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- Why divide by n-1 when estimating standard deviation? In many probability-statistics textbooks and statistical contributions, the standard deviation of a random variable is proposed to be estimated by the square-root of the unbiased estimator of the variance, i.e. dividing the sum of square-deviations by n-1, being n the size of a random sample. Does anybody know why such an estimator is anchored in the statistical literature? Is there any technical reason supporting the use of this estimator?
Your video explains very well about the necesity of using n-1 for estimating unbiadedly the population variance, but Juan José knows very well that. He is asking for the use of n-1 in the denominator of S , the estimator of the standard deviation of the population (Sigma).Following
- Shotgun metagenomics: what is the best way to analyse the data?
What workflow do you usually follow to process the metagenomic (shotgun) data?
I just got my data and I have been reading quite a bit about how to process them but I didn't get a well defined answer. Aside of the initial QC, some people assembly the reads, and others don't... is it better to blast the reads or contigs, or use prediction tools to evaluate protein families?...
Our sampling has been performed on triplicate on a time series that has been correlated with geochemical changes and one of the first things we are interested in is probably the potential correlation with functional changes; and if possible, the taxonomic changes (if they can be observed, not really that important). In case the data allow it, it could be interesting to reconstruct genomes.
I have experience processing 16S amplicon sequencing data from Illumina, including statistical analyses, and I have assembled and annotated a couple of fungal genomes, so I'm quite familiar with some software.
I have access to a computing cluster, so the resources are not a problem.
metaAmos is a good pipeline for shotgun metagenomic analysis. The pipeline consists of 13 steps and provides a visual summary of the results.
It can be a bit tricky to install but provides a complete pipeline using a modular approach so that you can try different tools for each step in the pipeline.Following
- In municipal wastewater treatment, there is currently a clear delimitation between secondary and tertiary treatment?
What basic treatment operations can be considered in each one?
Traditionally, primary and secondary biologic treatment included normally separation of settable solids and reduction of suspended solids and organic load, measured through Biochemical Oxygen Demand, BOD (and Chemical Oxygen Demand, COD), and tertiary treatment included mainly removal of nutrients and sometimes filtration and disinfection. With the development of the treatment processes what are the current trends?
My experience from designing WWTPs:
PRIMARY TREATMENT - raw influent is bar screened, then fine grit is removed followed by primary clarification to remove suspended solids before discharge into receiving waters which have enough flow to dilute remaining BOD:TSS (the Combined Sewer Overflow outfall discharge to rivers & oceans used this dilution principle to justify discharge of sewage contaminated waters). The primary sludge is usually anaerobically digested and the methane gas recovered to power the WWTP.
SECONDARY TREATMENT - in this case after primary clarification above, the primary effluent is biologically treated to remove dissolved organic matter by aeration methods using diffusers or fixed-film reactors to form a biological floc to be settled in secondary clarifiers which recirculates part of it as return activated sludge (RAS) to the aeration tanks, with the excess removed as waste activated sludge (WAS) to be treated in usually aerobic digesters. The secondary clarifier effluent is then disinfected with usually chlorine and discharged. Depending on the final discharge area, the BOD:TSS quality is usually 20:20 to 30:30 mg/l. If the secondary effluent is to be used for irrigation, then total nitrogen (TN) and total phosphorous (TP) removal is incorporated too.
TERTIARY TREATMENT - For highly sensitive receiving waters or WATER REUSE by the public, the secondary clarifier effluent from above is sent to sand or combination sand-carbon filters. This ensures an effluent with BOD:TSS:TN:TP not usually exceeding 5:3:3:1 mg/l. The filtered effluent is then high-level disinfected meaning longer detention times and higher residual chlorine so it can be used for irrigation of public areas and food crops. In some place the tertiary treatment also uses artificial wetlands/ponds.
In Florida, many WWTPs do not use primary clarifiers, primary treatment is provided by grit removal and then this influent is biologically treated in usually oxidation ditches, membrane batch reactors, aeration tanks with nitrification/denitrification because it is tertially treated by filtration and high level disinfection for reuse or discharge into designated wetlands.Following
- Can intestinal tuberculosis and crohns disease coexist in a single patient?
gastroenterology, tuberculosis, crohns
About 15-20% patients of Crohn's disease (CD) get antituberculous therapy before diagnosis and in some cases later in disease course. This underscores the practical difficulty of differentiating the two in community setting.
