Miracle-dz/UniFAR-FTUs huggingface dataset:
Quercetin-induced apoptosis prevents EBV infection

Epstein-Barr virus (EBV) is a human gamma-1 herpesvirus that establishes a lifelong latency in over 90% of the world's population. During latency, virus exists predominantly as a chromatin-associated, multicopy episome in the nuclei of a variety of tumor cells derived from B cells, T cells, natural killer (NK) cells, and epithelial cells. Licorice is the root of Glycyrrhiza uralensis or G. glabra that has traditionally cultivated in eastern part of Asia. Licorice was reported to have anti-viral, anti-inflammatory, anti-atopic, hepatoprotective, anti-neurodegenerative, anti-tumor, anti-diabetic effects and so forth. Quercetin and isoliquiritigenin are produced from licorice and highly similar in molecular structure. They have diverse bioactive effects such as antiviral activity, anti-asthmatic activity, anti-cancer activity, anti-inflammation activity, monoamine-oxidase inhibitor, and etc. To determine anti-EBV and anti-EBVaGC (Epstein-Barr virus associated gastric carcinoma) effects of licorice, we investigated antitumor and antiviral effects of quercetin and isoliquiritigenin against EBVaGC. Although both quercetin and isoliquiritigenin are cytotoxic to SNU719 cells, quercetin induced more apoptosis in SNU719 cells than isoliquiritigenin, more completely eliminated DNMT1 and DNMT3A expressions than isoliquiritigenin, and more strongly affects the cell cycle progression of SNU719 than isoliquiritigenin. Both quercetin and isoliquiritigenin induce signal transductions to stimulate apoptosis, and induce EBV gene transcription. Quercetin enhances frequency of F promoter use, whereas isoliquiritigenin enhances frequency of Q promoter use. Quercetin reduces EBV latency, whereas isoliquiritigenin increases the latency. Quercetin increases more the EBV progeny production, and inhibits more EBV infection than isoliquiritigenin. These results indicate that quercetin could be a promising candidate for antiviral and antitumor agents against EBV and human gastric carcinoma.
Nucleotide modifications in three functionally important regions of the Saccharomyces cerevisiae ribosome affect translation accuracy

Important regions of rRNA are rich in nucleotide modifications that can have strong effects on ribosome biogenesis and translation efficiency. Here, we examine the influence of pseudouridylation and 2'-O-methylation on translation accuracy in yeast, by deleting the corresponding guide snoRNAs. The regions analyzed were: the decoding centre (eight modifications), and two intersubunit bridge domains-the A-site finger and Helix 69 (six and five modifications). Results show that a number of modifications influence accuracy with effects ranging from 0.3- to 2.4-fold of wild-type activity. Blocking subsets of modifications, especially from the decoding region, impairs stop codon termination and reading frame maintenance. Unexpectedly, several Helix 69 mutants possess ribosomes with increased fidelity. Consistent with strong positional and synergistic effects is the finding that single deletions can have a more pronounced phenotype than multiple deficiencies in the same region. Altogether, the results demonstrate that rRNA modifications have significant roles in translation accuracy.
Triple-Color FRET Analysis Reveals Conformational Changes in the WIP-WASp Actin-Regulating Complex

