ARTICLE | doi:10.20944/preprints202207.0123.v1
Subject: Materials Science, General Materials Science Keywords: CoGa; electronic structure; magnetism; binary alloys
Online: 7 July 2022 (09:44:18 CEST)
The present work reports on the calculated electronic and magnetic structure of the binary Co-Ga system at high Co content. β-CoGa adopts a simple cubic CsCl type structure. Well-ordered CoGa does not exhibit collective magnetism but is a paramagnetic, metallic compound. Neither Co nor Ga deficiency induces magnetic order, however, ferromagnetism is observed for Co-Ga anti-site disorder. The magnetic moment per cell increases up to about 1.2 μB in the completely disordered body centered cubic structure. With increasing Co content, Co1+xGa1−x maintains the CsCl type structure and becomes ferromagnetic. Most important, a discontinuity of the magnetic order with composition is observed at about 10% excess Co, where a change from a low magnetic moment state to a high moment state is observed. This is accompanied by a change in the electronic structure and transport properties. The discontinuity is forced by the increasing exchange splitting related to the localized moment of the additional Co atoms that replace Ga. Subsequently, the magnetic moment increases continuously up to 2.5 μB for x=0.6. For x≳0.6, the structure changes to face centered cubic with random site occupation and the magnetic moment further increases. Above the magnetic discontinuity, the Curie temperature increases linearly with the Co content from the onset of ferromagnetism, until it reaches its maximum in pure Co.
ARTICLE | doi:10.20944/preprints202002.0303.v1
Subject: Mathematics & Computer Science, Analysis Keywords: fixed point; integral equation; binary relation
Online: 21 February 2020 (03:22:12 CET)
In this article, we introduce a relatively new concept of multi-valued (θ;R)-contractions and utilize the same to prove some xed point results for a new class of multi-valued mappings in metric spaces endowed with an amorphous binary relation. Illustrative examples are also provided to exhibit the utility of our results proved herein. Finally, we utilize some of our results to investigate the existence and uniqueness of a positive solution for the integral equation of Volterra type.
ARTICLE | doi:10.20944/preprints202211.0528.v2
Subject: Life Sciences, Genetics Keywords: DNA strands, complementary replication, DNA alphabets, binary opposition, binary numbers, dyadic groups, matrices, algebras, split-quaternions, root-complementarity.
Online: 20 December 2022 (01:29:16 CET)
This article is devoted to results of in-depth analysis of the system of binary-oppositional structures in DNA n-plet alphabets and their algebraic-matrix representations. These results show that the molecular complementary replication of DNA strands is accompanied by the presence of an algebraic version of the principle "like begets like" in matrix representations of DNA alphabets having internal structures. This algebraic version is based on binary-oppositional structures in the genetic molecular system, which can be represented by bynary numbers and corresponding matrices of DNA alphabets. The received results allow thinking that the phenomenon "like begets like" (or a complementary replication in a wide sense) is a systemic in the genetic organization and is connected with algebraic features of biological organization. Correspondingly, the biological principle "like begets like" can be additionally modeled by algebraic-matrix methods and approaches. Such algebraic-matrix modeling of the genetic coding system gives new ways for studying and understanding a key role of the named principle in genetic and other inherited physiological complexes. The author believes that further study of the algebraic relationships of the genetic system and inherited physiological complexes will be increasingly revealing the key biological role of the ancient principle "like begets like" at different levels of biological organization.
ARTICLE | doi:10.20944/preprints202206.0202.v1
Subject: Social Sciences, Economics Keywords: Machine Learning; Clusterization; Elbow Method; Prediction; Correlation Matrix; Principal Component Analysis; Binary and non-Binary regression models
Online: 14 June 2022 (09:54:46 CEST)
The following article presents an analysis of the determinants of diabetes using a dataset containing the surveys of 2000 patients from the Frankfurt Hospital in Germany. The data were analyzed using the following models, namely: Tobit, Probit, Logit, Multinomial Logit, OLS, WLS with heteroskedasticity. The results show that the presence of diabetes is positively associated with "Pregnancies", "Glucose", "BMI", "Diabetes Pedigree Function", "Age" and negatively associated with "Blood Pressure". A cluster analysis is realized using the fuzzy c-Means algorithm optimized with the Elbow method and three clusters were found. Finally a confrontation among eight different machine learning algorithms is realized to select the best performing algorithm to predict the probability of patients to develop diabetes.
ARTICLE | doi:10.20944/preprints202105.0649.v1
Subject: Engineering, Automotive Engineering Keywords: Binary switches; benchmarking; energy-delay product; reliability
Online: 26 May 2021 (15:14:15 CEST)
Binary switches, which are the primitive units of all digital computing and information processing hardware, are usually benchmarked on the basis of their ‘energy-delay product’ which is the product of the energy dissipated in completing the switching action and the time it takes to complete that action. The lower the energy-delay product, the better the switch (supposedly). This approach ignores the fact that lower energy dissipation and faster switching usually come at the cost of poorer reliability (i. e. higher switching error rate) and hence the energy-delay product alone cannot be a good metric for benchmarking switches. Here, we show the trade-off between energy dissipation, energy-delay product and error-probability, for both an electronic switch (a metal oxide semiconductor field effect transistor) and a magnetic switch (a magnetic tunnel junction switched with spin transfer torque). As expected, reducing energy dissipation and/or energy-delay-product generally results in increased switching error probability and reduced reliability.
ARTICLE | doi:10.20944/preprints202001.0318.v1
Subject: Mathematics & Computer Science, General & Theoretical Computer Science Keywords: efficient binary symbiotic; feature selection; classification; optimization
Online: 26 January 2020 (08:30:17 CET)
Feature selection is one of the main data preprocessing steps in machine learning. Its goal is to reduce the number of features by removing extra and noisy features. Feature selection methods must consider the accuracy of classification algorithms while performing feature reduction on a dataset. Meta-heuristic algorithms are the most successful and promising methods for solving this issue. The symbiotic organisms search algorithm is one of the successful meta-heuristic algorithms which is inspired by the interaction of organisms in the nature called Parasitism Commensalism Mutualism. In this paper, three engulfing binary methods based on the symbiotic organisms search algorithm are presented for solving the feature selection problem. In the first and second methods, several S-shaped and V-shaped transfer functions are used for binarizing the symbiotic organisms search algorithm, respectively. These methods are called BSOSS and BSOSV. In the third method, two new operators called BMP and BCP are presented for binarizing the symbiotic organisms search algorithm. This method is called EBSOS. The third approach presents an advanced binary version of the coexistence search algorithm with two new operators, BMP and BCP, to solve the feature selection problem, named EBSOS. The proposed methods are run on 18 standard UCI datasets and compared to base and important meta-heuristic algorithms. The test results show that the EBSOS method has the best performance among the three proposed approaches for binarization of the coexistence search algorithm. Finally, the proposed EBSOS approach was compared to other meta-heuristic methods including the genetic algorithm, binary bat algorithm, binary particle swarm algorithm, binary flower pollination algorithm, binary grey wolf algorithm, binary dragonfly algorithm, and binary chaotic crow search algorithm. The results of different experiments showed that the proposed EBSOS approach has better performance compared to other methods in terms of feature count and accuracy criteria. Furthermore, the proposed EBSOS approach was practically evaluated on spam email detection in particular. The results of this experiment also verified the performance of the proposed EBSOS approach. In addition, the proposed EBSOS approach is particularly combined with the classifiers including SVM, KNN, NB and MLP to evaluate this method performance in the detection of spam emails. The obtained results showed that the proposed EBSOS approach has significantly improved the accuracy and speed of all the classifiers in spam email detection.
ARTICLE | doi:10.20944/preprints202011.0462.v1
Subject: Physical Sciences, Acoustics Keywords: Eclipsing binary minima timing method; Transit timing variation method; Eclipsing binary stars; CM Draconis; TESS space mission; Computational Methods
Online: 18 November 2020 (09:51:19 CET)
The Kwee van Woerden (KvW) method for the determination of eclipse minimum times has been a staple in eclipsing binary research for decades, due its simplicity and independence of external input parameters. However, its estimates of the timing error have been known to be of low reliability. During the analysis of very precise photometry of CM Draconis eclipses from TESS space mission data, KvW’s original equation for the timing error estimate produced numerical errors, which evidenced a fundamental problem in this equation. This contribution introduces an improved way to calculate the timing error with the KvW method. A code that implements this improved method, together with several further updates over the original method is presented as well. An example application on the CM Draconis light curves from TESS is given, where we show that its timing error estimates of about 1 second are in excellent agreement with error estimates obtained by other means.
