Q&A

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  • Muhammad Azeem asked a question in Biochar:
    How can i get the good bands on DGGE gel?

    I have isolate the soil DNA with power soil DNA kit. The soil was amended with and without biochar. I have done PCR, it shows nice bands on 1 % agarose, but when i run on DGGE, i missed bands in half samples. DNA concentrations were almost same in all samples in the range of 13-22 ng/uL. The bands were visible in some samples with lower DNA quantity but not in higher. 

  • Sevim Korkmaz asked a question in Cerium:
    Can anyone explain why ceria particles UV-vis spectra is changing with the particles size?

    "The UV-VIS spectra of the cerium colloid nanoparticles in the range 300
    nm – 700 nm show at the visible light region of 350 nm to 550 nm, a plasmon peak at 443 nm, typical for cerium nanoparticles based on their absorption band (King, et al., 2011)." 

  • Paul Jennings added an answer in Ruminants:
    Is the metabolizable energy (ME) content of any feed higher in monogastrics compared to ruminants?

    For example, can you compare the ME contents of soybean meal (as an example of cake) and corn grain (sa an example of grain) for ruminants and monogastrics?

    Paul Jennings · MARJEN Consulting Group

    The ME value of any feed will vary with the type of animal to which it is fed. It should also be noted that Me value is a general guide as even within a class of animals the metabolic efficiency of individual animals will vary. This makes it extremely difficult to mathematically reconcile actual energy output with input for the individual animal.

    Additionally within the individual animal life cycle stage will also influence the efficiency with which the feed ME is utilized.

  • What is the link between attachment and self?

    I developed a model based on neural development that links the primitive need for safety (reptilian brain development) with the basic human needs of attachment, control and distress avoidance/pleasure (paleomamallian development) with the self (a high order construct based on frontal cortical development (neomamallian cortex) (see my book "Neuropsychotherapy Theoretical Underpinnings and Clinical Applications" Oct 2014) and am interested to compare other studies/theories of self based on neural principles.

  • What kind of statistical analysis should I use when comparing 2 individual data sets?

    The Number of testet individual will be 20 (intraindividual testing) and the data will be collected using a IGA score, which we still not know if it will go up to 5 or 7 scores. The average age might also be good to be included, but I´m not sure. Has anyone suggestions? Thank´s a lot in advance!

    Paul R. Yarnold · Optimal Data Analysis LLC

    Wow...

    I just spoke with an expert in this design.

    There is NO between-subjects factor, it is entirely within-subjects.

    Arm is a within-subjects factor (nested), and of course time is within-subjects. The small sample is indeed a problem from the perspective of statistical power, and the possibility of largely null data is the nail in the coffin.

    The expert agreed with me that either the CI approach, or the N-of-1 approach are likely the most straightforward. I truly feel like editing or deleting my prior comments, but I won't...

    Whew!  :-)

  • Lukaš Makky asked a question in Art:
    Are the problems of periphery and center still actual?

    We are preparing Conference (The Art on the Periphery and the Periphery in the Art) and according to abstracts it looks to be very interesting evening (for example there are abstracts about: fashion blogs, illustration in ABC books, about unrecognized artists, alternative theatres and music groups etc.). This question is just the output of my curiosity. So I would like to ask, if the notion of periphery and center is still actual, and what is known or understood as periphery in your countries. Or rather, how do you understand periphery in the field of fine art or art in general.

  • What is mathematics?

    "I think many physicists, including myself, agree that there should be some complete description of the universe and the laws of nature. Implicit in that assumption is the universe is intrinsically mathematical." – Simeon Hellerman

    Assuming that the universe is intrinsically mathematical, this leaves open the question: What is mathematics?

    Is it the case that mathematics is a hunt for structures in the universe? Or is it the case that mathematics and its discovery is independent of the universe?   Or is it both?   Or is it neither?

    Vitaly Voloshin · Troy University

    Mathematics is the ABSOLUTE  TRUTH HIDDEN IN THE NATURE. We simply discover it step by step during all our history.

