Miracle-dz/UniFAR-FTUs huggingface dataset:
Phase Synchronization and Spectral Coherence Analysis of EEG Activity During Mental Fatigue

In this article, 2 synchronization measures, phase locking value (PLV) and spectral coherence value (SCV), are used to characterize the changes of the phase synchronization and functional coupling of electroencephalogram (EEG) waves at different brain cortical areas for mental fatigue caused by a long-term cognitive task. The long-term cognitive task induces a significant decrease in the interhemispheric SCVs and PLVs of beta in central and parietal regions, a significant decrease in the intrahemispheric SCVs and PLVs of beta frequency band at the frontal–parietal and central–parietal, and frontal–central middle electrode pairs, suggesting EEG decreases in cooperative processing, strength of functional coupling, and flux of mutual information exchange in the corresponding inter- and intrahemispheres. However, when the mental fatigue level increases, the interhemispheric PLVs of theta are enhanced in the frontal region and C3–Cz electrode pair, and the intrahemispheric PLVs of theta are heightened at frontal–central middle electrode pairs. PLV and SCV measures could reflect the changes of the phase synchronization and functional coupling of EEG waves from time and frequency domains, which are sensitive to mental fatigue. Therefore, PLVs and SCVs can provide an effective and reliable way to quantify brain response to mental fatigue.
Image analysis tools and emerging algorithms for expression proteomics

Since their origins in academic endeavours in the 1970s, computational analysis tools have matured into a number of established commercial packages that underpin research in expression proteomics. In this paper we describe the image analysis pipeline for the established 2‐DE technique of protein separation, and by first covering signal analysis for MS, we also explain the current image analysis workflow for the emerging high‐throughput ‘shotgun’ proteomics platform of LC coupled to MS (LC/MS). The bioinformatics challenges for both methods are illustrated and compared, whereas existing commercial and academic packages and their workflows are described from both a user's and a technical perspective. Attention is given to the importance of sound statistical treatment of the resultant quantifications in the search for differential expression. Despite wide availability of proteomics software, a number of challenges have yet to be overcome regarding algorithm accuracy, objectivity and automation, generally due to deterministic spot‐centric approaches that discard information early in the pipeline, propagating errors. We review recent advances in signal and image analysis algorithms in 2‐DE, MS, LC/MS and Imaging MS. Particular attention is given to wavelet techniques, automated image‐based alignment and differential analysis in 2‐DE, Bayesian peak mixture models, and functional mixed modelling in MS, and group‐wise consensus alignment methods for LC/MS.
The Performance Ranking of Emerging Markets Islamic Indices Using Risk Adjusted Performance Measures

This paper evaluates the performance of Emerging Market (EM) Morgan Stanley Capital International (MSCI) Islamic indices of 20 countries located in 3 different regions; using 16 different risk adjusted performance measures (RAPMs). The conducted tests show that only Sharpe and M2 Ratios give the identical rankings, Pearson Linear Correlation Coefficient analysis was also performed to measure the correlation between the rankings of 16 RAPMs. The final rankings of the indices are obtained using the Borda count method. Our results suggest that, on a regional basis, the performances of Asian countries are found to be better than both Latin American and EMEA (Europe, Middle East and Africa) region countries. When the countries are examined individually, EM Colombia Islamic index comes first in the assessment; EM United Arab Emirates Islamic index comes at the last position.
Multiantennary group-specific polysaccharide of group B Streptococcus.

