Miracle-dz/UniFAR-FTUs huggingface dataset:
Ebola Virus VP35-VP40 Interaction Is Sufficient for Packaging 3E-5E Minigenome RNA into Virus-Like Particles

ABSTRACT The packaging of viral genomic RNA into nucleocapsids and subsequently into virions is not completely understood. Phosphoprotein (P) and nucleoprotein (NP) interactions link NP-RNA complexes with P-L (polymerase) complexes to form viral nucleocapsids. The nucleocapsid then interacts with the viral matrix protein, leading to specific packaging of the nucleocapsid into the virion. A mammalian two-hybrid assay and confocal microscopy were used to demonstrate that Ebola virus VP35 and VP40 interact and colocalize in transfected cells. VP35 was packaged into budding virus-like particles (VLPs) as observed by protease protection assays. Moreover, VP40 and VP35 were sufficient for packaging an Ebola virus minignome RNA into VLPs. Results from immunoprecipitation-reverse transcriptase PCR experiments suggest that VP35 confers specificity of the nucleocapsid for viral genomic RNA by direct VP35-RNA interactions.
Model Validation and DSGE Modeling

The primary objective of this paper is to revisit DSGE models with a view to bringing out their key weaknesses, including statistical misspecification, non-identification of deep parameters, substantive inadequacy, weak forecasting performance, and potentially misleading policy analysis. It is argued that most of these weaknesses stem from failing to distinguish between statistical and substantive adequacy and secure the former before assessing the latter. The paper untangles the statistical from the substantive premises of inference to delineate the above-mentioned issues and propose solutions. The discussion revolves around a typical DSGE model using US quarterly data. It is shown that this model is statistically misspecified, and when respecified to arrive at a statistically adequate model gives rise to the Student’s t VAR model. This statistical model is shown to (i) provide a sound basis for testing the DSGE overidentifying restrictions as well as probing the identifiability of the deep parameters, (ii) suggest ways to meliorate its substantive inadequacy, and (iii) give rise to reliable forecasts and policy simulations.
DLG5 variants contribute to Crohn disease risk in a Canadian population

Variants in the gene encoding the DLG5 scaffolding protein have been reported to be associated with increased risk of inflammatory bowel disease (IBD) and particularly Crohn's disease (Crohn disease; CD). These findings have not been uniformly replicated in follow‐up studies. In this study we genotyped a cohort of 402 Canadian CD and 179 ulcerative colitis (UC) patients and 537 healthy controls for three IBD/CD‐associated DLG5 variants. Our data reveal that the common DLG5 haplotype (A), which was previously considered protective for IBD, is associated with modest increases in risk for IBD (P=0.02) and CD (P=0.04). The effects of haplotype copy number on risk for IBD were minor, with the odds ratio (ORs) being 1.37 for the heterozygous risk genotype and 1.7 for the homozygous risk genotype. While we were unable to replicate the proposed association between the DLG5 c.113G>A variant and IBD, an association of IBD (P=0.02) and CD (P=0.04) with the rarer c.4136C>A variant was replicated in this cohort. These associations were restricted to the non‐Jewish subjects in this cohort and were not detected in the Ashkenazi Jewish population studied here. Within the non‐Jewish group, no associations were detected between the DLG5 variants and specific phenotypic features, such as site of disease, and there was no evidence of epistasis between DLG5 and any of the CD‐associated CARD15 or SLC22A4/A5 gene variants. Together, the results indicate a role for DLG5 variants in IBD susceptibility and suggest that further studies are warranted to evaluate this role in different IBD populations and to determine the functional pathways that couple DLG5 variants to IBD. Hum Mutat 27(4), 353–358, 2006. © 2006 Wiley‐Liss, Inc.
HCV‐infected cells and differentiation increase monocyte immunoregulatory galectin‐9 production