REVIEW | doi:10.20944/preprints202108.0521.v1
Subject: Mathematics & Computer Science, Probability And Statistics Keywords: non-applicability domain; binary classification; ignorance; decision-making
Online: 27 August 2021 (13:05:02 CEST)
We are of the opinion that during the design of a binary classifier one ought to consider adding an “I don’t know” answer. We provide the case for the introduction of this third category when a human needs to make a decision based on the answer from a binary classifier. We discuss the costs and potential benefits of its introduction. Colloquially, we have used the term “I don’t know”, but formally we refer to it as NotAvailable. A procedure to define NotAvailable predictions in binary classifiers, called all leave-one-out models (ALOOM), is presented as proof of the concept. Furthermore, we discuss the potential benefits of applying ALOOM in real life applications.
ARTICLE | doi:10.20944/preprints202103.0387.v1
Subject: Medicine & Pharmacology, General Medical Research Keywords: β-cyclodextrin; binary complex; antipsychotic drug; dissolution studies
Online: 15 March 2021 (13:44:03 CET)
Iloperidone (ILO) is a second-generation antipsychotic drug and a first-line treatment approved by USFDA in May 2009. Iloperidone belongs to Biopharmaceutical Classification Systems (BCS) class II; thus, it is poorly water-soluble, highly permeable, and has pH-dependent solubility. Cyclodextrins and their derivatives have a wide range of applications in different formulations due to their complexation ability, which improves the solubility, stability, safety, and bioavailability of a drug. We have tried the complexation of iloperidone with sulfobutyl ether-β-cyclodextrin (SEβCD) to improve its solubility and dissolution. Complexation was done by the kneading method. The characterization of the SEβCD complexes with Iloperidone was done by FTIR, differential scanning calorimetry (DSC), saturation solubility, etc. A multimedia dissolution of the complex was carried out and compared with the plain drug. A significant improvement in drug release was found from SEβCD complexes in all media when compared with the drug alone.
ARTICLE | doi:10.20944/preprints202103.0345.v1
Subject: Engineering, Automotive Engineering Keywords: interdigitated electrodes; pseudo binary biodiesel-diesel blends; impedance.
Online: 12 March 2021 (16:23:51 CET)
Non-standard diesel blends can be harmful to the environment and human health. In this context, a simple analytical method to estimate the biodiesel mixture ratio in diesel was developed based on the impedance spectroscopy (IS) associated with the interdigitated sensors. In this article, four different interdigitated sensors, variable comb spacing (G), were simulated using the COMSOL Multiphysics software. Based on finite element simulations, four interdigitated electrode architectures by manufactured and evaluated. According to the X-ray powder diffraction technique, the deposition of the conductive layer (Au°) over the surface of the dielectric substrate (SiO2) did not alter its phase composition. In the analysis of AFM and SEM, it was possible to observe irregular edges on the electrodes, possibly related to thin layers' manufacturing process and mechanical stability. Another characteristic observed in the AFM images was the height of the step of the gold layer of the sensor. Several cross-sections were obtained, and the mean step value is 225.71 ± 0.0032 nm. Although there are differences in the roughness, the whole sensor has nanometric roughness. Based on the finite element method simulation performed, it can be assumed that the geometric parameters more suitable for the manufacturing of the electrode are: W = 20 µm, L = 1000 µm, G = 50 µm e N = 40 digits. The electrical characterization performed by impedance spectroscopy showed that we could differentiate between biodiesel and diesel fuels and their pseudo-binary mixtures in the low-frequency region.
ARTICLE | doi:10.20944/preprints202005.0046.v1
Subject: Mathematics & Computer Science, General Mathematics Keywords: fixed point; q-contraction; binary relation; integral equation
Online: 4 May 2020 (02:54:58 CEST)
In this paper, inspired by Jleli and Samet [journal of inequalities and applications 38 (2014) 2 1–8] we introduce two new classes of auxiliary functions and utilize the same to define (q, y)R-weak 3 contractions. Utilizing (q, y)R-weak contractions, we prove some fixed point theorems in the setting 4 of relational metric spaces. We employ some examples to substantiate the utility of our newly proved 5 results. Finally, we apply one of our newly proved results to ensure the existence and uniqueness of 6 solution of a Volterra-type integral equation.
ARTICLE | doi:10.20944/preprints202203.0061.v1
Subject: Physical Sciences, Astronomy & Astrophysics Keywords: Galaxy; Interstellar; Radio Message; Civilization; Earth; Binary; Radio Telescope
Online: 3 March 2022 (10:24:20 CET)
An updated, binary-coded message has been developed for transmission to extraterrestrial intelligences in the Milky Way galaxy. The proposed message includes basic mathematical and physical concepts to establish a universal means of communication followed by information on the biochemical composition of life on Earth, the Solar System’s time-stamped position in the Milky Way relative to known globular clusters, as well as digitized depictions of the Solar System, and Earth’s surface. The message concludes with digitized images of the human form, along with an invitation for any receiving intelligences to respond. Calculation of the optimal timing during a given calendar year is specified for potential future transmission from both the Five-hundred-meter Aperture Spherical radio Telescope in China and the SETI Institute’s Allen Telescope Array in northern California to a selected region of the Milky Way which has been proposed as the most likely for life to have developed. These powerful new beacons, the successors to the Arecibo radio telescope which transmitted the 1974 message upon which this expanded communication is in part based, can carry forward Arecibo’s legacy into the 21st century with this equally well-constructed communication from Earth’s technological civilization.
ARTICLE | doi:10.20944/preprints202010.0416.v1
Subject: Physical Sciences, Astronomy & Astrophysics Keywords: Binary Black hole; entanglement; monogamy; gravitational waves; quantum optics
Online: 20 October 2020 (17:05:53 CEST)
Various techniques to tackle the black hole information paradox have been proposed. A new way out to tackle the paradox is via the use of pseudo-density operator. This approach has successfully dealt the problem with a two-qubit entangle system for a single black hole. In this paper, we present the interaction with a binary black hole system by using an arrangement of the three-qubit system of Greenberger–Horne–Zeilinger (GHZ) state. We show that our results are in excellent agreement with the theoretical value. We have also studied the interaction between the two black holes by considering the correlation between the qubits in the binary black hole system. The results depict a complete agreement with the proposed model. In addition to the verification, we also propose how modern detection of gravitational waves can be used on our optical setup as an input source, thus bridging the gap with the gravitational wave’s observational resources in terms of studying black hole properties with respect to quantum information and entanglement.
Subject: Mathematics & Computer Science, Applied Mathematics Keywords: Gabor atoms; wavelet entropy; binary metrics; acoustics; quantum wavelet
Online: 3 September 2020 (04:28:24 CEST)
Increased data acquisition by uncalibrated, heterogeneous digital sensor systems such as smartphones present new challenges. Binary metrics are proposed for the quantification of cyber-physical signal characteristics and features, and a standardized constant-Q variation of the Gabor atom is developed for use with wavelet transforms. Two different continuous wavelet transform (CWT) reconstruction formulas are presented and tested under different signal to noise ratio (SNR) conditions. A sparse superposition of Nth order Gabor atoms worked well against a synthetic blast transient using the wavelet entropy and an entropy-like parametrization of the SNR as the CWT coefficient-weighting functions. The proposed methods should be well suited for sparse feature extraction and dictionary-based machine learning across multiple sensor modalities.
ARTICLE | doi:10.20944/preprints201910.0095.v1
Subject: Physical Sciences, General & Theoretical Physics Keywords: landauer principle; binary logic; ternary logic; landauer bound; trit
Online: 9 October 2019 (08:16:16 CEST)
The Landauer principle asserts that “the information is physical”. In its strict meaning Landauer's principle states that there is a minimum possible amount of energy required to erase one bit of information, known as the Landauer bound W=kBTln2 where T is the temperature of a thermal reservoir used in the process and kB is Boltzmann’s constant. Modern computers use the binary system in which a number expressed in the base-2 numeral system. We demonstrate that the Landauer principle remains valid for the physical computing device based on the ternary and more generally N-based logic. The energy necessary for erasure of one bit of information (the Landauer bound) W=kBTln2 remains untouched for the computing devices exploiting a many-valued logic.
