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  • Rafik Karaman added an answer in Endothelial Progenitor Cells:
    Is there a universal exocytotic tag or sequence for proteins?

    I am a masters student and have a presentation of theoretical applications of regenerative medicine. I need a xenoenzyme to be exocytosed from an endothelial progenitor cell. I thought there would be a know tag/ sequence that could be incorporated to tell the cell to export the protein but I have had no luck finding any. How would you go about ensuring this protein is secreted by the cell?

    Any help is much appreciated. Thanks!

    Rafik Karaman

    Dear Stephen,

    I think that TTSS (T3SS,  Injectisome or Injectosome) a protein appendage found in several Gram-negative bacteria can be a good example.

    For details please use the following link:


    Hoping this will be helpful,


  • Samuel Ogbeibu added an answer in Organization:
    What is the best way for assessment of management support in success of an organization?

    What is the best way for assessment of management support in success of an organization?

    Samuel Ogbeibu

    First of all, there is NO best way in doing this as different firms approach their core management related practices differently. In this regard I would suggest you consider the kind and size of organisation which is also in terms of their structure, culture, strategic policies and performance evaluation strategies and processes as well. Please try to understand the firm's vision, mission and objectives statements as all these would help you as a guide, towards having an overview of the business management phenomena you wish to understand.

    Similarly, have in mind the present and past success cases of the firm so as to give you a benchmark towards a critical measurement of managements degree of support so far.

    You might want to look into the past and present management support systems for that same company with respect to failed and successful management operational projects over recent years. 

    Furthermore, try running a critical review and evaluation of the entire construct in a chronological manner in order to know which and or what business models, theories or principles to apply in this case and eventually it should be less tasking for you to prepare your own strategic business model which is tailored towards an effective and efficient way for the assessment of management support in success of this particular organization or group of organizations.

    Please let me know if you need further counsel okay.

  • Zongchao Han added an answer in Refractive Eye Surgery:
    Does anyone know a protocol for isolation of rod, cone, RPE and ganglion cells from the retina?

    Does anyone know a protocol for isolation of rod, cone, RPE and ganglion cells from retina?

    Zongchao Han

    Here it is. Thanks


  • Wenqiang Liu added an answer in Molecular Dynamics Simulation:
    How do I get the mean value of defects in a cascade simulation when variable timestep is being used?

    Hello everyone!

        I want to analyze the results of my cascade simulation, but one problem confused me.

        In some publications, the relationship of number of defects vs. simulation time is shown in pictures. I also want to plot a picture like the one in article Journal of Nuclear Materials 249 (1997) 77-86, which is shown as the first attachment.

        After the analysis of the defect numbers, I will get a file like the second attachment and I can plot Nd vs. time by using the second and the third columns. In order to reduce the statistic error, usually I should simulate, like saying, 10 cases with the same pka condition.

        My problem is that, because the variable timestep is applied in my simulation, the second column of my results which represents the simulation time would be different in the 10 cases. Then it seems it is not possible to get the mean value of the number of defects at the exactly same time and which means I cannot get a picture like the first attachment.

        Could anybody please give me some advice to help me solve this problem?

        Any help would be much appreciated!

    Best Regards


    + 1 more attachment

    Wenqiang Liu

    Dear Dr. Shao and Dr. Tramontina

    I am sorry for replying this late and I am afraid that I do not quite understand your answers. I am trying to make my question clearer. Could you please give me more help?

    After my simulation, I can get the defect numbers and a file like this:

    Step      time                    defects

    100       0.007195188      2

    1000    0.047129853      10

    10000  3.426915898      901

    Then I think I need to simulate 10 cases with the same PKA condition. Because the variable time step is applied, maybe the next file is like:

    Step      time                    defects

    100       0.008156612      3

    1000    0.054647746      13

    10000  3.532166466      920

    The other cases are similar, the time is different at the same steps. If I want to plot a picture of defect numbers vs. time, I cannot get the mean value of defect numbers at the exactly same time. And I am wondering what should I do?

    Thank you very much!

  • Enrique Espinosa added an answer in Small Molecules:
    How stable is NAD in human plasma samples at -80°?

    The plasma samples were obtained from 2005 to 2009, and have been stored at -80°C since. I know that many proteins are stable at this tempreature for long periods, but I don't know about small molecules like NAD (nicotinamide-adenine dinucleotide), which I want to measure. I also want to measure cADPR, ADPR, and NAADP.

    Enrique Espinosa

    Thanks very much. The sheet has two very useful references.

  • Rajan Vishwakarma added an answer in Steam Turbine:
    What are the design considerations to address higher thermal stresses for steam turbine casings at elevated temperature Zone (steam inlet) ?

    Apart from physical properties of material, To reduces higher thermal stresses in steam turbine casings especially in steam inlet, wall thickness optimisation, relaxing the extant of constraints, reducing the temperature differential across the wall may be the criterion.
    Can anyone comment on this or if any other criterion or way to reduce thermal stresses.

    Rajan Vishwakarma

    thanks for sharing papers related to TBC

    These papers are related to TBC for turbine blades. I need any example where TBC applied on steam turbine casings surface. 