Two interaction sites provide a mechanism to finely balance the activity and degradation of an actin-regulating protein complex. WhIPping WASp into Shape Changes in the actin cytoskeleton in T cells in response to T cell receptor (TCR) activation are mediated by a complex consisting of WIP, an actin-binding protein, and WASp, a protein that promotes actin nucleation. Through a fluorescence resonance energy transfer–based study that visualized protein-protein interactions in live cells, Fried et al. revealed a two-way, end-to-end interaction between WIP and WASp. In response to TCR stimulation, one of the interactions between WIP and WASp was lost, but the other interaction remained, resulting in a conformation-induced increase in activity that stimulated actin polymerization. The conformational change also enabled the ubiquitylation and degradation of WASp to inhibit activity of the complex. Thus, the conformational change functioned as both the on and off switch. Wiskott-Aldrich syndrome protein (WASp) is a key regulator of the actin cytoskeletal machinery. Binding of WASp-interacting protein (WIP) to WASp modulates WASp activity and protects it from degradation. Formation of the WIP-WASp complex is crucial for the adaptive immune response. We found that WIP and WASp interacted in cells through two distinct molecular interfaces. One interaction occurred between the WASp-homology-1 (WH1) domain of WASp and the carboxyl-terminal domain of WIP that depended on the phosphorylation status of WIP, which is phosphorylated by protein kinase C θ (PKCθ) in response to T cell receptor activation. The other interaction occurred between the verprolin homology, central hydrophobic region, and acidic region (VCA) domain of WASp and the amino-terminal domain of WIP. This latter interaction required actin, because it was inhibited by latrunculin A, which sequesters actin monomers. With triple-color fluorescence resonance energy transfer (3FRET) technology, we demonstrated that the WASp activation mechanism involved dissociation of the first interaction, while leaving the second interaction intact. This conformation exposed the ubiquitylation site on WASp, leading to degradation of WASp. Together, these data suggest that the activation and degradation of WASp are delicately balanced and depend on the phosphorylation state of WIP. Our molecular analysis of the WIP-WASp interaction provides insight into the regulation of actin-dependent processes.
Enhanced Spatial Modulation With Multiple Signal Constellations

In this paper, we introduce a new spatial modulation (SM) technique using one or two active antennas and multiple signal constellations. The proposed technique, which we refer to as Enhanced SM or ESM, conveys information bits not only by the index(es) of the active antenna(s), but also by the constellations transmitted from each of them. The main feature of ESM is that it uses a primary signal constellation during the single active antenna periods and some other secondary constellations during the periods with two active transmit antennas. The secondary signal constellations are derived from the primary constellation by means of geometric interpolation in the signal space. We give design examples using two and four transmit antennas and QPSK, 16QAM, and 64QAM as primary modulations. The proposed technique is compared to conventional SM as well as to spatial multiplexing (SMX), and the results indicate that in most cases, ESM provides a substantial performance gain over conventional SM and SMX while reducing the maximum-likelihood (ML) decoder complexity.
Direct Etching of High Aspect Ratio Structures Through a Stencil

This paper reports the feasibility of the fabrication of high aspect ratio structures on substrates via dry etching through a stencil mask placed onto the sample. It demonstrates the possibility to use standard equipment and processes with this novel masking technique, which allows the patterning of fragile and pre-structured surfaces, and avoids the use of resist or additional coating of the sample, reducing costs and processing time. Aspect ratios as high as 13:1 and pattern transfer with a gap of 100 ¿m are demonstrated.
Decomposition of Austenite in Austenitic Stainless Steels

Austenitic stainless steels are probably the most important class of corrosion resistant metallic materials. In order to attain their good corrosion properties they rely essentially on two factors: a high chromium content that is responsible for the protective oxide film layer and a high nickel content that is responsible for the steel to remain austenitic. Thus the base composition is normally a Fe-Cr-Ni alloy. In practice the situation is much more complex with several other elements being present, such as, Mo, Mn, C, N among others. In such a complex situation one almost never has a single austenite phase but other phases invariably form. Those phases are, with few exceptions, undesirable and they can be detrimental to the corrosion and mechanical properties. It is therefore of considerable importance to study the formation of such phases. In this work the decomposition of austenite in austenitic stainless steels is reviewed in detail. First the binary equilibrium diagrams relevant to the system Fe-Cr-Ni are briefly presented as well as other diagrams, such as the Schaeffler diagram, that traditionally have been used to predict the phases present in these steels as a function of composition. Secondly the precipitation of carbides and intermetallic phases is presented in detail including nucleation sites and orientation relationships and the influence of several factors such as composition, previous deformation and solution annealing temperature. Next, the occurrence of other constituents such as nitrides, sulfides and borides is discussed. TTT diagrams are also briefly presented. Finally the formation of martensite in these steels is discussed.
Erythropoietin-Receptor Gene Regulation in Neuronal Cells

