Miracle-dz/UniFAR-FTUs huggingface dataset:
Methods of DNA adduct determination and their application to testing compounds for genotoxicity

At the International Workshop on Genotoxicity Test Procedures (IWGTP) held in Washington, DC (March 25–26, 1999), a working group considered the uses of DNA adduct determination methods for testing compounds for genotoxicity. When a drug or chemical displays an unusual or inconsistent combination of positive and negative results in in vitro and in vivo genotoxicity assays and/or in carcinogenicity experiments, investigations into whether or not DNA adducts are formed may be helpful in assessing whether or not the test compound is a genotoxin. DNA adduct determinations can be carried out using radiolabeled compounds and measuring radioactive decay (scintillation counting) or isotope ratios (accelerator mass spectrometry) in the isolated DNA. With unlabeled compounds adducts may be measured by 32P‐postlabeling analysis of the DNA, or by physicochemical methods including mass spectrometry, fluorescence spectroscopy, or electrochemical detection, or by immunochemical methods. Each of these approaches has different strengths and limitations, influenced by sensitivity, cost, time, and interpretation of results. The design of DNA binding studies needs to be on a case‐by‐case basis, depending on the compound's profile of activity. DNA purity becomes increasingly important the more sensitive, and less chemically specific, the assay. While there may be adduct levels at which there is no observable biological effect, there are at present insufficient data on which to set a threshold level for biological significance. Environ. Mol. Mutagen. 35:222–233, 2000 © 2000 Wiley‐Liss, Inc.
Third Party Privacy Preserving Protocol for Perturbation Based Classification of Vertically Fragmented Data Bases

Privacy is become major issue in distributed data mining. In the literature we can found many proposals of privacy preserving which can be divided into two major categories that is trusted third party and multiparty based privacy protocols. In case of trusted third party models the conventional asymmetric cryptographic based techniques will be used and in case of multi party based protocols data perturbed to make sure no other party to understand original data. In order to enhance security features by combining strengths of both models in this paper, we propose to use data perturbed techniques in third party privacy preserving protocol to conduct the classification on vertically fragmented data bases. Specially, we present a method to build Naive Bayes classification from the disguised and decentralized databases. In order to perform classification we propose third party protocol for secure computations. We conduct experiments to compare the accuracy of our Naive Bayes with the one built from the original undisguised data. Our results show that although the data are disguised and decentralized, our method can still achieve fairly high accuracy.
Quality, Safety, and Value in Pediatric Orthopaedic Surgery

Enhancing patient safety and the quality of care continues to be a focus of considerable public and professional interest. We have made dramatic strides in our technical ability to care for children with pediatric orthopaedic problems, but it has become increasingly obvious that there are also significant opportunities to improve the quality, safety, and value of the care we deliver. The purpose of this article is to introduce pediatric orthopaedic surgeons to the rationale for and principles of quality improvement and to provide an update on quality, safety, and value projects within Pediatric Orthopaedic Society of North America.
Estimation method of surface texture parameters by inverse analysis of dynamic characteristics

The surface texture describes the surface topography formed by micro asperities on a surface of a solid member. The Hertz-Mindlin theory is one of contact theories based on the mechanics of elasticity. The main parameters for the theory are the number of the asperity peaks per unit area, the radius of the curvature at the asperity peak and the standard deviation of the asperity peak heights. These parameters are collectively named as the surface texture parameters. Most of the conventional approaches to obtain these parameters are curve ﬁttings applied on the surface texture. However, the 3D measurement with a spatial resolution of a micron is required in the measurement of the surface texture, and the measurable area is limited. This study has developed a novel method to estimate the surface texture parameters by the inverse analysis of the dynamic characteristics of the target. In the proposed method, the natural frequency of the target is obtained by the hammering test and the ﬁnite element analysis with the interfacial element based on the Hertz-Mindlin theory. Then the set of the surface texture parameters minimizing the residual between the test result and the analysis result is derived. In order to verify the proposed method, a series of hammering tests was carried out by using specimens with bolted joints. Using the test results, the surface texture parameters were estimated by the proposed method. From the estimation results, it conﬁrmed that the calculation results of the natural frequency in the inverse analysis had good agreement with the results of the hammering test. The estimation accuracy of the proposed method was comparable to that of the 3D surface texture measurement in terms of ﬁtting the quadratic surfaces.
Performance and construction of polar codes on symmetric binary-input memoryless channels