  • Bikash Ranjan Sahoo asked a question in Gromacs:
    How to fix the error in Gromacs 5.0.x for Umbrella sampling MD simulation MD simulation?

    Dear All,

    I am trying to run US in gromacs for my protein-lipid system in version 5.0.2.

    I tried to simulate the same system using the attached pull.mdp file in Gromacs 4.6.x. It was running fine.
    Now I have upgraded my gromacs to 5.0.2. It is giving many warnings and an error.

    WARNING 1 [file pull.mdp, line 70]:
    Unknown left-hand 'pull_ngroups' in parameter file

    WARNING 2 [file pull.mdp, line 70]:
    Unknown left-hand 'pull_ncoords' in parameter file
    (12 similar warnings followed by fatal error for all pull code parameters).

    I saw your post and came to know that you have succeed in running in 5.0.2.

    Could you please check the attached pull.mdp file and suggest me how to modify it. I also have tried the tutorial pull.mdp file (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/Files/md_pull.mdp). But, I am getting almost same error for my system.

    Thanking you in anticipation
    Best regards

  • Giok P Chua asked a question in Composting:
    EarthWorm Poo & Urine from Moringa or Sweet Dates....Test Reports?

    With its beneficial nutritional values, anyone knows or has reserach test reports on the before & after of moringa/sweet dates bioproducts after composting by earthworms

    Looking at using the composting by-products for biofertilizers, amtimicrobial pesticides

    Best Regards

    Appreciate your kind assistance

  • Renjie Liu asked a question in ASF:
    What is the condition of the ASF distribution for Fischer-Tropsch synthesis ?

    Such as the temperature, pressure, H/CO

  • Amipara Manilal D added an answer in Patch Antenna:
    What are substrate dimensions of a circular patch antenna?

    In Balanis we are having active patch radius formulas, but I could not find any substrate dimensions.  

    What are substrate length and widths of a circular micro strip patch antenna.

    Amipara Manilal D

    Substrate dimensions are equal or greater than patch dimensions. The radius is equal to ground patch radius & thickness can be designed as per the impedance.

    The ground patch conductor and live patch conductor thickness is very less (Very thin layer) and to support two layers, to keep them separate (Uniformly), it is required to be supported. The support is provided by substrate (Electrical effect is added advantage). Hence substrate dimensions should be the dimensions of biggest one, generally, ground one. 

  • Sidharta Chatterjee asked a question in Phosphates:
    What are the determinants of extracellular phosphate concentration?

    Can anyone provide some references/articles that discusses in good detail the mechanism of renal handling of PO43- , and factors that modulate phosphate reabsorption and its excretion?

  • Louis Brassard added an answer in Cognitive Systems:
    Is Chalmers' so-called "hard problem" in consciousness real?

    In his 2014 book "Consciousness and the Brain: Deciphering How the Brain Codes Our Thoughts" Stanislas Dehaene wrote "Chalmers, a philosopher of the University of Arizona, is famous for introducing a distinction between the easy and the hard problems. The easy problem of consciousness, he argues, consists in explaining the many functions of the brain: how do we recognize a face, a word, or a landscape? How do we extract information form the senses and use it to guide our behavior? How do we generate sentences to describe what we feel?

    “Although all these questions are associated with consciousness,” Chalmers argues, “they all concern the objective mechanisms of the cognitive system, and consequently, we have every reason to expect that continued work in cognitive psychology and neuroscience will answer them. By contrast the hard problem is the “question of how physical processes in the brain give rise to subjective experience … the way things feel for the subject. When we see for example, we experience visual sensations, such as that of vivid blue. Or think of the ineffable sound of a distant oboe, the agony of an intense pain, the sparkle of happiness or the meditative quality of a moment lost in thought … It is these phenomena that poses the real mystery of the mind”."

    Stanislas Dehaene's opinion is "that Chalmers swapped the labels: it is the “easy” problem that is hard, while the “hard” problem just seems hard because it engages ill-defined intuitions. Once our intuition is educated by cognitive neuroscience and computer simulations, Chalmers’ “hard problem” will evaporate".

    Personally, I agree with Stanislas Dehaene's opinion.

    Louis Brassard


    When a person say something about how she feel. How she does that is subjective. But the report itself , the exterior expression of her feeling state is objective because in the public domain. If you base a study on such subjectively produced reports, you study is objective and so the subjectivity has been eliminated on your side although it was there for the production of the reports used in the study.

  • Samantha Karunarathna asked a question in Mushroom:
    What is the best way of getting DNA out from a mushroom specimen 70-80 years old, and amplify the ITS region?

    Note: the DNA of the sample possibly degraded in to 100 bp fragments.

  • Ariel Linden added an answer in SPSS:
    Do I include the baseline value of the outcome variable as one of the repeated outcome measures in a Generalised Estimating Equation analysis?