The lectin galectin‐9 may help establish and maintain chronic hepatitis C virus infection. Galectin‐9 is elevated in the liver and sera of hepatitis C virus patients, induces apoptosis of hepatitis C virus‐specific T cells, and increases inhibitory regulatory T cells. Kupffer cells stain strongly for galectin‐9 protein in hepatitis C virus patients. In the current study, we determined stimuli that induce galectin‐9 production by monocytes and macrophages in hepatitis C virus infection. With the use of real‐time PCR and flow cytometry, we analyzed galectin‐9 mRNA and protein from human monocytes cocultured with hepatitis C virus‐infected cells or noninfectious hepatitis C virus subgenomic replicon cells. We focused on finding the stimuli for galectin‐9 production. Additionally, we measured galectin‐9 during monocyte‐to‐macrophage maturation. Finally, we examined galectin‐9 in peripheral monocytes from hepatitis C virus patients using flow cytometry. Galectin‐9 mRNA increased 8‐fold when primary monocytes were exposed to hepatitis C virus‐‐infected cells. Maximum induction required proximity or contact and did not require IFN‐γ or hepatitis C virus virions. Coculture of monocytes with subgenomic replicon cells increased galectin‐9 5‐fold, and purified exosomes from infected cells stimulated galectin‐9 production. Stimulation of monocyte TLR3, ‐7, and ‐8 increased galectin‐9 production. Differentiation of monocytes to macrophages increased galectin‐9, and nonclassic monocytes from hepatitis C virus patients had the highest levels of galectin‐9. Hepatitis C virus‐infected cells stimulated monocytes to produce galectin‐9 in close proximity, possibly, in part, as a result of exosomes and endosomal TLRs. Differentiation of monocytes to macrophages increased galectin‐9. Nonclassic monocytes from hepatitis C virus patients express the highest galectin‐9 levels, suggesting they may contribute to elevated galectin‐9 and adaptive immune inhibition in hepatitis C virus infection.
Principal component analysis - a tutorial

Dimensionality reduction is one of the preprocessing steps in many machine learning applications and it is used to transform the features into a lower dimension space. Principal component analysis (PCA) technique is one of the most famous unsupervised dimensionality reduction techniques. The goal of the technique is to find the PCA space, which represents the direction of the maximum variance of the given data. This paper highlights the basic background needed to understand and implement the PCA technique. This paper starts with basic definitions of the PCA technique and the algorithms of two methods of calculating PCA, namely, the covariance matrix and singular value decomposition (SVD) methods. Moreover, a number of numerical examples are illustrated to show how the PCA space is calculated in easy steps. Three experiments are conducted to show how to apply PCA in the real applications including biometrics, image compression, and visualisation of high-dimensional datasets.
A decoupled adaptive tracking filter for real applications

A decoupled adaptive tracking filter for maneuvering targets under nonlinear measurement environment is presented. A modified input estimation method is implemented in a line-of-sight Cartesian coordinate system. Since the proposed filter has a decoupled structure, computation is drastically reduced without degrading performance. Also, due to small cross-correlation between pseudomeasurement noises, accuracy of maneuver detection is improved.
Interlimb coordination deficits in patients with parkinson's disease during the production of two‐joint oscillations in the sagittal plane

TwoK. U. Leuven, Heverlee, Belgiumlimb coordination patterns involving cyclical flexionK. U. Leuven, Heverlee, Belgiumextension movements, performed in the same or in different directions, were studied in patients with Parkinson's disease and a group of elderly subjects. The three patterns referred to the homologous (both arms or legs), homolateral (right or left arm and leg), and heterolateral (right arm and left leg or vice versa) limb segment combinations that were performed in the sagittal plane from a seated position. Findings revealed that interlimb coordination deficits were evident in patients with Parkinson's disease. Moreover, mean cycle duration and its variability were increased, particularly during the production of nonhomologous limb movements in different directions. These temporal findings suggest that movement slowness was not a primary consequence of an intrinsic inability to move the limb segments at the required speed but rather reflected an intentional strategy to cope with the complexity of the coordination pattern. Finally, movement amplitude was substantially smaller and more variable in patients with Parkinson's disease, suggestive of hypometria during the production of these cyclical tasks.
Reproducibility of nighttime salivary cortisol and its use in the diagnosis of hypercortisolism compared with urinary free cortisol and overnight dexamethasone suppression test.

