Miracle-dz/UniFAR-FTUs huggingface dataset:
A bioinformatic implementation of mutual information as a distance measure for identification of clusters of variables

The size of data sets produced in genetic experiments is steadily increasing. Very often there are many more variables than observations, leading to the so-called ``large $p$, small $n$" problem. For such data, clustering and distance based procedures are useful tools for identifying groups of variables associated with outcomes of interest. We develop a novel approach using mutual information as a measure of distance (here dependency) between probability distributions that is valid for comparisons between pairs of variables that are both continuous, both discrete, or one of each. This gives an overall information matrix to be used as a distance matrix in clustering procedures and to define a so-called weighted network of associations between variables. We present computational aspects of implementing our procedures in R. References T. M. Cover and J. A. Thomas. Elements of information theory . Wiley, 2006. doi:10.1002/0471200611 . Z. Dawy, B. Goebel, J. Hagenauer, C. Andreoli, T. Meitinger, and J. C. Mueller. Gene mapping and marker clustering using Shannon's mutual information. IEEE/ACM Transactions on Computational Biology and Bioinformatics , 3(1):47--56, 2006. doi:10.1109/TCBB.2006. 9 . J. J. Faith, B. Hayete, J. T. Thaden, I. Mogno, J. Wierzbowski, G. Cottarel, S. Kasif, J. J. Collins, and T. S. Gardner. Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol , 5(1):e8, 2007. doi:10.1371/journal.pbio. 0050008 . T. F. Fuller, A. Ghazalpour, J. E. Aten, T. A. Drake, A. J. Lusis, and S. Horvath. Weighted gene coexpression network analysis strategies applied to mouse weight. Mammalian Genome , 18(6):463--472, 2007. doi:10.1007/s00335-007-9043-3 . A. Ghazalpour, S. Doss, B. Zhang, S. Wang, C. Plaisier, R. Castellanos, A. Brozell, E. E. Schadt, T. A. Drake, A. J. Lusis, et al. Integrating genetic and network analysis to characterize genes related to mouse weight. PLoS Genet , 2(8):e130, 2006. doi:10.1371/journal.pgen. 0020130 . Hung T. Nguyen. On modeling of linguistic information using random sets. Information Sciences , 34(3):265 -- 274, 1984. doi:10.1016/0020-0255(84)90052-5 . P. Qiu, A. J. Gentles, and S. K. Plevritis. Fast calculation of pairwise mutual information for gene regulatory network reconstruction. Computer Methods and Programs in Biomedicine , 94(2):177--180, 2009. doi:10.1016/0020-0255(84)90052-5 . S. J. Sheather and M. C. Jones. A reliable data-based bandwidth selection method for kernel density estimation. Journal of the Royal Statistical Society. Series B (Methodological) , pages 683--690, 1991. M. P. Wand and M. C. Jones. Kernel smoothing . Chapman and Hall/CRC, 1995. B. Zhang and S. Horvath. A general framework for weighted gene co-expression network analysis. Statistical Applications in Genetics and Molecular Biology , 4(1):1128, 2005. doi:10.2202/1544-6115.1128 .
In vitro and in vivo nutrient digestibility in sheep of rations with and without residue from the extraction of tamarind pulp Digestibilidade in vitro e in vivo de nutrientes em ovinos para rações

