Simple and effective: the principle of PCR

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Simple allele-discriminating PCR for cost-effective and rapid genotyping and mapping

Simple allele-discriminating PCR for cost-effective and rapid genotyping and mapping

To discriminate single base changes between wild type and the mutant allele, a forward primer that exclusively anneals to WT and another forward primer that exclu- sively anneals to the mutant allele are designed. These two allele-specific (AS) primers are paired with a common reverse primer for standard PCR reactions. The AS primers are designed based on the principle that if the existing SNP mismatch results in a weak destabilization between the AS primer and its non-template target, a strong desta- bilizing mismatch will be introduced at the penultimate site. Conversely, if the SNP mismatch already has a strong destabilizing effect, a weak destabilizing mismatch should be introduced at the penultimate site. If a medium desta- bilizing effect exists at the SNP mismatch, a weak or medium mismatch will be created at the penultimate site. Table 1 indicates the weak, medium, strong, or maximum destabilization effect of each mismatched pair, based on Little (1995) [16]. In general, the purine-pyrimidine mis- pairing (G-T and A-C) are more stable and exhibit a weaker destabilization effect than the purine-purine or pyrimidine-pyrimidine mismatches as purine-pyrimidine mismatches still form two hydrogen bonds in a geometry similar to G-C and A-T, and they do not require contract- ing or expanding the double helix. Pyrimidine-pyrimidine or purine-purine mispairings, in contrast, are more unsta- ble because of the altered geometry in the double helix as well as reduced hydrogen bonding. For more detailed analyses of thermodynamics of mismatches, one can con- sult Peyret et al. (1999) [18].
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Evaluation of Simple and Cost-Effective DNA Preparation and Subsequent PCR Amplification for Clinically Relevant Mycobacteria

Evaluation of Simple and Cost-Effective DNA Preparation and Subsequent PCR Amplification for Clinically Relevant Mycobacteria

Technical complexity as well as the equipment and consumables required make the use of enzymatic lysis, detergents, and other commercial extraction methods time consuming and expensive. In order to find the optimal procedures to minimize processing time, costs and bio safety risks, we evaluated8 protocols for extracting DNA from cultures of MTB and NTM for the direct PCR detection of mycobacteria.

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Use of Amplification Refractory Mutation System PCR Assay as a Simple and Effective Tool To Detect HIV 1 Drug Resistance Mutations

Use of Amplification Refractory Mutation System PCR Assay as a Simple and Effective Tool To Detect HIV 1 Drug Resistance Mutations

Simple and Effective Tool To Detect HIV-1 Drug Resistance Mutations Aubin J. Nanfack, a,b,c Lucy Agyingi, d,e Jean Jacques N. Noubiap, e,f Johnson N. Ngai, e Vittorio Colizzi, b,g Phillipe N. Nyambi a,h Department of Pathology, New York University School of Medicine, New York, New York, USA a ; Department of Immunology and Applied Biotechnology, University of Rome Tor Vergata, Rome, Italy b ; Chantal Biya International Reference Center, Sequencing Unit, Yaounde, Cameroon c ; Faculty of Sciences, University of Dschang, Dschang, Cameroon d ; Serology Unit, Medical Diagnostic Center, Yaounde, Cameroon e ; Internal Medicine Unit, Edéa Regional Hospital, Edéa, Cameroon f ; UNESCO Chair of Interdisciplinary Biotechnology, University of Rome Tor Vergata, Rome, Italy g ; Veterans Affairs New York Harbor Healthcare Systems, New York, New York, USA h
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CharBot : a simple and effective method for evading DGA classifiers

CharBot : a simple and effective method for evading DGA classifiers

These findings expose a dangerous weakness in modern DGA classifiers: they can be circumvented using a simple algorithm and they cannot be easily trained to detect it well. We speculate that this weakness is inherent in any model that relies solely on domain name strings to perform DGA classification. CharBot works by introducing a small number of typographical errors in benign domain names from the Alexa data set. As such, the statistical properties of the names it generates will be almost identical to those of the Alexa domains. This makes it nearly impossible for a classifier to draw any significant distinction between Alexa names and CharBot names. Moreover, any other set of legitimate domains that should be accepted by a classifier with high probability could in principle be used instead of Alexa by a CharBot attack. Therefore, we do not believe these attacks can be mitigated without relying on additional side infor- mation. Such information might include the IP addresses the domains resolve to, how many times the domains were queried and when, etc. This has been explored in other works already [3], [10], [16]–[18]. To our knowledge, we are the first to expose this type of weakness in DGA classifiers that do not use side information. We would, therefore, recommend that the community focuses its research efforts on DGA classifiers that utilize side information and not just rely on the domain name string by itself.
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Absolutely New, Simple and Effective Theory of Movement Steadiness

