Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparisons among the Novel Measurements Based on Chi Square Criterion for Sequence Dissimilarity and Their Applications to Phylogeny

In this paper, some new measurements based on Chi square test are presented. Protein sequences are characterized by the frequency of occurrence of the 20 amino acids. Each frequency of a protein sequence is deemed as a sample for various populations. The value of Chi square in the Chi square test is used to measure the dissimilarity of each pair of the protein sequence. Furthermore, some transformations based on the Chi square value are done to measure the dissimilarity. For example, taking the unbalance of the length of protein sequences into consideration, we standardize the length of protein sequence as 1000 with the same frequency of amino acid. Other transformations are listed as follow, such as, the P value according to the Chi square distribution and the normal distribution quantile according to the P value. Based on the data for the Eutherian orders using concatenated H-stranded amino acid sequences, we compare the phylogeny trees with these measurements for sequence dissimilarity. In line with the results, some phylogeny trees are agreed with the commonly accepted one for the Eutherians.
Objective II: Human Bioavailability and anti-inflammatory properties of Mango Polyphenols (Comparison lean and obese over 24h, and 10 and 42 days)

s: R Barnes, K Krenek, S Talcott, S Talcott. Profile of Gallic Acid Metabolites in Urine After the Intake of Mango (Mangifera indica, L.) cv. Keitt in Humans. Experimental Biology 2015, Boston H Kim, R Barnes, C Fang, S Talcott, S Mertens-Talcott. Intestinal Microbiota and Host Metabolism Respond Differentially in Lean and Obese Individuals Following Six-Week Consumption of Galloyl Derivatives from Mango (Mangifera Indica L.) Pulp. Experimental Biology 2017, Chicago C Fang, H Kim, R Barnes, S Talcott, S Mertens-Talcott. Daily Mango (Mangifera Indica L.) Consumption For 42 Days Differentially Modulates Metabolism And Inflammation In Lean And Obese Individuals. Experimental Biology 2017, Chicago SU Mertens-Talcott, H Kim, S Talcott, R Barnes. Adaptation of Gallic Acid, Galloyl Glycoside, and Gallotannin Metabolism and Excretion after 42 Days of Mango (Mangifera Indica L.) Consumption. Experimental Biology 2017, Chicago Chuo Fang, Hyemee Kim, Ryan C Barnes, Stephen T Talcott, Susanne U MertensTalcott. Daily Mango (Mangifera Indica L.) Consumption for 42 Days Differentially Modulates Metabolism and Inflammation in Lean and Obese Subjects. Interdisciplinary Regional NORC meeting, Texas A&M University, May 2017. Manuscripts/peer reviewed publications: R Barnes, K Krenek, S Talcott, S Talcott. Urinary metabolites from mango (Mangifera indica L. cv. Keitt) galloyl derivatives and in vitro hydrolysis of gallotannins in physiological conditions. Mol. Nutr. Food Res. 2016, 60, 542–550
Theoretical Description of Ultrasonic Propagation and Scattering Phenomena in Polycrystalline Structures Aiming for Simulations on Nondestructive Materials Characterization and Defect Detection

In microscopically inhomogeneous media ultrasonic scattering at grain and/or phase boundaries causes sound velocity dispersion and attenuation. These effects as well as the amplitudes of the scattering waves can be used for materials characterization. Concomitant, scattering at the microstructure of materials hampers defect detection and evaluation because the so-called structural noise superposes defect signals, and velocity dispersion corrupts defect positioning. Hence, the simulation of ultrasonic propagation and nondestructive testing procedures must contain microstructural scattering phenomena. In a general approach, the scattering wave energy flux densities in microscopically inhomogeneous materials are derived from the formal infinite Born series presentation of ultrasonic displacement vectors, the solutions of the elastodynamic equation of motion. The energy flux densities are ensemble averaged respective the microscopic inhomogeneity and evaluated for single phase polycrystals in lowest non-zero order. The resultant directional and frequency dependent scattering wave amplitudes are discussed in the context of results from the literature.
Adaptive Error-Prediction Aging Sensor for On-Line Monitoring of Performance Errors

