsequent analysis and imaging.
Thank you,
Best Regards,
Dr. Lenin Kumar B
  • asked a question related to Fixatives
Question
1 answer
Dear researchers
I have salmonella Florenced labeled bacteria and want to do invasion (caco2 and LMH cells) and then fixing for evaluating with microscope
I have problem in fixing could you please let me know about the best protocol which solve my problem and successfully fixed the cells
Thank alot in advance
Cheers
Relevant answer
Answer
Cell fixatation Protocol for Salmonella invasion assay. following this protocol, you should be able to achieve consistent and high-quality fixation of your cells, allowing you to accurately assess the invasion and cellular interactions with Salmonella.
Thank you.
  • asked a question related to Fixatives
Question
6 answers
What would happen if nitrogen-fixing plants could no longer fix nitrogen from the atmosphere and what would happen if nitrogen-fixing bacteria disappeared?
Relevant answer
Answer
If this will not take place then organisms will not be able to grow and function properly, they will start showing different signs as in plants, they start to become yellowish and they produce less fruits and flowers Nitrogen will usually not be made accessible to plants in usable forms (ammonia and nitrate), limiting their growth and development. Because plants are the main producers, this can also have an impact on the entire food chain. If nitrogen-fixing plants and bacteria were no longer able to fix nitrogen from the atmosphere, organisms would not be able to grow, and the food chain would be impacted:
· Plants: Plants that are deficient in nitrogen may appear pale or yellowish, and produce fewer flowers and fruits. Without nitrogen fixation, plants would not be able to access nitrogen in usable forms, such as ammonia and nitrate, which are essential for their growth and development.
· Food chain: Because plants are the main producers, the lack of nitrogen fixation would impact the entire food chain.
· Soil fertility: If there are no bacteria on the roots of leguminous plants, the soil's fertility would decrease and the plants would become nitrogen deficient.
· Organisms: Most organisms are unable to use atmospheric nitrogen directly. Without nitrogen fixation, the chemicals necessary for the structural and functional growth of organisms would not be generated.
· Symbiotic relationships: If nitrogen fixation does not occur, the symbiotic relationships between some nitrogen-fixing bacteria and plant groups like legumes would stop functioning.
Organisms are unable to grow in the absence of nitrogen fixation. Plants that are deficient in nitrogen appear pale or yellowish. They produce quite fewer flowers & fruits than other plants.
  • asked a question related to Fixatives
Question
4 answers
Application of neural networks in shape prediction
Is there a fixed code used in shape prediction in neural networks?
Relevant answer
Answer
The persistent diagram (from persistent homology) can be used to get a vector that can uniquely encode shape information. check readme of this repo : https://github.com/GUDHI/TDA-tutorial/tree/master
  • asked a question related to Fixatives
Question
1 answer
I fixed it with 4% paraformaldehyde and then stained it with DAPI.
Relevant answer
It’s high chance that it’s mycoplasma contamination. If you want to be sure, you should perform PCR using any commercial kits or some antigen test kits as well. But judging from the clear fluorescence around the nucleus, it’s better to assume that it is mycoplasma contaminated and to throw out this particular cell stock.
  • asked a question related to Fixatives
Question
2 answers
Hi everyone, I'm currently working on an autodock4 and I've received those warning in my running process. I don't know how to fix or how it affects to my final results. Attached below are my dpf file and cmd warning.
Thanks for your advices.
Relevant answer
Answer
  • asked a question related to Fixatives
Question
2 answers
seti or search of intelgenece articial nee to be fixed due to masss solar systems outhere thta expelled laser beam light ollimated wel beign so is neede to modificated the seti in a new device of armenta velasquez like radi ho can detect the laser signals
Relevant answer
Answer
SETI (Search for Extraterrestrial Intelligence) does not need to be fixed exclusively on radio-collimated signals, but radio waves are a primary focus because they can travel vast distances through space with minimal interference. However, SETI also explores other methods, including optical and infrared signals, to broaden the search for potential extraterrestrial communications.
  • asked a question related to Fixatives
Question
3 answers
In the fight against global warming, does the biochar really have the capacity to absorb more carbon than it takes to produce it and biochar help fix climate change?
Relevant answer
Answer
Yes, biochar can sequester more carbon over its lifetime than is released during its production. Biochar is an eco-friendly adsorbent made from natural biomass or agricultural waste that contains 35–95% carbon. During production, 50% of the original carbon in the biomass is captured and stored in the biochar. When added to soil, biochar can also capture carbon that would otherwise return to the atmosphere as CO2. Biochar can lock carbon in the soil for centuries, acting as a carbon sink and helping to fight climate change. biochar can help address climate change. Biochar is a carbon removal technique that can help reduce carbon dioxide (CO2) emissions, the main greenhouse gas that humans have added to the atmosphere and that contributes to climate change. Biochar can be used in soils to help grow crops and enhance soil fertility. When buried in the ground, the carbon in biochar can remain in the soil for hundreds or thousands of years, which can help create a "carbon negative" system. Biochar has the potential to absorb more carbon than it takes to produce it and could help reduce global emissions. There are many ways to fight global warming, including individual actions, government and business pressure, and conservation-based solutions:
· Carbon sequestration
Biochar removes carbon from the active cycle of the atmosphere and stores it in the inactive carbon cycle. This can help displace fossil fuel-based fertilizers, which release nitrous oxide, a greenhouse gas that's 310 times more potent than CO2.
· Soil fertility
Biochar can improve soil fertility, which can make agriculture more sustainable.
· Water retention
Biochar can help improve water retention in soil.
· Fuel byproducts
Sustainable biochar practices can also produce fuel byproducts that can provide clean, renewable energy.
· Individual actions
· Reduce energy use: Use LED light bulbs, energy-efficient appliances, and adjust your thermostat. You can also wash your laundry in cold water and hang things to dry instead of using a dryer.
· Change your transportation: Walk, bike, take public transportation, or carpool when possible. You can also consider taking a train or bus for longer distances.
· Change your diet: Eat more vegetables and plant-based meals, and consider shifting from a mixed to a vegetarian diet.
· Shop local and buy sustainable: Buy local and seasonal foods, and avoid products with a lot of packaging.
· Government and business pressure
Pressure governments and businesses to keep fossil fuels in the ground, invest in renewable energy, and switch to sustainable transportation.
· Conservation-based solutions
Restore nature to absorb more carbon, protect forests and oceans, and create marine protected areas.