Absolutely New, Simple and Effective Theory of Movement Steadiness

Up to now, Liapunov's method of the positive-definite functions has remained the most common. However, this method has serious shortcomings. Liapunov's method is based on the sufficient conditions of the stable motion. But, it is known that the sufficient conditions almost always are less effective for searching the solution for any problems than the necessary conditions. And if by means of sufficient conditions it is impossible to solve the problem, then it does not mean that the solution does not exist. As the necessary conditions of the stable motion (in accordance with its definition) are regarded in assumption of existence of the stable motion, these conditions almost always permit to find this stable motion if one exists. Whereas by means of the sufficient conditions it often turns out impossible in principle to find the desirable solution for the problem.
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A Simple Model of the Difference Principle

A Simple Model of the Difference Principle

Note that the contribution curve, the curve OP, supposes that social coop- eration defined by the basic structure is mutually advantageous. It is no longer a matter of shuffling about a fixed stock of goods ([1], p. 77). It would be impossible to consider the difference principle using any standard market model lacking this sort of mechanism because the difference principle is reduced to the (average) utilitarian principle in such models. We will expand on this point at a later stage. However, we must stress that a mechanism caused by external increasing returns is an example of reciprocity. We do not assert that it is the mechanism by which the second principle is fulfilled. What we hope to accomplish in this paper is to show how mutual benefits are naturally built into social increasing returns and that they will then give us an intuition how the second principle can be realized in societies characterized by property-owing democracy or liberal socialism.
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Principle for Effective Engagement

Principle for Effective Engagement

D 5.1 – Principles for Effective Engagement only available from the 1990s, which show that the majority of Spaniards opposed nuclear energy and the development of nuclear power stations, and that these levels of opposition and rejection of nuclear expansion in Spain are high when compared to other EU countries, such as the U.K., and are more comparable to public opinion in Germany. Social movements in the 1970s, 1990s and mid 2000s demonstrate this. Following the fall of the Franco Regime, anti-nuclear protests during the 1970s were associated with strong regional identities. In the Basque case, this translated into violent action, with 13 lives being lost. In 1976 this movement progressed and became increasingly organised, with the Committee for the Defence of a No Nuclear Basque Coast (CDCVNN) forming through an a amalgamation of anti-nuclear neighbourhood associations, cultural groups and professional associations. In 1991 during the Gulf War the campaign ‘Living without nuclear’ was launched, which saw approximately half a million signatures collected, requesting a referendum to close nuclear power plants in Spain. In 2007, more than 600,000 signatures were collected and brought to Brussels demanding the shutdown of plants, uranium mining and research on their effects on health.
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A Simple Mathematical Formulation of the Correspondence Principle

A Simple Mathematical Formulation of the Correspondence Principle

ABSTRACT In this paper we suggest a simple mathematical procedure to derive the classical probability density of quantum systems via Bohr’s correspondence principle. Using Fourier expansions for the classical and quantum distributions, we assume that the Fourier coefficients coincide for the case of large quantum number. We illustrate the procedure by analyzing the classical limit for the quantum harmonic oscillator and the particle in a box, although the method is quite general. We find, in an analytical fashion, the classical distribution arising from the quantum one as the zeroth order term in an ex- pansion in powers of Planck’s constant. We interpret the correction terms as residual quantum effects at the micro- scopic-macroscopic boundary.
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Implications of the principle of effective stress

Implications of the principle of effective stress

Shear bands arise in sand when the elastic energy of the grain fabric attains a critical point with respect to its elastic strain. Rather fractal patterns of shear bands arise with dilation as critical phenomena, with them spatial fluctua- tions diverge so that Cauchy stress fields and gradients are contestable. The principle of effective stress is still legiti- mate for saturated sand with shear bands by using spatial averages of stress, pore pressure and void fraction as the p w -neutrality of the mineral is not impaired by spatial fluctuations. This works also for saturated clay if the vis- cosity of the solid fabric is taken into account. Different to Terzaghi’s and Hvorslev’s standpoint, the resistance to drained shearing after over-consolidation can be explained without an effective cohesion, while the total cohesion without drainage can be attributed to suction which can lead to a cavitation of pore water.
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Mill's 'very simple principle': Liberty, utilitarianism and socialism