    I am doing a Generalised Linear Model analysis(GEE)  and need some advice. I am comparing two well-randomised groups for an outcome measured at 5 follow up points, and the only real difference between groups at baseline is the baseline value of the outcome variable. I want to know if I should include the baseline measure of this outcome as one of the 'repeated measures' or just use it as a covariate.  I suppose my lack of understanding of how GEEs work is the issue here. If it works by comparing the regression lines (over time)  between the two groups (and thus the comparison is simply of the gradient of the lines) then it makes perfect sense to include the baseline measure in with the 5 follow up measures. But if there is also some comparison of the absolute magnitudes of the outcome variable at each time point  in each group then including the baseline in the repeated measures would surely be a source of bias: the baseline difference could potentially contribute to any conclusion of a difference at follow up (or might eradicate any true difference). So do I include the baseline measure in the 'repeated measures' or do I just include it as a covariate? I'm using SPSS by the way. Thanks in advance!

    Ariel Linden

    Hi Mark,

    The set up for the model depends on how your data is laid out. The way you describe the model in the second post is how one would perform a difference-in-difference analysis. However, each individual in the data will have two rows of data, one for the pre period and one for the post period, indicated by a 0 or 1 on a variable called Post (in the following example):

    Y = a + b1Tr + b2Post + b3Tr*Post +  bkXk + e,

    where Y is an interval-scaled outcome variable, Tr is the treatment indicator (0/1), Post is a post period indicator (0/1), and Tr*Post is an interaction term that represents the difference-in-differences, (bkXk simply represents additional covariates as needed)

    b3 (pred) = (¯y2,Treat - ¯y1,Treat) - (¯y2,Control - ¯y1,Control)

    I hope this helps


  • David Dunaetz added an answer in Rock Art:
    How can mainstream anthropologists and archaeologists in the United States persuade our colleagues of the value of rock art?

    Do you agree that the full potential of rock art studies has not been embraced in the US?

    Do you feel that rock art is still seen by many as a marginal subject for scholarly study?

    David Dunaetz

    As a social psychologist who is interested in both anthropology and archaeology, I have felt that this field has been dismissed as unimportant in the general population.

    In general, to make people value something (e.g., rock art studies), people need to see its relevance to at least one of the following domains:

    1. Does it enhance their personal well-being? What does it provide them?

    2. Does it help them develop strong, healthy relationships with others?

    3. Does it make them feel good about who they are? Does it enhance their identity before others?

    4. Does it promote fairness and justice?

    If you can frame your studies so that it responds to at least one of these domains, these studies will be more likely appreciated by your colleagues.

  • Rafik Karaman added an answer in Cystic Fibrosis:
    Which inhaled antibiotic is best for chronic B. cepacea infection in CF patients?

    ceftazidime or meropenem?

    Rafik Karaman

    Dear Carlos,

    Attached please find a paper entitled " Treatment of lung infection in patients with cystic fibrosis: Current and future strategies"that discusses all antibiotics used for chronic B cepacea.

    I have copied some paragraphs for quick view:

    5.1. Approved aerosol antibiotics
    5.1.1. Tobramycin
    Tobramycin is an aminoglycoside antibiotic that has long been used as an aerosol therapy for CF. TIS was the first aerosol antibiotic approved for CF and has been a workhorse chronic medication and is included in the CF treatment guidelines [59],[60] and [61] for the suppression of P. aeruginosa infection, resulting in improved lung function and prevention of pulmonary exacerbations. The approved dose is 300 mg nebulized twice daily every other month. TIS is available in most countries.

    Tobramycin is also available in another nebulized formulation (Bramitob®, Chiesi) [62]. The total dose is the same as for TIS, but it is more concentrated (75 mg/mL versus 60 mg/mL) to decrease nebulization time. In a double-blind randomized study, 247 CF patients with chronic P. aeruginosa infection were randomized to receive nebulized 300 mg/4 mL tobramycin or placebo over a 24-week study period in 4-week on and off cycles. At week 20, FEV1 was significantly increased in the intention-to-treat population versus placebo. Treatment induced a trend toward decreased hospitalizations, increased nutritional status, and was well tolerated. The approved dose is 300 mg nebulized twice daily every other month. Bramitob is currently available only in European countries.

    Tobramycin has also been developed as a dry powder formulation (TOBI® Podhaler®, TIP™, Novartis) for the management of chronic P. aeruginosa infection in CF patients. Tobramycin inhalation powder (TIP) capsules are formed of low density porous particles (PulmoSphere™), which exhibit improved flow and dispersion by inhalation via the passive T-326 dry powder inhaler (Podhaler). The dose was developed to replicate the pharmacokinetics of TIS [63]. Two controlled studies investigated the efficacy and safety of TOBI Podhaler. The EAGER trial enrolled 553 CF patients comparing TIP to TIS over 3 cycles of treatment [64]. The EVOLVE trial, including 102 CF patients [65], was placebo-controlled for 1 cycle followed by open label treatment with the TOBI Podhaler for 2 additional cycles of treatment. The Podhaler formulation displayed similar tolerability and efficacy to TIS and significantly improved FEV1 compared with placebo. Cough was the most frequently reported adverse reaction related to the dry powder in both clinical studies. The recommended dose is 112 mg (four 28 mg capsules) inhaled twice daily in alternating cycles of 28 days on treatment followed by 28 days off treatment. TIP is currently available in some European countries, South America, and Canada.