—This paper presents a new aging sensor architecture for error prediction of performance errors in synchronous digital circuits. The aging sensor is based on a new flip-flop with built-in logic that predicts the errors by monitoring long-term performance degradation of CMOS digital systems. The main advantage is that the sensor’s long-term degradation effects increase its sensitivity to performance error prediction. Moreover, the reduction of the power-supply voltage (V) and the increase of the temperature (T) also make the sensor to increase its sensitivity, making the sensor to adapt its monitoring capability with aging and VT variations. Performance failure prediction is implemented by the detection of late transitions at flip-flop data input, caused by aging (namely, due to NBTI), or to physical defects activated by long lifetime operation, or even by a worst-case operating condition (namely, V and/or T). Extensive SPICE simulations allowed achieving a new flip-flop with additional aging sensor capability, however with negligible performance degradation, because the sensing circuitry is out of the signal path. Simulation results are presented for two CMOS technologies (65nm and 22nm), using Berkeley Predictive Technology Models (PTM). It is shown that PVTA (Process, power supply Voltage, Temperature and Aging) variations on the sensor enhance error prediction capability.
Analytical determination of the workspace of symmetrical spherical parallel mechanisms

This paper presents a methodology for the analytical determination and representation of the workspace boundaries of symmetrical spherical parallel mechanisms (SPMs). The methodology is based on an intuitive orientation representation which, while not well known, has proven to be very useful for the analysis of symmetrical parallel mechanisms. The latter, previously introduced as "tilt-and-torsion angles," are briefly described. Then, relatively simple analytical expressions are found for the workspace boundaries of general symmetrical SPMs. Next, using these expressions and a simple numerical procedure, a fast algorithm is proposed for representing the so-called constant-torsion workspace. Finally, several examples are provided
Southeast Marine Recreational Fishery Statistical Survey: Distance and Catch Based Choice Sets

In this paper we estimate the economic value associated with marine recreational fishing in the southeast United States using the random utility model. The data used is the Southeast (North Carolina to Louisiana) Marine Recreational Fishery Statistics Survey (SE MRFSS). The geographic extent of the market and potential catch are used to determine the effect of choice set definition on random utility model parameter and welfare estimates. We find that choice sets based on distance or catch do not lead to large differences in the compensating variation of a fishing trip. Defining choice sets based on catch does lead to insignificant estimates of the effect of one measure of site quality on site selection. We also find differences in the value of an additional fish when comparing alternative measures of site quality.
ASKNet: Automatically Generating Semantic Knowledge Networks

The ASKNet project uses a combination of NLP tools and spreading activation to transform natural language text into semantic knowledge networks. Network fragments are generated from input sentences using a parser and semantic analyser, then these fragments are combined using spreading activation based algorithms. The ultimate goal of the project is to create a semantic resource on a scale that has never before been possible. We have already managed to create networks more than twice as large as any comparable resource(1.5 million nodes, 3.5 million edges) in less than 3 days. This report provides a summary of the project and its current state of development.
Impedance-controlled, minimally-assistive robotic training of severely impaired hemiparetic patients

The paper describes a pilot study in the robotic training of severely impaired hemiparetic patients. It provides arguments in favor of impedance control, with a backdrivable manipulandum characterized by a very low level of the intrinsic mechanical impedance, and proposes a method of minimally assistive robotic training that focuses on outward reaching movements of large amplitude. This type of training is well accepted by the patients and appears to help them decrease the dominating flexion patterns that characterize their pathology
(Near) Dimension Independent Risk Bounds for Differentially Private Learning

In this paper, we study the problem of differentially private risk minimization where the goal is to provide differentially private algorithms that have small excess risk. In particular we address the following open problem: Is it possible to design computationally efficient differentially private risk minimizers with excess risk bounds that do not explicitly depend on dimensionality (p) and do not require structural assumptions like restricted strong convexity? In this paper, we answer the question in the affirmative for a variant of the well-known output and objective perturbation algorithms (Chaudhuri et al., 2011). In particular, we show that under certain assumptions, variants of both output and objective perturbation algorithms have no explicit dependence on p; the excess risk depends only on the L2-norm of the true risk minimizer and that of training points. Next, we present a novel privacy preserving algorithm for risk minimization over simplex in the generalized linear model, where the loss function is a doubly differentiable convex function. Assuming that the training points have bounded L∞-norm, our algorithm provides risk bound that has only logarithmic dependence on p. We also apply our technique to the online learning setting and obtain a regret bound with similar logarithmic dependence on p. In contrast, the existing differentially private online learning methods incur O(√p) dependence.
Non-intrusive regularization for least-squares multichannel equalization for speech dereverberation

Acoustic multichannel equalization techniques for speech dereverberation are known to be highly sensitive to estimation errors of the room impulse responses. In order to increase robustness, it has been proposed to incorporate regularization. However, the optimal regularization parameter which yields the highest perceptual speech quality has generally been determined intrusively, limiting the practical applicability. In this paper, we propose an automatic non-intrusive procedure for determining the regularization parameter based on the L-curve. Experimental results show that using such an automatic non-intrusive regularization parameter in a recently proposed partial multichannel equalization technique (P-MINT) leads to a very similar performance as using the intrusively determined optimal regularization parameter. Furthermore, it is shown that the automatically regularized P-MINT technique outperforms state-of-the-art multichannel equalization techniques such as channel shortening and relaxed multichannel least-squares, both in terms of reverberant tail suppression and perceptual speech quality.
Changes in the distribution of a spectrin-like protein during development of the preimplantation mouse embryo