BACKGROUND/METHODS Nighttime salivary cortisol (NSC) has been suggested to be a useful diagnostic test for Cushing's syndrome (CS). In the absence of published data on its day-to-day variability, we assessed the reproducibility of NSC by repeated measurements in healthy volunteers. Its diagnostic performance was compared with 24-h urinary free cortisol (UFC) and 1 mg overnight dexamethasone suppression test in 12 patients with CS, 20 healthy volunteers, 14 referred patients in which CS was excluded or not firmly established, 16 obese patients, and 20 women in late pregnancy. RESULTS NSC showed a superior reproducibility in healthy volunteers with a low day-to-day variability as reflected by an intraclass correlation coefficient of 0.78. The receiver operating characteristic curve-estimated cutoff of 6.1 nmol/liter (0.22 microg/dl) demonstrated a sensitivity and specificity of 100% (area under the receiver operating characteristic curve, 1.0; 95% confidence interval, 0.94-1.0) in the diagnosis of CS. NSC, 24-h UFC [after adjusting the local laboratory cutoff to 504 nmol/d (183 microg/d)], and the urinary cortisol/creatinine ratio showed a tendency to be superior to 1 mg dexamethasone suppression test in correctly identifying CS. In late pregnancy, the preserved diurnal variation at a higher level of salivary cortisol reduced the specificity of NSC to 75%. CONCLUSION Based on its remarkable reproducibility, easy noninvasive nature, and at least similar diagnostic performance, NSC appears to be a preferable alternative to 24-h UFC as a first-line screening test for CS. The cutoff values of NSC, 24-h UFC, and urinary cortisol/creatinine ratio have to be carefully adjusted using assay and center-specific reference ranges of sufficiently large populations.
Active bioacoustic measurement for human-to-human skin contact area detection

This paper describes a method to acquire the human-to-human skin contact area quantitatively. "Touch" is human's fundamental communication and is reckoned to have positive effects physically and emotionally. Indeed, physical stimulation is applied for clinical treatments for mental disorders. However, there is no existing technique to quantitatively measure the amount of touch (area, position, time length, etc.). Our method employs an active bioacoustics measurement technique to quantify the skin-to-skin contact area. A proposed system consists of a vibration unit and a sensing unit. A couple of users wear the units respectively. When they touch with each other, acoustic (elastic) waves propagate through their bodies via the skin contact zone. We consider that the amplitude of the waves which reach the sensing unit depends on the contact zone area. A result of our fundamental experiment supports our expectation.
Superstars and Underdogs: An Examination of the Long Tail Phenomenon in Video Sales

The rise of online channels facilitates the distribution of a wide range of products and services. Academics and industry observers agree that online distribution will fundamentally change the number and variety of products that consumers purchase. However, there is sharp disagreement about what type of change will occur. Proponents of the “long tail” idea argue that a sharp increase in the variety of products offered through online channels will fuel a shift in consumption away from hits to a much larger number of lower-selling niche products. While the long-tail view predicts an increase in the heterogeneity of consumption patterns, the well-known superstar effect promises the exact opposite. As consumers have access to their favorite content wherever they are whenever they demand it, consumption patterns will become more, not less uniform, this theory predicts. To shed light on this debate, we study the distribution of revenues across products in the context of the U.S. home video industry for the 2000 to 2005 period. We find superstar and long-tail effects in home video sales, but each effect comes with a twist. There is a long-tail effect in that the number of titles that sell only a few copies every week increases almost twofold during our study period. But at the same time, the number of non-selling titles rises rapidly; it is now four times as high as in 2000. Many underdogs thus in fact appear to be losers. We also find evidence of a superstar effect. Among the best-performing titles, an ever-smaller number of titles accounts for the bulk of sales. The caveat here is that today’s superstars lack the punch of earlier generations: video sales generally decrease over time across all quantiles of the sales distribution, but this effect is most pronounced among best-selling titles. Our findings have important implications for entertainment companies. Exploiting the tail might prove unprofitable if many titles do not sell at all. At the same time, producing superstars is more difficult than ever. The trends we uncover thus point to significant challenges for the entertainment industry.
Maximum power point tracking using fuzzy logic control for photovoltaic system