Because erythropoietin (Epo) is intensively studied as neuroprotective agent, Epo receptor (EpoR) regulation in neurons is of particular interest. Herein, we investigated molecular mechanisms of EpoR regulation in neuronal cells including the role of GATA transcription factors. First, developmental downregulation of EpoR expression in murine brain was observed. A differential expression pattern of the Gata factors was found in these specimens as well as in murine adult neural stem cells (NSC) and primary rat neurons, astrocytes, and microglia. Human SH-SY5Y cells served as a model to analyze EpoR regulation. In vitro binding of GATA-2, -3, and -4 to the 5′-flanking region was demonstrated. In reporter gene assays, the activity of a region containing two GATA binding sites was significantly induced when these GATA factors were overexpressed. However, GATA factors alone did not affect endogenous EpoR expression. Importantly, EpoR transcripts have doubled under hypoxia. Furthermore, we analyzed the methylation pattern close to the GATA motifs. Indeed, demethylation with 5-Aza-2′-deoxycytidine (Aza) resulted in upregulation of EpoR mRNA. Additionally, several CpGs were mostly nonmethylated in SH-SY5Y cells, but methylated in specific regions of the human adult brain. Thus, methylation may be involved in developmental EpoR downregulation.
Reversible Diffraction Efficiency of Photochromic Polymer Gratings Related to Photoinduced Dimensional Changes

In this Full Paper, the possibility of reversibly changing the diffraction efficiency of gratings, fabricated by soft molding lithography on polymer films, containing photochromic molecules, is demonstrated. In particular, alternating UV and visible laser irradiation of the gratings causes the doped photochromic molecules to undergo transformations, which induce reversible dimensional changes to the samples. As a result, reversible changes are monitored in the intensity of the beams of a diode laser, transmitted and diffracted from the gratings. These changes affect the diffraction efficiency, which is increased upon irradiation with UV and decreased after irradiation with visible laser light. Such gratings are promising candidates for the fabrication of modern optical components such as optical switching devices.
Characterization of vitellogenin gene expression in round goby (Neogobius melanostomus) using a quantitative polymerase chain reaction assay

A growing concern over endocrine disruption in aquatic species has prompted the development of molecular assays to monitor environmental impacts. This study describes the development of quantitative polymerase chain reaction (qPCR) assays to characterize the expression of two vitellogenin (Vtg) genes in the invasive round goby (Neogobius melanostomus). Fragments from the 18SrRNA (housekeeping gene), Vtg II, and Vtg III genes were cloned and sequenced. The qPCR assays were developed to detect hepatic Vtg expression in goby. The assays detected induction of both Vtg genes in nonreproductive males following a two‐week laboratory exposure to 17β‐estradiol (≥1 mg/kg i.p. injection). The assays were applied to goby from Hamilton Harbour, Lake Ontario (Canada), including those from sites where feminization and intersex of goby has been documented. Both Vtg genes had significantly higher expression in females compared to males. Male reproductive goby adopt either parental or sneaker tactics; Vtg II expression was higher in sneaker than in parental males but parental and nonreproductive males did not differ from each other. The Vtg III expression was significantly higher in sneaker males followed by parental males and nonreproductive males, respectively. The Vtg II and III expression in nonreproductive males was elevated in the contaminated site with documented intersex. This assay provides an important tool for the use of an invasive species in monitoring endocrine disruption in the Great Lakes region. Environ. Toxicol. Chem. 2010;29:2751–2760. © 2010 SETAC
DNA Sequence Assembly and Genetic Algorithms - New Results and Puzzling Insights

Applying genetic algorithms to DNA sequence assembly is not a straightforward process. Significantly improved results in terms of performance, quality of results, and the scaling of applicability have been realized through non-standard and even counter-intuitive parameter settings. Specifically, the solution time for a 10kb data set was reduced by an order of magnitude, and a 20kb data set that was previously unsolved by the genetic algorithm was solved in a time that represents only a linear increase from the 10kb data set. Additionally, significant progress has been made on a 35kb data set representing real biological data. A single contig solution was found for a 752 fragment subset of the data set, and a 15 contig solution was found for the full data set. This paper discusses the new results, the modifications to the previous genetic algorithm used in this study, the experimental design process by which the new results were obtained, the questions raised by these results, and some preliminary attempts to explain these results.
Bmc Complementary and Alternative Medicine Treatments of Pelvic Girdle Pain in Pregnant Women: Adverse Effects of Standard Treatment, Acupuncture and Stabilising Exercises on the Pregnancy, Mother, Delivery and the Fetus/neonate