  • Dena Gassner added an answer in Adults With Autism:
    Are there any books that outline teaching empathy to adults with autism?

    I am working with post-secondary students of low-average intelligence and with autism. I am interested in using book clubs to build empathy skills and other social skills. I need book suggestions or any research of this kind. 

    I do not know about assessments  specifically but I would look at reading facial expressions--this is computer generated and there are assessments about that. I would look for word searches for these various labels at the publishers I mentioned above. 

  • What are some of the impacts of 3D printing in construction and does it contribute to a sustainable construction?

    From the perspective of sustainable construction, I would like to research on some of the positive /negative impacts of 3D printing in the construction industry including some of the sustainable and environmental factors including technique, material, embodied energy and cost in comparison to regular method of construction.  

  • Nashon Adero added an answer in Heritage:
    How can a architect go about design sustainable features for heritage buildings?

    Heritages buildings are already existing, but we can remove them, even they are very old and not sustainable for the future, so what should architect to do for these buildings to become more sustainable?

    Nashon Adero · The Technical University of Kenya

    Work with rehabilitation engineers to ensure the buildings are re-structured for safety and durability while preserving important aspects of heritage/bequest values. The architect comes in handy in enhancing and preserving the message that such buildings should convey, especially through visual impact.

  • Christian O Isichei added an answer in Hepatitis B:
    Is anyone interested in doing data analysis and writing up of a huge set of data about HBV from my work?

    This should make a good paper and you will be an author. This work (the analysis and writing up) should finish in the next two months. If you have time and do not have busy schedule, please contact.  You should be a very good statistician and writer. No time waster please (This is not paid work), the only reward you get is the authorship! 

    Christian O Isichei · University of JosTeaching Hospital

    Grateful for this networking

  • Daniel Feger added an answer in Enteritis:
    How long can a compound be stable in DMSO for?

    I am slightly concerned about my overexpression studies where one of my BCG strains should confer resistance to my control compound, but it seems like either the compound cannot enter the cell or either it is not functional. Could also multiple freeze-thawing cycles affect its stability? Should I prepare fresh solutions from powder?

    Daniel Feger · ProQinase GmbH

    Hi Ramón, the stability of a compound in DMSO or in other solvent solutions depends strongly from the special characteristics of the compound. In our experience, there are compounds which are very stable and resistent to multiple freeze-thawing cycles in DMSO. Other compounds are very sensitive, like Calcein-AM from Life Technologies, which we only use as fresh dissolved solutions. In this case the characteristic of DMSO to easily take up moisture is a big problem. To achieve a maximum of stability of your DMSO solution you should also use a compound concentration which is as high as possible (e.g. 10 mM), this is also true for all kind of compound solutions. Since you don't know whether your compound enter the cell, I would recommend to use only freshly prepared solutions in your experiment.

  • Jorge Herbstein added an answer in Autopsy:
    In your country, in some cases, can you state the cause of death and manner of death, after only external examination or partial autopsy?
    Sometimes, in many Islamic countries, there is restriction and minimization of autopsy rate due to religious or social thoughts. In your opinion, what is the best to do, apologize for stating a cause of death or state it in a conservative manner. Sometimes, a cause of death is evident e.g. firearm to the head or severe cut throat ... etc.
    Jorge Herbstein · University of Buenos Aires

    In my country all the medico-legal autopsies  must be: complete, methodical, systematical and illustrated and we do not determine and state the manner of death, same that in South Africa. 

    As you say: "Sometimes, a cause of death is evident e.g. firearm to the head or severe cut throat ... etc." but, for example, in a gunshot wound to the head it could be an homicide or an suicide and how can you determinate the range of fire without an autopsy  ???

    Regards from Argentina

    PS: sorry for my bad English.