The mouse blastocyst expresses a 240,000-mol-wt polypeptide that cross- reacts with antibody to avian erythrocyte alpha-spectrin. Immunofluorescence localization showed striking changes in the distribution of the putative embryonic spectrin during preimplantation and early postimplantation development. There was no detectable spectrin in either the unfertilized or fertilized egg. The first positive reaction was observed in the early 2-cell stage when a bright band of fluorescence delimited the region of cell-cell contact. The blastomeres subsequently developed continuous cortical layers of spectrin and this distribution was maintained throughout the cleavage stages. A significant reduction in fluorescence intensity occurred before implantation in the apical region of the mural trophoblast and the trophoblast outgrowths developed linear arrays of spectrin spots that were oriented in the direction of spreading. In contrast to the alterations that take place in the periphery of the embryo, spectrin was consistently present in the cortical cytoplasm underlying regions of contact between the blastomeres and between cells of the inner cell mass. The results suggest a possible role for spectrin in cell-cell interactions during early development.
Antibacterial and Synergistic Activity of Pentacyclic Triterpenoids Isolated from Alstonia scholaris

(1) Background: Alstonia scholaris (Apocynaceae) is an important medicinal plant that has been historically used in “Dai” ethnopharmacy to treat infectious diseases in China. Although various pharmacological activities have been reported, the antimicrobial constitutes of A. scholaris have not yet been identified. The objective of this study is to evaluate the antibacterial constitutes from the leaf extract of A. scholaris and to assess the synergistic effects of isolated compounds with antibiotics against bacterial pathogens. ; (2) Methods: The chemical constitutes isolated from the leaf extract of A. scholaris were structurally identified by NMR. The antibacterial and synergistic effect of compounds was assessed by calculating the minimal inhibitory concentration (MIC), checkerboard dilution test, and time-kill assay. ; (3) Results: Six pentacyclic triterpenoids were structurally identified as (1) lupeol, (2) betulin, (3) 3-hydroxy-11-ursen-28,13-olide, (4) betulinic acid, (5) oleanolic acid and (6) ursolic acid. Both oleanolic and ursolic acid showed antibacterial activity but were limited to Gram-positive bacteria. Ursolic acid showed a synergistic effect with ampicillin and tetracycline against both Bacillus cereus and S. aureus. ; (4) Conclusion: These findings reflect that pentacyclic triterpenoids are the antibacterial chemicals in A. scholaris. The ability of ursolic acid to enhance the activity of antibiotics can constitute a valuable group of therapeutic agents in the future.
FIXED-WINDOW CONSTANT MODULUS ALGORITHMS : ADAPTIVE

Adaptive implementations of two recently proposed block-iterative algorithms, referred to as xed-window constant modulus algorithms (FWCMA), are developed. Their transient behavior, in relation to the delay at which the user sequence is recovered, is discussed and compared with other existing variations of CMA. The adaptive FWCMA-2 appears to be particularly promising, attaining convergence with little data. It retains the merits of its batch counterpart, namely, fast convergence, robustness to ill-conditioning, no required step-size tuning, and relatively low complexity. The built-in control over the converged delay translates into more reliable and predictable transient behavior. Equalizer calculation can be initiated from any ini-tialization, and at any time instant, to attain convergence instantaneously without storing any received data. Thus, diierent initializations can be used to easily obtain multiple equalizers recovering the signal at diierent delays or recovering distinct users under a near-far situation.
Nonlinear dynamics of a Liénard delayed-feedback optoelectronic oscillator

We present an optoelectronic oscillator (OEO) that is capable of generating complex and rich dynamics including stable periodic oscillations and broadband chaos. The OEO under analysis here is based on a resonant tunneling diode (RTD) oscillator driving a laser diode and a time-delayed feedback loop. The RTD based OEO is well described as a a Liénard oscillator with delayed-feedback. When subjected to external perturbation, the RTD-OEO generates periodic and chaotic states that are controlled by the delayed-feedback loop characteristics. The implemented numerical Liénard optoelectronic oscillator provides a simple way to study time-delayed dynamical systems containing negative resistance oscillators.
Design and evaluation of a selective compressed memory system