Due to its aromatic content, biochar can persist in the environment for an extended period and absorb greenhouse gases (GHG). Each year, biochar effectively captures an estimated amount of CO2 ranging from 1 to 35 gigatons (GtCO2) and 78 to 477 GtCO2 over this century. However, the amount of carbon biochar sequesters depends on several factors, including the feedstock used, the pyrolysis process, and how the biochar is managed. As biochar with a high surface area and porosity has a higher adsorption capacity. The surface functional groups on biochar are also important, and are controlled by the biomass and temperature used during production. To maximize the benefits of biochar while minimizing any potential drawbacks, it's important to consider ethical concerns about land usage and biomass sources, as well as responsible production practices. But where charcoal is used for cooking and heat, biochar is used in soils to help grow crops. It can also help address climate change. Biochar is one of several “carbon removal” techniques that target carbon dioxide (CO2), the most important climate-warming greenhouse gas humans have been adding to the atmosphere. Eating more vegetables, fruits, whole grains, legumes, nuts, and seeds, and less meat and dairy, can significantly lower your environmental impact. Producing plant-based foods generally results in fewer greenhouse gas emissions and requires less energy, land, and water.
  • asked a question related to Fixatives
Question
2 answers
I've trimmed my sequences in Geneious, exported them as fasta documents, and imported them into fasta. I'd like to use Mesquite to align my sequences. To do so, I downloaded Muscle align from Github and keep running into this error: MUSCLE Align quit, possibly because of an error (1). Please examine StandardOutputFile and StandardErrorFile in the analysis directory for information.
The StandErrorFile says :
Invalid command line
Unknown option in
Help appreciated!
Relevant answer
Answer
Yeah, I had to go download an older version from github. Not sure if messaging is allowed here but I can send it to you if you need.
  • asked a question related to Fixatives
Question
2 answers
I am looking to stain live Saccharomyces cerevisiae cells using DAPI (Thermo cat # 62248) but have currently been unsuccessful. Does anyone have a protocol to stain these cells without having to fix them using either DAPI or Hoechst, I want to be able to visualize the nucleus in live cell? Also does it matter if you use DAPI or Hoechst, is one better than the other?
Relevant answer
Answer
May consider using Permai fluorescence dye.
  • asked a question related to Fixatives
Question
4 answers
I need to Postfix mice brains. I slice the brains using microtome at 40 microns. These are Postnatal days 7, 11, 14, and 21. I am using half the brain for other analysis, so I need to fresh freeze it while the other half is fixed.
What should be the best protocol to follow?
Relevant answer
Answer
thank you so much for the feedback :)
  • asked a question related to Fixatives
Question
2 answers
Hey..I want to start electrocatalysis for small molecule activation, but the problem is that I am not getting that how do I fix the scan rate. I read some literature where in some of them people are keeping 0.1 V/s, somewhere 0.05 V/s, or somewhere 1.0 V/s, hence I am confused.
Kindly help me in this regard.
Thanks for giving your valuable time and considerations.
Relevant answer
Answer
Hi,
You should explore the electrochemical response of your catalyst/material at varying scan rates, as the CVs will provide different information depending on the time scale of your experiments. Please refer to specialized textbooks for more details (e.g. those by Bard or Savéant).
Besides, the choice of the scan rate for meaningful CVs to display in a main text figure will also depend on your system, and benchmarking based only on this variable is not easy, and not always useful.
Hope it helps!
  • asked a question related to Fixatives
Question
2 answers
How do we fix the appearing problem in VNA? The attached window appears during the calibration, and in the end, the measurement results cannot be viewed.
Relevant answer
Answer
1. **Check the VNA software version and update if necessary**: Ensure that you are using the latest version of the VNA software, as updates often include bug fixes and improvements.
2. **Verify the VNA hardware connections**: Ensure that all the cables and connections to the VNA are secure and properly connected. Check for any damaged or loose connections.
3. **Perform a full reset of the VNA**: Power off the VNA, wait a few seconds, and then power it back on. This can sometimes resolve software-related issues.
4. **Check for any interference or environmental factors**: Ensure that the VNA is placed in a suitable environment, away from any potential sources of interference, such as other electronic devices or electromagnetic fields.
5. **Calibrate the VNA properly**: Carefully follow the calibration process as per the manufacturer's instructions. Ensure that the calibration standards are in good condition and that the calibration is performed correctly.
6. **Check the VNA settings**: Verify that the VNA settings, such as the frequency range, power level, and measurement parameters, are configured correctly for your specific application.
7. **Consult the VNA manufacturer's support**: If the issue persists, contact the VNA manufacturer's support team. They may be able to provide more specific guidance or identify any known issues with the VNA model you are using.
good luck; partial credit ai
  • asked a question related to Fixatives
Question
1 answer
I want to fix it to run APEA, the problem is when I run the APEA in the heater give me a error, but the temperatura difference is about 160 F.
Someone can help me?
The simulation is in Hysys
Excuse me about my English language skills
Relevant answer
Answer
May I ask if you have solved this problem? How did you solve it?
  • asked a question related to Fixatives
Question
7 answers
For a grid connected BESS (lets say 100 MW/200 MWh system, LFP battery), if we charge the BESS in such a way that whenever we can access power from the solar that will charge the BESS. Hence it can be like, the BESS can have 10 partial charging and 10 partial discharging per day. Instead of direct 2 hours of fixed charging and 2 hours of fixed discharging, does these sort of continuous partial charge-discharge do any harm to the BESS in terms of degradation, performance, or any other technical issue?
Look forward to your answer. Thanks in advance.
Relevant answer
Answer
Hi Shaikat Debnath
YOU: It gives me a proper idea about the basic philosophy of the degradation
I think that a damage philosophy that has been successfully applied to many other problems would be useful for batteries. This philosophy has different levels with :
- evaluating publications by their size, statistical power and impact on resources. This is a quantitative method that avoids over-evaluating studies and multiplying work in uncertain directions.
- the collection of observations relating to damage processes that are linked to fundamental physical-chemical processes,
- the search for an experimental damage law,
- transforming this law into an equation of state that links the factors of the damage law to the parameters of a reliability law.
- the final stage is the choice of appropriate characterization methods.
YOU :Is there any simple model or equation that would give an approximate idea about the percentage of the battery degradation?
A very simple calculation gives the lifetime of a battery as a function of its operating history. However, I don't share this calculation with you, as it would be impossible to understand without understanding the damage mechanism. It is very simple to understand, but there are many forks in the road.