    5.2. Aztreonam lysine for inhalation
    The nebulized monobactam aztreonam lysine inhalation solution (AZLI, Cayston®, Gilead) was approved in 2010 for improvement of respiratory symptoms in CF patients 6 years old and over with chronic P. aeruginosa infection. Cayston® is delivered via the PARI eFlow platform through a portable Altera handset which controls particle size for optimal airway deposition, minimizes delivery time, and increases particle delivery efficiency. Inhalation time in clinical trials averaged 2 min for each 75 mg dose[66] and [67]. The recommended dose is 75 mg inhaled thrice daily, with a minimum of four hours between doses, in alternating cycles of 28 days on treatment followed by 28 days off treatment.

    In several clinical studies Cayston® has been shown to be safe and efficacious in suppressing chronic P. aeruginosa lung infection in CF patients [66], [67], [68] and [69]. In a randomized, placebo-controlled study of 164 CF patients [67], Cayston significantly improved CFQ-R Respiratory Symptoms Score (RSS) and FEV1 after one cycle of use at 28 days, with a treatment difference compared to placebo of 9.7 points and 10.3%, respectively. In a second pivotal trial of 211 patients with CF [66], Cayston increased the median time to need for additional antipseudomonal antibiotics for symptoms of pulmonary exacerbation by 21 days, versus placebo. In the open-label follow-on study of these two trials, Cayston safety and efficacy was examined in 274 patients over 18 [68]. FEV1 values, CFQ-R RSS, and body weight increased with each 28 day course of Cayston, and this effect was maintained over 18 months. No significant safety concerns were observed in studies over 12 months [70] and 18 months [68]; including no evidence of development of antibiotic resistance.

    In a 6 month active comparator trial of 273 CF patients receiving either Cayston® or TIS, Cayston® was superior to TIS with regard to lung function improvements, with a treatment difference of 7.8% at 28 days and 2.7% at 24 weeks. Significant reductions in pulmonary exacerbations and mean change in CFQ-R RSS after 28 days of Cayston treatment were also seen, compared to TIS. In the follow-on 6 month open-label extension of this active comparator trial, the FEV1 response of previous TIS subjects who were switched to Cayston® improved and was sustained over time. Patients receiving Cayston® also gained weight throughout the 12 month trial, compared to those who received TIS who initially lost weight and then improved upon switch to Cayston® [70]. Cayston® is available in the EU, Switzerland, USA and Canada. Cayston® is licensed for use in patients 6 years and older.

    5.2.1. Colistin
    The polymyxin derivative colistimethate sodium increases Gram-negative bacterial membrane permeability causing cell death. It has been used by inhalation for many years in CF patients for the treatment of chronic P. aeruginosa lung infection [8]. Colobreathe® (Forest Laboratories) contains 1,662,500 IU of colistimethate sodium inhalation powder, for the management of chronic P. aeruginosa pulmonary infections in CF patients, aged 6 years and older [71]. In a phase III open-label trial, Colobreathe® (125 mg twice daily) was not inferior to TIS, based on change in FEV1 % predicted after 24 weeks [71]. Colobreathe® was safe and well tolerated in adult and pediatric subjects with CF [71]. Colobreathe® may be available in some EU countries in 2012.

    5.3. Medications in development
    5.3.1. Liposomal amikacin
    Liposomes are biodegradable vesicles composed of single or multiple phospholipid layers, which may protect entrapped polycationic antibiotics, such as aminoglycosides, from inactivation by polyanionic components present in sputum, such as mucins or DNA. In airways, liposomes can also be taken up by macrophages. Based on this notion, liposomal amikacin for inhalation (Arikace®, INSMED) comprised of neutral charge liposomes has been developed to improve the penetration of the aminoglycoside antibiotic into mucus plugs and P. aeruginosa biofilms [72]. Clinical studies with Arikace, delivered via the eFlow® nebulizer system, revealed a sustained release of amikacin in CF lungs [73]. The clinical pharmacokinetics and pharmacodynamics of Arikace have been evaluated in Phase Ib studies in 24 CF patients with chronic P. aeruginosa infection who received 500 mg of Arikace once daily for 14 days [73]. Randomized, placebo-controlled dose escalating phase II trials in CF patients with chronic P. aeruginosainfection showed a dose response and indicated that Arikace, delivered at a dose of 560 mg once daily for 28 consecutive days, followed by 28 days off drug, demonstrated superior clinical benefit compared to placebo as measured by significant and sustained improvement in lung function and reduction in P. aeruginosa density [74]. Also, patients receiving Arikace showed superior improvement in their respiratory symptoms as compared to those on placebo [74]. In addition, Arikace® was well-tolerated [74].

    5.3.2. Ciproinhale
    Ciprofloxacin dry powder inhaler (DPI) has been developed for the management of chronic P. aeruginosa infection in CF patients. Ciprofloxacin DPI uses the PulmoSphere® technology. Phase I studies with ciprofloxacin DPI in pediatric and adult CF patients showed that high concentrations in the lung were achieved with very low systemic exposure following single and multiple dose administration. A Phase II study of ciprofloxacin DPI, given at 2 dose levels (32.5 and 48.75 mg) twice a day for 28 days, showed significant decrease in P. aeruginosa density compared to placebo, but did not significantly improve the primary endpoint FEV1. There was also no significant change in other endpoints such as respiratory symptoms or exacerbations [75].

