tag:beta.briefideas.org,2005:/all?page=20Journal of Brief Ideas: Ideas from the last week2018-09-16T18:53:48Ztag:beta.briefideas.org,2005:Idea/4872018-09-16T18:53:48Z2021-03-09T06:00:31ZComponents of Expertisehttps://doi.org/10.5281/zenodo.1419803Herling (2000:13) in his "Operational definitions of expertise and competence" outlined three basic components of expertise: knowledge; problem-solving; and experience.
Here, I propose a more sophisticated differentiation that involves four types of knowledge:
1) Epistemic Knowledge;
2) Tooled Knowledge;
3) Meta-Cognitive Knowledge;
4) Idiosyncratic Knowledge.
Epistemic knowledge refers to the understanding and the formation of principles and generalizable causal relationships. Epistemic principles are highly likely to cross domain boundaries.
Tooled knowledge refers to specialized techniques of fact-finding, interpretation, or analysis. They are highly domain-specific.
Meta-Cognitive Knowledge refers to knowledge about one's own cognition. It involves constantly improving one's schemata regarding one's own optimal cognitive and psychic functioning.
Idiosyncratic Knowledge is divided into two types. Personal Idiosyncratic Knowledge refers to personal experiences that are not (yet) integrated into higher order functional schemata. Social Idiosyncratic Knowledge refers to social knowledge of highly arbitrary nature, which one has to learn as an instrument to function better in the society.
It is important to note that all types of knowledge can be either derived by the person themselves via Peircean abduction, or they can be acquired through systematic training or education.Araki, Michaeltag:beta.briefideas.org,2005:Idea/4782018-07-29T08:12:03Z2020-10-18T13:32:41ZDetecting the delimiter in CSVs that liehttps://doi.org/10.5281/zenodo.1402269File extensions for data sharing sometimes lie about their contents.
Here is an algorithm to infer the actual delimiter of a CSV, TSV or any related format:
- Assume that alpha-numeric characters (A-Z, a-z, 0-9) and the period/full stop (.) are cannot be delimiters.
- Begin with input text _a_.
- Store a short sample of _a_ as _b_, by copying _n_ lines from the input text _a_.
- Rank every character that appears in _b_ by frequency, creating candidate delimiters _c_
- For every candidate delimiter _d_ in _c_, split each line in _b_. If every line has the same number of splits, _d_ is the delimiter.
An implementation of this idea is available [on Zenodo](https://zenodo.org/record/1323186) and within the [Python Package Index](https://pypi.org/project/detect-delimiter/).McNamara, Timtag:beta.briefideas.org,2005:Idea/4682018-06-29T11:05:04Z2020-08-09T06:00:51ZThe Academic Venture Coachbook for the Social Sciences and Humanitieshttps://doi.org/10.5281/zenodo.1302045Academic entrepreneurship concept has been in place for a while, but not many well-documented research studies approached it from the angle of making academic entrepreneurship a genuinely commercially-viable venture. Even in highly-cited books such as Scott Shane’s Academic Entrepreneurship: University Spinoffs and Wealth Creation, useful ideas are tied to the key concept of ‘spinoff’, which is too simplistic, and too ideal, for the genuine meaning of commercial venture, which basically represents a continuum of entrepreneurial activities and processes. Also, there has been little discussion about the academic venture in the social sciences and humanities, except the specific ones of economics and business. The idea of the Academic Venture Coachbook represents a serious attempt to:
a) Coach a researcher in the social sciences and humanities in performing their research duties, with adequate preparations for future ‘academic business’;
b) Walk her/him through the process that provides an analogy between a researcher and an entrepreneur (so that they are not ‘different animals’); and,
c) Show the real calculus of cost-benefit analysis and necessary-sufficient conditions, with pecuniary rewards, should be an essential part of the calculation.