  • Any advice on Patient-Centered Outcomes Research Institute (PCORI) grants?
    PCORI is new in the US as of last year. If you look at their web site (www.pcori.org), they want "patient-centered" and "comparative" research. I'm guiding my colleagues as to research design as we write our grants, but would love it if anyone who has succeeded or failed at getting one of these grants could provide some insight into "what went right" as well as "what went wrong". Thank you!
    Michael Griffiths · Howard University

    The instigators of these Grants seldom have the historical Donabedian understanding of the issue of health care outcome based evaluation.  I unfortunately come from those times and the current understanding of the issues is at best limited. Please see Donabedian's original article on Structure Process Outcome in the 65? APHA Journal

  • D H Steve Zou added an answer in Peer Review:
    What is the criteria to be a reviewer? Can all authours be reviewers?

    I wish to know the criteria for a reviewer. Can all authors could be reviewers? Should editor go strictly by reviewer reports on acceptance/rejection of manuscript, even the recommendations are sloppy. I welcome a lively debate on this topic.

    D H Steve Zou · Editor-in-Chief

    "The International Journal of Geohazards" has strict guidelines and criteria for reviewers. We normally only select scholars with the required expertiese and good reputation as reviewers. To avoid the type of problem of "all recommendations are sloppy", the Editor-in-Chief of this journal has a final say on acceptance or rejection. More detail at "https://sites.google.com/site/ijgeoh/instructions-for-reviewers"

  • Simon Andrew Reid added an answer in Health Systems:
    How do you estimate specific disease prevalence for a population when all that is available is prevalence data from the public health system?

    In the absence of data from the private health sector, estimating health care costs will fall short if we are to only consider those utilizing the public health system. Is there a way (academic methodology) for applying a multiplier to cover that unmet population?

    Simon Andrew Reid · University of Queensland

    Why not try a number of methods and just explore how much difference exists in the estimates.  The danger is that you will never know which estimate is "most" wrong.  I would then be inclined to look at the validity of the range of estimates by consulting with a range of local experts who would be expected to know the local conditions, i.e. clinicians local epidemiologists etc.  There are iterative techniques for eliciting expert opinion that could be adapted to use the experts to rank the estimates.  It is not perfect but I think in most circumstances it is good to get some verification from an independent source, data or human.  Sort of like generating confidence intervals using the "human brain" method.

  • Geng Ouyang added an answer in Formal Logic:
    What happens if mathematics is inconsistent?
    By Godel's incompleteness theorem it is impossible to prove consistency of the current widely accepted foundation of mathematics ZFC within ZFC. But this theorem says nothing about existence or non-existence of a possible formal proof for inconsistency of ZFC within ZFC that means it is possible that some day set theorists or other working mathematicians find an inconsistency between two mathematical theorems.

    My first question is about any possible option which could be chosen by set theorists, logicians and mathematicians in this imaginary situation.

    Another question is about possible impacts of discovering an inconsistency in mathematics on philosophy of mathematics and some fields of human knowledge like theoretical physics which use mathematics extensively.
    ------------------------
    It seems weakening the current axiomatic foundation of mathematics in any sense (including removing a particular axiom or moving to another weaker axiomatic system) causes an expected problem. In fact avoiding the contradiction by means of weakening our axiomatic system (which seems the only accessible choice) sends some accepted parts of current mathematics into the realm of "non-mathematics". Thus in this case we need to choose between different parts of mathematics that which one is good and useful and which one is not. This could be the matter of many discussions. For example if the Axiom of Choice (AC) is a part of that contradiction then by removing it from the foundation we will lose many useful tools of mathematics including many essential theorems like "Every vector space has a basis" that harms linear algebra extensively.
    ------------------------
    Geng Ouyang · MinNan Normal University

    As a researcher, I am sincerely looking for the different opinions to improve the work, would you please be so kind as to tell me where I do wrong, welcome to join the discussion. The foundation of infinite related area in our science is really very week. Through discussions we can get better understanding on the topic, any ideas are devoted to our scientific work.
    Sincerely yours!
    Geng

  • Nashon Adero asked a question in Creative Arts:
    Which training aspects need priority from childhood to enhance the capacity of graduates of engineering and other applied sciences to be innovators?