ARTICLE | doi:10.20944/preprints202208.0201.v1
Subject: Life Sciences, Genetics Keywords: auto-encoder; high sparse binary data; feature extraction; SNV integration
Online: 10 August 2022 (10:27:32 CEST)
Genomics involving tens of thousands of genes is a complex system determining phenotype. An interesting and vital issue is that how to integrate highly sparse genetic genomics data with a mass of minor effects into prediction model for improving prediction power. We find that deep learning method can work well to extract features by transforming highly sparse dichotomous data to lower dimensional continuous data in a non-linear way. This idea may provide benefits in risk prediction based on genome-wide data associated e.g. integrating most of the information in the genotype data. Hence, we developed a multi-stage strategy to extract information from highly sparse binary genotype data and applied it for risk prediction. Specifically, we first reduced the number of biomarkers via a univariable regression model to a moderate size. Then a trainable auto-encoder was used to extract compact representations from the reduced data. Next, we performed a LASSO problem process over a grid of tuning parameter values to select the optimal combination of extracted features. Finally, we applied such feature combination to two prognostic models, and evaluated predictive effect of the models. The results of simulation studies and real data applying indicated that these highly compressed transformation features could better improve predictive performance and did not easily lead to over-fitting.
ARTICLE | doi:10.20944/preprints202106.0224.v1
Subject: Engineering, Automotive Engineering Keywords: Binary system; Surfactant modification; Orange peel; Artificial neural network modeling
Online: 8 June 2021 (12:38:57 CEST)
This study presents the consecutive modification of orange peel (OP) by NaOH and sodium dodecyl sulfate (SDS) for simultaneous elimination of basic dyes from the binary system and modeling the adsorption process using an intelligent tool. The natural and modified biosorbents were characterized by variety of analyses such as: field emission scanning electron microscopy with energy dispersive X-ray, N2 physisorption and Fourier transform infrared spectroscopy techniques. The influence of various variables on dye removal like pH, the quantity of biosorbents, dyes concentration, contact time, and temperature in the binary system were investigated and optimized by an artificial neural network (ANN) model as an intelligent tool. The optimum quantity of the sorbent was found to be 0.30 g for orange peel (OP) and 0.25 g for NaOH-treated OP (NOP) and SDS-decorated NOP (SNOP) at pH = 7. The kinetics and thermodynamics investigations showed that the removal of dyes obeyed the pseudo-second-order kinetic model and were spontaneous and exothermic in nature. Moreover, in order to describe the mechanism of sorption process, desorption studies of dyes were carried out. The desorption percentages of methylene blue (MB) in water and HCl were found to be in the range of 1.93%–4.76% and 18.87%–28.76%, respectively; in addition, the desorption percentages of crystal violet (CV) in water and HCl were obtained to be in the range of 4.11%–7.41% and 32.84%–43.00%, respectively; which could be a recommendation ion exchange or electrostatic attachment of dyes onto biosorbents. The ANN predictions matched with the experimental data very well (0.95308 < R2 < 0.99191 and 0.98335 < R2 < 0.99773 for MB and CV, respectively) which indicated high accuracy of the ANN model. In addition, the relative importance of each parameter was calculated by Garson’s equation.
ARTICLE | doi:10.20944/preprints201904.0244.v1
Subject: Keywords: salient object; local binary pattern; histogram features; conditional random field
Online: 22 April 2019 (11:40:11 CEST)
We propose a novel method for salient object detection in different images. Our method integrates spatial features for efficient and robust representation to capture meaningful information about the salient objects. We then train a conditional random field (CRF) using the integrated features. The trained CRF model is then used to detect salient objects during the online testing stage. We perform experiments on two standard datasets and compare the performance of our method with different reference methods. Our experiments show that our method outperforms the compared methods in terms of precision, recall, and F-Measure.
ARTICLE | doi:10.20944/preprints202007.0019.v1
Subject: Mathematics & Computer Science, Information Technology & Data Management Keywords: COVID-19; Coronavirus; reopen; sentiment analysis; Twitter; Census; Binary Logit Model
Online: 3 July 2020 (08:35:46 CEST)
Investigating and classifying sentiments of social media users (e.g., positive, negative) towards an item, situation, and system are very popular among the researchers. However, they rarely discuss the underlying socioeconomic factor associations for such sentiments. This study attempts to explore the factors associated with positive and negative sentiments of the people about reopening the economy, in the United States (US) amidst the COVID-19 global crisis. It takes into consideration the situational uncertainties (i.e., changes in work and travel pattern due to lockdown policies), economic downturn and associated trauma, and emotional factors such as depression. To understand the sentiment of the people about the reopening economy, Twitter data was collected, representing the 51 states including Washington DC of the US. State-wide socioeconomic characteristics of the people (e.g., education, income, family size, and employment status), built environment data (e.g., population density), and the number of COVID-19 related cases were collected and integrated with Twitter data to perform the analysis. A binary logit model was used to identify the factors that influence people toward a positive or negative sentiment. The results from the logit model demonstrate that family households, people with low education levels, people in the labor force, low-income people, and people with higher house rent are more interested in reopening the economy. In contrast, households with a high number of members and high income are less interested to reopen the economy. The accuracy of the model is good (i.e., the model can correctly classify 56.18\% of the sentiments). The Pearson chi2 test indicates that overall this model has high goodness-of-fit. This study provides a clear indication to the policymakers where to allocate resources and what policy options they can undertake to improve the socioeconomic situations of the people and mitigate the impacts of pandemics in the current situation and as well as in the future.
ARTICLE | doi:10.20944/preprints201905.0198.v1
Subject: Mathematics & Computer Science, Artificial Intelligence & Robotics Keywords: Support vector machine, Local binary pattern, crowd analysis, crowd density estimation
Online: 16 May 2019 (08:33:07 CEST)
Crowd density estimation is an important task for crowd monitoring. Many efforts have been done to automate the process of estimating crowd density from images and videos. Despite series of efforts, it remains a challenging task. In this paper, we proposes a new texture feature-based approach for the estimation of crowd density based on Completed Local Binary Pattern (CLBP). We first divide the image into blocks and then re-divide the blocks into cells. For each cell, we compute CLBP and then concatenate them to describe the texture of the corresponding block. We then train a multi-class Support Vector Machine (SVM) classifier, which classifies each block of image into one of four categories, i.e. Very Low, Low, Medium, and High. We evaluate our technique on the PETS 2009 dataset, and from the experiments, we show to achieve 95% accuracy for the proposed descriptor. We also compare other state-of-the-art texture descriptors and from the experimental results, we show that our proposed method outperforms other state-of-the-art methods.
ARTICLE | doi:10.20944/preprints201809.0120.v1
Subject: Behavioral Sciences, General Psychology Keywords: Transgender, non-binary gender identity, adolescence, health, well-being, gender nonconforming
Online: 6 September 2018 (15:31:10 CEST)
Purpose: Young transgender and non-binary are exposed to situations of discrimination and have a greater risk of violence. The purpose of this study is to analyze which protective, violence and health and well-being factors have more influence on transgender and non-binary people compared to cisgender people. Method: The sample comprised 856 people between 14 and 25 years old. A survey including questions about sociodemographic information and protective, violence and health and well-being factors was designed ad hoc for this study. Results: The results show non-binary group received the least support from family and friends, higher risk of suffering cyberbullying and a higher feel isolated and unhappy. Non-binary and transgender have suffered more verbal attacks both inside and outside their school and physical attacks at school than cisgender young. Conclusions: These results are important and may contribute to promote public policies and clinical interventions to favor the integration of non-binary and transgender people in our society.