Such a coachbook idea should also be an example of an ‘academic product’ that can be sold for real cash, i.e., a genuine venture.Vuong, Quan Hoangtag:beta.briefideas.org,2005:Idea/4672018-06-26T23:46:54Z2018-06-27T06:01:26ZCros-IP: A Novel Co-immunoprecipitation Method for Characterising Direct/Indirect Protein Interactions.https://doi.org/10.5281/zenodo.1298748Co-immunoprecipitation (co-IP) is considered the gold standard in vitro technique for characterising protein-protein interactions. However, the technique is limited by the inability to differentiate direct/indirect interactions of proteins. This publication presents a novel IP technique named ‘Cros-IP’ (Figure 1: Protocol Flow Diagram) that has been validated by experiments (data not shown). Antibody immobilised to beads containing Protein A/G is incubated with cell lysate/protein mixture, and spun/washed using the conventional co-IP method, with the exception that the tris-based buffers should be replaced by phosphate-based buffers due to the presence of a primary amine on the tris compound. After unbound (non-interacting) proteins in the cell lysate have been thoroughly washed away, the beads-antibody-protein complex is incubated with the protein crosslinker disuccinimidyl suberate (DSS) for 2 hours on ice. The protein complex is then eluted using a sodium dodecyl sulfate (SDS)-based buffer. This technique takes advantage of the considerably inconsistent crosslinking rate of DSS, with a series of crosslinked protein products expected to be formed. The product consisting the antigen (target protein) crosslinked with interacting proteins (Figure 1, Product B) can be used to characterise the sequence of protein interactions of an in vivo protein complex via SDS-PAGE/Western blotting and/or mass spectrometry characterisation.Su, Shih-Pingtag:beta.briefideas.org,2005:Idea/4642018-06-26T00:16:49Z2018-06-26T06:00:32ZReport a relative proportion of patients ruled-out or ruled-in with a diagnostic testhttps://doi.org/10.5281/zenodo.1297700One measure of the performance of a diagnostic test is the proportion of patients the test stratifies as likely not to have the condition (ruled-out:RO) or to have the condition (ruled-in:RI). This proportion depends on the prevalence of the disease in the cohort. This means that it is not valid to compare tests performed in cohorts with differing prevalences. However, this is exactly what is often done in the discussion section of academic papers. Usually there is a target sensitivity (t_sn) for the test which means that the maximum proportion ruled-out at that sensitivity is:
```
ROmax=(TN + TP(1/t_sn -1))/(TN + TP/t_sn)
```
Where TN=True Negative, TP=True Positive. Note for ROmax, there are zero False Positives (FP). Also, in the case where t_sn=1 (False Negatives, FN=0), R0max=1-prevalence.
Similarly, if there is a target specificity (t_sp) the maximum proportion ruled-in is:
```
RImax=(TP + TN(1/t_sp -1))/(TP + TN/t_sp)
```
Note, in the case where t_sp=1 (FP=0), RImax=prevalence.
Therefore, to better be able to compare between studies, both the measured proportion of those ruled-out and those ruled-in should be normalised to their maximum possible values:
```
Adjusted proportion ruled-out = measured proportion ruled-out / ROmax
Adjusted proportion ruled-in = measured proportion ruled-in / RImax
```
Pickering, John Williamtag:beta.briefideas.org,2005:Idea/4622018-06-23T19:39:23Z2018-07-06T17:11:57ZOCD, ST JOHN'S WORT AND IRON.https://doi.org/10.5281/zenodo.1297179MAOI and St John's Wort treatments for OCD may have a similar radical-based mechanism. Six years' unrelieved total compulsive thinking was cured by the MAOI Phenelzine, with also a role for radical-releasing phenols which enter the CNS very little .1. (Journal of Brief Ideas article "Oxidative stress, MAOIs and OCD"). Side-effects lead to a search for alternatives. St John's Wort extract proved ineffectual (at 5 x 333 mg whole herb equivalent per day), but cure was greatly improved when ferrous fumarate was added to St John's Wort (at 2 x 14 mg per day). This improved cure, just as on the MAOI, did not happen until after several weeks, but followed 24 - 48 hours after the advent of peripheral serotonin release patterns. This suggests that the enabling of radical-based releasing of serotonin is a crucial first stage, as on MAOIs, as excess iron ions are known to increase the radical effects behind gut serotonin release by cisplatin and pyrogallol, for example. .2.
.1. Neurology,Psychiatry and Brain Research 5(4):181, 8(4):185, 10(4):149.
.2. European Journal of Pharmacology: Environmental Toxicology and Pharmacology.(1993) 248:329-331. STEWART, JOHNtag:beta.briefideas.org,2005:Idea/4592018-05-17T19:56:17Z2018-06-12T16:54:17ZImagery in Rock and Ancient Art Influenced by Pareidolic Response to Environmental Stimulihttps://doi.org/10.5281/zenodo.1250209A Pareidolic Response to Environmental Stimuli occurs when it is triggered by a certain richly textured surface or object . This human trait is a result of a survival mechanism, where the environment is quickly scanned for potential threats. A well known example is seeing animals in clouds. The curious experience has been artistically communicated in modern culture, on the internet via image sharing of trees resembling people and faces emerging from woodgrain texture. Indigenous cultures name mountain ranges for the people or animals visible in the rock contours. Photography books depict figures perceived in vegetation, and daVinci admitted using it to create scenes. As a human trait, it would have been active, perhaps even more pronounced in the Upper Paleolithic, and in ancient times. Without knowledge of the scientific explanation, a Pareidolic event would have significant impact on ancient people, resulting in an artistic communication of the beings perceived.