This study evaluated the digestibility of nutrients by, and parameters associated with, in vitro fermentation using different inocula (sheep ruminal fluid and feces) as well as the in vivo digestibility in sheep that were fed rations with 50% concentrate containing either no (0%) residue from the extraction of tamarind pulp (RETP) or 15% RETP. To determine the in vitro digestibility (IVD) of nutrients, two sheep, weighing 40.38 ± 2.10 kg, were used as inoculum donors. To determine the in vivo digestibility of nutrients, we used four sheep and a 3×2 factorial experimental design, with three methods of digestion of nutrients and two experimental rations (0% and 15% RETP). The variables were subjected to analysis of variance and the variables that showed differences at 5% probability were further analyzed using the Tukey test at 5% significance. The IVD using different inocula did not significantly differ (p>0.05) from the in vivo digestibility in sheep for dry matter (DM), organic matter (OM), and neutral detergent fiber (NDF). The different methods for determining nutrient digestibility did not affect (p>0.05) the digestibility of DM, OM, crude protein (CP), NDF, and acid detergent fiber (ADF) in rations with 0% and 15% RETP. However, the IVD of CP for rations containing 0% and 15% RETP incubated with both inocula was lower (p<0.05) than the CP digestibility in vivo. The in vivo digestibility of ADF for rations containing 0% and 15% RETP was higher (P<0.05) than the IVD using sheep ruminal fluid and feces as inocula. The pH values and concentration of ammonia nitrogen (NH3-N) after in vitro incubation for 24 h and the in vivo assay were not different (p>0.05) for the rations containing 0% and 15% RETP, but the pH and NH3-N of both fermented and rumen contents differed (p<0.05) depending on the inocula used and the in vivo assay. In summary, the digestibility of DM, OM, and NDF can be determined by the in vitro fermentation method using the ruminal fluid or feces of sheep as inocula in rations containing 0% or 15% RETP. However, in vitro fermentation is not a suitable method for the determination of pH and NH3-N concentration.
Influence of Modified Atmosphere Packaging on the Survival of Salmonella Enteritidis PT 8 on the Surface of Chilled Chicken Legs

The aim of this study was to find whether low numbers of Salmonella in the presence of natural microflora will survive on the surface of chicken legs stored in 30% CO 2 /70% N 2 and 20% CO2/80% O2. In four experiments, a total of 240 pieces of chicken leg were inoculated with a Salmonella Enteritidis, PT 8, wildtype strain resulting in initial concentrations of approximately 4 log, 2.5 log, 1.5 log and 0.5 log cells per piece and kept under selected modified atmospheres for 14 days. Counts of Salmonella were determined by the Most Probable Number method (MPN) at days 0, 3, 7, 10 and 14 of storage. No significant increase or decrease in Salmonella numbers was observed in the atmosphere of 20% CO 2 /80% O 2 . In the atmosphere of 30% CO 2 /70% N 2 there was a significant decrease in cell numbers at days 10 and 14; however, this decrease was proved only in experiments with an initial Salmonella concentration of 4 log and 1.5 log cells per piece. We proved that even low numbers of S. Enteritidis in the presence of natural microflora survive well on the surface of poultry stored at 3 °C in both modified atmospheres we tested. In the case of temperature abuse even products with low initial numbers of Salmonella may constitute a health risk for consumers. Enumeration, Enteritidis, chicken legs, MPN, MAP Poultry meat is very popular among consumers, though it is also the type of meat with the highest risk of the presence of Salmonella. In addition to eggs and egg products, poultry meat and poultry meat products are considered one of the main sources of salmonellosis, the incidence of which in the Czech Republic is continually one of the highest in the European Union. The most commonly identified causative agent of salmonellosis, as well as the most commonly isolated Salmonella serotype in poultry meat, is Salmonella Enteritidis (EFSA, 2009).
A New Methodology of Multicriteria Decision-Making in Supplier Selection Based on -Numbers

Supplier selection is a significant issue of multicriteria decision-making (MCDM), which has been heavily studied with classical fuzzy methodologies, but the reliability of the knowledge from domain experts is not efficiently taken into consideration. -number introduced by Zadeh has more power to describe the knowledge of human being with uncertain information considering both restraint and reliability. In this paper, a methodology for supplier selection using -numbers is proposed considering information transformation. It includes two parts: one solves the issue of how to convert -number to the classic fuzzy number according to the fuzzy expectation; the other solves the problem of how to get the optimal priority weight for supplier selection with genetic algorithm (GA), which is an efficient and flexible method for calculating the priority weight of the judgement matrix. Finally, an example for supplier selection is used to illustrate the effectiveness the proposed methodology.
The Holland and Andre Study on Extracurricular Activities: Imbalanced and Incomplete

The Holland and Andre study on extracurricular activities is imbalanced and incomplete—imbalanced in that because the authors fail to provide a theoretical framework as well as definitions of key terms, both of which would guide their presentation, the inclusion of research studies is skewed heavily toward one aspect of extracurricular activities; incomplete in that the authors fail to provide a literature review comprehensive enough to support the conclusions they draw. These shortcomings make it difficult to understand the relationship between extracurricular activities and student development and, thus, to have confidence in the authors’ recommendations for future research. We agree, however, on the importance of a research effort in this area.
Parameter estimations of geometric extreme exponential distribution based on dual generalized order statistics