    5.3.3. Levofloxacin
    A novel formulation of levofloxacin, levofloxacin inhalation solution (MP-376, Aeroquin) is being developed for the management of chronic P. aeruginosa infection in CF patients. As with inhaled ciprofloxacin, pharmacokinetic studies show high levels in sputum with low systemic exposure [76]. In a phase II study [76], 151 patients with CF were randomized to one of three doses of MP-376 (120 mg every day, 240 mg every day, and 240 mg twice a day) or placebo for 28 days. The primary efficacy endpoint was the change in sputum P. aeruginosa density. All doses of MP-376 reduced P. aeruginosasputum density at day 28. A dose-dependent increase in FEV1 was observed between the 240 mg MP-376 twice-daily group and placebo. A significantly reduced need for other anti-P. aeruginosa antibiotics was observed in all MP-376 treatment groups compared with placebo. MP-376 was generally well tolerated relative to placebo.

    5.3.4. Fosfomycin/tobramycin
    A broad spectrum combination antibiotic, consisting of fosfomycin and tobramycin, is currently developed for the management of chronic bacterial infection in CF patients. A phase II study has been completed (NCT00794586) in which the safety and efficacy of 2 dose combinations of fosfomycin/tobramycin for inhalation (FTI), following a 28-day course of AZLI in CF patients and P. aeruginosa lung infection has been evaluated [77].

    5.3.5. What is the best strategy of chronic suppressive antibiotics for P. aeruginosa?
    It is reasonable when initiating therapy for chronic airways infection to implement a strategy as was used during drug development; that is, an approved inhaled antibiotic should be used in repeated cycles of 4 weeks of treatment, followed by 4 weeks off treatment. However, the original strategy of four-week on–off cycle of TIS [78], chosen for decreasing the development of resistance during antibiotic therapy, has been challenged as to whether it is the optimum treatment strategy noting the observation of a decrease in lung function during the off cycle [78]. The development of new antibiotic formulations has now given clinicians and patients greater opportunity to determine the best treatment approach. Potential strategies could employ continuous antibiotic rather than an intermittent approach, or to use a rotation of antibiotics rather than a single antibiotic. Thus, it is recommended that therapeutic options for inhaled antibiotic therapy in patients with chronic P. aeruginosa infection include an intermittent one month-on one month-off regime for inhaled aminoglycosides or continuous administration for inhaled colistin. In parallel with re-evaluation of all other aspects of care, a change of the inhalation antibiotic regimen should be considered in patients who frequently suffer from acute exacerbations or whose lung function deteriorates rapidly. Patients may remain on an intermittent one month-on one month-off regime but administering another inhaled antibiotic in the off month cycle or administering continuously inhaled antibiotic is also rationale and may benefit those patients with unstable disease. Current evidence from short-term studies suggests that inhaled antibiotics are safe and that the benefit outweighs the possible risk.

    Combining different antibiotics in a given CF patient for treating chronic P. aeruginosalung infection may prove useful, based on in vitro observations [79] and [80] and animal experiments [80].

    Hoping this will be helpful,


  • Chieng jin yu added an answer in Hiatal Hernia:
    Does anyone know about GERD induced irritative cough?

    Gastroesophageal reflux disease, or GERD , is a digestive disorder that affects the lower esophageal sphincter (LES), the ring of muscle between the esophagus and stomach. Many people, including pregnant women, suffer from heartburn or acid indigestion caused by GERD. Doctors believe that some people suffer from GERD due to a condition called hiatal hernia. In most cases, GERD can be relieved through diet and lifestyle changes; however, some people may require medication or surgery.

    Chieng jin yu

    GERD related chronic cough is known as one of the GERD related extraesophageal manifestation (suggested to refer to Montreal classification). All non-smoking patients with chronic cough but normal chest X rays and are not taking ACEI, should be suspected of GERD related chronic cough.

    Poe et al. found that GER alone accounted for cough in 13% of their study population.

    TWO mechanisms:
    (a) Irritation of the respiratory tract by aspiration

    (b) Stimulation of an esophageal-bronchial cough reflex (Vagal mediated)

    Low specificity of studies to diagnose chronic cough:

    - OGDS showed only 15% esophagitis in 45 patients with chronic cough by Baldi et al.

    - 24-h esophageal pH monitoring has low specificity in diagnosing abnormal esophageal acid exposure in patients with reflux associated chronic cough. 53% of the patients had pathological reflux. by Baldi et al. 

    American College of Gastroenterology recommends that PPI  should be tried to treat extraesophageal symptoms in patients who also have typical symptoms of GERD.


  • Yoshinori Shiozawa added an answer in Rationality:
    How do the economists define self-interest and rationality?

    How do the economists define self-interest and rationality so as to make these concepts different from the animal instincts, beast behaviour, and barbarism? What is that which forms and what is that which does not form the self-interest? Moreover, are these the behavioural guides for all individuals? Are these the collective guides for policy making? 

    Given the propensity for free riding in each economic-beast, does not the collective policy results into a collective free riding of those who make policies over those who do not?