The group-specific antigen of group B Streptococcus is composed of four different oligosaccharide units of Mw 766 (III), 1277 (II), 1462 (IV), and 1788 (I). The major constituent sugars of the oligosaccharides are alpha-L-rhamnopyranose, alpha-D-galactopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranosyl, and D-glucitol except that III does not contain alpha-D-galactopyranosyl or 2-acetamido-2-deoxy-beta-D-glucopyranosyl residues and IV contains no D-glucitol but has one additional beta-L-rhamnopyranosyl residue. The structures of II and III have been previously elucidated [Michon, F. , Katzenellenbogen, E. , Kasper, D. L. , & Jennings, H. J. (1987) Biochemistry 26, 476-486]. In the group B antigen all the oligosaccharides are linked by one type of phosphodiester bond from O6 of the D-glucitol residue of one oligosaccharide to O6 of the alpha-D-galactopyranosyl residue of the next to form a complex and highly branched multiantennary structure. However, despite the heterogeneous nature of its component oligosaccharides, some order has been identified in the biosynthesis of the group B antigen from chemical and enzymatic sequence studies. Because III lacks an alpha-D-galactopyranosyl residue but has a D-glucitol residue, it is situated at the reducing terminus of all the branches of the group B antigen where it is always adjacent to a II moiety. Conversely, IV has an alpha-D-galactopyranosyl residue but has no D-glucitol and is therefore located at the reducing terminus of the group B antigen where it probably functions as a linker molecule between the group B polysaccharide and the cell wall peptidoglycan of the group B streptococcal organisms. Oligosaccharide I contains two alpha-D-galactopyranosyl residues and one D-glucitol residue and thus constitutes the branch point in the group B antigen, whereas II contains one of each of the above residues and therefore is situated in linear interchain positions. The group B antigen is highly branched and probably has a unique multiantennary structure.
The Kinase Activity of IL-1 Receptor-associated Kinase 4 Is Required for Interleukin-1 Receptor/Toll-like Receptor-induced TAK1-dependent NFκB Activation*

Two parallel interleukin-1 (IL-1)-mediated signaling pathways have been uncovered for IL-1R-TLR-mediated NFκB activation: TAK1-dependent and MEKK3-dependent pathways, respectively. The TAK1-dependent pathway leads to IKKα/β phosphorylation and IKKβ activation, resulting in classic NFκB activation through IκBα phosphorylation and degradation. The TAK1-independent MEKK3-dependent pathway involves IKKγ phosphorylation and IKKα activation, resulting in NFκB activation through dissociation of phosphorylated IκBα from NFκB without IκBα degradation. IL-1 receptor-associated kinase 4 (IRAK4) belongs to the IRAK family of proteins and plays a critical role in IL-1R/TLR-mediated signaling. IRAK4 kinase-inactive mutant failed to mediate the IL-1R-TLR-induced TAK1-dependent NFκB activation pathway, but mediated IL-1-induced TAK1-independent NFκB activation and retained the ability to activate substantial gene expression, indicating a structural role of IRAK4 in mediating this alternative NFκB activation pathway. Deletion analysis of IRAK4 indicates the essential structural role of the IRAK4 death domain in receptor proximal signaling for mediating IL-1R-TLR-induced NFκB activation.
Noninvasive monitoring of end‐tidal CO2 via nasal cannulas in spontaneously breathing children during the perioperative period

Objective: To determine the correlation between end‐tidal CO2 and Paco2 values measured via nasal cannulas in spontaneously breathing children during the perioperative period. Design: Prospective evaluation. Setting: Pediatric intensive/intermediate care unit in a tertiary care referral center. Patients: Thirty postoperative surgical and trauma patients aged ≤18 yrs (average age 7.8 yrs [range 6 months to 16 yrs] and average weight 28.3 kg (range 8.5 to 69). Measurements and Main Results: Spontaneously breathing, nonintubated patients with an arterial cannula in place were selected for study. End‐tidal CO2 was sampled from nasal cannulas by a sidestream aspirator and was estimated by infrared spectroscopy. The difference between Paco2 and end‐tidal CO2 was compared using linear regression analysis. A total of 55 blood gas measurements were obtained on the 30 patients. The Paco2 to end‐tidal CO2 gradient was ≤4 torr in 54 of the 55 samples. The mean Paco2 was 39.5 ± 3.3 torr (5.27 ± 0.44 kPa) with a mean end‐tidal CO2 value of 39.7 ± 3.8 torr (5.29 ± 0.51 kPa). Linear regression analysis of arterial vs. end‐tidal CO2 yielded a slope of 0.992 and p = . 0001. Conclusions: End‐tidal CO2 measurement by infrared spectroscopy provided an accurate estimation of Paco2 in this patient population. Its use may limit the need for invasive monitoring and/or repeated arterial blood gas analysis. (Crit Care Med 1994; 22:1805–1808)
Localizer: fast, accurate, open-source, and modular software package for superresolution microscopy