Mill's 'very simple principle': Liberty, utilitarianism and socialism

The "strong"/"weak" distinction gives rise to more difficulties than it solves. For one thing, it totally removes the clarity and simplicity from the operation of Mill's "very simple" principle. Mill puts forward the principle as a convenient yardstick for answering "the practical question" of where to set the limit of social control encroaching on individual independence3-3 . What Gray and Ten are saying is that this yardstick will not suffice, and it is necessary to consider further, supplementary, criteria about whether the individual understands what he is doing, or is "clearly" acting as a result of "considered rational deliberation". This introduces far greater complexity, uncertainty and, indeed, arbitrariness into the application of Mill's principle. Moreover, it is hard to believe that the state can possibly know what goes on in people's minds - whether they have made rational deliberations or understand what they are doing - and, even if it could, the arrogation by the state of the discretion to make such judgements involves an enormous extension of state power. The world of the "Thought Police" beckons.
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Simple Tips For Creating Effective Ads

Simple Tips For Creating Effective Ads

But if humor isn’t part of your day-to-day persona, you might find it uncomfortable or awkward to make it the centerpiece of your advertising. Humor is also very subjective, so use it with caution. If you’re working with agencies or other third parties, and you’re not entirely convinced that a humorous slant is effective, try something more straightforward. Finally, humor has a short shelf life. Your first humorous ad can get stale rather quickly. If you can’t use a humorous concept consistently in several, if not many, different pieces of your

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Simple and Effective Theory of Movement Steadiness

Simple and Effective Theory of Movement Steadiness

Smol’yakov Eduard Rimovich. Simple and Effective Theory of Movement Steadiness. International Journal of Theoretical and Applied Mathematics. Vol. 5, No. 6, 2019, pp. 113-117. doi: 10.11648/j.ijtam.20190506.15 Received: November 10, 2019; Accepted: December 2, 2019; Published: December 11, 2019 Abstract: It is proposed the very simple and quick method for estimation of the asymptotic stability of any nonlinear dynamic systems, in particular, of the high-dimensional systems for which Tailor series of the right-hand sides of the differential equations converge very slowly. In such problems, the sum of terms of the order of smallness higher than two can substantially exceed the value of any term of second order. In this case, Lyapunov’s methods cannot guarantee correct stability estimate at all. The new method does not use the notion of Liapunov function and, therefore, one has no numerous shortcomings of all Liapunov methods. In this paper, it is proposed to replace the very complex problem of the searching for Liapunov function with a very simple problem of the searching maximum of the function of n coordinates (that is of the velocity of variation in metrics of the perturbed state space). However, one is not intended for the linear systems.
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Tax-effective giving. made simple

Tax-effective giving. made simple

Tax-effective giving made simple 15 Conclusion Charities that receive donations from individuals may be able to increase the value of those donations by structuring them tax efficiently. Gift Aid is the best know tax relief and is a very effective route for increasing the value of cash donations from UK taxpayers. It can be administratively burdensome, but the benefits will usually outweigh the costs.

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The principle of effective delegation from prophet muhammad life

The principle of effective delegation from prophet muhammad life

People might be reluctant to achieve a targeted task, or they might lose motivation in a workplace. A leader has a significant role in reinforcing the reasons for working. Accordingly, before delegating tasks, the purpose of achieving it has to be fully realized by the performers. A leader should not merely explain the reason for doing the task, but also how to approach it, using non-verbal skills if needed to enhance the meaning of words. Having said that, the Prophet has provided clear pictures of how he motivates, explains tasks and uses various approaches to express how to perform various tasks. In addition, clarifying the reasons for doing a task and developing trustful relationships are more powerful motivations, unlike the use of force. Cultivating a culture of openness and trust creates a climate of mutual respect, unlike an atmosphere of power, force and coercion. When workers are fearful they are less effective. This point was apparent in the Prophet’s method of delegation. He did not delegate tasks before having a precise understanding of others and matching the task to the person’s qualifications and strengths. This is clear when he gave responsibilities to his companion with whom he had a long relationship. In addition, when the tasks are suitable and interest the person, they retain their attention and perform them enthusiastically, for example when the Prophet appointed his companion Abu Bakr to lead the Muslim prayers. Not only assigning appropriate tasks, but also using complimentary titles and stimulating a sense of competition increases people's keenness to perform tasks, such as when the Prophet asked “Is there among us a knight who can guard us tonight?” In Maslow's hierarchy of needs, satisfying the needs of self- esteem can influence behaviors.
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The principle of effective stress and triaxial compression testing of peat