ARTICLE | doi:10.20944/preprints201705.0086.v1
Subject: Materials Science, General Materials Science Keywords: binary liquid alloy; chemical ordering; sodium; theoretical study; Warren-Cowley parameter
Online: 9 May 2017 (11:28:07 CEST)
A simple model has been used to investigate the nature of chemical order in Na-Pb and Na-Hg liquid binary alloy at 700K and 673K respectively. The energy parameter obtained from the model was used to calculate the concentration dependent mixing properties such as Gibb’s free energy of mixing, Concentration fluctuations in the long wavelength limit and the Warren-Cowley chemical short range order parameter. Results obtained showed that both alloys are hetero-coordinated throughout the entire concentration and there is tendency for segregation and demixing to take place in the liquid alloys. We observed that Na-Hg liquid alloy is more strongly interacting binary alloy and chemically ordered than Na-Pb liquid alloy.
ARTICLE | doi:10.20944/preprints202209.0223.v1
Subject: Life Sciences, Other Keywords: Covid; Covid testing; sample pooling; resources; time; binary system; probability; positivity rate
Online: 15 September 2022 (08:14:36 CEST)
In Los Angeles, at one point, the Covid-19 testing positivity rate was 6.25%, or one in sixteen. This translates to, on average, one in sixteen specimens testing positive and the vast majority testing negative. Usually, we run sixteen tests on sixteen specimens to identify the positive one(s). This process can be time consuming and expensive. Since a group of negative specimens pooled together for testing will produce a negative result, one single test could potentially eliminate many specimens. Only when the pooled specimen tests positive do we need further testing to identify the positive one(s). Based on this concept, we designed a strategy that will identify the positive specimen(s) efficiently. Assuming one in sixteen specimens is positive, we find that only four tests are needed. Furthermore, we can run them simultaneously, saving both resources and time. Although, in the real world, we cannot make the assumption of only one positive specimen, the same strategy works with slight modification and proves to be much more efficient than the conventional testing. Our strategy returns an answer 48% of the time in four tests and one time cycle. Overall, the average number of tests is seven or eight depending on the follow-up testing, and the average time cycle is about one and a half.
ARTICLE | doi:10.20944/preprints202201.0258.v1
Subject: Mathematics & Computer Science, Artificial Intelligence & Robotics Keywords: Skin cancer; Deep learning; Hybrid feature extractor; Local binary pattern; Feature extraction
Online: 18 January 2022 (12:43:50 CET)
Skin cancer is an exquisite disease globally nowadays. Because of the poor contrast and apparent resemblance between skin and lesions, automatic identification of skin cancer is complicated. The rate of human death can be massively reduced if melanoma skin cancer can be detected quickly using dermoscopy images. In this research, an anisotropic diffusion filtering method is used on dermoscopy images to remove multiplicative speckle noise and the fast-bounding box (FBB) method is applied to segment the skin cancer region. Furthermore, the paper consists of two feature extractor parts. One of the two features extractor parts is the hybrid feature extractor (HFE) part and another is the convolutional neural network VGG19 based CNN feature extractor part. The HFE portion combines three feature extraction approaches into a single fused feature vector: Histogram-Oriented Gradient (HOG), Local Binary Pattern (LBP), and Speed Up Robust Feature (SURF). The CNN method also is used to extract additional features from test and training datasets. This two-feature vector is fused to design the classification model. This classifier performs the classification of dermoscopy images whether it is melanoma or non-melanoma skin cancer. The proposed methodology is performed on two ordinary datasets and achieved the accuracy 99.85%, sensitivity 91.65%, and specificity 95.70%, which makes it more successful than previous machine learning algorithms.
ARTICLE | doi:10.20944/preprints202002.0330.v1
Subject: Engineering, Electrical & Electronic Engineering Keywords: distributed generation; energy resource management; optimization; mixed-binary linear programming; smart buildings
Online: 23 February 2020 (15:30:01 CET)
Efficient alternatives in energy production and consumption are constantly investigated by increasingly strict policies. In this way, the pollutant emissions that contribute to the greenhouse effect reduce and sustainability of the electricity sector increase. With more than a third of the world's energy consumption, buildings have great potential to contribute these sustainability goals. Additionally, with growing incentives in the Distributed Generation (DG) and Electric Vehicle (EV) industry, it is believed that Smart Buildings (SBs) can be a key in the field of residential energy sustainability in the future. In this work, an energy management system in SBs are developed to reduce the power demanded of a residential building. In order to balance the demand and power provided by the grid, microgrids such as Battery Energy Storage System (BESS), EVs and Photovoltaic Generation panels (PV) are used. Here, a Mixed Binary Linear Programming formulation (MBLP) is proposed to optimize the charge and discharge scheduling of EVs and also BESS. In order to show the efficiency of the model, a case study involving three scenarios and an economic analysis is considered. The results point a 65% reduction in peak load consumption supplied by grid and a 28.4% reduction in electricity consumption costs.
ARTICLE | doi:10.20944/preprints201812.0142.v2
Subject: Life Sciences, Genetics Keywords: DNA sequences, literary texts, probability, binary opposition, alphabet, tensor product, quantum informatics
Online: 18 February 2019 (17:22:56 CET)
Impressing discoveries in the field of the genetic code have been described by its researchers by means of the terminology borrowed from linguistics and the theory of communications. Leading experts on structural linguistics believe for a long time already that languages of human dialogue were formed not from an empty place, but they are continuation of genetic language or, anyhow, are closely connected with it, confirming the idea of information commonality of organisms. The aticle continues the theme about a connection of linquistic languages with the genetic language. It describes results of comparative study of long Russian literary texts (novels by L.Tolstoy, F.Dostoevsky, A.Pushkin, etc.) and long sequences of hydrogen bonds in double helixes of DNA of different organisms. Formalisms of quantum informatics are used in modeling some of these results taking into account thoughts of many researches about possible using principles of quantum informatics in organisation of living bodies.
ARTICLE | doi:10.20944/preprints201705.0206.v1
Subject: Life Sciences, Microbiology Keywords: Clostridium difficile; ST201; binary toxin-positive; whole genome sequencing; comparative genomic analysis
Online: 30 May 2017 (06:15:11 CEST)
A novel binary toxin-positive non-027, non-078 Clostridium difficile strain designated LC693 whose sequence type was ST201 was isolated from the fecal sample of a patient with severe diarrhea in China. To understand the pathogenesis basis of C. difficile ST201, this recently recovered isolate LC693 was then chosen for whole genome sequencing. The project finally generated an estimated genome size of approximately 4.07 Mbp. The genome sequence was then analyzed together with the other two ST201 strains VL-0104 and VL-0391 and compared to the epidemic 027/ST1 and 078/ST11 strains. Phylogenetic analysis demonstrated that the ST201 strains belonged to clade 3. Genome size of the three ST201 strains ranged from 4.07 Mb~4.16 Mb, with an average GC content between 28.5%~28.9%. The ST201 genomes contained more than 40 antibiotic resistance genes and 15 of them were predicted to be associated with vancomycin-resistance, suggesting that they may have a strong antibiotic resistance. The ST201 strains contained a typical clade 3 specific PaLoc with a Tn6218 element inserted, and those genes harbored on their PaLoc that participated in the toxin expression and regulation were highly homologues to the epidemic 027 and 078 strains, with the exception of tcdC. A truncated TcdC was found in the ST201 strains, which is suggestive to have a contribution to the toxin production of the ST201 strains. In addition, the ST201 strains contained intact binary toxin coding and regulation genes, which is also proposed to contribute to the virulence. Genome comparison of the ST201 strains with the epidemic 027 and 078 strain identified 641 genes specific for the C. difficile ST201, and a number of them were predicted as fitness and virulence associated genes. The identification of those genes also contributes to the pathogenesis of the ST201 strain. To our knowledge, this is the first study that the genome sequence of C. difficile ST201 was discussed in detail, and the present study would have a contribution to understanding the pathogenesis basis of C. difficile ST201.