    Yoshinori Shiozawa

    (2) Philosophical background

    Philosophy is not a part of economics. In this sense, I will talk economics from outside. However, the philosophical problem which I want to talk is nested too deeply in economics and in many aspects it is difficult to discern philosophy and economics here. 

    Reason is at the core the modern philosophy or modern thought. Descartes' most famous book is titled Discourse on the Method of Rightly Conducting One's Reason and of Seeking Truth in the Sciences. Kant has written two books on Reason. Logic is a science how Reason works or ought to work. (I will modify this understanding later.) Hegel wrote two books on Logic. Husserl wrote Logical Investigation and stated to create phenomenology. J. P. Sartre wrote Critique of Dialectical Reason. Whitehead and Russell's Principia Mathematica tried to produce foundations of mathematics basing on logic.  

    All great modern philosophers thought about reason and logic. I have no intention to deny that reason is one of most important faculty of human being. However, logic (classical or modern) is standing on complete rationality. It is the logic of omniscient and omnipotent being, It is not a logic of human being. Modern philosophy is not in general well aware of this fact. Fuzzy logic of L. A. Zadeh is more close to human logic but it is not constructed as such. (The mathematical induction on bald man that I cited in my last post is borrowed from a fuzzy logic textbook.) 

    To emphasize that we are moderately rational or we have only a bounded rationality does not imply that we deny or ignore or oppose to reasoning. A strong underground stream of modern philosophy is romanticism. Post modern thought has a strong tendency to deny reason and rationality, because they are essential part of modern thought. I am opposed to this kind of romanticism. Reason and rationality played an important role in creating free democratic world. I have no intention to deny the achievement of the modern world and the modern thought that produced it. In the consideration of economics or in the discussion of economic methodology, rationality is a kind of epistemological obstruction. A part of this reason has already been explained in my last post on Paradigmatic necessity. Distinction between moderate rationality and complete rationality (or excessive rationality in a more expressive terminology) is quite difficult. It is understandable that some of our readers in this question page have difficulty to understand it. However, there is a new trend in sciences (not very much in philosophy yet). It is the complexity. 

    Let me introduce briefly what is complexity. Warren Weaver (a director of the natural science division of the Rockefeller Foundation) published in 1948 a paper with the title Science and Complexity. He presented the next schema of the history of sciences (in the order of periods, types of problems, typical sciences) 

    Up to 19th c.  Problems of simplicity  Classical mechanics 

    • First half of 20th c.    Problems of disorganized complexity   Statistical and quantum mechanics
    •  Second half of 20th c.  Problems of organized complexity   Sciences to be created.
    • Second half of 20th c.  Problems of organized complexity   Sciences to be created.

    Note that the third stage is Weaver's expectation for the future. Weaver presented his prospect of the sciences for the second half of the 20 the century. He envisioned develop a new type of sciences.  

    I have no space to enter into the details of Weaver's prospect. I am sorry that there is no good summery or account of Weaver's idea in Wikipedia (no comments in headings Warren Weaver or Complex Systems. A short comment in heading Complexity). The paper is now reprinted as a chapter of Facets of Systems Science, Springer, 1991 and you can download it. Please read the paper for the details.

    Weaver's idea was not realized until 1970's. In this decade, various movements occurred in search of complexity sciences and 1980's it became flourished. Santa Fe Institute is one example of this wide movement. 

    There are two important points in Weaver's scheme. First, philosophy of science mainly study physics. It does not fully recognize the difference of problems of organized complexity. Second, each phase of science has its typical mathematics. Classical physics or classical mechanics used effectively differential equations. The statistical and quantum mechanics in the second phase is based on probability theory. And yet we have no mathematics which is well adapted to sciences of complexity. 

    A hint is given by the fact that probability theory became a powerful part of mathematics at the same time of establishment of second phase physics. Complexity sciences are burgeoning in every field of science and technology. Complexity economics is one of them. Although they are developing rapidly, it is remarkable that we still lack mathematics and logic which correspond to complexity sciences. One of new tools which emerged is Agent Based Simulations (ABS), but they are not well established tool of sciences. See on this point the paper below. 

    The difficulty of complexity sciences is probably juxtaposed with a much longer wave of scientific methods. We may dress a similar scheme as Weaver's: 

    • Classical Greece   Theory         Logics and mathematics
    • Modern Physical Sciences        Experiments
    • Complexity      Sciences             Computer simulation (ABS in economics)

    See the paper indicated above for a similar but detailed discussion. 

    Computer simulation is processed by a predetermined algorithm and the process is called computation or calculus. (Note this latter differs substantially from differential and integral calculus). We now know that there are close similarity between calculus and logic. It is named Curry-Howard correspondence (We have a good account of this correspondence in Wikipedia). 

    We may get two hints form Curry-Howard correspondence. First, the correspondence is established between intuitionistic logic and typed λ-calculus. Intuitionism in mathematics was proposed by L. E. J. Brower. He is famous with his fixed point theorem. At the beginning of the 20th century, mathematics was in a crisis with Cantor's paradox and later Russell's paradox. Brower, in opposition to Hilbert’s formalism and to Whitehead and Russell's logicalism, proposed intuitionism. He proposed to replace classical logic by intuitionistic logic. 