Channel polarization is a method of constructing capacity achieving codes for symmetric binary-input discrete memoryless channels (B-DMCs) [1]. In the original paper, the construction complexity is exponential in the blocklength. In this paper, a new construction method for arbitrary symmetric binary memoryless channel (B-MC) with linear complexity in the blocklength is proposed. Furthermore, new upper bound and lower bound of the block error probability of polar codes are derived for the BEC and arbitrary symmetric B-MC, respectively.
EXTRACTING FEATURE SUBSPACE FOR KERNEL BASED LINEAR PROGRAMMING SUPPORT VECTOR MACHINES

We propose linear programming formulations of support vector machines (SVM). Unlike standard SVMs which use quadratic programs, our approach explores a fairly small dimensional subspace of a feature space to construct the nonlinear discriminator. This allows us to obtain the discriminator by solving a smaller sized linear program. We demonstrate that an orthonormal basis of the subspace can be implicitly treated by eigenvectors of the Gram matrix defined by the associated kernel function. When the number of given data points is very large, we construct a subspace by random sampling of data points. Numerical experiments indicate that the subspace generated by less than 2% of the entire training data points achieves reasonable performance for a fairly large instance with 60000 data points.
Seamless registration of dual camera images using optimal mask-based image fusion

In an image fusion, misalignment errors are generated in the boundaries between objects and background. To solve this problem, this paper presents an image fusion method using the optimal mask that contains main objects. The proposed method consists of three steps: i) pre-processing and global warping to register a tele-view image to a wide-view image, ii) generating seam-based optimal mask to detect the noticeable region, and iii) image fusion using the mask and local warping based on motion estimation. This method provides high quality fusion results without misalignment. For this reason, the proposed method can apply in various areas that need the image synthesis.
Estimation and Comparison of the Weighted Kappa Coefficients of Binary Diagnostic Tests: A Review

Sensitivity and specificity are classic parameters to assess and to compare the precision of binary diagnostic tests in relation to a gold standard. Another parameter to assess and to compare the performance of binary diagnostic tests is the weighted kappa coefficient, which is a measure of the beyond-chance agreement between the binary diagnostic test and the gold standard, and it is a function of the sensitivity and the specificity of the diagnostic test, the disease prevalence and the relative loss between the false positives and the false negatives. In this study, we carry out a review of the weighted kappa coefficient, its estimation for a single diagnostic test and the hypothesis tests to compare the weighted kappa coefficients of two or more diagnostic tests, both when the gold standard is applied to all of the subjects in a random sample and when the gold standard is only applied to a subset of subjects in a random sample. The results were applied to different examples.
A Review on Research on Replacement of CH4 in Natural Gas Hydrates by Use of CO2

This paper introduces the research advances on replacement of CH 4 in Natural Gas Hydrates (NGHs) by use of CO 2 and discusses the advantages and disadvantages of the method on the natural gas production from such hydrates. Firstly, the feasibility of replacement is proven from the points of view of kinetics and thermodynamics, and confirmed by experiments. Then, the latest progress in CH 4 replacement experiments with gaseous CO 2 , liquid CO 2 and CO 2 emulsion are presented Moreover, the superiority of CO 2 emulsion for replacement of CH 4 is emphasized. The latest experiment progress on preparation of CO 2 emulsions are introduced. Finally, the advancements in simulation research on replacement is introduced, and the deficiencies of the simulations are pointed. The factors influencing on the replacement with different forms of CO 2 are analyzed and the optimum conditions for the replacement of CH 4 in hydrated with different forms of CO 2 is suggested.
Parallel plate slot coupler modeling using two dimensional frequency domain transmission line matrix method