ARTICLE | doi:10.20944/preprints201612.0049.v2
Subject: Physical Sciences, General & Theoretical Physics Keywords: Quantum Liouville equation; metric compatibility condition; Joint probability; Binary Data Matrix; Ricci flow
Online: 25 February 2022 (02:34:16 CET)
In this paper after introducing a model of binary data matrix (BDM) for physical parameters of an evolving system (of particles), we develop a Hilbert space as an ambient space to derive induced metric tensor on embedded parametric manifold identified by associated joint probabilities of particles observables (parameters). Parameter manifold assumed as space-like hypersurface evolving along time axis, an approach that resembles 3+1 formalism of ADM and numerical relativity. We show the relation of endowed metric with related density matrix. Identification of system density matrix by this metric tensor, leads to the equivalence of quantum Liouville equation and metric compatibility condition while covariant derivative of metric tensor has been calculated respect to Wick rotated time or spatial coordinates. After deriving a formula for expected energy per particles, we prove the equality of this expected energy with local scalar curvature of related manifold. We show the compatibility of BDM model with Hamilton-Jacobi formalism and canonical forms. On the basis of the model, I derive the Ricci flow like dynamics as the governing dynamics and subsequently derive the action of BDM model and Einstein field equations. Given examples clarify the compatibility of the results with well-known principles such as equipartition energy principle and Landauer’s principle. This model provides a background for geometrization of quantum mechanics compatible with curved manifolds and information geometry. Finally, we conclude a “bit density principle” which predicts the Planck equation, De Broglie wave particle relation, , Beckenstein bound and Bremermann limit.
ARTICLE | doi:10.20944/preprints201810.0740.v2
Subject: Social Sciences, Microeconomics And Decision Sciences Keywords: political polarization; echo-chambers; social networks; binary voter model; discussion dynamics; opinion dynamics model
Online: 17 December 2018 (10:11:31 CET)
Polarization in online social networks has gathered a significant amount of attention in the research community and in the public sphere due to stark disagreements with millions of participants in topics surrounding politics, climate, the economy and other areas where an agreement is required. There are multiple approaches to investigating the scenarios in which polarization occurs and given that polarization is not a new phenomenon but that its virality may be supported by the low cost and latency messaging offered by online social media platforms; an investigation into the intrinsic dynamics of online opinion evolution is presented for complete networks. Extending a model which utilizes the Binary Voter Model (BVM) to examine the effect of the degree of freedom for selecting contacts based upon homophily, simulations show that different opinions are reinforced for a period of time when users have a greater range of choice for association. The facility of discussion threads and groups formed upon common views further delays the rate in which a consensus can form between all members of the network. This can temporarily incubate members from interacting with those who can present an alternative opinion where a voter model would then proceed to produce a homogeneous opinion based upon pairwise interactions.
ARTICLE | doi:10.20944/preprints202207.0145.v2
Subject: Physical Sciences, General & Theoretical Physics Keywords: dispersion of light; gravitational field; fundamental physics constant; vacuum; speed of light; spectroscopic binary system; double gravitational lens
Online: 19 August 2022 (08:04:34 CEST)
In any region of a space, the gravitational field cannot be eliminated. The speed of light in a vacuum has never been observed and cannot be observed with current technology. Till now, only the speed of light in a gravitational field has been observed. Here, it is presented that light could be dispersion in a gravitational field analogous to the dispersion of light in the Newtonian prism experiment. The relativistic mass density on the surface of a neutron star is on the level of 1017kgm-3 while on the surface of the Earth is only 6.63*10-7kgm-3, the speed of light acted by the gravitational field of a neutron star is much larger than that by the Earth. Therefore, light dispersion in strong gravitational field could be generally observed from the picture of a star and it should have been observed through the spectroscopic binary system.
ARTICLE | doi:10.20944/preprints202203.0362.v1
Subject: Mathematics & Computer Science, Applied Mathematics Keywords: game theory; economic relation; problem reductions; binary and regression problems; machine learning; boosting, neural network
Online: 28 March 2022 (12:11:49 CEST)
Starting from a very simple economic scenario, we build on it a game and then we introduce a general strategy able to reduce a regression problem to an equivalent binary classification problem. This reduction scheme (that we call adaptive reduction or also dynamic reduction) can be also used to derive a new boosting algorithm for regression problems named bOOstd. The bOOstd algorithm is very simple to implement, and it can use any learning algorithm with no priori assumptions. We present a conjecture for bOOstd performances, which ensures a little error on training set. More important we can also provide a very good theoretical upper bound for the generalization error. We give a set of preliminary experimental results that seems to confirm our conjecture for bOOstd performances on training set and the theoretical assumptions for the generalization error. We also provide a possible justification of why boosting often does not overfit. Finally, we leave some open problems and argue that in the future an adaptive single boosting (with an unique code) algorithm for binary, multi class and regression problems can be derived.
ARTICLE | doi:10.20944/preprints202104.0256.v1
Subject: Mathematics & Computer Science, Numerical Analysis & Optimization Keywords: Multi-database Mining; Graph Clustering; Coordinate Descent; Convex Optimization; Similarity Measure; Binary Entropy Loss; Fuzziness Index
Online: 9 April 2021 (10:20:06 CEST)
Clustering algorithms for multi-database mining (MDM) rely on computing $(n^2-n)/2$ pairwise similarities between $n$ multiple databases to generate and evaluate $m\in[1, (n^2-n)/2]$ candidate clusterings in order to select the ideal partitioning which optimizes a predefined goodness measure. However, when these pairwise similarities are distributed around the mean value, the clustering algorithm becomes indecisive when choosing what database pairs are considered eligible to be grouped together. Consequently, a trivial result is produced by putting all the $n$ databases in one cluster or by returning $n$ singleton clusters. To tackle the latter problem, we propose a learning algorithm to reduce the fuzziness in the similarity matrix by minimizing a weighted binary entropy loss function via gradient descent and back-propagation. As a result, the learned model will improve the certainty of the clustering algorithm by correctly identifying the optimal database clusters. Additionally, in contrast to gradient-based clustering algorithms which are sensitive to the choice of the learning rate and require more iterations to converge, we propose a learning-rate-free algorithm to assess the candidate clusterings generated on the fly in a fewer upper-bounded iterations. Through a series of experiments on multiple database samples, we show that our algorithm outperforms the existing clustering algorithms for MDM.
ARTICLE | doi:10.20944/preprints202005.0451.v1
Subject: Mathematics & Computer Science, Applied Mathematics Keywords: Bilateral Line Local Binary Patterns; Facial matrix; Statistical subspace; Face recognition; Calibrated SVM model; Ensemble learning
Online: 27 May 2020 (12:07:19 CEST)
Local binary pattern is one of the visual descriptors and can be used as a powerful feature extractor for texture classification. In this paper, a novel representation for face recognition is proposed, called it Bilateral Line Local Binary Patterns (BL-LBP). This scheme is an extension of Line Local Binary Patterns descriptors in the statistical learning subspace. The present bilateral descriptors are fused with an ensemble learning of calibrated SVM models. The performance of this scheme is evaluated using 5 standard face databases. It is found that it is robust against illumination variation, diverse facial expressions and head pose variations and its recognition accuracy reaches 98 percent, running on a mobile device with a processing speed of 63 ms per face. Results suggest that our proposed method can be very useful for the vision systems that have limited resources where the computational cost is critical.
ARTICLE | doi:10.20944/preprints201806.0456.v1
Subject: Mathematics & Computer Science, Algebra & Number Theory Keywords: binary system(groupoid); minimum (mutual) covering set; (mutual) shortest distance; (di)frame graph; d/BCK-algebra
Online: 28 June 2018 (04:48:32 CEST)
In this paper, we observe that if X is a set and (Bin(X), □) is the semigroup of binary systems on X, then its center ZBin(X) consists of the locally-zero-semigroups and that these can be modeled as (simple) graphs and conversely. Using this device we show that we may obtain many results of interest concerning groupoids by reinterpreting graph theoretical properties and at the same time results on graphs G may be obtained by considering them as elements of centers of the semigroups of binary systems (Bin(X), □) where X = V(G), the vertex set of G.