I am in the process of completing some training material which will be available in about two months.
YOU: Would love to get referred to any paper as well.
Bibliographic research has not so far been able to find any precedence for this approach.
YOU :Does continues partial charging/discharging do any harm to the BESS performance and degradation?
You will find a damage law in the field of partial discharges, but it has not been proven as such and its explanations are not physical chemistry.
I hope these comments will encourage you to follow your intuition.
Claude
  • asked a question related to Fixatives
Question
4 answers
Hi users,  I want to create an itp file for my ligand (ligand with ruthenium) complex, im using MCPB.Py for generating itp for my structure during the process i got the following error kindly please help. MCPB.py -i dna.in -s 3 The input file you are using is : dna.in The following is the input variable you have: The variable ion_ids is :  [1201] The variable ion_info is :  [] The variable ion_mol2files is :  ['Ru.mol2'] The variable original_pdb is :  complex_fixed_h.pdb The variable add_bonded_pairs is :  [] The variable add_redcrd is :  0 The variable additional_resids is :  [] The variable anglefc_avg is :  0 The variable bondfc_avg is :  0 The variable chgfix_resids is :  [] The variable cut_off is :  2.8 The variable force_field is :  ff19SB The variable frcmod_files is :  ['LIG.frcmod'] The variable gaff is :  1 The variable group_name is :  dna The variable ion_paraset is :  12_6 (Only for the ions using the nonbonded model). The variable large_opt is :  1 The variable lgmodel_chg is :  -99 The variable lgmodel_spin is :  -99              -99 means program will assign a charge automatically. The variable naa_mol2files is :  ['LIG.mol2'] The variable scale_factor is :  1.0              ATTENTION: This is the scale factor of frequency. The              force constants will be scaled by multiplying the square              of scale_factor. The variable smmodel_chg is :  -99 The variable smmodel_spin is :  -99              -99 means program will assign a charge automatically. The variable software_version is :  gau The variable sqm_opt is :  0 The variable water_model is :  OPC The variable xstru is :  0 ****************************************************************** *                                                                * *======================RESP Charge fitting=======================* *                                                                * ****************************************************************** ***Generating the 1st stage resp charge fitting input file... ***Generating the 2nd stage resp charge fitting input file... ***Doing the RESP charge fiting... =========================Checking models========================== ***Check the large model... Good. The charges and atom numbers are match for the large model. Good. There are 27 atoms in the large model. ***Check the standard model... Traceback (most recent call last):   File "/home/saranya/amber20/bin/MCPB.py", line 692, in <module>     resp_fitting(stpdbf, lgpdbf, stfpf, lgfpf, mklogf, ionids, ff_choice,   File "/home/saranya/amber20/lib/python3.9/site-packages/pymsmt/mcpb/resp_fitting.py", line 521, in resp_fitting     raise pymsmtError('Error: the charges and atom numbers are mismatch ' pymsmt.exp.pymsmtError: Error: the charges and atom numbers are mismatch for the standard model!
Relevant answer
Answer
Thank you very much, Please what will be the input file for step 3 Saranya Vasudevan
I am trying to understand the mismatch of the atoms
Thank you in advance
  • asked a question related to Fixatives
Question
3 answers
I have calculated maximum debonding force between sma fiber and epoxy for a fixed interfacial shear strength but in one paper author plotted interfacial bond strength. Can anyone tell me how to get interfacial bond strength in ansys
Relevant answer
Answer
Hi Kartikeya,
I'm still a bit uncertain about the data. Let me make some comments and see if they help. The relate to the attached picture.
  • Let's say that there is a stress distribution along the interface between the SMA fibre and the epoxy.
  • Let's say that the whole interface fails when the peak value of the stress distribution reaches a critical level (called the "strength").
  • Under these circumstances, we are assuming that the peak value of the stress distribution along of the interface at failure would be independent of bond length because it is a "material property".
  • It is possible that the "average" joint line stress determined by the failure load divided by the joint line area is not independent of joint line length because the stress distribution is non-uniform. It is possible that most of the load is carried by the first bit of the fibre and longer fibres do not carry much load at positions away from the top of the interface. If so, the average stress would reduce with interface length. This would show that the average stress on fibre interface at failure is not a "material property".
Regards,
Simon
  • asked a question related to Fixatives
Question
4 answers
Hi everyone,
I ran a Generalised Linear Mixed Model to see if an intervention condition (video 1, video 2, control) had any impact on an outcome measure across time (baseline, immediate post-test and follow-up). I am having trouble interpreting the Fixed Coefficients table. Can anyone help?
Also, why are the last four lines empty?
Thanks in advance!
Relevant answer
Answer
Alexander Pabst I would add that the first thing to do is a likelihood ratio test to see if having the fixed effects in the model was better fitting than a model without them. I see that the two of the interaction terms may be significant but that's contingent on the overall system of variables being 'significant'. Personally I don't use Wald tests, their approximation sometimes isn't very good. I would use stepwise LRT to determine whether a term (or system of terms) should be included in the model (although for some situations in a mixed model one needs to use something like the BIC).
  • asked a question related to Fixatives
Question
3 answers
Hello, I am trying to fix Pseudomonas aeruginosa PAO1 cells with 4% formaldehyde for 20-30 minutes (on ice and in the dark) for fluorescent microscopy. I am attempting to stain the DNA and outer membrane, but have not been successful with this fixation method. The dyes give weak signals and appear to be exported out, suggesting the bacteria are not completely fixed with formaldehyde. Does anyone have a reliable protocol for PAO1 fixation, including concentration, time, quenching, etc.? Any help would be greatly appreciated.
Relevant answer
Answer
Unfortunately all of my work has been on mammalian lines.
Good luck with the fixation
  • asked a question related to Fixatives
Question
2 answers
how to fix this error,
from phq_readin : error # 1
DFPT with the Blochl correction is not implemented
I am attaching my ph.in file.
Relevant answer
Answer
Dear Shehla Rao
It seems ph.x calculation does not have the ability to read the output file of SCF calculation.
I suggest to recompile Quantum espresso to solve the problem.
  • asked a question related to Fixatives
Question
2 answers
Hi everyone
I have got this test in a fixed excitation and various emissions. In some wavelengths there are overflows which make the resulted analyze different from other carbon dots.
Is it normal or there are some issues?
Relevant answer
Thanks for your response.
I will consider this factors.
  • asked a question related to Fixatives
Question
3 answers
I have a problem with geo-referencing a shape file. How can I fix it when it appears in mines despite selecting WGSWGS 84 / UTM zone 38N?