In this study, we consider the maximum likelihood and Bayes estimation of the parameters of geometric extreme exponential distribution based on dual generalized order statistics. However, the Bayes estimator does not exist in an explicit form for the parameters. We used an approximation based on Lindley method for obtaining Bayes estimates under squared error loss function. We also discuss the asymptotic variance-covariance matrix of maximum likelihood estimators of two parameters. Through Monte Carlo simulation, we compare the maximum likelihood and Bayes estimates of the parameters. And we include one real data analysis. 3174 Chansoo Kim, Young Han Bae and Woosuk Kim Mathematical Subject Classification: 62C10, 62F10, 62F15, 62G30
Forecasting S&P 500 Stock Index Using Statistical Learning Models

Forecasting the movement of stock market is a long-time attractive topic. This paper implements different statistical learning models to predict the movement of S&P 500 index. The S&P 500 index is influenced by other important financial indexes across the world such as commodity price and financial technical indicators. This paper systematically investigated four supervised learning models, including Logistic Regression, Gaussian Discriminant Analysis (GDA), Naive Bayes and Support Vector Machine (SVM) in the forecast of S&P 500 index. After several experiments of optimization in features and models, especially the SVM kernel selection and feature selection for different models, this paper concludes that a SVM model with a Radial Basis Function (RBF) kernel can achieve an accuracy rate of 62.51% for the future market trend of the S&P 500 index.
Comparative study on earthquake and ground based transmitter induced radiation belt electron precipitation at middle latitudes

Abstract. We examined (peak-to-background flux ratio p/b > 20) energetic electron bursts in the presence of VLF activity, as observed from the DEMETER satellite at low altitudes (~700 km). Our statistical analysis of measurements during two 6-month periods suggests that: (a) the powerful transmitter NWC causes the strongest effects on the inner radiation belts in comparison with other ground-based VLF transmitters, (b) the NWC transmitter was responsible for only ~1.5 % of total electron bursts examined during the 6-month period (1 July 2008 to 31 December 2008), (c) VLF transmitter-related electron bursts are accompanied by the presence of a narrow band emission centered at the radiating frequency emission, whereas the earthquake-related electron bursts are accompanied by the presence of broadband emissions from a few kHz to >20 KHz, (d) daytime events are less preferable than nighttime events, but this asymmetry was found to be less evident when the powerful transmitter NWC was turned off and (d) seismic activity most probably dominated the electromagnetic interactions producing the electron precipitation at middle latitudes. The results of this study support the proposal that the detection of radiation belt electron precipitation, besides other kinds of studies, is a useful tool for earthquake prediction research.
A Precision RC-locked Oscillator

In this thesis, the development and implementation of a new precision RC-locked oscillator topology suitable for wireless sensor networks (WSNs) is described. The objective of this thesis was to investigate the performance of the proposed topology and to compare this with the state-of-the-art in terms of accuracy and power consumption. The new oscillator was implemented in a 0.16 µm CMOS process. The prototype was su? ciently functional to be tested. It achieved a frequency inaccuracy of ±0.9% (3? based on 12 samples) from -40C to 125C, consuming 37 µW power. The achieved performance is comparable to the state-of-the-art, for a wider temperature range and for signi? cantly more samples.
Study of Outflows in Luminous Quasars at Redshift ∼0.4–0.8