ARTICLE | doi:10.20944/preprints201710.0187.v1
Subject: Mathematics & Computer Science, Analysis Keywords: medical image classification; local binary patterns; characteristic curves; whole slide image pro-cessing; automated HER2 scoring
Online: 31 October 2017 (03:10:22 CET)
This paper presents novel feature descriptors and classification algorithms for automated scoring of HER2 in Whole Slide Images (WSI) of breast cancer histology slides. Since a large amount of processing is involved in analyzing WSI images, the primary design goal has been to keep the computational complexity to the minimum possible level and to use simple, yet robust feature descriptors that can provide accurate classification of the slides. We propose two types of feature descriptors that encode important information about staining patterns and the percentage of staining present in ImmunoHistoChemistry (IHC) stained slides. The first descriptor is called a characteristic curve which is a smooth non-increasing curve that represents the variation of percentage of staining with saturation levels. The second new descriptor introduced in this paper is an LBP feature curve which is also a non-increasing smooth curve that represents the local texture of the staining patterns. Both descriptors show excellent interclass variance and intraclass correlation, and are suitable for the design of automatic HER2 classification algorithms. This paper gives the detailed theoretical aspects of the feature descriptors and also provides experimental results and comparative analysis.
ARTICLE | doi:10.20944/preprints201710.0181.v1
Subject: Mathematics & Computer Science, Analysis Keywords: ultrasound image analysis; speckle noise; synthetic ultrasound images; texture features; local binary patterns; image quality assessment
Online: 30 October 2017 (09:37:59 CET)
Speckle noise reduction is an important area of research in the field of ultrasound image processing. Several algorithms for speckle noise characterization and analysis have been recently proposed in the area. Synthetic ultrasound images can play a key role in noise evaluation methods as they can be used to generate a variety of speckle noise models under different interpolation and sampling schemes, and can also provide valuable ground truth data for estimating the accuracy of the chosen methods. However, not much work has been done in the area of modelling synthetic ultrasound images, and in simulating speckle noise generation to get images that are as close as possible to real ultrasound images. An important aspect of simulated synthetic ultrasound images is the requirement for extensive quality assessment for ensuring that they have the texture characteristics and gray-tone features of real images. This paper presents texture feature analysis of synthetic ultrasound images using local binary patterns (LBP) and demonstrates the usefulness of a set of LBP features for image quality assessment. Experimental results presented in the paper clearly show how these features could provide an accurate quality metric that correlates very well with subjective evaluations performed by clinical experts.
ARTICLE | doi:10.20944/preprints202205.0192.v1
Subject: Physical Sciences, Astronomy & Astrophysics Keywords: galaxy center; supermassive black hole; black hole binary; VLBI; submillimeter radio wave; decameter radio wave; event horizon
Online: 13 May 2022 (11:01:08 CEST)
In 2011, by 1.3 mm wavelength VLBI radio wave observations of the SgrA*, Fish, V. L. et al showed that the emissions tightly related to the formation of a black hole shadow have a remarkably large time-varying feature within a region of less than 50 μas. The present paper suggests that the origin of the time variation in the observed emission is due to effects of the orbital motion of the existing super-massive black hole binary orbiting at SgrA* with a period of 2150±2.5 s. This suggestion is based on observations of decameter radio wave pulses from SgrA*. We show a good correlation between the time variation in the coherent flux density of the VLBI results and the time variation model of estimated emission intensities based on the periodic motion of the super-massive black hole binary by applying parameters deduced from the decameter radio wave pulse observation model (DRWP-Model). With further confirmation by Fourier analyses of the potential periodicity of the VLBI data that show the same periods of DRWP Model, we conclude that the time variation detected by the 1.3 mm wavelength radio wave VLBI is evidence of an existing super-massive black hole at Sgr A*.
ARTICLE | doi:10.20944/preprints202202.0331.v1
Subject: Physical Sciences, Acoustics Keywords: equivalence-principle; Einstein-Lift; EP; formal binary logic; inhomogenious gravity- field; acceleration- field; radial-field; tidal-forces
Online: 25 February 2022 (09:46:25 CET)
Mass plays a strange multiple role in classical physics. This results in a difference between gravity and all other forces - a difference that stood at the beginning of Einstein's development of his general theory of relativity. The equivalence principle (EP) deals with homogenious gravitational fields, which, in fact, don‘t exist in nature. There is only an approximation for this field in Einstein-Lift possible for local situations. Nevertheless this EP can be true, because in classical formal binary logic there can be formulated a true conclusion from a wrong premise or assumption.
ARTICLE | doi:10.20944/preprints202202.0170.v1
Subject: Life Sciences, Virology Keywords: influenza virus; RNA-polymerase; RNA-polymerase II; protein-protein interaction; PPI; cap snatching; transcription; binary complementation assay
Online: 14 February 2022 (09:51:21 CET)
Influenza virus transcription is catalyzed by the viral RNA-polymerase (FluPol) through a cap-snatching activity. The snatching of the cap of cellular mRNA by FluPol is preceded by its binding to the flexible C-terminal domain (CTD) of the RPB1 subunit of RNA-polymerase II (Pol II). To better understand how FluPol brings the 3’-end of the genomic RNAs in close proximity to the host-derived primer, we hypothesized that FluPol may recognize additional Pol II subunits/domains to ensure cap-snatching. Using binary complementation assays between the Pol II and FluPol subunits and their structural domains, we revealed an interaction between the N-third domain of PB2 and RPB4. This interaction was confirmed by a co-immunoprecipitation assay and found to occur with the homologous domains of influenza B and C FluPols. Residues [1-72] of RPB4 were found critical in this interaction. Numerous punctual mutants generated at conserved positions between influenza A, B and C FluPols in the N-third domain of PB2 exhibited strong transcriptional activity defect. These results suggest that FluPol interacts with several domains/subunits of Pol II, the CTD to bind Pol II initiating host transcription and a second on RPB4 to locate FluPol at the proximity of the 5’-end of nascent host mRNA.
HYPOTHESIS | doi:10.20944/preprints202201.0364.v1
Subject: Chemistry, Organic Chemistry Keywords: origin of life; hydrothermal biochemistry, information storage, continental crust model, supercritical fluids, open system, binary proto-synthetase
Online: 25 January 2022 (04:17:03 CET)
The storage of biochemical information, which is a prerequisite for the development of the first cell, is an unsolved problem affecting all concepts of the origin of life. However, if the protected environment in the continental crust is taken into account, completely new possibilities emerge for identifying processes that may have been crucial for the formation of the first cell. Under this background, we can hypothesize that, before cellular life began, a self-sustaining cycle of molecular reaction steps with information storage in RNA existed outside of a cell. This cycle was made possible in an open system bound to gas-permeable tectonic fracture zones with a high proportion of CO2 and N2. The formation of peptides and vesicles in supercritical CO2 and the chemical evolution of peptides have already been proven for the upper continental crust. Further considerations include the interactions of vesicles with catalytic peptides and the emergence of proto-tRNA. In combination with the formation of proto-tRNA synthetases, which consist of only two amino acid species and associated proto-tRNAs, the first RNA as an information storage system could have been formed with the information of proto-enzymes.
ARTICLE | doi:10.20944/preprints202101.0360.v3
Subject: Life Sciences, Genetics Keywords: DNA alphabets, genomes, percentages of n-plets, binary-oppositions, tensor family of matrices, tetra-groupings, quantum biology, algebraic holography.
Online: 23 June 2021 (11:49:51 CEST)
The article presents the author's results of studying hidden rules of structural organizations of long DNA sequences in eukaryotic and prokaryotic genomes. The results concern some rules of percentages (or probabilities) of n-plets in genomes. To reveal such rules, the author considers genomic DNA nucleotide sequences as multilayers sequences of n-plets and studies the percentage contents of n-plets in different layers. Unexpected rules of invariance of total sums of percentages in certain tetra-groupings of n-plets in different layers of genomic DNA sequences are revealed. These discovered rules are candidates for the role of universal genomic rules. A tensor family of matrix representations of interrelated DNA-alphabets of 4 nucleotides, 16 doublets, 64 triplets, and 256 tetraplets is used in the study. This matrix approach allows revealing algebraic properties of the mentioned genetic rules of probabilities, which are useful for developing algebraic and quantum biology. Some analogies of the discovered genetic phenomena with phenomena of Gestalt psychology are noted and discussed. The author connects the received results about the genomic percentages rules with a supposition of P. Jordan, who is one of the creators of quantum mechanics and quantum biology, that life's missing laws are the rules of chance and probability of the quantum world. Additional attention is paid to the algebraic features of the system of structured DNA alphabets and their relationship with the methods of algebraic holography, known in the technique of processing discrete signals. The concept of algebraic-holographic genetics is being developed for the understanding of inherited holographic properties of organisms.