Relevant answer
Answer
When working with Geographic Information Systems (GIS), specifically when using the WGS 84 / UTM zone 38N coordinate system, it's not uncommon to encounter issues where the coordinate system appears to be incorrect. Here’s a step-by-step guide to troubleshoot and fix this issue:
1. Verify Coordinate System Settings
  • Check Layer Properties: Ensure that the layer’s coordinate system is correctly set to WGS 84 / UTM zone 38N. In QGIS, for example, you can do this by right-clicking the layer, selecting "Properties," and then navigating to the "Information" or "General" tab.
  • Project CRS: Make sure the overall project is set to the same coordinate system. In QGIS, you can check this by looking at the CRS displayed in the bottom-right corner of the window or by going to "Project" > "Properties" > "CRS."
2. Re-project the Data
  • If your data was initially in a different coordinate system, you might need to re-project it. In QGIS, you can do this by right-clicking the layer and selecting "Export" > "Save Features As." In the CRS section, choose WGS 84 / UTM zone 38N.
3. Check for CRS Conflicts
  • Sometimes, a layer might have a CRS assigned that does not match the actual coordinates. In such cases, re-assigning the CRS without re-projecting can fix the issue. To do this in QGIS, right-click the layer, select "Set Layer CRS," and choose the correct CRS.
4. Examine Data Integrity
  • Ensure that your data points are within the expected geographic area for UTM zone 38N. Data that appears outside of this zone might indicate a problem with the initial data import or incorrect CRS assignment.
5. Review Import/Export Processes
  • If you are importing data from external sources (e.g., shapefiles, CSVs), make sure that the import process correctly interprets the coordinate system. Double-check the import settings and ensure the CRS is explicitly defined.
6. Use CRS Transformation Tools
  • Utilize GIS tools designed to handle CRS transformations. In QGIS, the "Reproject Layer" tool under the "Vector" menu can be useful. This tool allows you to transform the layer’s CRS to match the project CRS.
7. Consult Software Documentation
  • Refer to the documentation of the GIS software you are using. Different GIS platforms (e.g., QGIS, ArcGIS) have specific workflows and tools for managing CRS and projections.
8. Check for Software Updates
  • Ensure your GIS software is up-to-date. Occasionally, bugs related to CRS handling are resolved in newer versions.
Example Scenario:
Imagine you have imported a shape file that you believe is in WGS 84 / UTM zone 38N, but it appears in a different location on your map. By following the steps above, you would:
  1. Verify that the layer’s properties correctly identify it as WGS 84 / UTM zone 38N.
  2. Check the project CRS to ensure it matches.
  3. If there’s a discrepancy, re-project the data using the "Reproject Layer" tool.
  4. Confirm that the data points are in the expected geographic area for UTM zone 38N.
By systematically checking each of these aspects, you can identify and fix the issue with the coordinate system in your GIS project
  • asked a question related to Fixatives
Question
6 answers
We are currently trying to calculate the lattice thermal conductivity of several metals (Ni, Cu, Pd, Ag, Pt and Au) using the non-equilibrium Müller-Plathe method in LAMMPS. We are considering big supercells (20x20x20 unit cells, 70k+ atoms) for each elemental metal separately. The interactions between atoms are mediated by the well-known MEAM potential. The heat flux is tallied using the fix thermal/conductivity command, and temperature profiles are recorded using the compute chunk/atom and fix ave/chunk commands. Please find attached the typical input run for reference. We have successfully run this for other systems (molecular liquids governed by OPLS-AA), but for MEAM metals we found that the temperature profiles are basically erratic noise. While the lattice thermal conductivity of metals should low, we do not expect it to be completely negligible.
Is anyone aware of existing problems with the application of the Müller-Plathe method together with the MEAM potential? Is there particular requirements for such a case? We have played with the Nevery and Nswap parameters in the fix thermal/conductivity command with no success.
Thank you in advance for your attention.
*****
include "system.in.init"
read_data "system.data"
include "system.in.settings"
include "system.in.charges"
neigh_modify every 1 delay 0 check yes
variable t equal 0.001
variable T equal 298.0
variable P equal 1.013
variable s equal 5
variable c equal 10000
variable d equal $s*$c
variable kB equal 8.617333262E−5
minimize 1.0e-6 1.0e-8 1000 100000
reset_timestep 0
timestep $t
thermo_style custom step etotal temp press lx ly lz density
thermo 1000
fix 1 all nvt temp $T $T 10.0
run 500000
unfix 1
fix 2 all npt temp $T $T 10.0 iso $P $P 100.0
run 2000000
unfix 2
reset_timestep 0
thermo_style custom step etotal epair ke temp press
thermo 1000
fix 3 all nvt temp $T $T 10.0
run 10000000
unfix 3
reset_timestep 0
fix 4 all nve
fix 5 all thermal/conductivity 100 z 50
compute ke all ke/atom
variable temp atom c_ke/(1.5*${kB})
compute layers all chunk/atom bin/1d z lower 0.02 units reduced
fix MP all ave/chunk $s $c $d layers v_temp file temp.profile ave one
thermo_style custom step etotal epair ke temp press f_5
thermo 1000
run 10000000
unfix MP
unfix 5
unfix 4
Relevant answer
Answer
Dear Iván Carrillo-Berdugo,
Thank you for the answer.
Actually, I am a new user of LAMMPS, and I am trying to test thermal conductivity calculations on metals that already have defects in the lattice. For this, I am using the SNAP potential (though I can try EAM as well), but the problem remains the same. I am using the input script provided in the LAMMPS example for the Müller-Plathe method, making changes according to my metal. The variable tdiff is defined in this script.