We perform a systematic study of outflow in the narrow-line region (NLR) of active galactic nuclei (AGNs) at z ∼ 0.4–0.8 based upon a large sample of ∼900 quasars at z ∼ 0.4–0.8. The sample is extracted from the Sloan Digital Sky Survey by mainly requiring that (1) the g-band magnitude is brighter than 19 mag and (2) the [O iii]λ5007 emission line has a signal-to-noise ratio larger than 30. Profiles of multiple emission lines are modeled by a sum of several Gaussian functions. The spectral analysis allows us to identify (1) a prevalence of both [O iii]λ5007 line blue asymmetry and bulk velocity blueshift of both [Ne iii]λ3869 and [Ne iii]λ3426 lines, when the [O ii]λ3727 line is used as a reference. The velocity offset of the [O iii]λ5007 line is, however, distributed around a value of zero, except for a few outliers. (2) Not only the significant [O iii]λ5007 line asymmetry, but also the large bulk velocity offsets of [Ne iii]λ3869 and [Ne v]λ3426 emission lines tend to occur in the objects with high L/LEdd, which is considerably consistent with the conclusions based on local AGNs. With three MBH estimation methods, the significance level of the trend is found to be better than 2. 9σ, 3. 2σ, and 1. 8σ for [O iii], [Ne iii], and [Ne v], respectively. After excluding the role of radio jets, the revealed dependence of NLR gas outflow on L/LEdd allows us to argue that the pressure caused by the wind/radiation launched/emitted from a central supermassive black hole is the most likely origin of the outflow in these distant quasars, which implies that the outflow in luminous AGNs up to z ∼ 1 have the same origin.
Q uantification of eutrophic aerial compounds in Galicia ( NW Spain ) : Part 2 – NO x inventory

This study is the second part of a series where NH3 and NOx emission inventories for Galicia (NW Spain), a region with a great risk of eutrophication, have been developed. The principal sources of NOx emissions in Galicia and their associated uncertainty have been calculated in this paper. The results prove that industrial and mobile sources produce 90% of the emissions, principally due to road transport, power and cogeneration plants. Use of fertilizers or fuels for residential purposes, burning of agricultural waste, soils, fires and lightning are minor sources of emissions. In the case of fires, in regions specially affected like Galicia, attention must be paid to variations in number and type of burnt areas from one year to another, because it can significantly change total NOx emissions. The emissions produced by agricultural, fishery and forest vehicles and machines as well as by maritime and railway traffic are the main focus of uncertainty due to the lack of specific data for Galicia like type, age and power of the machines. Other important focuses of uncertainties are the emissions from soils and fires owing to the absence of a more specific methodology.
Determination of Bioavailable Contaminants in the Lower Missouri River following the Flood of 1993

The semipermeable membrane device (SPMD) technology was employed to determine the presence of bioavailable organochlorine pesticides (OCs), polychlorinated biphenyls (PCBs), and polyaromatic hydrocarbons (PAHs) in the water of the main stem of the lower Missouri River and three of its tributaries. The SPMDs were deployed in 1994 following the extensive flood of 1993. Specifically, the SPMDs were deployed for 28 days at Wilson State Park, IA; Nebraska City, NE; Parkville, MO; the Kansas River in Kansas City, KS; Napoleon, MO; the Grand River; Glasgow, MO; the Missouri River upstream from the confluence of the Gasconade River; the Gasconade River; and Hermann, MO. Contaminant residues were found at all sites and at higher concentrations than found in the earlier pre-flood sampling. For example, in the present study, dieldrin was found to range from a low of 110 ng/sample in the Gasconade River to a high of 2000 ng/sample at Glasgow, while in the pre-flood sampling, dieldrin ranged from a low of 64 ng/sample.
North-Holland Supply-side economics and endogenous growth

Convex models of endogenous economic growth have proven useful as analytic laboratories for the evaluation of fiscal policy experiments. Unlike the basic neoclassical growth model of Solow (1956) and Cass (1965), which attributes cross-economy differences in growth rates to differences in rates of exogenous technological progress, these newer models isolate channels through which public policy can influence long-run growth. In particular, Jones and Manuelli (1990), King and Rebel0 (1990), Rebel0 (1991), and Jones, Manuelli, and Rossi (1993) find that tax policies have potentially large effects on long-run
EFFECT OF COMPOUND FORMULATION ON THE PRODUCTION AND PROPERTIES OF EPOXIDISED NATURAL RUBBER (ENR-25) FOAMS