The principle of effective stress and triaxial compression testing of peat

j 1 j 2 Peat deposits comprise the fragmented remains of dead plant vegetation that have accumulated under waterlogged conditions. Effective stress theories developed for mineral soils are routinely applied in practice for peat, although there are fundamental issues regarding the application of conventional soil mechanics to peat, on account of its extremely high water content, fibrous nature, low shear strength and high compressibility, and also the flexible, permeable and compressible nature of the porous organic solids. This paper presents an experimental study intended to contribute to the ongoing and increasing debate about the degree to which conventional soil mechanics approaches can be applied to peat. A programme of isotropic consolidated-drained triaxial compression tests was performed on saturated fibrous peat under the same effective confining pressure, but developed by applying different cell- and back-pressure combinations. Effects of mini-structure and fibre content on mechanical response were considered by testing undisturbed, reconstituted and refined (blended) peat materials. Similar volumetric strain–time and stress–strain–time responses experienced by identically prepared triaxial specimens were persuasive regarding the applicability of the principle of effective stress to peat, although there is no firm conclusion, since significant challenges occurred in performing these tests and in interpreting the data.
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A Simple PCR Method for Rapid Genotype Analysis ofMycobacterium ulcerans

A Simple PCR Method for Rapid Genotype Analysis ofMycobacterium ulcerans

Institute of Tropical Medicine, Antwerp, Belgium 2 Received 3 November 1999/Accepted 23 January 2000 Two high-copy-number insertion sequences, IS2404 and IS2606, were recently identified in Mycobacterium ulcerans and were shown by Southern hybridization to possess restriction fragment length polymorphism between strains from different geographic origins. We have designed a simple genotyping method that captures these differences by PCR amplification of the region between adjacent copies of IS2404 and IS2606. We have called this system 2426 PCR. The method is rapid, reproducible, sensitive, and specific for M. ulcerans, and it has confirmed previous studies suggesting a clonal population structure of M. ulcerans within a geographic region. M. ulcerans isolates from Australia, Papua New Guinea, Malaysia, Surinam, Mexico, Japan, China, and several countries in Africa were easily differentiated based on an array of 4 to 14 PCR products ranging in size from 200 to 900 bp. Numerical analysis of the banding patterns suggested a close evolutionary link between M.
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A Simple Technique for Optimizing the Implementation of the Aperture Theorem Based on Equivalence Principle

A Simple Technique for Optimizing the Implementation of the Aperture Theorem Based on Equivalence Principle

technique is developed based on the FDTD method. As well-known, the Yee cells cannot model the non-regular shapes very well. The TSF technique is only for the long thin slot. It can be a problem when it is used in the multiscale structures. The equivalence principle is introduced to increase the accuracy of the results in [14]. But because the denominators of the coefficient in the updating equations contain the electric fields which are zero in some moments in the simulation, it is not easy to use in practice. And the slot needs to be just in the center of the Yee cell in the TSF technique. And the results become inaccurate when the width of the slot equals the length of the cell’s edge. When using other numerical methods alone, such as FEM and MOM, much denser meshes are needed in the aperture region.
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A Simple and Effective Hierarchical Phrase Reordering Model

A Simple and Effective Hierarchical Phrase Reordering Model

7 Conclusions and Future Work In this paper, we presented a lexicalized orientation model that enables phrase movements that are more complex than swaps between adjacent phrases. This model relies on a hierarchical structure that is built as a by-product of left-to-right phrase-based decod- ing without increase of asymptotic running time. We show that this model provides statistically signifi- cant improvements for five NIST evaluation sets and for two language pairs. In future work, we plan to extend the parameterization of our models to not only predict phrase orientation, but also the length of each displacement as in (Al-Onaizan and Papineni, 2006). We believe such an extension would improve translation quality in the case of larger distortion limits. We also plan to experiment with discrimi- native approaches to estimating reordering probabil- ities (Zens and Ney, 2006; Xiong et al., 2006), which could also be applied to our work. We think the abil- ity to condition reorderings on any arbitrary feature functions is also very effective in the case of our hi- erarchical model, since information encoded in the trees would seem beneficial to the orientation pre- diction task.
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A Simple and Cost Effective Raman- Fluorescence Spectrometer

A Simple and Cost Effective Raman- Fluorescence Spectrometer

The laser is used to probe a sample to elicit Raman scattering, the filtering optics are a series of filters that serve to filter out noise due to Rayleigh scattering, the monochromat[r]

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Simple and Effective Multi Paragraph Reading Comprehension

Simple and Effective Multi Paragraph Reading Comprehension

The no-answer and merge approaches were moderately effective, we suspect because they at least expose the model to more irrelevant text. However, these methods do not address the fun- damental issue of requiring confidence scores to be comparable between independent applications of the model to different paragraphs, which is why we think they lagged behind. The sigmoid objec- tive function reduces the paragraph-level perfor- mance considerably, especially on the TriviaQA datasets. We suspect this is because it is vulner- able to label noise, as discussed in Section 2.2.

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