Subject: Mathematics & Computer Science, Algebra & Number Theory Keywords: Covid-19; computational modelling; space time framework; multigrid implementation; update binary rules; Von Neumann and Moore neighbourhoods.
Online: 6 January 2021 (14:49:09 CET)
This paper presents a discrete compartmental Susceptible-Exposed-Infected-Recovered/Dead (SEIR/D) model to address the expansion of Covid-19 pandemic. When time passes, the status of the cells is determined by binary rules that update following both a neighbourhood and a delay pattern. The model assumes the environmental parameters have a crucial impact on the expansion of the disease so a grid is assigned to each parameter to model the single effect caused by this parameter. The expansion is then the weighted sum of all the grids. This proposal shows how the grid architecture, along with an update rule and a neighbourhood pattern is a valuable tool to model the pandemic expansion. This model has already been analyzed in previous works and compared with the corresponding continuous models solved by ordinary differential equations (ODE), coming to find the homologous parameters between both approaches. Thus, it has been possible to prove that the combination neighborhood-update rule is responsible for the rate of expansion and recovering/death of the illness. The delays (between Susceptible and Asymptomatic, Asymptomatic and Infected, Infected and Recovered/Dead) may have a crucial impact on both the peak of Infected and the Recovery/Death rate. This theoretical model has been successfully tested in the case of the dissemination of information through mobile social networks and in the case of plant pests.
ARTICLE | doi:10.20944/preprints201611.0058.v1
Subject: Physical Sciences, Condensed Matter Physics Keywords: spot-profile analysis; one dimensional physics; low energy electron diffraction; binary surface technique; supercell model; domain boundary
Online: 10 November 2016 (15:50:29 CET)
Motivated by diffraction experiments on the reconstructed Si(111) due to deposition of rare earth elements (Dy, Tb) and silicide formation we analyse the splitting and non-splitting of superstructure spots. For this purpose, we model diffraction patterns for one dimensional structures generated by the binary surface technique and use supercell models to keep the analysis simple. Diffraction pattern are calculated in the framework of the kinematical diffraction theory and they are analyzed as a function of the domains and domain boundaries. Basic properties of the diffraction pattern are analyzed for model systems of a two-fold and a three-fold periodicity. The rules derived from these calculations are applied to the "real-world" system of Si(111)-()-RESi (RE = Dy or Tb). Depending on the combination of domains and domain boundaries of different types a plethora of different features are observed in the diffraction patterns. These are analyzed to determine the sizes of both domain boundaries and domains from experimentally observed splitting of specific superstructure spots.
ARTICLE | doi:10.20944/preprints202107.0638.v1
Subject: Keywords: Image Processing; Automated Plant Diseases Detection; Histogram Oriented Gradient (HOG); Local Binary Pattern (LBP); Support Vector Machine (SVM)
Online: 28 July 2021 (17:18:04 CEST)
: On earth, plants play the most important part. Every organ of a plant plays a vital role in the ecological field as well as the medicinal field. But on the whole earth there are several species of plants are available. Different plants have different diseases. Therefore it is needed to identify the plants and their diseases to prevent loss. Now to identify the plants and their diseases manually is very time consuming. In this research an automatic plant and their disease detection system is proposed. For experimental purposes, high-quality leaf images are accepted for training and testing. For detecting the healthy and diseased area in a leaf, region-based and color-based region thresholding techniques were used. For feature selection Histogram Oriented Gradient (HOG) and Local Binary Pattern (LBP) method were applied. Finally for classification two-class and multi-class Support Vector Machine (SVM) was used. It is observed that both feature selection processes with SVM give 99% accuracy. Finally to understand the automated system a graphical user interface was created for all users.
ARTICLE | doi:10.20944/preprints201911.0301.v2
Subject: Life Sciences, Genetics Keywords: genetic code; DNA; alphabet; amino acids; hypercomplex numbers; doubly stochastic matrix; binary numbers; dyadic groups; tensor product; palindrome
Online: 17 March 2020 (03:02:27 CET)
The article shows materials to the question about algebraic features of the genetic code and about the dictatorial influence of the DNA and RNA molecules on the whole organism. Presented results testify in favor that the genetic code is an algebraic code related with a wide class of algebraic codes, which are a basis of noise-immune coding of information in communication technologies. Structural features of the genetic systems are associated with hypercomplex double (or hyperbolic) numbers and with bisymmetric doubly stochastic matrices. The received results confirm that represented matrix approaches are effective for modeling genetic phenomena and revealing the interconnections of structures of biological bodies at various levels of their organization. This allows one to think that living organisms are algebraically encoded entities where structures of genetic molecules have the dictatorial influence on inherited structures of the whole organism. New described algebraic approaches and results are discussed.
ARTICLE | doi:10.20944/preprints202009.0572.v1
Subject: Medicine & Pharmacology, General Medical Research Keywords: randomized controlled clinical trials; mathematical model; binary system; statistical analysis; epidemiological model; junk science; reductionist treatments; failure of medicine
Online: 24 September 2020 (08:13:15 CEST)
Modern medicine adopted four presumptions when it evolved from ancient experienced-based mind-body medicine. To understand its failure in finding cures for chronic diseases, we examined four presumptions, and found that statistical population of health properties does not exist for most research purposes, mathematical models are misused to model intensive properties, synthetic drugs are inherently more dangerous than nature-made medicines under their respective application conditions, and reductionist treatments are inferior and inherently dangerous. We found that clinical trials are valid only for research where treatment effect is much stronger than the total effects of all interfering or co-causal factors or errors introduced by misused mathematical models can be tolerated. In all other situations, clinical trials introduce excessive errors and fail to detect treatment effects, or produce biased, incorrect or wrong results. We further found that chronic diseases are manifestation of small departures in multiple process attributes in distinctive personal biological pathways networks, that modern medicine lacks required accuracy for accurately characterizing chronic diseases, and that reductionist treatments are good at controlling symptoms and safe for short term uses. For all stated reasons, as long as modern medicine continues relying on the flawed presumptions, it can never find predictable cures for chronic diseases. By implication, predictable cures to chronic diseases are adjustments to lifestyle, dietary, emotional, and environmental factors to slowly correct departures in process attributes responsible for chronic diseases.
ARTICLE | doi:10.20944/preprints202109.0403.v1
Subject: Life Sciences, Biophysics Keywords: RKIP expression regulation; Stochastic binary regulation of gene expression; Treatment targeting RKIP levels increase; Reduction of heterogeneity of treatment response
Online: 23 September 2021 (11:43:54 CEST)
In this manuscript we use an exactly solvable stochastic binary model for regulation of gene expression to analyse the dynamics of response to a treatment aiming to modulate the number of transcripts of RKIP gene. We demonstrate the usefulness of our method simulating three treatment scenarios aiming to reestablish RKIP gene expression dynamics towards pre-cancerous state: i. to increase the promoter’s ON state duration; ii. to increase the mRNAs’ synthesis rate; iii. to increase both rates. We show that the pre-treatment kinetic rates of ON and OFF promoter switching speeds and mRNA synthesis and degradation will affect the heterogeneity and time for treatment response. Hence, we present a strategy for reducing drug dosage by simultaneously targeting multiple kinetic rates. That enables a reduction of treatment response time and heterogeneity which in principle diminishes the chances of emergence of resistance to treatment. This approach may be useful for inferring kinetic constants related to expression of antimetastatic genes or oncogenes and on the design of multi-drug therapeutic strategies targeting master regulatory genes.