In this study, Epoxidized Natural Rubber (ENR-25) formulations are compounded and tested to obtain a stable expandable rubber foam as well as to determine the foam cell physical morphology and its mechanical properties. The experiment was carried out by employing different ratio of rubber blend between ENR-25 and natural rubber (SMR-L), different amount of blowing agent which is Sodium Bicarbonate and different ratio of accelerator between Tetramethylthiuram-disulfenamide (TMTD) and N-cyclohexyl-2-benzotiazolsulfenamide (CBS). Cure characteristics of the compounded rubber were determined using Monsanto Rheometer and the expandable rubber foam is produced using compression moulding technique with utilization of heat transfer process. The generated foam cell morphology is analyzed using image analyzer and SEM while the mechanical properties of the foam are examined by using Instron machine to determine its compression stress. On the other hand, swelling test using the Flory-Rhener equation is also done to support the substitute results. The data shows that at the ratio of 60 phr ENR-25 and 40 phr SMR-L is able to deliver stable rubber foam. Furthermore, increasing the amounts of blowing agent evidently increased the foam cell size, inducing smaller cell in between the foam cell wall, decreasing the value of compression stress and compression set. It was also observed that increasing the ratio of CBS in the compounded rubber will increase the cell size, creating thicker foam cell wall, increasing the value of compression stress and compression set.
Deoxyribonucleic Acid Homology and Taxonomy of the Genus Bacillus

The taxonomic relationships among 56 strains of 16 species of the genus Bacillus were studied by deoxyribonucleic acid (DNA)-DNA hybridization. In general, no significant DNA homology was detected between two strains of different species, except for a group of species consisting of B. subtilis, B. amyloliquefaciens, B. licheniformis, and B. pumilus and for another group of species including B. cereus and B. thuringiensis. Species of the former group were related, but they were independent of each other as their DNA homologies were 19% or less. The DNA homology indexes of three strains of B. thuringiensis to B. cereus T, so far tested, showed high DNA homologies (54 to 80%). This fact indicates that B. thuringiensis should be an identical species to B. cereus. The intraspecific DNA homology indexes of 16 strains of B. pumilus were 51% or more to strain IFO 12092 as the standard, and those of 10 strains of B. coagulans were 76 to 113% to strain ATCC 7050 as the standard. Thus, the species identification of B. pumilus and B. coagulans by the conventional taxonomic method was well in accord with the DNA homology data. On the other hand, significant heterogeneities were suggested among the strains of B. circulans and among those of B. sphaericus by the DNA homology data of the three and five strains so far tested, respectively. Although B. lentus was described to be closely related to B. firmus in Bergey's Manual (8th ed., 1974), the interspecific DNA homology index between these two species was 3%. It was concluded that these two species are independent.
A Kind of Potential Practical Sensors of Metamaterial in Electromagnetic Flaw Nondestructive Testing

We present a new kind of method of electromagnetic flaw nondestructive testing with coating of metamaterials and simulation near electromagnetic field property for test crack. The simulation of improving a Nondestructive testing (NDT) probe electromagnetic radiant property by Metamatrials (MMs) covering a tiny current element is investigated and analyzed using Ansoft HFSS based on finite element method (FEM), which permittivity and permeability are negative. Electromagnetic model: Ideal MMs ball shell with inner radius of 1 mm and outer radius variation, and the shell’s relative permittivity and relative permeability are all –3.0, dielectric loss tangent and magnetic loss tangent are all 0.1; and exciting current element length is with 0.3 mm, diameter 0.2 mm, value 1 mA at frequency 10 GHz; and simulation is with radiation boundary conditions. The simulating near electromagnetic field variety with ratio of inner radius and out radius, and so near or local field of MMs sensor on a surface crack, as well as comparing near field value of sensor with coating common material are finished. Results can be seen that MMs film sensor near electromagnetic field and radiation properties are obviously better than other two kinds of structures without coating medium and coating with common medium, and Metamaterial may be opened out some new kinds of sensors in electromagnetic flaw nondestructive testing for potential practical applications in future.
Output-reference tracking problem for discrete-time systems with input saturations

Nonlinear state feedback controllers are exhibited for locally stabilising linear discrete-time systems with both saturating actuators and additive disturbances when the output must track a certain time-varying reference level. The objective is to bring the steady-state error due to disturbances to zero, by using a saturated controller and a dead-zone function. The objective is two-fold: to determine both a stabilising controller and a region of the state space over which the stability of the resulting closed-loop system is ensured, when the controls are allowed to saturate.