The important questions are whether the two diseases can coexist throughout their course, or whether Mycobacterium tuberculosis initiate CD by producing altered gut mucosal immunity like other gut microbiota and more recently whether it can cause disease exacerbation in patients of CD on immunosuppressives. Though Myc paratuberculosis has strong zoonotic potential and the organism has been isolated from specimen of CD, the effect of its eradication have given inconclusive results in different series and hence its association with causation of CD is poor. It is now clear that a large portion of IBD risk loci are shared with other complex immune-mediated diseases, primary immunodeficiencies and mycobacterial disease, pointing towards shared pathogenic mechanisms between ‘distinct’ diseases. The associations with gene coding for proteins involved in autophagy and innate immunity point towards the importance of defective processing of intracellular bacteria (like mycobacteria) in CD. The genetic overlap between CD and susceptibility to infection with Mycobacterium leprae is particularly intriguing. A total of seven out of eight susceptibility loci, including NOD2, IL23R, RIPK2 and TNFSF15, for infection with Mycobacterium leprae have also been associated with CD, although with genetic effects in different directions for some of these associations. It is still to be explored whether this shared immunogenetic risk profile underpins a true causative role for mycobacteria in CD, or rather represent the result of convergent evolutionary adaptations to several pathogens. There are case reports of TB occuring in long standing CD on immunosuppressives.Following
- Is neural network optimization technique is feasible for local earthquake tomography or 1-D velocity modeling?
I am looking for some examples on how to start local earthquake tomography with the use of Neural network non linear optimization. I have found some previous works on the topic, But I am not much clear on how to apply the methodology on this problem. How to define the parameters? How to formulate our goal function for the tomography data. I am mainly interested in local earthquakes p and S- wave travel time data and invert it for the seismic velocity model. Is there some one working on this topic? Any help regarding my problem would be appreciated.
The Hopfield neural networks (HNN) is feasible for this problem.Following
- What is the difference between embedded flash(eFlash) and NVRAM that used flash?
I looked over the internet that NVRAM might use many type of non-volatile memory, such as flash, FeRAM, MRAM, etc.. I got confused about NVRAM that used flash and embedded flash. Some references about them will be really helpful.
Maybe this article could help you.
- How long is the maximum distance between two FRT site, which could making FRT-mediated recombination occuring?
I am trying to make gene deletion using FRT-mediated recombination in Drosophila. There are two p-element insertion with FRT sites across one particular gene. The distance between these two FRT site is 7Kb, I am wondering about whether or not these two FRT could work?Following
- Why do we get two different AUC in HPLC while running same plasma sample twice ?
I am running plasma samples in HPLC to detect a compound. The problem I am facing is that I am getting two different AUC while running same sample twice (as first time AUC is 3.25 and 2nd time 25 with same retention time). I am using C18 reverse phase column. I have proceed the plasma sample to eliminate all proteins and injecting 10ul of sample to HPLC. My run time is 25 min and my compound retention time is 11min and after that almost straight line till 25min, so I don't wash column before injecting the same sample. In all my plasma samples I am getting two different AUC for same compound while running them second time. Can anyone help me to find the solution??
Sunil: Regeneration of the column is not needed and I do not recommend the general procedure you referenced as it does not address the specific contaminants retained on the column. It also takes about four hours to run which is not very practical after each run. Those referenced general procedures would be fine for an older unknown NP or RP column that was not used with plasma samples as a first step to try and clean it.
A column wash is required and standard operating procedure after each run. It must be tailored to the specific sample(s) injected or loaded onto the column. It will be different for different methods and samples. *Just like we tailor an analysis method to our samples, for best results, the wash method is also custom tailored to the method.
Yes, I too strongly recommend a better sample cleanup procedure. This is always good advice. The better the job you do here, the less problems you will have with the chromatography. Don't rely on the column to be your sample filter! ;)
Reenu: BTW: I am not saying that the specific problem you are experiencing is caused by lack of column washing. It is the most likely reason for it, but their are hundreds of other reasons too. Column washes are also required and if you are not doing them after plasma injections, then we need to address all of the areas which are not optimized first, before we look elsewhere. Please share the details of your method so I can suggest an appropriate wash step. The more info you share, the better the job I can do in helping you.Following
- Why is the value of my regression intercept over 7,000 when the function has only one dependent and one independent variable and 40 observations?
- Is it possible to provide single chiral molecules as drug entities for use ?