I have the error :ERROR: Variable tdiff: Fix in variable not computed at a compatible time (src/variable.cpp:1854)
Last command: run 20000
{# sample LAMMPS input script for thermal conductivity of liquid LJ
# Muller-Plathe method via fix thermal_conductivity
# settings
variable x equal 10
variable y equal 10
variable z equal 20
variable rho equal 0.6
variable t equal 1.35
variable rc equal 2.5
#variable rho equal 0.85
#variable t equal 0.7
#variable rc equal 3.0
# setup problem
units lj
atom_style atomic
lattice fcc ${rho}
region box block 0 $x 0 $y 0 $z
create_box 1 box
create_atoms 1 box
mass 1 1.0
velocity all create $t 87287
pair_style lj/cut ${rc}
pair_coeff 1 1 1.0 1.0
neighbor 0.3 bin
neigh_modify delay 0 every 1
# 1st equilibration run
fix 1 all nvt temp $t $t 0.5
thermo 100
run 1000
velocity all scale $t
unfix 1
# 2nd equilibration run
compute ke all ke/atom
variable temp atom c_ke/1.5
fix 1 all nve
compute layers all chunk/atom bin/1d z lower 0.05 units reduced
fix 2 all ave/chunk 10 100 1000 layers v_temp file profile.mp
fix 3 all thermal/conductivity 10 z 20
variable tdiff equal f_2[11][3]-f_2[1][3]
thermo_style custom step temp epair etotal f_3 v_tdiff
thermo_modify colname f_3 E_delta colname v_tdiff dTemp_step
thermo 1000
run 20000
# thermal conductivity calculation
# reset fix thermal/conductivity to zero energy accumulation
fix 3 all thermal/conductivity 10 z 20
variable start_time equal time
variable kappa equal (f_3/(time-${start_time})/(lx*ly)/2.0)*(lz/2.0)/f_ave
fix ave all ave/time 1 1 1000 v_tdiff ave running
thermo_style custom step temp epair etotal f_3 v_tdiff f_ave
thermo_modify colname f_3 E_delta colname v_tdiff dTemp_step colname f_ave dTemp
run 20000
print "Running average thermal conductivity: $(v_kappa:%.2f)"}
  • asked a question related to Fixatives
Question
1 answer
Hi there,
I am trying to fix, stain, and image cells in mitosis with an antibody against gamma-H2AX. I do not synchronize my cells as part of my research looks at genome integrity, so I usually just grow them to a higher confluency and search for cells in metaphase or anaphase manually. I have been fixing with 4% formaldehyde at 37C for 10 minutes, and blocking with 5%BSA in TBS+0.01%Triton-X. I do this at 37C because I don't want the microtubules to depolymerize in response to cold fixative. However, I always seem to get non-specific background staining. There are a lot of little foci all over the place. I notice that they frequently colocalize with microtubules on the spindle, but I don't know why that would be happening. Would it be better if I used Ice cold methanol instead? Would this ruin any analysis I do on cells in metaphase in anaphase due to microtubule depolymerization?
Thanks!
Relevant answer
Answer
Dear Noel,
In my experience, methanol minus 20C, 6 min is better for staining microtubules. Depolymerization of MT does not occur and no additional membrane permeabilization is required before immunofluorescence staining with antibodies. It is important that the methanol temperature is no warmer than minus 20C and its volume per cover glass is at least 10 ml. I usually prerared little bottles with fixative in the evening and left it in the freezer overnight. Before fixation, I rinsed the cells on the glass with warm PBS at 37 C, and removed a drop of PBS with a filter (on the side opposite to the cells) so that it did not get into the methanol. The main thing is to prepare everything in advance and act quickly. After fixing the coverslip with cells, they are washed with PBS at room temperature. Methanol should be taken with a minimum percentage of water.
Best regards,
Rustem Uzbekov
  • asked a question related to Fixatives
Question
1 answer
Hi!
I was opening CST file, it showed this problem.
Do anyone know how to fix it?
I have tried restart my computer, but it didn't work.
Relevant answer
Answer
The process responsible for showing you the 3d model is failing to respond normally and resulted in a crash.
this issue can be due to your 3d-model complexity, system driver malfunction or your device might need an upgrade in specs.
  • asked a question related to Fixatives
Question
2 answers
"epigenetic information is stored in a digital-analog format, susceptible to alterations induced by diverse environmental signals and cellular damage" and potentially polish can fix those scratches(
Relevant answer
Answer
En principio el envejecimiento no es una enfermedad, por lo que no hay que curarlo. Sin embargo, factores externos, pueden modificar la regulación epigenética con la expectativa de mejorar el deterioro aumentado que acompaña al envejecimiento. Todo lo que evite reacciones oxidativas sin duda para mí mejorará la regulación epigenética y el deterioro del envejecimiento.
  • asked a question related to Fixatives
Question
3 answers
I suspect my cells are contaminated with mycoplasma. I fixed the cells with 4% PFA and stained them with DAPI. Below is the image I obtained. I don't observe the typical small, rounded DAPI foci outside the nuclei. Instead, there's a slightly cloudy blue color in the center of the image. Could this indicate mycoplasma contamination? Thanks!
Relevant answer
Answer
Determining whether your cells are contaminated with mycoplasma requires careful observation and testing. Mycoplasma contamination is common in cell cultures and can lead to altered cell behavior, growth rates, and experimental results. Signs of contamination may include abnormal cell morphology, changes in growth patterns, or unexpected changes in gene expression. To confirm contamination, specific tests such as PCR, culture methods, or enzyme-based assays can be employed. Regular monitoring and good laboratory practices, including maintaining strict aseptic techniques and using mycoplasma-free reagents, are essential to prevent and detect contamination early. If you suspect contamination, it’s crucial to act quickly to address the issue and ensure the integrity of your experiments.
  • asked a question related to Fixatives
Question
2 answers
Hi everyone! I tried to perform a classic One Way Anova with the package GAD in R, followed by a SNK test, which I always used, but it didn't work with this dataset, and I got the same error for both tests, which is the following:
"Error in if (colnames(tm.class)[j] == "fixed") tm.final[i, j] = 0 :
missing value where TRUE/FALSE needed"
I understand there is something that gives NA values in my datatset but I do not know how to fix it. There are no NA values in the dataset as itself. Here is the dataset:
temp Filtr_eff
gradi19 11.33
gradi19 15.90
gradi19 10.54
gradi26 11.01
gradi26 -1.33
gradi26 9.80
gradi30 -49.77
gradi30 -42.05
gradi30 -32.03
So, I have three different levels of the factor temp (gradi19, gradi26 and gradi30) and my variable is Filtr_eff. I also already set the factor as fixed.
Please help me, how do I fix the error? I could do the Anova with another package (library car worked for example with this dataset) and I could do tukey instead of SNK, but I want to understand why I got this error since it never happened to me..thanks!