A slot coupler for coupling between via-defined waveguides is analyzed using the 2D frequency domain transmission line matrix (2D-TLM) method. The general 2D-TLM model for a slot coupling between parallel plate waveguides is useful in the design of advanced low cost millimeter-wave packaging. The via waveguide coupler is modeled and the model verified by comparison to measurement.
Tools Engineered Specifically for Information Space Organization 1. Introduction and Motivation

The burgeoning " information overload " problem plaguing today's technology users is well-documented. On nearly every front, the amount of data collected electronically far outstrips our ability to keep pace with understanding it. We have embedded devices with sensors that continually gather data; online digital libraries that regularly add new material as well as old; supermarket chains that capture and archive our every purchase; and of course the World Wide Web, which by conservative estimates is growing at a rate of over a hundred pages per minute[78]. It's no secret that by themselves, these vast megabytes mean nothing. In general, only the interpretation and deep analysis by human beings gives rise to productive knowledge that can be of practical benefit. Anything less is a waste of time. The tools currently available to assist in this quest for knowledge are principally two: query languages, in their various forms, and the discipline of data mining. The former is well-known to virtually any consumer of data – users (or programs) pose a series of concrete inquiries to some kind of interface, which attempts to extract bits of knowledge from an enormous data store. Sometimes a query is an intricate piece of code, such as an SQL statement, that navigates and pulls together a series of tables and values to arrive at a precise answer. In other cases, for instance a Google web search, it's more of a shot in the dark: a group of terms suggests the desired content which the search engine aims to find. In either case, between the human and the information lies a narrow channel through which questions are posed and results given. Researchers in the fields of query optimization and information retrieval have invested tremendous effort in improving this channel, in order to make the results speedier and more satisfactory. Data mining takes a different approach; the emphasis is less on ad hoc interaction and more on the discovery of patterns deeply embedded in the data which can only be uncovered by exhaustive statistical analysis. In some cases, human observers bring a great deal of structure to the data at the outset: they know the relevant categories to which individual data records belong, and seek complex rules by which future records can be automatically classified. Or they may approach a large data set with a particular subset of variables in mind, and want to verify mathematical correlations between …
The Enzyme Activity and Substrate Specificity of Two Major Cinnamyl Alcohol Dehydrogenases in Sorghum (Sorghum bicolor), SbCAD2 and SbCAD41

Substrate catalysis by cinnamyl alcohol dehydrogenases from Sorghum bicolor deduced from crystal structures, site-directed mutagenesis, and kinetics. Cinnamyl alcohol dehydrogenase (CAD) catalyzes the final step in monolignol biosynthesis, reducing sinapaldehyde, coniferaldehyde, and p-coumaraldehyde to their corresponding alcohols in an NADPH-dependent manner. Because of its terminal location in monolignol biosynthesis, the variation in substrate specificity and activity of CAD can result in significant changes in overall composition and amount of lignin. Our in-depth characterization of two major CAD isoforms, SbCAD2 (Brown midrib 6 [bmr6]) and SbCAD4, in lignifying tissues of sorghum (Sorghum bicolor), a strategic plant for generating renewable chemicals and fuels, indicates their similarity in both structure and activity to Arabidopsis (Arabidopsis thaliana) CAD5 and Populus tremuloides sinapyl alcohol dehydrogenase, respectively. This first crystal structure of a monocot CAD combined with enzyme kinetic data and a catalytic model supported by site-directed mutagenesis allows full comparison with dicot CADs and elucidates the potential signature sequence for their substrate specificity and activity. The L119W/G301F-SbCAD4 double mutant displayed its substrate preference in the order coniferaldehyde > p-coumaraldehyde > sinapaldehyde, with higher catalytic efficiency than that of both wild-type SbCAD4 and SbCAD2. As SbCAD4 is the only major CAD isoform in bmr6 mutants, replacing SbCAD4 with L119W/G301F-SbCAD4 in bmr6 plants could produce a phenotype that is more amenable to biomass processing.
NMDA-Mediated Ca2+ Influx Drives Aberrant Ryanodine Receptor Activation in Dendrites of Young Alzheimer's Disease Mice