Background: Previous publications indicate that acupuncture is efficient for the treatment of pelvic girdle pain, PGP, in pregnant women. However, the use of acupuncture for PGP is rare due to insufficient documentation of adverse effects of this treatment in this specific condition. The aim of the present work was to assess adverse effects of acupuncture on the pregnancy, mother, delivery and the fetus/neonate in comparison with women that received stabilising exercises as adjunct to standard treatment or standard treatment alone.
Choroidal thickness profile in healthy Indian children

Purpose: The purpose was to study choroidal thickness and its profile based on location in healthy Indian children using enhanced depth spectral-domain-optical coherence tomography (SD-OCT). Methods: In this cross-sectional observational study 255 eyes of 136 children with no retinal or choroidal disease were consecutively scanned using enhanced depth SD-OCT. Eyes with any ocular disease or axial length (AXL) >25 mm or < 20 mm were excluded. A single observer measured choroidal thickness from the posterior edge of the retinal pigment epithelium to the choroid/sclera junction at 500-microns intervals up to 2500 microns temporal and nasal to the fovea. Generalized estimating equations were used to evaluate the correlation between choroidal thickness at various locations and age, AXL, gender and spherical equivalent (SEq). Results: Mean age of the subjects was 11.9 ± 3.4 years (range: 5–18 years). There were 62 Females and 74 males. The mean AXL was 23.55 ± 0.74 mm. Mean subfoveal choroidal thickness was 312.1 ± 45.40 μm. Choroid was found to be thickest subfoveally, then temporally. Age, AXL and SEq showed a significant correlation with choroidal thickness, whereas gender did not affect choroidal thickness. Conclusion: Our study provides a valid normative database of choroidal thickness in healthy Indian children. This database could be useful for further studies evaluating choroidal changes in various chorioretinal disorders. Age and AXL are critical factors, which negatively correlated with choroidal thickness.
Motor and Sensory Conduction in Infancy and Childhood: Reappraisal

Maximum motor and sensory conduction along peripheral nerve increased with age, from 20 m/sec at a conceptional age of 33 weeks to 33 m/sec at one month after term. From one month to four years of age the increase was 20 m/sec, the velocity along adult nerve being reached at three to four years of age. Therefore abnormalities in motor and sensory conduction velocity must always be compared with findings in normal nerves matched for age. Data obtained on the nerves of infants are less uniform than in adults. Some of the scatter may be unavoidable because of the difficulty of establishing the precise age of the newborn; some of the scatter is due to inadequate control of temperature and other parameters.
Multivariate Analysis of Blood Oxygen Saturation Recordings in Obstructive Sleep Apnea Diagnosis

This study focuses on the analysis of blood oxygen saturation (SaO2) from nocturnal pulse oximetry (NPO) to help in the diagnosis of the obstructive sleep apnea (OSA) syndrome. A population of 148 patients suspected of suffering from OSA syndrome was studied. A wide set of 16 features was used to characterize changes in the SaO2 profile during the night. Our feature set included common statistics in the time and frequency domains, conventional spectral characteristics from the power spectral density (PSD) function, and nonlinear features. We performed feature selection by means of a step-forward logistic regression (LR) approach with leave-one-out cross-validation. Second- and fourth-order statistical moments in the time domain (M2t and M4t), the relative power in the 0.014-0.033 Hz frequency band (PR), and the Lempel-Ziv complexity (LZC) were automatically selected. 92.0% sensitivity, 85.4% specificity, and 89.7% accuracy were obtained. The optimum feature set significantly improved the diagnostic ability of each feature individually. Furthermore, our results outperformed classic oximetric indexes commonly used by physicians. We conclude that simultaneous analysis in the time and frequency domains by means of statistical moments, spectral and nonlinear features could provide complementary information from NPO to improve OSA diagnosis.
Take your seats: leftward asymmetry in classroom seating choice