PS: I attached the R and txt files
Relevant answer
Answer
Thanks, Anna; I have the same problem as yours, and your solution helped me. Many thanks
  • asked a question related to Fixatives
Question
3 answers
I have a problem, in additive manufacturing (here specifically LPBF), if you make parts with different shapes through a fixed printing process, the parts will deform due to different geometry resulting in different stress concentrations. However, for the same shape of the part, the use of different printing process parameters to manufacture the part, will have an impact on its deformation? Such as different laser power, scanning rate, etc. (of course, if the part can be successfully manufactured)
Relevant answer
Answer
Hi,
Yes, of course, this issue was discussed in section 4.2 of this paper:
  • asked a question related to Fixatives
Question
2 answers
Hello everyone,
I am very much new in quantum espresso and Boltztrap2. I have faced a problem regarding the fermi energy of semiconductor.I have done scf and nscf calculation for Perovskite material. But there in the nscf file output I have got HOMO and LUMO , not the fermi energy as it is a semiconductor material . As per Quantum Espresso input file description for semiconductor and insulator occupation will be fixed. but using this i cannot get the Fermi energy . In the boltztrap calculation I have to give the fermi energy value. Can you please suggest what should I do?
Relevant answer
Answer
Jasurbek Gulomov Thanks a lot.Very good explanation. But I have problem in using Boltztrap for calculating the thermoelectric property. Using smearing though I have got the fermi level but I have obtained the Seebeck coefficients 10 times higher than the published value. So, I am looking for the problem
  • asked a question related to Fixatives
Question
3 answers
I'm trying to fitting Cu Auger peak into various state (Cu0, Cu+, CuI etc..)
In Cu0, one of the peak's FWHM is 0.84 but when I try to enter smaller value than 0.89, "input error" is occured. How can I put smaller value?
And plus how can I 'fix' the FWHM of other values? Whenever I try to optimize peaks, the values are changing.
Relevant answer
Answer
Thank you for your kind information. I didn't know about "fwhm constr." range, and now I know what it is. Now I can adjust this value for 0.84 eV. Why I use 0.84eV is that I'm trying to use Cu LMM curve-fitting parameters. I attach the table.
Thank you very much for your time.
  • asked a question related to Fixatives
Question
1 answer
Will this affect properties such as band and DOS? If yes, then how can I fix this? This calculation has been done in WIEN2K.
Relevant answer
Answer
Change in number of electrons can occur if u have changed the pseudopotentials used.
  • asked a question related to Fixatives
Question
2 answers
I need a PET + Solvent mixture to feed it to a fixed bed reactor for steam reforming.
Relevant answer
Answer
PET is insoluble in water, diethyl ether, and many common organic solvents. However, it is soluble in DMSO, nitrobenzene, phenol, and o-chlorophenol. The reforming can be done with fixed bed reactor using Ni over La2O3-Al2O3 support with temperature 700 degree C to 800 degree Cent. PET can be efficiently converted to hydrogen and valuable fuels at optimized condition. Production of hydrogen from plastic waste could be a prospective key to the ecological problems resulted from waste.the steam reforming of Polyethylene terephthalate (PET) dissolved in phenol can be conducted in a fixed bed reactor using above mentioned catalyst.
The following five factors studied be maintained
1. Temperature of the furnace
2. Feed flow rate
3. Mass flow
4. Phenol((C6H5OH))concentration and
5. Concentration of PET solution (E),
  • asked a question related to Fixatives
Question
1 answer
How to store SDS-PAGE for fluorescent imaging without fixatives?
I am running protein samples on SDS-PAGE that are tagged with fluorophores. If I place the gel in a destain solution of 60%water/30%methanol/10% acetic acid, the chemistry reverses and I lose the fluorophore. Is there an alternative storage solution I can use to get my gel to the imager to capture the fluorescence without chemical fixatives? After imaging, I then proceed to Coomassie Blue staining in acetic acid and methanol, at which point I am not worried about losing the fluorophore.
Relevant answer
Answer
If you image the gel immediately after it finishes running, it should not be necessary to use a fixing agent. The bands will not diffuse significantly in a few minutes.
  • asked a question related to Fixatives
Question
3 answers
I have samples with monocytes and THP-1 cells fixed in paraformaldehyde 1% and would like to stain with these fluorescent probes if it is possible.
Relevant answer
Answer
Much like Kush, ER-staining followed by fixation basically ablated the ER signal and when present looked diffuse. On the other hand, I have fixed and then ER-stained (ER-Tracker Green, #8787, Cell Signaling Technologies) the cells and saw good signal but diffuse. Fixing the cells definitely changes the morphology of the ER and increases signal background (even in other channels). I have not tried other color variants.
  • asked a question related to Fixatives
Question
6 answers
What is the role of technology in mitigating climate change and which is a technological fix to mitigating climate change?
Relevant answer
Answer
Technology helps reduce the impact of climate change by cutting down greenhouse gas emissions and promoting sustainable practices. One technological fix is renewable energy sources, like solar and wind power, which replace fossil fuels and reduce carbon pollution.
  • asked a question related to Fixatives
Question
2 answers
I'm currently trying to do some EMSA using P32. The first two gels looked perfect, with sharp bands and no background. However, all the following ones looked like the blot below. I'm not doing anything different. All my buffers and gels were freshly prepared, and I even produced fresh nuclear extracts to make sure my other batch was not degraded, and it still looks like that. So far, I've repeated it five times, but nothing's changed. Has anyone had the same problem or an idea of what I can do?
Relevant answer
Answer
Ryan Yellamaty Thank you for your answer.
After I run my gel I put it in a 10% ethanol and 10% acetic acid solution for 45 min after which I air dry the gel for 2 h using Whatman (under the chemical hood). For exposure I use a phosphor storage screen and I use a Phosphorimager (Typhoon) to scann my gel after 16h. The gel is not as dry as it would be after using a vacuum dryer but is feels dry to the touch. Due to the solution it will not shrink and so far it also did not warp.
I'm not sure if I can change something at the instrument but I can ask.
  • asked a question related to Fixatives
Question
4 answers
Traceback (most recent call last):
File "/home/aarushi/gromacs/cgenff_charmm2gmx_py3_nx2.py", line 54, in <module>
import networkx as nx
File "/home/aarushi/gromacs/myenv/lib/python3.10/site-packages/networkx/__init__.py", line 114, in <module>
import networkx.generators
File "/home/aarushi/gromacs/myenv/lib/python3.10/site-packages/networkx/generators/__init__.py", line 14, in <module>
from networkx.generators.intersection import *
File "/home/aarushi/gromacs/myenv/lib/python3.10/site-packages/networkx/generators/intersection.py", line 13, in <module>
from networkx.algorithms import bipartite
File "/home/aarushi/gromacs/myenv/lib/python3.10/site-packages/networkx/algorithms/__init__.py", line 16, in <module>
from networkx.algorithms.dag import *
File "/home/aarushi/gromacs/myenv/lib/python3.10/site-packages/networkx/algorithms/dag.py", line 23, in <module>
from fractions import gcd
ImportError: cannot import name 'gcd' from 'fractions' (/usr/lib/python3.10(m(m((((((((myenv)
could you please help me fixing this error?