    It can be argued that the dominant approach to education in most countries does not inculcate in students, from early stages, the innovative skills we need in the 21st century's  amazing era of digital revolution/ the Conceptual Age. Reading and writing dominate the early stages, yet skills in scientific inquiry, creative arts, spatial thinking, and seeing the big picture (systems thinking) also need to be introduced early and progressively using curricular and extra-curricular activities to ensure that we get graduates who can innovate locally relevant solutions. Referring to your country, are these skills being ingrained from the early stages of learning? What would you recommend to improve output?

  • How to estimate diseases-specific medical expenditure?
    How can we estimate disease-specific medical expenditure when costs come together. For example, it is difficult for respondent to distinguish cost of diabetes and hypertension, hypertension and heart diseases, and so on. These types of disease come together, sought same doctor, and purchases medicine in same time.
    I know regression method through multiple imputation to allocate medical costs.
    Can anyone suggest another method to perform this?
    Michael Griffiths · Howard University

    We did a project on this very issue in the 1980's by selecting primary ICD9 codes for diseases, capturing modifying or contributory diagnoses and source of admissions data to identify the charged cost of a particular hospital relative to the patients diagnoses.  You can develop a multivariable equation and retrospectively impute the contribution of each ICD9 code. 

  • Nathan Dawthorne added an answer in Phenomenology:
    In phenomenological research, does keeping a reflexive journal help to address issues of subjectivity?

    I am looking at ways to strengthen a small masters project which will only use interviews as a data collection method and I will be the only person analysing data (using basic thematic coding...I think). I'm acutely aware that results are likely to be highly subjective (hopefully to my participants, but possibly to me) and wonder if a reflexive journal might help to at least acknowledge this difficulty.

    Nathan Dawthorne · The University of Western Ontario

    Here's some thoughts

    - make sure you detail how you came about the questions you pose to your interviewees 

    - reflect on the setting of the interview and the ways it is influencing you, your interaction, and the interviewee

    - reflexive journaling is important however if you could tell us what your research project is, it may allow us to offer more refined advice on the topic (ex: if your interviews involve accounts of traumatic events, then I believe this approach is imperative for more than just dealing with the intersubjectivity of your research)

  • Whether MYO1C gene expressed in colorectal tumors, and is the gene expression level would be different between different tumor stages?

    What reagent stock we need to process it and what method should be suitable for it?

    What is the protocol and what material should we need to find MYO1C gene expression in colorectal cancer?

  • How to remove ghost bands which are as bright as my linearized plasmid bands? How to prevent it?

    For the past few days I have been getting ghost bands in plasmid mini prep as well as restriction digests. My vector and insert sizes are 10 and 8 kb respectively. I am also getting 2 - 3 more bands between 5-3 kb sizes.

    Does anyone have an idea why this happens and how to prevent this?

    Thanks

    Venkatesh Endalur Gopinarayanan · Tufts University

    Thanks Christopher. It seems the problem is with electroporation and ligation mix. The same ligation mix with chemical transformation doesn't seem to have those unwanted bands.

  • Uvernes A Somarriba added an answer in Concrete:
    I need to represent a change of space in a period of time with GIS tool. ¿How can structure the database to do so?

    In concrete, I need to represent a historical evolution of the construction works in a period of time. So I have a list of architects that were working in distinct buildings in different dates. That is, architect "A" in 1455 was working in building “X” and then in 1457 was working in “Y” building....

    Uvernes A Somarriba · The Ottawa Hospital

    (AId, date, GIS coordinates)

    (Bkey, Building, GIS coordinates)

    (AId, architect)

    Then, use joins. 

  • Thought and opinions on a hospital implementing an "Overcapacity Protocol"/"Full Capacity Protocol"?
    Is it a safer option than just 'warehousing' patients in an ED? In comparison, what are some limitations?