Abstract. We present Localizer, a freely available and open source software package that implements the computational data processing inherent to several types of superresolution fluorescence imaging, such as localization (PALM/STORM/GSDIM) and fluctuation imaging (SOFI/pcSOFI). Localizer delivers high accuracy and performance and comes with a fully featured and easy-to-use graphical user interface but is also designed to be integrated in higher-level analysis environments. Due to its modular design, Localizer can be readily extended with new algorithms as they become available, while maintaining the same interface and performance. We provide front-ends for running Localizer from Igor Pro, Matlab, or as a stand-alone program. We show that Localizer performs favorably when compared with two existing superresolution packages, and to our knowledge is the only freely available implementation of SOFI/pcSOFI microscopy. By dramatically improving the analysis performance and ensuring the easy addition of current and future enhancements, Localizer strongly improves the usability of superresolution imaging in a variety of biomedical studies.
Bactericidal activities of peptide antibiotics against multidrug-resistant Enterococcus faecium

Multidrug-resistant Enterococcus faecium has emerged as a serious pathogen for which no effective therapy has been established. In this report, we describe the activities of two peptide antibiotics, ramoplanin and daptomycin, against 15 isolates of E. faecium resistant to vancomycin, ampicillin, and aminoglycosides using time-kill experiments. Both antibiotics were rapidly bactericidal when tested in broth; however, the addition of 50% serum resulted in significant regrowth. The combination of ampicillin with either ramoplanin or daptomycin largely prevented this regrowth. These peptide antibiotics showed good activity against these pathogens. While the development of daptomycin has been halted, ramoplanin may hold promise for the therapy of multidrug-resistant E. faecium, especially when combined with ampicillin.
PENGARUH RASIO LIKUIDITAS, PROFITABILITAS, SOLVABILITAS, AKTIVITAS DAN PENILAIAN PASAR TERHADAP RETURN SAHAM

ABSTRAK Penelitian ini bertujuan untuk mengetahui pengaruh likuiditas, profitabilitas, solvabilitas, rasio aktivitas dan penilaian pasar terhadap return saham pada perusahaan manufaktur di Bursa Efek Indonesia periode 2011-2015. Sampel yang digunakan dalam penelitian ini yaitu 35 perusahaan yang dipilih dengan menggunakan teknik purposive sampling. Metode analisis yang digunakan adalah regresi linear berganda melalui metode observasi non partisipan. Pengujian secara parsial menunjukkan bahwa variabel likuiditas, profitabilitas, rasio aktivitas dan penilaian pasar berpengaruh positif dan signifikan terhadap return saham, sedangkan variabel solvabilitas berpengaruh negatif signifikan terhadap return saham. Kata kunci : return saham, likuiditas, profitabilitas, solvabilitas, rasio aktivitas, penilaian pasar ABSTRACT This study aimed to determine the effect of liquidity, profitability, solvability, activity ratio and market valuation on the stock return of manufacturing companies in the Indonesian Stock Exchange (Bursa Efek Indonesia) on a period of 2011-2015. The samples are 35 companies choosed by using purposive sampling technique. The analytical method used is multiple linier regressions through non participant observation methods. Results showed that, partially, the variables of liquidity, profitability, activity ratio and market valuation have a positive and significant impact on stock return, while the solvability have a significant negative effect on stock return. Keywords : stock return, liquidity, profitability, solvability, activity ratio, market valuation
THE COMPARISON OF PERFORMANCE OF ISLAMIC AND CONVENTIONAL UNIT TRUST FUNDS IN MALAYSIA

This research reports on the findings of a study that examined the performance of Islamic unit trust funds in comparison with the conventional trust funds in Malaysia. The objectives of the study were to compare the nature and characteristics of both funds, assess their risks and returns profiles, measure the degree of diversification and compare the consistency of performance ranking. The performance of both funds was analyzed over a period of 36 months commencing from February 2000 to January 2003 and evaluated based on the standard performance measures for funds known as Adjusted Sharpe, Treynor and Adjusted Jensen Alpha Indices. The composite index of the Kuala Lumpur Stock Exchange (KLSE) represented the market benchmark for the conventional funds while the Islamic funds used Syariah index as proxy for the market. The findings revealed that on average, the Islamic funds failed to outperform the performance of conventional fund. However, the Islamic funds seemed to have lower risks than the conventional funds. Even so, the independent sample t-test results showed that there was no significant difference in the means performance of both funds.
Secondary voltage control areas through energy levels