ARTICLE | doi:10.20944/preprints202008.0241.v1
Subject: Mathematics & Computer Science, Artificial Intelligence & Robotics Keywords: gene expression profiles; lung cancer; clustering; classification; binary classifiers; SOTA clustering algorithm; clustering quality criteria; ROC analysis; fuzzy inference system
Online: 10 August 2020 (08:01:10 CEST)
In this paper, we present the results of the research concerning extraction of informative gene expression profiles from high-dimensional array of gene expressions considering the state of patients' health using clustering method, ensemble of binary classifiers and fuzzy inference system. Applying of the proposed stepwise procedure can allow us to extract the most informative genes taking into account both the subtypes of disease or state of the patient's health for further reconstruction of gene regulatory networks based on the allocated genes and following simulation of the reconstructed models. We used the publicly available gene expressions data as the experimental ones which were obtained using DNA microarray experiments and contained two types of patients' gene expression profiles: the patients with lung cancer tumor and healthy patients. The stepwise procedure of the data processing assumes the following steps: in beginning, we reduce the number of genes by removing non-informative genes in terms of statistical criteria and Shannon entropy; then, we perform the stepwise hierarchical clustering of gene expression profiles at hierarchical levels from 1 to 10 using SOTA clustering algorithm with correlation distance metric. The quality of the obtained clustering was evaluated using complex clustering quality criterion which is considered both the gene expression profiles distribution relative to center of the clusters were these gene expression profiles are allocated and the centers of the clusters distribution. The result of this stage execution was selection of the optimal cluster at each of the hierarchical levels which corresponded to minimum value of the quality criterion. At the next step, we have implemented classification procedure of the examined objects using four well known binary classifiers: logistic regression, support-vector machine, decision trees and random forest classifier. The effectiveness of the appropriate technique was evaluated based on the use of ROC analysis using criteria included as the components the errors of both the first and the second kinds. The final decision concerning extraction of the most informative subset of gene expression profiles was taken based on the use of fuzzy inference system, the inputs of which are the results of the appropriate single classifiers operation and output is the final solution concerning state of the patient's health. To our mind, the implementation of the proposed stepwise procedure of the informative gene expression profiles extraction create the conditions for increasing effectiveness of the further procedure of gene regulatory networks reconstruction and the following simulation of the reconstructed models considering the subtypes of the disease and/or state of the patient’s health.
ARTICLE | doi:10.20944/preprints201904.0011.v2
Subject: Life Sciences, Genetics Keywords: DNA sequence; helix; nucleotide frequencies; DNA epi-chains; helical antennas; Fröhlich's theory; long-range coherence; epigenetics; quantum biology; binary representation
Online: 14 May 2019 (06:22:48 CEST)
One of creators of quantum mechanics P. Jordan in his work on quantum biology claimed that life's missing laws were the rules of chance and probability of the quantum world. The article presents author’s results of studying frequencies (or probabilities) of nucleotides on so-called epi-chains of long DNA sequences of various eukaryotic and prokaryotic genomes. DNA epi-chains are algorithmically constructed subsequencies of DNA nucleotide sequences. According to the algorithm of construction of any epi-chain of the order n, the epi-chain is such nucleotide subsequence, in which the numerations of adjacent nucleotides differ by natural number n (n = 1, 2, 3, 4,…). Correspondingly each epi-chain of order n ≥ 2 contains n times less nucleotides than the original DNA sequence. The presented results unexpectedly discover that in long single-stranded and double-stranded DNA of any tested genome its DNA epi-chains of different orders n (values n are not too large) have practically identical frequencies (or probabilities) of each kind of nucleotides. These data allow considering DNA as a regular rich set of epi-chains, which can play a certain role in genetic and epigenetic phenomena as the author belives. Appropriate rules of nucleotide frequencies on epi-chains of long DNA sequences are formulated for further their tests on a wider set of genomes. These results testify on existence of long-range coherence in long DNA and remind the Fröhlich's theory of long-range coherence in biological systems. The phenomenological data are discussed from different standpoints: the DNA double helices and helical antennas with circular polarizations of electromagnetic waves; relations with the Fröhlich's theory; numerical analysis of DNA epi-chains under binary representations of nucleotides. Results are useful for developing quantum and algebraic biology.
ARTICLE | doi:10.20944/preprints202109.0021.v1
Subject: Mathematics & Computer Science, Probability And Statistics Keywords: Effect size; correlation coefficient; association measure; covariance; mean square contingency coefficient; mean square effect half-size; Pearson’s Phi; 2 × 2 table; binary crosstab; gross crosstab; contingency table
Online: 1 September 2021 (14:28:47 CEST)
Evidence-based medicine (EBM) is in crisis, in part due to bad methods, which are understood as misuse of statistics that is considered correct in itself. This article exposes two related common misconceptions in statistics, the effect size (ES) based on correlation (CBES) and a misconception of contingency tables (MCT). CBES is a fallacy based on misunderstanding of correlation and ES and confusion with 2 × 2 tables, which makes no distinction between gross crosstabs (GCTs) and contingency tables (CTs). This leads to misapplication of Pearson’s Phi, designed for CTs, to GCTs and confusion of the resulting gross Pearson Phi, or mean-square effect half-size, with the implied Pearson mean square contingency coefficient. Generalizing this binary fallacy to continuous data and the correlation in general (Pearson’s r) resulted in flawed equations directly expressing ES in terms of the correlation coefficient, which is impossible without including covariance, so these equations and the whole CBES concept are fundamentally wrong. MCT is a series of related misconceptions due to confusion with 2 × 2 tables and misapplication of related statistics. The misconceptions are threatening because most of the findings from contingency tables, including CBES-based meta-analyses, can be misleading. Problems arising from these fallacies are discussed and the necessary changes to the corpus of statistics are proposed resolving the problem of correlation and ES in paired binary data. Since exposing these fallacies casts doubt on the reliability of the statistical foundations of EBM in general, we urgently need to revise them.
HYPOTHESIS | doi:10.20944/preprints202105.0437.v1
Subject: Keywords: Binary digits, Mobius strips, Figure-8 Klein bottles, Dark matter, Dark energy, Topological insulators, Topological superconductors, Topological universe, Weyl fermion, Majorana fermion, Vector-tensor-scalar geometry, Higgs-like body/consciousness
Online: 19 May 2021 (08:23:47 CEST)
The part of this article dealing with topological insulators and topological superconductors was first written about two years ago - the ideas in the part about the topological universe originated six years ago or more. It’s rather strange that I never put the two parts together in writing before. My belief in unification is unshakeable - I’ve been convinced for years that the universe must be composed of topology. Since Earth is part of the cosmos, entanglement means it must have topological materials. The reverse is also true: topological materials on Earth are well known to science - so in a unification, space and time inevitably possess topological composition. Topological materials (topological insulators, topological superconductors) can be less mystifying if they’re related to the paradigm-shifting deterministic view of quantum mechanics which is described in the universal topology (the “rubber-sheet geometry” of the cosmos): see my previous submission “Hypothesis of Quantum Gravity - Resulting from a Static, Topological Universe Resulting from the Positives and Negatives of the Steady State and Big Bang Theories" at https://www.preprints.org/manuscript/202105.0239/v1 (the first section of this present article is a quick summary of the relevant parts).
HYPOTHESIS | doi:10.20944/preprints202106.0598.v1
Subject: Keywords: Plant communication; Binary digits; Vector-tensor-scalar geometry; Mobius strip; Figure-8 Klein bottle; Consciousness; Electromagnetic-gravitational interaction; Higgs boson; Artificial Intelligence; Quantum Gravity; Theory of Everything, Life after death/before life (before conception)
Online: 24 June 2021 (10:20:25 CEST)
According to Swiss-American Doctor of Sciences and Agricultural Engineer Jean-Pierre Jost, "plants communicate with each other by the quality of light emitted by their leaves or by means of stress hormones and other volatile chemicals. They also make use of cocktails of chemicals, pheromones, shape and colors to attract pollinators whereas other signals repel unwanted organisms. Insects are able to decode such messages and respond accordingly. Plants are apparently also communicating by sounds and electric signals." (1) How do plants do these things? Of course, it's easy to imagine it's all purely mechanical. But at the risk of sounding like a mysticism fanatic, I wonder if plants' activities are part of a spectrum of consciousness that pervades the entire universe. This spectrum would result from everything in the universe having the BITS or BInary digiTS of electronics as their ultimate composition. As explained in this hypothesis, something I call vector-tensor-scalar geometry is essential to my hypothesis. VTS geometry produces the particles of chemicals and pheromones, and refers to communication via electric signals when it speaks of electromagnetic-gravitational interaction. There's another consequence if everything in the universe is ultimately composed of electronic BITS and the cosmos is a spectrum of consciousness/artificial intelligence. It's impossible for an absence of consciousness to exist, either after death or before conception.