Relevant answer
Answer
I have uninstall the old version of network and installed the 2.3 version by still this error pops up. Can you help.me fix this error.
  • asked a question related to Fixatives
Question
2 answers
I have scan data of multiple individuals over a while and
their positional photographs were taken at certain fixed instances during focal sampling. I want to obtain the inter-individual distances of these sets of individuals from the scan data. Can any software help me extract this positional data for the focal individuals from these photographs?
Thank you so much for your attention and participation.
Relevant answer
Answer
Ankana Sanyal Ankana, I'll add to David Nkem Davids recommendations. I like Image J by itself - but especially for the community of users who've created an extensive knowledge base and plug-ins. A search for Image J __ https://imagej.net/ij/ ___will yield a links to the user & developer forums
  • asked a question related to Fixatives
Question
3 answers
I have to remove OCT from the tissue completely and fix the OCT-removed tissue in paraffin. Please suggest the best way.
Relevant answer
Answer
Unfortunately, once the tissue is frozen you're kind of out of luck. You can try a slow thaw and then repeated PBS washes to remove the OCT and sucrose cryoprotection.
If the tissue is just in OCT and not frozen or just in sucrose, that's significantly easier. You can get a good idea how how much sucrose is left in the tissue by using different gradients. If the tissue still sinks in let's say, 5% sucrose, you have some more washes to go. Once the tissue is fully cleared of sucrose, I would fix again (especially if you're thawing a block) for another 24 hours before paraffin processing.
  • asked a question related to Fixatives
Question
1 answer
I've run it three times to try different parameters, but it stops changing after running for a short while. Please help me understand how to fix this. Is there a problem with the sequence or the parameters?
6471000 -- (-192324.911) [-190903.882] (-191836.670) (-203192.846) * (-192291.336) (-195396.079) (-197058.880) [-190667.824] -- 36:24:32 6472000 -- (-192324.911) [-190903.882] (-191836.670) (-203199.097) * (-192291.336) (-195396.079) (-197058.880) [-190667.824] -- 36:23:56 6473000 -- (-192324.911) [-190903.882] (-191836.670) (-203206.485) * (-192291.336) (-195396.079) (-197058.880) [-190667.824] -- 36:23:22 6474000 -- (-192324.911) [-190903.882] (-191836.670) (-203186.976) * (-192291.336) (-195396.079) (-197058.880) [-190667.824] -- 36:22:47 6475000 -- (-192324.911) [-190903.882] (-191836.670) (-203176.349) * (-192291.336) (-195396.079) (-197058.880) [-190667.824] -- 36:22:12 Average standard deviation of split frequencies: 0.143548 6476000 -- (-192324.911) [-190903.882] (-191836.670) (-203174.778) * (-192291.336) (-195396.079) (-197058.880) [-190667.824] -- 36:21:37 6477000 -- (-192324.911) [-190903.882] (-191836.670) (-203190.326) * (-192291.336) (-195396.079) (-197058.880) [-190667.824] -- 36:21:02 6478000 -- (-192324.911) [-190903.882] (-191836.670) (-203201.748) * (-192291.336) (-195396.079) (-197058.880) [-190667.824] -- 36:20:27 6479000 -- (-192324.911) [-190903.882] (-191836.670) (-203196.704) * (-192291.336) (-195396.079) (-197058.880) [-190667.824] -- 36:19:52 6480000 -- (-192324.911) [-190903.882] (-191836.670) (-203173.040) * (-192291.336) (-195396.079) (-197058.880) [-190667.824] -- 36:19:18 Average standard deviation of split frequencies: 0.143548 6481000 -- (-192324.911) [-190903.882] (-191836.670) (-203178.787) * (-192291.336) (-195396.079) (-197058.880) [-190667.824] -- 36:18:43 6482000 -- (-192324.911) [-190903.882] (-191836.670) (-203151.441) * (-192291.336) (-195396.079) (-197058.880) [-190667.824] -- 36:18:08 6483000 -- (-192324.911) [-190903.882] (-191836.670) (-203159.321) * (-192291.336) (-195396.079) (-197058.880) [-190667.824] -- 36:17:33 6484000 -- (-192324.911) [-190903.882] (-191836.670) (-203156.963) * (-192291.336) (-195396.079) (-197058.880) [-190667.824] -- 36:16:58 6485000 -- (-192324.911) [-190903.882] (-191836.670) (-203142.242) * (-192291.336) (-195396.079) (-197058.880) [-190667.824] -- 36:16:24 Average standard deviation of split frequencies: 0.143548
Relevant answer
Answer
If the avg SE is not going down then the runs are failing to converge which means that there is too little phylogenetic information in the sequence alignment.
Note that the likelihood scores have not changed either over the 11,000 generations you show here,
Six million plus generations should result in multiple lowering plateaus of better fit. But this does not seem to be happening.
If you wish you could send me the alignment and I could assess whether the data is possibly informative.
  • asked a question related to Fixatives
Question
6 answers
So let's say I wanted to do a research with this topic:
"Factors affecting QOL of beta-thalassemic patients"
Study Design: Cross Sectional
Number of Independent Variables: 21
Dependent Variables: mean QOL score
Statistical Analysis: Descriptive statistics, bivariate analysis, followed by multiple linear regression
Power: 80%
Significance level: 0.05
Aim of study: figuring out which of the 21 independent variables included significantly affect the QOL of beta-thalassemic patients
First of all, is it correct for me to use G*power F test to do a power analysis with A priori to determine my minimum sample size or should I be using something else?
If yes, then which test do I use? Do I use the "Linear multiple regression: fixed model, R-squared deviation from zero", or "Linear multiple regression: fixed model, R-squared increase" or should I use something else entirely? Thank you for helping out!
Relevant answer
Answer
What I'm suggesting is that you do a stepwise multiple regression. This procedure successively deletes variables which do not add significantly to prediction. (There are three alternative procedures forward inclusion which progressively adds significant predictors, backwards elimination which progressively deletes nonsignificant predictors, and stepwise (proper) which starts forward but retests deleted alternatives with the addition of each new predictor.) It is because all stepwise alternatives are based on R-squared increase that I think it's the appropriate choice for estimating statistical power.