In this paper, a fuzzy logic control (FLC) based “Mamdani” is proposed to control the maximum power point tracking (MPPT) for a photovoltaic (PV) system. The proposed technique uses the fuzzy logic control to specify the size of incremental current in the current command of MPPT. As results indicated, the convergence time of maximum power point (MPP) of the proposed algorithm is better than that of the conventional Perturb and Observation (P&O) technique.
Microalbuminuria Precedes the Development of NIDDM

Several studies have indicated that insulin resistance, elevated blood pressure (BP), and dyslipidemia precede the onset of non-insulin-dependent diabetes mellitus (NIDDM). Little data, however, exist on the presence of renal disease in prediabetic subjects. We measured albumin excretion in a cross-sectional population study in subjects 65–74 years of age living in eastern Finland in relation to the risk of developing diabetes 3.5 years later. The prevalence of microalbuminuria (urinary albumin-to-urinary creatinine ratio ≥ 2 mg/mmol) was 1.3-, 1.8-, and 2.0-fold higher among subjects with impaired glucose tolerance (n = 242), newly diagnosed NIDDM subjects (n = 92), and previously diagnosed NIDDM subjects (n = 136), respectively, compared with subjects with normal glucose tolerance (n = 826). Nondiabetic subjects with microalbuminuria had multiple abnormalities in cardiovascular risk factors including elevated BP, high triglyceride concentration, high insulin concentration, and a low high-density lipoprotein cholesterol concentration, a cluster of risk factors typical for prediabetic individuals. The relationship between microalbuminuria and the incidence of NIDDM over the 3.5-year follow-up was studied in 891 subjects who were free of diabetes at baseline. Converters to diabetes (n = 69) had a higher prevalence of hypertension (68.1 vs. 54.4%, P < 0.05) and a higher prevalence of microalbuminuria (43.5 vs. 30.4%, P < 0.05) than nonconverters (n = 822). In logistic regression analysis, microalbuminuria predicted the development of NIDDM independently of BP level. However, after adjustment for plasma glucose and insulin levels at baseline, the difference in the prevalence of microalbuminuria between converters and nonconverters was not statistically significant. These results suggest that microalbuminuria may be a feature of the prediabetic state and that the increase in albumin excretion rate may be related to increases in glucose and insulin concentrations.
Exact solution to the exit-time problem for an undamped free particle driven by Gaussian white noise.

The noise-induced escape problem from a stable state is ubiquitous in many branches of mathematics, physics, chemistry, and engineering [1—5]. The problem has been the subject of intense research since the end of the last century when Arrhenius law was first published and most especially after the landmark work of Kramers in 1940 [6]. From a dynamical point of view the escape problem is closely related with the evaluation of the mean exit time (MET) out of an interval of a diffusing particle moving in a potential V(x), under the influence of a heat bath. In many cases the dynamics of the system is governed by the following stochastic differential equation for the position X(t) of the particle,
Modeling and analysis of a rotating turret winder in roll-to-roll manufacturing systems

The process of manufacturing products using roll-to-roll (R2R) methods involves unwinding of thin, flexible material in rolled form into machinery for processing and winding of the processed material into a roll. This paper describes modeling and control of a rotating turret winder in the rewind section of a R2R printing press. Governing equations for web speed and web tension within the rewind section are described by taking into consideration the motion of the rotating turret winder. Data from production runs of an industrial R2R printing press are analyzed to determine web behavior during a wound roll change sequence accomplished by the rotating turret. Model simulations are conducted and data from these simulations are compared with typical data from production runs. The key challenges associated with controlling web speed and web tension in a rewind section containing a rotating turret winder are discussed along with recommendations for machine and control design to achieve improved regulation of process parameters.
YY1 expression predicts favourable outcome in follicular lymphoma