Deficits in synaptic function, particularly through NMDA receptors (NMDARs), are linked to late-stage cognitive impairments in Alzheimer's disease (AD). At earlier disease stages, however, there is evidence for altered endoplasmic reticulum (ER) calcium signaling in human cases and in neurons from AD mouse models. Despite the fundamental importance of calcium to synaptic function, neither the extent of ER calcium dysregulation in dendrites nor its interaction with synaptic function in AD pathophysiology is known. Identifying the mechanisms underlying early synaptic calcium dysregulation in AD pathogenesis is likely a key component to understanding, and thereby preventing, the synapse loss and downstream cognitive impairments. Using two-photon calcium imaging, flash photolysis of caged glutamate, and patch-clamp electrophysiology in cortical brain slices, we examined interactions between synaptically and ER-evoked calcium release at glutamatergic synapses in young AD transgenic mice. We found increased ryanodine receptor-evoked calcium signals within dendritic spine heads, dendritic processes, and the soma of pyramidal neurons from 3xTg-AD and TAS/TPM AD mice relative to NonTg controls. In addition, synaptically evoked postsynaptic calcium responses were larger in the AD strains, as were calcium signals generated from NMDAR activation. However, calcium responses triggered by back-propagating action potentials were not different. Concurrent activation of ryanodine receptors (RyRs) with either synaptic or NMDAR stimulation generated a supra-additive calcium response in the AD strains, suggesting an aberrant calcium-induced calcium release (CICR) effect within spines and dendrites. We propose that presenilin-linked disruptions in RyR signaling and subsequent CICR via NMDAR-mediated calcium influx alters synaptic function and serves as an early pathogenic factor in AD.
ICAP, a new flash wear-leveling algorithm inspired by locality

In this paper, we extend a trivial wear-leveling algorithm to reduce the management overhead of leveraging the number of write operations over all data blocks. By exploiting access locality, most parts of a mapping table of a flash translation layer (FTL) keep unchanged since wear leveling is adopted only when a block tends to be unreliable. Because the mapping table is changed rarely, we can reduce the mounting time by record most portion of the mapping table on the flash drive. Furthermore, we can give short codes to the data blocks that erased frequently (because the locality) when recording the erase counts in a log structure. We observe that the algorithm can extend the lifetime of a flash drive and reduce mounting time in most situations.
Analysis of flagellar size control using a mutant of Chlamydomonas reinhardtii with a variable number of flagella

A mutant of Chlamydomonas reinhardtii with a variable number of flagella per cell has been used to investigate flagellar size control. The mutant and wild-type do not differ in cell size nor in flagellar length, yet the size of the intracellular pool of flagellar precursor protein can differ dramatically among individual mutant cells, with, for example, triflagellate cells having three times the pool of monoflagellate cells. Because cells of the same size, but with very different pool sizes, have flagella of identical length, it appears that the concentration of the unassembled flagellar precursor protein pool does not regulate flagellar length. The relation between cell size, pool size, and flagellar length has also been investigated for wild-type cells of different sizes and ploidies. Again, flagellar length appears to be maintained independent of pool size or concentration.
Attentional Focus Effects in Standing Long Jump Performance: Influence of a Broad and Narrow Internal Focus