    When demands for urgent and emergent care continue to mount and no Emergency Department (ED) care spaces are available for these emergent and urgent patients and all usual actions for rapid admissions to inpatient beds have been maximized, the Over Capacity Protocol should be initiated. This protocol is intended to ensure systematic actions are undertaken to ensure admitted patients being cared for in the ED will be appropriately admitted to an inpatient unit. The protocol may be extended to other areas of the hospital, for example critical care, as required. (Fraser Health).
    Michael Griffiths · Howard University

    The sub-acute care model was used in the 1980's to some success.  There were a number of private companies, one in Maryland that pursued this as a business model.  For a brief time this relived Hospital systems of longer than reasonable time in the hospital for recovery.  As you know this model was replaced by Rehabilitation facilities but to my knowledge this transition is still fraught with challenges.  The system is driven by the re-imbursement system unfortunately and not by patient care or effective needs. 

  • Can electroporation of ligation mix (alcohol precipitated) cause shearing of dna?

    So I have a ligation mix which when I transform through electroporation doesn't give me a single band of plasmid ( checked by linearizing it). Instead I seem to get 3 additional bands of less size. If I do the same procedure with MES transformation, I get the band of my size. Can anyone explain this? Is there a way to overcome this?

  • Mohammad N. Abdulrahim asked a question in Strings:
    Is the Burau representation of the braid group on 4 strings faithful?

    For n=3, the burau representation is faithful.

    For n \geq 5, the Burau representation is unfaithful

  • Ahmed Abdeen Hamed added an answer in Text Analysis:
    Does anyone have a climate change corpus that I can use?

    Dear respected scientists and colleagues,

    I am looking for a climate change corpus to do text analysis on it. If you have one or you know a journal that I can download their abstracts I would be very much obliged.

    Thanks,

    -Dr.Hamed

    Ahmed Abdeen Hamed · University of Vermont

    Thanks you very much for taking the time to respond and share the resource. Very much appreciated. I actually need thousands of publications with their titles and abstracts if possible. Do you know any corpus of this description?

  • Julie Lord added an answer in Drug Incompatibility:
    Are there any drug incompatibility references available indicating "time gap" as a factor to be considered during multiple drugs administration?

    Drug compatibility and  incompatibility  is an important consideration for nurses in drug administration, especially when multiple drugs are administered rapidly per three way connectors either through central lumen or peripheral line.

    Though safety of medication administration is ensured through "10 Rights ", to remain alert for potential harm & additional information about  "gap in time " between two or multiple drugs administration  is most significant for patient safety.

    Julie Lord · Alfred Hospital

    If  multiple drugs  are to be administered rapidly per three way connectors either through central lumen or peripheral line and you don't have specific compatability data to indicate that they're okay together (eg from Trissel or other similar reference) you should always flush with a compatible fluid between each drug

    Time itself is not a factor but the drugs shouldn't come into contact with each other, hence the need for flushing the line.  This is not quite so critical with central lines as peripheral ones due to the rapid and large volume dilutional factors in the former situation.

  • Yanmei Xiao added an answer in Transgenes:
    Which plant binary vector has 1X35S promoter to drive the transgene and Bar as a selectable marker?

    Which plant binary vector has a 1X normal 35S promoter to drive the transgene and Bar as a selectable marker? I want to transform Arabidopsis plants. Thanks.

    Yanmei Xiao · University of California, Davis

    pMLBart

  • Marcin Zalewski added an answer in Carabidae:
    Pellet analysis and Ground beetle Body Mass reference?

    Hello to all, 

    I 've currently analysed pellets from Lesser Kestrels throughout different seasons. I think that would be worthy to make some correlations with the prey body mass. I have some data from insect reference collections but I still need more.I would be greatfull if anyone knows where can I found data about European Ground beetles (Carabidae) weight. 

    Thanks in advance!

    Konstaninos Vlachopoulos

    Marcin Zalewski · Polish Academy of Sciences

    Hi, i think you should rather use body weight  instead of length. Here you can find equation how to link  length and weight  

    https://www.researchgate.net/publication/232724744_Local_and_regional_interspecific_abundance__body_weight_relationships_of_ground_beetles

    good luck