Despite an overall body symmetry, human behavior is full of examples of asymmetry, from writing or gesturing to kissing and cradling. Prior research has revealed that theatre patrons show a bias towards sitting on the right side of a movie theatre. Two competing theories have attempted to explain this seating asymmetry: one posits that expectation of processing demand drives the bias; the other posits that basic motor asymmetries drive the bias. To test these theories we assessed the real-world classroom seating choices of university students using photographs. A bias for students to choose seats on the left side of the classroom was observed, in contrast to the right side bias observed in theatre seating studies. These results provide evidence in support of a processing-expectation bias.
Overview of the RANSAC Algorithm

The RANdom SAmple Consensus (RANSAC) algorithm proposed by Fischler and Bolles [1] is a general parameter estimation approach designed to cope with a large proportion of outliers in the input data. Unlike many of the common robust estimation techniques such as M-estimators and least-median squares that have been adopted by the computer vision community from the statistics literature, RANSAC was developed from within the computer vision community. RANSAC is a resampling technique that generates candidate solutions by using the minimum number observations (data points) required to estimate the underlying model parameters. As pointed out by Fischler and Bolles [1], unlike conventional sampling techniques that use as much of the data as possible to obtain an initial solution and then proceed to prune outliers, RANSAC uses the smallest set possible and proceeds to enlarge this set with consistent data points [1]. The basic algorithm is summarized as follows: Algorithm 1 RANSAC 1: Select randomly the minimum number of points required to determine the model parameters. 2: Solve for the parameters of the model. 3: Determine how many points from the set of all points fit with a predefined tolerance . 4: If the fraction of the number of inliers over the total number points in the set exceeds a predefined threshold τ , re-estimate the model parameters using all the identified inliers and terminate. 5: Otherwise, repeat steps 1 through 4 (maximum of N times). The number of iterations, N , is chosen high enough to ensure that the probability p (usually set to 0.99) that at least one of the sets of random samples does not include an outlier. Let u represent the probability that any selected data point is an inlier 1
Nested Stochastic Possibility Frontiers with Heterogeneous Capital Inputs

This paper studies the productivity impact of heterogeneous capital inputs of selected EU-15 member countries and of the U.S. at the macroeconomic level. The stochastic possibility frontiers approach of Battese and Coelli (1992) applied here is used to identify neutralities or non-neutralities between different heterogeneous capital and labor inputs. Owing to the introduction and estimation of two-stage nested translog possibility production frontiers, the otherwise huge parameter space for the seven input factors included in the model is reduced significantly. This gives more robust estimates of the remaining parameters. Due to the detailed data, specific types of biased technological change in heterogeneous capital inputs can be tested. Furthermore, time-varying inefficiency trajectories for each country are obtainable. Annual data from 1980 to 2004, calculated and published by the Groningen Growth and Development Centre, are used in the empirical analysis. The results obtained shed new light on how fast technological progress in a global economy can shift comparative advantages between countries. In particular the different factor specific impacts of ICT and non-ICT capital stocks give a more detailed picture of the structural dynamics between factor inputs than do most other empirical studies using more aggregate factor input data.
Towards Risk-Based Management of Critical Infrastructures: Enabling Insights and Analysis Methodologies from a Focused Study of the Bulk Power Grid

This report summarizes research on a holistic analysis framework to assess and manage risks in complex infrastructures, with a specific focus on the bulk electric power grid (grid). A comprehensive model of the grid is described that can approximate the coupled dynamics of its physical, control, and market components. New realism is achieved in a power simulator extended to include relevant control features such as relays. The simulator was applied to understand failure mechanisms in the grid. Results suggest that the implementation of simple controls might significantly alter the distribution of cascade failures in power systems. The absence of cascade failures in our results raises questions about the underlying failure mechanisms responsible for widespread outages, and specifically whether these outages are due to a system effect or large-scale component degradation. Finally, a new agent-based market model for bilateral trades in the short-term bulk power market is presented and compared against industry observations.