Abstract Becker, KA and Smith, PJK. Attentional focus effects in standing long jump performance: Influence of a broad and narrow internal focus. J Strength Cond Res 29(7): 1780–1783, 2015—The content of instructions that strength coaches give can have a significant impact on how an athlete or client performs. Research on motor learning has shown an advantage of instructions focusing on the effects of movements (external focus) over those focusing on the movements themselves (internal focus) in the performance of motor skills. Internally focused cues are abundant in coaching, therefore the purpose of this study was to test whether some internally focused cues might be more helpful than others. Participants (68) were randomly assigned to either an external focus (EX), broad internal focus (B-IN), narrow internal focus (N-IN), or a control group (CON), and performed 5 standing long jumps. All groups were instructed that the goal was to jump as far as possible. In addition, the EX group was told to “jump as far past the start line as possible. ” The B-IN group was told to “use your legs. ” The N-IN group was told to “extend your knees as rapidly as possible,” and the CON group received no additional instruction. An analysis of covariance showed that the EX group (198.09 ± 31.89 cm) jumped significantly farther than both the B-IN group (173.74 ± 35.36 cm), p = 0.010 and the N-IN group (178.53 ± 31.17 cm), p = 0.049, with no group different from the CON group. The results suggest that a broad internal focus is no more effective than a narrow internal focus, and that an external focus leads to the greatest jump distance. Strength and conditioning professionals should carefully word their instructions to induce an external focus of attention whenever possible.
Smart Partnerships to Increase Equity in Education

This exploratory analysis of smart partnerships identifies the risk of increasing the digital divide with the deployment of data analytics. Smart partnerships in education appear to include a process of evolution into a synergy of strategic and holistic approaches that enhance the quality of education with digital technologies, harnessing ICT “smartly” both in relation to learning and support of the partnership itself. To guide strategic development as data analytics start to emerge in the schooling sector, two cases of large multi-stakeholder partnership initiatives aiming to increase access to education with ICT nationwide in India and Malaysia are analyzed. Mapping the partners’ collaborative activities in Davis’ Arena of change with digital technologies enabled the identification of both local and global influences in that ecological framework, which inform the choice of partners and their roles to increase equitable access to education. Research and development is recommended so that multi-stakeholder partnerships leverage data analytics alongside technology enhanced learning in the schooling sector with strategies that proactively increase equity.
Glucose Limitation Induces GCN4Translation by Activation of Gcn2 Protein Kinase

ABSTRACT Phosphorylation of the α subunit of eukaryotic initiation factor 2 (eIF-2α) is a well-characterized mechanism regulating protein synthesis in response to environmental stresses. In the yeastSaccharomyces cerevisiae, starvation for amino acids induces phosphorylation of eIF-2α by Gcn2 protein kinase, leading to elevated translation of GCN4, a transcriptional activator of more than 50 genes. Uncharged tRNA that accumulates during amino acid limitation is proposed to activate Gcn2p by associating with Gcn2p sequences homologous to histidyl-tRNA synthetase (HisRS) enzymes. Given that eIF-2α phosphorylation in mammals is induced in response to both carbohydrate and amino acid limitations, we addressed whether activation of Gcn2p in yeast is also controlled by different nutrient deprivations. We found that starvation for glucose induces Gcn2p phosphorylation of eIF-2α and stimulates GCN4translation. Induction of eIF-2α phosphorylation by Gcn2p during glucose limitation requires the function of the HisRS-related domain but is largely independent of the ribosome binding sequences of Gcn2p. Furthermore, Gcn20p, a factor required for Gcn2 protein kinase stimulation of GCN4 expression in response to amino acid starvation, is not essential for GCN4 translational control in response to limitation for carbohydrates. These results indicate there are differences between the mechanisms regulating Gcn2p activity in response to amino acid and carbohydrate deficiency. Gcn2p induction of GCN4 translation during carbohydrate limitation enhances storage of amino acids in the vacuoles and facilitates entry into exponential growth during a shift from low-glucose to high-glucose medium. Gcn2p function also contributes to maintenance of glycogen levels during prolonged glucose starvation, suggesting a linkage between amino acid control and glycogen metabolism.