We are working on the synthesis of intermediates required for drug synthesis. Molecules may contain several chiral centres , which will be easy method for resolution of the racemic mixture ?
The answer to your question is, unfortunately, very case dependent. Without knowing the details it is really virtually impossible to provide good feedback.
In general, resolution of salts with chiral acids or bases, or resolution of esters with chiral acids or alcohols, or resolution of amides with chiral amines or acids are just some examples. Chiral chromatography is another.Following
- How long can we store competent Agrobacterium cells?
I'm facing problem in transformation of Agrobacterium cells via electroporation, the electrocompetent cells are about 15 months older, stored at -80 degree C. Anybody face the same problem?
Agrobacterium cells remain viable at -80 degree C for long periods. It is advisable to use standard strains available commercially.Following
- What is the best strategy for jamming frequency hopping&Direct sequence Hybrid spread spectrum signals?
What is the best strategy for jamming frequency hopping&Direct sequence Hybrid spread spectrum signals ?
A quick search with Google gives access to the following Thesis
PERFORMANCE EVALUATION OF DIFFERENT JAMMING STRATEGIES OVER UNCODED NONCOHERENT FAST FREQUENCY HOPPING FSK COMMUNICATION SYSTEMS
- What is your favorite scientific graph plotting software on Mac? I'm using Mac for writing my paper with TexPad, LaTex editor. However, creating a scientific graph in Mac is very difficult for me. I'm using Mjo, an open source graph plot but it can't handle complex number on axis. Any suggestion?
The most intuitive scientific plotting and statistics software that I have ever used on the Mac is GraphPad Prism. However, I do not think that it handles complex numbers directly. Origin Pro has more features than Prism and it can handle complex numbers directly. Origin Pro is for Windows only, but it can run in a Mac using Parallels or VMware Fusion to create a virtual Windows machine.Following
- What do you usually do to find the right journal for your research paper? Selecting the right journal for your academic paper is like meeting friends. You have to know what kind of scientific article and research you have, write the article with the necessary ingredients that are expected of it, be where editors and journals are, find an academic journal that publishes articles on the subject you have chosen, and when love arises, if necessary, insist a little.
However, there are still people who believe in the theory of probabilities when publishing in journals: sending the paper to a list of journals, one after the other until it is accepted. This is a fairly poor approach, because selecting an appropriate journal is as important as writing a good article.
Dear @Rafael, there are many good tools for choosing appropriate Journal for your paper. I am free to attach some of them. Hope it will be helpful.Following
- Mittag-Leffler functions? 1) E_a(z) is an entire function of order 1/a. Can you suggest a good reference about this topic?
2) How many derivatives do the functions E_a(z) and E_a(z^a) have at z=0?
entire function of finite order, by A. I. MarkushevichFollowing
- Is copper biocompatible (for Bio implants)?
Whether Cu is biocompatible ? If it is alloyed with bio compatible material such as Zirconium, what will be the biocompatibility of the binary alloy system?
Toxicity of copper(II) ions is well known for biological systems. copper is heavy metal which is essential for metabolism just in trace amount and at higher concentrations it can lead to poisoning. generally copper is not a desirable biomaterial(as well as most metals) and in the case of implantation in physiological media could leak toxic ions. in my opinion synthesis of alloy metallic implant with Zirconium is not proper method dealing with this problem because it dose not address properly the toxic ion problem of copperFollowing
- In the number of patients with allergic rhinitis have increased over the years?
what do you think about the reason for this ?Following
- How we can take advantage of the processing of unstructured data ?
How we can take advantage of the processing of unstructured data to improve distance education (e-Learning) in general, and the online research in the same context of learning specifically? are there any of existing produtcs or mechanisms in this way?Following
- Where can I find information about coupling two models ( WRF & ROMS )?
I wanted to couple WRF V3.4.1 and ROMS (Regional Ocean Modeling System) to study some properties of air-sea interaction. Where can i find valuable information about setting and other setup information in web?
I have a very low configured computer resource (A small server with 12 gb ram). Is it possible to run the models in there for 5 days data?
Thanks in advance
I would also encourage you to use COAWST, as did Sandro Carniel. Its very easy and pretty much comes already configured.
You can also find information about it in the ROMS forumFollowing
- In case of deposited film on any electrode (say graphite), what might be the reasons for not getting any characteristic peaks from Powdr XRD analysis?