    Intuitionistic logic does not admit the laws of excluded middle and double negation. For many people this logic may be very strange but is now established as a part of mathematical logic. This logic still assumes complete rationality but approaches a bit nearer to human logic, because it is necessary to give constructive procedure when one wants to prove existence of an entity. 

    Second hint that we may draw from Curry-Howard correspondence is the relation between mathematics and computation (simulation in the case of economics). In my opinion, this correspondence means that mathematics and computation are on the opposite extremes of the scale of various types of reasoning. In between the two there is a huge unknown area of logic and reasoning. We have not yet explored this area at all. 

    It is time to reconsider the nature of our reasoning. Organized complexity presents a new and difficult task before us. We should originate a new logic for economics and for social sciences. Market economy is a huge network of exchanges. The trouble with this network is that they are organically related with each other. Probability theory is not always applicable, because at the base of probability theory we have independence hypothesis which excludes organic relationship. 

    The necessity to distinguish human and social sciences was felt by various philosophers and theoreticians around the turn to the 20th century. They claimed that human and social sciences are essentially different from natural sciences by the names such as History, Moral Science and Cultural Science. They were right but they did not succeeded in make a breakthrough, because in my opinion they did not have nay idea like Weaver and the concept of complexity. 

    Some scholars are interested in complex phenomena such as those exhibited by the chaos theory. Remind for example the economist I cited in my previous post. He was interested in the chaos theory and wanted to demonstrate that an macroeconomic dynamical system shows chaos. This is only a small part of the complexity. 

    Complexity is related to various aspects of our study. There are at least three aspects: 

    • (1) Complexity for human agents
    • (2) Complexity of a system and its processes
    • (3) Complexity for the scientific research

    In Paradigmatic necessity, I discussed two aspects concerning (1) and (3). The present post is mainly related to (3). It seems Santa Fe Institute is mainly concerned with aspect (2). 

    To sum up my long post, neglect complexity questions lies in the depth of economics and yet most economists do not recognize even the existence of the problem. This is the most serious aspect of our epistemological obstruction. This is the reason why we need some deep philosophical reflections or critique of our scientific reason.


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      DESCRIPTION: Agent-based simulation brings a host of possibilities for the future of economics. It provides a new analytical tool for both economics and mathematics. For a century and a half, mathematics has been the major tool of theoretical analysis in economics. It has provided economics with logic and precision, but economics is now suffering; economics in the 20th century made this clear. Theorists know that the theoretical framework of economics is not sound and its foundations are fragile. Many have tried to sidestep this theoretical quagmire and failed. Limits of mathematical analysis force theorists to adopt mathematically tractable formulations, though they know these formulations contradict reality. This demonstrates how economics lacks a tool of analysis that is well suited to analyzing the economy’s complexity. Agent-based simulation has the potential to save economics from this dead end and can contribute to reconstructing economics from its very foundations. Achieving this mission requires those engaging in agent-based simulation to have an in-depth understanding of economics based on its critical examinations. This guided tour leads readers around the backside of economics, tells what is wrong with economics and what is needed for its reconstruction, and provides hints for a new direction open to incorporation of agent-based simulation. This is the first draft for Chapter 1 of H. Kita, K. Taniguchi, and Y. Nakajima (Eds.) Simulation of Financial Markets with Agent-Based Model, to appear in 2016, by Springer (Vol. 9 in Evolutionary Economics and Social Complexity Science Series)
  • Ariel Linden added an answer in Experience Sampling Method:
    Can I use experience sampling methods in a single case experimental design study? or is using daily diary more appropriate for SCED?

    I'm wanting to run a study examining the effectiveness of intervention components and wanting to check which method for data collection is possible/most appropriate.  I've also been told that with the large amount of data collected with ESM interrupted time series analysis would be more appropriate than, for example, percentage of non-overlapping data, or percentage of data exceeding the median... Would really appreciate any advice! Thanks!

    Ariel Linden

    As a follow up to my previous post, I am attaching a link to a paper that introduces a program I wrote that performs interrupted time series analysis. It would be a good idea for you to read the introduction to get a better idea when, and how this type of analysis is appropriate.


    • Source
      [Show abstract] [Hide abstract]
      ABSTRACT: This article introduces the ITSA command, which performs interrupted time series analysis for single and multiple group comparisons. In an interrupted time series analysis, an outcome variable is observed over multiple, equally spaced time periods before and after the introduction of an intervention which is expected to interrupt its level and/or trend. The ITSA command estimates the effect of an intervention on an outcome variable for either a single treatment group or when compared with one or more control groups. Additionally, its options allow the user to control for autocorrelated disturbances and to estimate treatment effects over multiple periods.
      Stata Journal 06/2015; 15(2):480-500.

    + 1 more attachment

  • Amarasiri Desilva added an answer in Chronic Kidney Disease:
    How can we identify CKDU patients in their early stages of stage 1 and 2?

    In Sri Lanka, CKDu patients come to know about their disease only when they reach stages 3 and above, by which time their kidneys are mostly damaged. If there is a way in which we could identify the CKDu patients in early stages, through awareness programs they could be motivated to seek treatment at the hospitals, and as a result their life span can be prolonged. 