  • asked a question related to Fixatives
Question
1 answer
Is there any way to somehow normalize these coefficients? How can I fix this problem?
Relevant answer
Answer
That's what happens when you have redundant variables, probably they are directly correlated between them. In that case, why would you want to use both for the prediction? If it's a matter of robustness you can do a weighted average of the predictors and then build the model.
  • asked a question related to Fixatives
Question
2 answers
I have been trying to install PowerMarker on my Windows 10 PC but it is not working.
One of the requirements for PowerMarker installation is MS NET Framework 1.1.4322 condition, however, Windows 10 no longer supports this 1.1.4322 version.
I'd need assistance, please.
Relevant answer
Answer
@Mohammad, many thanks for your suggestion. It worked perfectly well. Cheers.
  • asked a question related to Fixatives
Question
9 answers
Hi everyone,
I want to Apply Tests for Special Causes in p-chart, but the sample size for each group is different. So I don’t have a fixed UCL and LCL. Just a question can I apply Tests for Special Causes? Can I calculate index when I don’t have a fixed LCL and UCL.
Thanks,
Relevant answer
Answer
i meant what is the minimum of total sample per subgroup to use p-chart?
  • asked a question related to Fixatives
Question
6 answers
Hi, i am currentyl fitting mno2 material into the peak at Mn 2p 3/2 and Mn 2p 1/2. in the right side of the peak, the tip highlighted in red is still not fit enough. is there any idea how to fit the top so that the black lines all matched the blue raw data lines?I already estimated the initial value and the fix it and then run the first itenery. after that i ticked of the fix button and let it run again. But it is still not fit enough.
Thank You very much for your kind assistance
Relevant answer
Answer
Understood Dr. Weippert. Thank You for your guidance. I am still new to the XPS technique. Your comments really helped me better understand this technique.
  • asked a question related to Fixatives
Question
1 answer
I know that it is recommended during fixing column but I am curious if there are much more cases. Maybe it has a lot of applications ;)
Relevant answer
Answer
I have used it for cleaning columns, especially for ion exchange columns. It is also good if you install at a size exclusion column and there is a bubble in the tubing to remove it.
  • asked a question related to Fixatives
Question
2 answers
1 ton charcoal fixes 3,7 t CO2. The global charcoal production is 54 mio tons, in which 200 mio t CO2 are fixed. 200 times the currently produced charcoal will fix the entire CO2 emitted globally per year!!! CO2 emission about 30 bln t per year: means this will be fixed in 10 bln t charcoal.
The entire annually CO2 can be fixed in a volume 2,7 km * 2,7 km*2,7 km and could be dumped in e.g. open pit mining sites where the coal was exploited (give it back).
Rapid growing biomass may be used. Charcoal production cost may be assumed the in the order of 200$ per ton, results in an annual investment of 2000 bln $ globally. THIS IS THE SAME AS WHAT ARE MILITARY WEAPON EXPENDITURES.
This is possible...in principle!
Please tell me where I am wrong in my rough brainstorming.
Relevant answer
Answer
That varies. The retort-manufacturer SPDC says for a simple drum-retort Vario-L: input 1,9 m3 biomass (wood, grass, roots, corn-residues...) and output 0,9 m3 charcoal. This is volume...
Regarding the mass: 1 t input and about 300-500 kg charcoal.
The loss is C-volatiles, syngas, water....
The amazing idea is: use photosynthesis (for free) and partial oxidation (for free).
  • asked a question related to Fixatives
Question
2 answers
Which type of stain can be used?
Relevant answer
Answer
1. **Fixation**: Tissues are fixed using a formalin solution³. This step preserves the structure of the cells and tissues in the sample.
2. **Trimming and Transferring**: Fixed specimens are trimmed to the appropriate size and transferred to labeled cassettes³.
3. **Dehydration, Clearing, and Embedding**: The samples are then dehydrated, cleared, and embedded in paraffin wax³. Dehydration involves removing water from the sample, usually with alcohol. Clearing makes the sample transparent and prepares it for embedding.
4. **Sectioning**: Sectioning with a microtome produces thin tissue slices which are transferred to glass slides³.
This is a general protocol and might need to be adjusted depending on the specific type of plant seed you are studying. For example, protocols have been developed for rapid clearing and staining of fixed Arabidopsis ovules¹, and for studying crassinucellate ovules of the sugar beet².
Please note that these steps should be carried out in a lab under the guidance of a trained professional, as they involve the use of chemicals and specialized equipment. Always follow safety guidelines when handling chemicals and equipment. If you're planning to do this in a lab, make sure you have the necessary permissions and guidance.
(1) Histology Slide Preparation: 5 Important Steps - Bitesize Bio. https://bitesizebio.com/13398/how-histology-slides-are-prepared/.
(2) Protocol for rapid clearing and staining of fixed ... - Plant Methods. https://plantmethods.biomedcentral.com/articles/10.1186/s13007-019-0505-x.
(3) Refinement of a clearing protocol to study ... - Plant Methods. https://plantmethods.biomedcentral.com/articles/10.1186/s13007-019-0452-6.
(4) An optimized histological proceeding to study the ... - Plant Methods. https://plantmethods.biomedcentral.com/articles/10.1186/s13007-020-00604-6.
  • asked a question related to Fixatives
Question
4 answers
Hi,
I am trying to do an Ordinal Logistic Regression (OLR) in R since this is the regression analysis that I need to use for my research.
I followed the tutorial video I found in YouTube in setting up the two sample models. Here are the 2 codes for the models:
modelnull <- clm(as.factor(PRODPRESENT)~1,
data = Ordinaldf,
link = "logit")
model1 <- clm(as.factor(PRODPRESENT)~Age+ as.factor(Gender)+Civil Status,
data = Ordinaldf,
link = "logit")
Next, I followed what the instructor did in doing anova and an error message prompted. It says, Error in UseMethod("anova") : no applicable method for 'anova' applied to an object of class "c('double', 'numeric')"
Is there something wrong in setting up the two sample models, hence, an error message in prompting? What needs to be done to fix the error?
Please help.
Thank you in advance.
Relevant answer
Answer
This comes from the depth of R. It means that the command anova() expects a different object type. Usually, it would simply be two model objects, like:
anova(modelnull, model1)
The object you pass to anova() is a vector of numbers. Looks like you have passed a vector of coefficients to anova, not a model object.