I am getting only the subtrate (electrode) peaks and not the electrodeposited samples peaks although i can see visually the smooth deposition of Ni and Ni(OH)2 onto it. I wonder what are the possibilities of not getting any PXRD peaks although EDAX and other elemental analysis prove its presence. The thickness of the deposition is about ~ 5-6 micrometers (from AFM and SEM cross sectional image).
Please suggest what might be the case.
The most simple reason could be that the deposited phase is amorphous. In your xrd pattern there is the presence of a broad peak at about 20°? Or is it possible to see bumps in the background?Following
- Who can help me with some reviews about the ethical issues of resuscitation?
I'm looking for some reviews, experiences,... about the ethical issues of resuscitation. Who can help me out?
Radiology. 2012 Dec;265(3):976; author reply 977. doi: 10.1148/radiol.12121485.
The Lazarus syndrome and the ethics of evidence-based versus experience-based medicine.
Lazarus syndrom is the answerFollowing
- How can I identify the critical quality attributes for a software system?
I'm looking for the concept of what is a critical attribute/characteristic of a software system.
Most information sources list security, dependability, safety, and reliability as critical attributes, but, they are considered critical for all kind of systems, or each system has specific critical attributes.
Thanks in advance.
You could use Quality Attribute Workshop, is a Scenario based SEI Method for defining the quality attributes and the tradeoffs considering the stakeholders.Following
- Can we use microwaves on large scale synthesis of organic compounds ?
We are working on the microwave assisted reactions. However, Is it possible to carry out on the synthesis on industrial scale ?
Yes! It is similar to photochemistry in this respect.
However, as in photochemistry, flow reactors is the way to go, I wish to thank Dr. Mushtaq Ahmad for providing two very good references, which also include what I just said about the advantages of flow reactors.Following
- Does anyone know how to combine density data to quantified disturbance in order to map risk for a given species?
I would like to know which formula would be correct to calculate a value of risk for marine mammals knowing the noise generated by human activities and the density of animals. Data are provided in 0.05° grid and I would like to obtain a map of predicted risk of disturbance for mammals.
Following Garthe and Hüppop 2004 (wind farm sensivity index calculation), I was thinking to do this :
Risk = (ln (density + 1) X noise)
Do you think it is correct ?
- When using the floral dip method to transform Arabidopsis, is the endosperm in the seed also transformed?
I want to express GFP in the endosperm using an endosperm specific promotor and I was wondering whether the endosperm is transformed as well when performing the floral dip or just the egg cell?
I have not seen any report suggesting endosperm in seed of Arabidopsis is transformed using floral dip method.Following
- What could be possible question to be asked to marketing manager to find out the present state of integrated marketing communication in their company?
I am doing qualitative research on "The present state of Integrated Marketing Communication in Mobile company of Nepal". Any suggestion in preparing Interview questionnaire to be asked to Marketing Manager will be appreciated?
Please look into the Clow and Baack text entitled Integrated Advertising, Promotion, and Marketing Communication. You also want to try to get to the heart of IMC--that is, are they using multiple channels, each with a single voice saying one message. Questions that get to this notion will let you know if they are truly using IMC.
- My cell line U87MG is getting detached after splitting, what could be the reason?
few weeks back there was fungal infection in some of my petridishes. So, I thoroughly clened the incubator using bleach and rectified alcohol, revived fresh stocks, prepared everything fresh and started using sodium azide in the humidity pan 1g/L autoclaved water (earlier I used to use copper sulphate 1g/L). Now, the infection has dissappeared but my cells are dettaching after the first splitting I do after stock revival. what could be the reason for it.
I agree with Attila; even a small amount of azide in incubator atmosphere can stress your cells. Or perhaps you have chlorine from bleach still blowing off from cleaned incubator parts.Following
- Anyone works on Bacteriophage from P. multocida
I want to ask some questions, any infomation it will be great
- Given a linear ODE, x'=Ax, where A is a Hamiltonian matrix, I transform via x=Ty s.t. T^(-1)AT is in Jordan canonical form. Is T a symplectic matrix?
Essentially, I want to know if the transformation to the eigenbasis of a linear Hamiltonian system is a symplectic transformation. I suspect that in general it will not be, unless one is careful with the scaling of the eigenvectors before placing in the columns of T, but I haven't found any obvious answers to this question in texts on Hamiltonian Dynamics (Meyer & Hall, Marsden & Ratiu, Arnold).
You can think about another way if you want:
For a linear Hamiltonian system, it is possible to find a symplectic transformation which puts the system in Jordan canonical form.Following