This research explores any potential for an on-chip cache compression which can reduce not only cache miss ratio but also miss penalty, if main memory is also managed in compressed form. However, the decompression time causes a critical effect on the memory access time and variable-sized compressed blocks tend to increase the design complexity of the compressed cache architecture. This paper suggests several techniques to reduce the decompression overhead and to manage the compressed blocks efficiently which include selective compression, fixed space allocation for the compressed blocks, parallel decompression, the use of a decompression buffer, and so on. Moreover a simple compressed cache architecture based on the above techniques and its management method are proposed. The results from trace-driven simulation show that this approach can provide around 35% decrease in the on-chip cache miss ratio as well as a 53% decrease in the data traffic over the conventional memory systems. Also, a large amount of the decompression overhead can be reduced, and thus the average memory access time can also be reduced by maximum 20% against the conventional memory systems.
Engagement of major histocompatibility complex class II molecules by superantigen induces inflammatory cytokine gene expression in human rheumatoid fibroblast-like synoviocytes

Cells in the rheumatoid synovium express high levels of major histocompatibility complex (MHC) class II molecules in vivo. We have therefore examined the ability of engagement of MHC class II molecules by the superantigen Staphylococcal enterotoxin A (SEA) to activate interleukin 6 (IL-6) and IL-8 gene expression in type B synoviocytes isolated from patients with rheumatoid arthritis. SEA had a minimal or undetectable effect on the expression of either gene in resting synoviocytes, as determined by Northern blot and specific enzyme-linked immunosorbent assay. However, induction of MHC class II molecule expression after treatment of synoviocytes with interferon gamma (IFN- gamma) enabled the cells to respond to SEA in a dose-dependent manner, resulting in an increase in both the level of steady-state mRNA for IL- 6 and IL-8, and the release of these cytokines into the supernatant. IFN-gamma by itself had no effect on the expression of either cytokine. Pretreatment of the cells with the transcription inhibitor actinomycin D prevented the increase in cytokine mRNA induced by SEA, whereas cycloheximide superinduced mRNA for both cytokines after stimulation by SEA. Taken together, these results indicate that signaling through MHC class II molecules may represent a novel mechanism by which inflammatory cytokine production is regulated in type B rheumatoid synoviocytes, and potentially provides insight into the manner by which superantigens may initiate and/or propagate autoimmune diseases.
Think Twice Before You Buy! How Recommendations Affect Three-Stage Purchase Decision Processes

Consumer decision-making is usually modeled as a two-stage process of initial screening and subsequent in-depth consideration of attractive alternatives. Recent evidence indicates, however, that consideration is not necessarily the direct precursor of choice: consumers may narrow their consideration sets further to the choice set. We examine how choices in a three-stage purchase decision process evolve by observing consumer behavior in an online shopping experiment. Specifically, we examine the effects of system- and user-generated recommendations (SGR and UGR) moderated by gender. Our contribution to information systems research is threefold. First, we suggest a new experimental design for observing the stages in purchasing processes. Second, we show that effects of SGR and UGR indeed vary between stages. UGR reduce consideration set size and increase females’ choice probability while SGR reduce males’ transition probabilities. Third, our results suggest that omitting choice set formation can lead to incorrect estimates of choice probabilities.
Identification of acoustic signals of surface discharges on glass insulator under different contamination levels

Surface discharge is a common phenomenon that normally occurs on the insulator surface under wet contamination condition. The generation of small sparks from the surface discharge would develop many types of signals. In this work an acoustic method is used to detect and capture the signals of surface discharges. The tests were carried out on cleaned and polluted glass insulators by using surface tracking and erosion test procedure of IEC 587. Three conditions of contamination levels were considered, which are light, medium and heavy based on ESDD levels. A laboratory experiment was done by making the models of these discharges. The test equipment including antennas as a means of detection and digital processing techniques for signal analysis were used. Wavelet signal processing was used to recover the surface discharge acoustic signal by eliminating the noises of many natures. Experimental results shows that the actual signals of surface discharge are related to the levels of insulator contamination.
Authenticated binding update in Mobile IPv6 networks

Mobile IPv6 allows mobile nodes to remain reachable while moving around in the Internet. In Mobile IPv6, each mobile node is always identified by its home address, regardless of its current point of attachment to the Internet. While situated away from its home, a mobile node is also associated with a care-of address, which provides information about the mobile node's current location. This chapter reviews security threats and solutions in Mobile IPv6 with particular emphasis on security of binding update operation - a central and mandatory operation to achieve efficient mobility support in Mobile IPv6. The binding update operation allows a mobile node to inform its home agent and its correspondent nodes about its new care-of address. Unauthenticated or malicious binding updates, however, open the door for intruders to perform redirect attacks - malicious acts which redirect traffic from home agent or correspondent nodes to locations chosen by intruders. We present various methods for securing the binding update operation, analyze their security and performance, and point out possible future research directions.