Novel strategies for identifying voltage control areas in large power systems are proposed. These are founded on the modal energy levels and the instantaneous energy of oscillatory modes for determining voltage control areas of large power systems. The modal energy levels are used for identifying the minimum number of areas into the grid, and the minimum number of control buses per area in order to make a suitable secondary voltage control into the system. The energy levels are conceived regarding the topology of the grid and the dynamic analysis. Then, the instantaneous energy is provided by the Taylor-Fourier transform (TFT), which is taken into account for determining a set of sensible buses during the transient behavior. Both strategies are applied in the New England power system corroborating the applicability and the validity of the proposition.
Cell fate decisions in the Drosophila dorsal vessel depend on the multiadapter protein inscuteable

The Drosophila dorsal vessel consists of two cell types, contractile cardiomyoblasts that form a linear tube‐like structure, and the loosely associated pericardial cells. All heart cells originate during embryogenesis from the early dorsal mesoderm under the influence of external and internal signals. Recently, it was shown that a subset of heart cells arise throughout asymmetric cell division, dependent on the function of Notch, Sanpodo, and Numb. Here, we show that Inscuteable, a multiadapter protein required for asymmetric cell division, participates in the formation of specific heart cells to distinguish between a myogenic (cardiomyoblast) and a nonmyogenic (pericardial cell) fate. genesis 40:218–222, 2004. © 2004 Wiley‐Liss, Inc.
Line‐shape analysis of J‐resolved NMR spectra: application to metabolomics and quantification of intensity errors from signal processing and high signal congestion

NMR spectroscopy remains one of the primary analytical approaches in metabolomics. Although 1D 1H NMR spectroscopy is versatile, highly reproducible and currently the most widely used technique in NMR metabolomics, analysis of complex biological samples typically yields highly congested spectra with severely overlapping signals making unambiguous metabolite identification and quantification almost impossible. Consequently there is a growing use of 2D NMR methods, in particular 1H J‐resolved (JRES) spectroscopy, which spreads the high signal density into a second dimension. One potentially powerful method to deconvolute these JRES spectra, facilitating metabolite quantification, is via line‐shape fitting. However, the mathematical functions describing the JRES NMR line‐shape, in particular after applying apodisation functions and JRES specific processing, including tilting and symmetrisation, remain uncharacterised. Furthermore, possible quantitation errors arising from processing JRES spectra have not been evaluated, nor have the potentially adverse quantitative effects of overlapping dispersive tails of closely spaced signals in the 2D spectrum. Here we address these issues and evaluate the suitability of the JRES experiment for accurate complex mixture analysis. Specifically, we have examined changes in NMR line‐shape and signal intensity after application of different apodisation functions (SINE and SEM) and JRES specific processing (tilting and symmetrising), comparing simulated and experimental data. We also report a significant quantitation error of up to 33%, dependent upon apodisation, due to overlap of the dispersive tails of closely spaced resonances. Finally, we have validated the use of these mathematical line‐shape functions for metabolite quantitation of 2D JRES spectra, by comparison to corresponding 1D NMR datasets, using both gravimetrically‐prepared chemically defined mixtures as well as biological tissue extracts. Copyright © 2009 John Wiley & Sons, Ltd.
Genetic Variation in Prostate-Specific Antigen–Detected Prostate Cancer and the Effect of Control Selection on Genetic Association Studies

Background: Only a minority of the genetic components of prostate cancer risk have been explained. Some observed associations of SNPs with prostate cancer might arise from associations of these SNPs with circulating prostate-specific antigen (PSA) because PSA values are used to select controls. Methods: We undertook a genome-wide association study (GWAS) of screen-detected prostate cancer (ProtecT: 1,146 cases and 1,804 controls); meta-analyzed the results with those from the previously published UK Genetic Prostate Cancer Study (1,854 cases and 1,437 controls); investigated associations of SNPs with prostate cancer using either “low” (PSA < 0.5 ng/mL) or “high” (PSA ≥ 3 ng/mL, biopsy negative) PSA controls; and investigated associations of SNPs with PSA. Results: The ProtecT GWAS confirmed previously reported associations of prostate cancer at three loci: 10q11.23, 17q24.3, and 19q13.33. The meta-analysis confirmed associations of prostate cancer with SNPs near four previously identified loci (8q24.21,10q11.23, 17q24.3, and 19q13.33). When comparing prostate cancer cases with low PSA controls, alleles at genetic markers rs1512268, rs445114, rs10788160, rs11199874, rs17632542, rs266849, and rs2735839 were associated with an increased risk of prostate cancer, but the effect-estimates were attenuated to the null when using high PSA controls (Pheterogeneity in effect-estimates < 0.04). We found a novel inverse association of rs9311171-T with circulating PSA. Conclusions: Differences in effect-estimates for prostate cancer observed when comparing low versus high PSA controls may be explained by associations of these SNPs with PSA. Impact: These findings highlight the need for inferences from genetic studies of prostate cancer risk to carefully consider the influence of control selection criteria. Cancer Epidemiol Biomarkers Prev; 23(7); 1356–65. ©2014 AACR.
A large-scale, in vivo transcription factor screen defines bivalent chromatin as a key property of regulatory factors mediating Drosophila wing development