    Amarasiri Desilva

    Dr. Ranga Migara Weerakkody, could you provide me with a little more details on the project that is being done by the Peradeniya Team (Prof. SAM Kularathne and Prof. Kamani Wanigasuriya et al) on identification of early CKDu biomarkers? Are there any publications?  

  • Amipara Manilal D added an answer in Satellite Communication:
    SSPA or TWTA, which one should I consider to design High power amplifier in c-band satellite communication?

    SSPA is linear and TWTA is more efficient. How are linearity and efficiency of high power amplifier related? Where should I concentrate more; on linearity or efficiency? 

    Amipara Manilal D

    Both of the amplifiers are excellent in their area of application. 

    Which one to select is depend upon the application. The signal where you need distortion/harmonic  free signal, linear amplifier is preferred and for high power, one need to go for efficient amplifier.

    TWTA offers high power as compare to SSPA and SSPA is linear as compare to TWTA. 

  • Madhur Anand asked a question in Hemothorax:
    Is it really required to direct chest tubes up in pneumothorax and down in effusions and hemothorax?

    How you evaluate these traditional teachings of directing ICD tubes towards apex of lung in pneumothorax and base in hydro/hemothorax? Are they still relevant?

  • David Dunaetz added an answer in Quality of Work Life:
    Hi! Does anyone know about journals/articles/research that are related to mediator for quality of work life and mediator for career success?

    I am looking for mediator between quality of work life and career success.Any idea about such mediator? I hope that you can provide me with green lights by sharing latest journals and research about mediator for quality of work life and mediator for career success too. Your assistance is highly appreciated.Thank you. 

    David Dunaetz

    Here's an article linking quality of work life to career success.


    Likely mediators to consider would be motivation and performance.

  • Yusrifar K Tirta added an answer in Cephalopods:
    Is there any alternative preservation for kidney tissues besides Bouin fixative for molecular studies?

    I'd like to ask a few questions;

    People said that Bouin fixative is not recommended for molecular studies and ethanol does the work much better. Let say what I am try to fixate is a parasite reside in the cephalopods body (kidney). First I need to fixate the kidney smear containing parasites for characterization using microscopy and then I need to do molecular technique for the parasite itself for more analysis.

    1. What should I do for the sample preservation? In case I need to bring it overseas.

    2. Is it really that bad to extract DNA from the bouin fixated tissues or parasite? Is it impossible?

    Thank you. 

    Yusrifar K Tirta

    Dear Raju,

    Thank you for your answer.

    What i mean by molecular studies is that i want to do DNA extraction from the tissue, not exactly the tissue itself, but the parasite which attached on the tissue.

    I see, so probably it is better to use two different preservation method for microscopy and molecular study. In case getting the sample is difficult, how long does frozen parasite can preserve DNA in a good condition?

    Thank you

  • Glenn Bingham added an answer in Applied Linguistics:
    How should I determine the underlying forms of these noun stems?

    Hello everyone, I have some data from Ganda (Luganda), which is a language in the Bantu language family. I can not determine which are the underlying forms for their noun stems. I give the data as in the follows. 

    singular                     plural                    My assumption

    lulagala                     ndagala                    dagala

    lwatika                       ɲjatika                       jatika

    lweyo                         ɲjeyo                        jeyo

    luuyi                          ɲjuyi                          juyi

    lugambo                    ŋŋambo                    ŋambo

    lulimi                          nnimi                         nimi

    luyombo                    ɲɲombo                    ɲombo

    lwendo                       ɲɲendo                    ɲendo

    lunaku                       nnaku                       naku

    luyola                        ɲjola                          jola

    lupapula                    mpapula                   papula

    This question has been bothering me for a very long time. If I assume the above stems, it would be easy to explain the plural alternations, it is to add the plural prefix n- to the stems, but it would be hard to explain how the singular forms are formed, the singular prefix is lu- or lw- (before vowels). Your ideas and suggestions are highly appreciated!

    Glenn Bingham


    If you were my student, my only complaint would be that you waited too long to reach out to the world for insight. Science is a cooperative effort. Share the insight with the class (and give credit when due).

    (And thanks Angelina for the added data.)

  • Siddique Tomal asked a question in Comsol Multiphysics:
    How to draw a piezoelectric sandwich with COMSOL Multiphysics?

    There is an article where the modeling of a piezoelectric sandwich has been done with the help of AceFEM but I'm wishing to do this with COMSOL so help me in this context. Specially how to draw such sandwich in COMSOL?

  • Xingjian Xu added an answer in Sterilization:
    What is the most suitable approach for sterilizing sulphur?

    Hei, I want to sterilize sulphur.  UV irradiation sterilization or  high pressure of steam sterilization, which one is the most appropriate? 

    Xingjian Xu

    Pure sulphur powder

  • Muhammad Iqbal Hossain asked a question in Software Testing:
    Can anyone please suggest some SCI/SCI(E) indexed "free" journal for Software testing?

    Can anyone please suggest some SCI/SCI(E) indexed "free" journal for Software Engineering/testing?