Aims Follicular lymphoma is the second most common type of non-Hodgkin's lymphoma worldwide. The majority of patients diagnosed as having follicular lymphoma have an indolent form of the disease, but a subset of patients have aggressive disease with a shorter survival interval. Optimal treatment stratification requires a distinction between these two groups, though there are presently few prognostic biomarkers available. The transcription factor YY1 has been shown to play an important role in cancer biology. The authors have previously reported a correlation of Yin Yang 1 (YY1) mRNA levels with survival in FL. This study aimed to validate these findings at the protein level. Methods Quantification of YY1 protein was carried out on 26 FL biopsy samples using quantum dot labelled immunohistochemistry. Ki-67 percentage, grade, YY1 protein levels and T cell and macrophage markers were used in a multivariable analysis for survival in 26 cases of FL. Results Expression levels of YY1 protein were significantly increased in patients alive in comparison with those dead after follow-up (p≤0.025). Kaplan–Meier analysis showed association of higher expression levels of YY1 with longer survival (p≤0.01) (hazard ratio 3.33, 95% CI 1.26 to 8.85). The multivariable analysis identified YY1 protein level as the strongest predictor of outcome (p≤0.018), with none of the other markers being significantly associated with outcome. Conclusion These results support the prognostic utility of YY1 in FL, indicating potential as a clinical biomarker.
Phase Synchronization analysis of Heart Rate Variability and Systolic Blood Pressure Variability under Postural Stress

In this paper, the coupling between heart rate variability (HRV) and systolic blood pressure variability is analyzed using a non-linear measure called phase synchronization index (PSI). 20 healthy subjects alongwith 20 post myocardial patients undergong postural stress were used for analysis. The results were validated on standard EuroBaVar dataset. Results demonstrate that i) for healthy subjects PSI in the low frequency (LF) range i.e. (0.04-0.15) Hz is greater than PSI in the high frequency (HF) range i.e. (0.151-0.4) Hz in the lying position. ii) LF-PSI is less than HF-PSI in the standing position ii) for post AMI patients, LFPSI is greater than HF-PSI irrespective of the change in posture. In conclusion, it is found that there is a coupling between HRV and SBPV that varies in the LF and HF regions. This coupling changes with a change in the posture from lying to standing due to change in the autonomous drive occurring due to predominance of vagal over the sympathetic drive. This change is suppressed in the post AMI patients due to possible inactivity of the Baroreflex control.
Analysis of polynomial-phase signals by the integrated generalized ambiguity function

The aim of this work is the performance analysis of a method for the detection and parameter estimation of mono or multicomponent polynomial-phase signals (PPS) embedded in white Gaussian noise and based on a generalized ambiguity function. The proposed method is shown to be asymptotically efficient for second-order PPS and nearly asymptotically efficient for third-order PPSs. The method presents some advantages with respect to similar techniques, like the polynomial-phase transform, for example, in terms of (i) a closer approach to the Cramer-Rao lower bounds, (ii) a lower SNR threshold, (iii) a better capability of discriminating multicomponent signals.
Higher order finite-time consensus protocol for heterogeneous multi-agent systems

This paper studies the higher order finite-time consensus protocol for heterogeneous multi-agent systems (HMASs). By adding a power integrator method and using heterogeneous domination method, two kinds of consensus protocols are proposed with state feedback and output feedback, respectively. First, for the leaderless and leader-follower HMASs, the continuous finite-time consensus protocols are proposed. Then, by designing a finite-time observer, the output-feedback finite-time consensus protocol is developed. Finally, simulations are performed to illustrate the effectiveness of the theoretical results.
Analysis of the heart rate variability and stratification of the risk of cardiac patients with Chagas’ disease

According to the World wide Organization of the Health, the number of people infected with the Tri-panosoma Cruzi is considered between 16 and 18 million, causal agent of the Chagaspsila disease, and in 100 million the people exposed to the affectation risk. When concluding in 1983 a study longitudinal epidemiologist in patients with the disease evaluated every 3 years, the cardiac affectation: chronic Chagasic myocarditis (MCHC) increased from a 17% at the beginning of the study to a 49, 4% after 15 years. Previous studies of the variability of cardiac frequency in patients with the Chagaspsila disease, show alterations in the spectral indices of the HRV. We analyze the 24-hour heart rate by Holter recordings in 62 patients with ECG alterations (CH2), 32 patients without ECG alterations (CH1) who had positive serological findings for disease of Chagaspsila and 36 healthy subjects (control) matched for sex and age. We find a orthogonal base that is able to discriminate the groups from circadian profiles, control and CH2, and stratify the groups CH1.