Environmental triggers and the corresponding art include:
the moon (man in the moon) - Inca and Haida art
rock surface - cave art (traced directly)
trees - (Baobab) Australian Aboriginal art
tree limbs and shadows - some stick men
rocks reflected shoreline - Haida
Lava - Maori and Hawaiin
Desert vegetation - HopiNeumann, Ericatag:beta.briefideas.org,2005:Idea/4582018-05-10T12:10:40Z2018-05-18T06:01:14ZRestricted SDM: Predicting habitat suitability from species occurrence onlyhttps://doi.org/10.5281/zenodo.1248991Species Distribution Models are commonly used to predict species habitat suitability. The data needed to build such a model usually consist of a range of environmental variables together with a target variable - the species occurrence itself (often in presence/absence format, or just presence).
An interesting idea that can be applied to this problem is to rely on the species occurrence only. The assumption here is similar to a market basket analysis: similar species should co-occur, much likely to a shopping cart containing frequently purchased together items, such as ketchup and french fries. In this case our features become different species, and our observations are different sites where they are either present or absent. We can use such a model to predict the probability of a new species occurring when some of the others have already been identified. Possible difficulties in using this approach are class imbalance, large dimensionality and sparsity in the data. Dimensionality reduction techniques such as PCA can be useful in this case and improve the prediction performance.
Attached are some preliminary results, predicting the occurrence of the Great horned owl (_Bubo virginianus_) from the [ebird](https://ebird.org/) reference dataset.Angelov, Boyantag:beta.briefideas.org,2005:Idea/4512018-04-05T11:33:47Z2020-07-17T13:07:43ZMicrobial butanol tolerance: mediated by toxicity or by phase equilibrium?https://doi.org/10.5281/zenodo.1219005It is conventionally assumed that the achievable concentration of a bio-alcohol molecule by fermentation is limited by the toxicity of that molecule to the micro-organisms producing it. In the case of ethanol, for example, extremely high titers have been achieved by developing resistant strains of micro-organism. Butanol, conversely, has proven remarkably stubborn to this same sort of progression. Despite widespread efforts, concentration above 2% have not been achieved.
2% also happens to be the limit of solubility of butanol in water. It seems intuitive that intra-cellular phase separation would result in highly toxic localized concentrations of butanol, and generally disrupt material transport through cell membranes. This would suggest that butanol titers are fundamentally limited by phase equilibrium and that conventional research to improve butanol tolerance will prove fruitless.
This hypothesis could be tested experimentally in one of two ways. Firstly, ethanol-producing organisms could be cultivated in a 2% butanol solution. If toxicity is severe then they would be highly inhibited in this environment but if phase equilibrium is the limit then they will cope well. Alternatively, higher temperatures improve solubility. Hence, if butanol tolerance increases with temperature it can be inferred that solubility is limiting.Stacey, Neil Thomastag:beta.briefideas.org,2005:Idea/4502018-04-01T12:52:18Z2018-04-05T06:00:49ZA combinatorial approach towards treating cancer through Cisplatinhttps://doi.org/10.5281/zenodo.1212226Cisplatin is an effective chemotherapeutic drug against a vast variety of cancers. It is a cytotoxic drug that kills cancer cells by forming DNA adducts, thereby damaging the DNA leading to apoptosis. However, the clinical use of cisplatin is limited by severe side effects in healthy tissues with nephrotoxicity being the major issue (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3756417/). The side effects are mainly due to the accumulation of cisplatin in kidney, especially when the drug is transported through organic cation transporter II expressed in the basolateral membrane of proximal tubule cells. This induces p53 which activate PUMAα (pro-apoptotic protein) in renal tubular cells which leads to renal failure due to apoptosis (https://www.hindawi.com/journals/scientifica/2012/473829/).
However, this can be prevented by pre-treatment with QiShenYiQi pills (QSYQ), a compound in Chinese medicine which significantly decreases histological damage and cisplatin-induced increase in plasma urea levels and creatinine levels (https://www.researchgate.net/publication/321989615_QiShenYiQi_Pills_a_Compound_Chinese_Medicine_Prevented_Cisplatin_Induced_Acute_Kidney_Injury_via_Regulating_Mitochondrial_Function). Thereby we propose, a combinatorial treatment approach towards cancer through cisplatin and QSYQ, where the later can decrease the cisplatin-induced nephrotoxicity and enhance the clinical use of cisplatin chemotherapy without any side effects.
Jainarayanan, Ashwin K.Sharma, Ankush