Transcription factors (TFs) are key regulators of cell fate. The estimated 755 genes that encode DNA binding domain-containing proteins comprise ∼5% of all Drosophila genes. However, the majority has remained uncharacterized so far due to the lack of proper genetic tools. We generated 594 site-directed transgenic Drosophila lines that contain integrations of individual UAS-TF constructs to facilitate spatiotemporally controlled misexpression in vivo. All transgenes were expressed in the developing wing, and two-thirds induced specific phenotypic defects. In vivo knockdown of the same genes yielded a phenotype for 50%, with both methods indicating a great potential for misexpression to characterize novel functions in wing growth, patterning, and development. Thus, our UAS-TF library provides an important addition to the genetic toolbox of Drosophila research, enabling the identification of several novel wing development-related TFs. In parallel, we established the chromatin landscape of wing imaginal discs by ChIP-seq analyses of five chromatin marks and RNA Pol II. Subsequent clustering revealed six distinct chromatin states, with two clusters showing enrichment for both active and repressive marks. TFs that carry such “bivalent” chromatin are highly enriched for causing misexpression phenotypes in the wing, and analysis of existing expression data shows that these TFs tend to be differentially expressed across the wing disc. Thus, bivalently marked chromatin can be used as a marker for spatially regulated TFs that are functionally relevant in a developing tissue.
Test power reduction with multiple capture orders

This paper proposes a method to reduce the excess power dissipation during scan testing. The proposed method divides a scan chain into a number of sub-chains, and enables only one sub-chain at a time for both the scan and capture operations. To efficiently deal with the data dependence problem during the capture cycles, we develop a multiple-capture-orders method to guarantee the full scan fault coverage. A test pattern generation procedure is developed to reduce the test application time and a test architecture based on a ring control structure is adopted which makes the test control very simple and requires very low area overhead. Experimental results for large ISCAS'89 benchmark circuits show that the proposed method can reduce average and peak power by 86.8% and 66.1% in average, respectively, when 8 sub-chains are used.
Precise methane absorption measurements in the 1.64 μm spectral region for the MERLIN mission

In this article we describe a high‐precision laboratory measurement targeting the R(6) manifold of the 2ν3 band of 12CH4. High‐fidelity modeling of this absorption spectrum for atmospheric temperature and pressure conditions will be required by the Franco‐German, Methane Remote Sensing LIDAR (MERLIN) space mission for retrievals of atmospheric methane. The analysis uses the Hartmann‐Tran profile for modeling line shape and also includes line‐mixing effects. To this end, six high‐resolution and high signal‐to‐noise ratio absorption spectra of air‐broadened methane were recorded using a frequency‐stabilized cavity ring‐down spectroscopy apparatus. Sample conditions corresponded to room temperature and spanned total sample pressures of 40 hPa–1013 hPa with methane molar fractions between 1 µmol mol−1 and 12 µmol mol−1. All spectroscopic model parameters were simultaneously adjusted in a multispectrum nonlinear least squares fit to the six measured spectra. Comparison of the fitted model to the measured spectra reveals the ability to calculate the room temperature, methane absorption coefficient to better than 0.1% at the online position of the MERLIN mission. This is the first time that such fidelity has been reached in modeling methane absorption in the investigated spectral region, fulfilling the accuracy requirements of the MERLIN mission. We also found excellent agreement when comparing the present results with measurements obtained over different pressure conditions and using other laboratory techniques. Finally, we also evaluated the impact of these new spectral parameters on atmospheric transmissions spectra calculations.