Miracle-dz/UniFAR-FTUs huggingface dataset:
Pompe's disease.

Over the past 25 years, the widespread application of genetic and biochemical techniques has revolutionized the way physicians, particularly neurologists, characterize and even name diseases. Pompe's disease, or glycogen storage disease type II, provides an excellent illustration of how an understanding of the molecular basis of a disease alters fundamental elements of clinical nosology and therapy.
A Randomized-Controlled Trial Examining the Effects of Reflexology on Anxiety of Patients Undergoing Coronary Angiography

Background: The anxiety reduction before coronary angiography has clinical advantages and is one of the objectives of nursing. Reflexology is a non-invasive method that has been used in several clinical situations. Applying reflexology might have effect on the reduction of anxiety before coronary angiography. Objectives: The aim of this randomized clinical trial was to investigate the effect of reflexology on anxiety among patients undergoing coronary angiography. Patients and Methods: This trial was conducted in Shahid Beheshti Hospital, in Kashan, Iran. One hundred male patients who were undergoing coronary angiography were randomly enrolled into intervention and placebo groups. The intervention protocol was included 30 minutes of general foot massage and the stimulation of three reflex points including solar plexus, pituitary gland, and heart. The placebo group only received the general foot massage. Spielbergers state trait anxiety inventory was used to assess the anxiety experienced by patients. Data was analyzed using Man-Witney, Wilcoxon and Chi-square tests. The stepwise multiple regressions used to analyze the variables that are involved in anxiety reduction. Results: The mean range of anxiety decreased from 53.24 to 45.24 in reflexology group which represented 8 score reduction (P = 0.0001). The reduction in anxiety was 5.9 score in placebo group which was also significant (P = 0.0001). The anxiety reduction was significantly higher in reflexology group (P = 0.014). The stepwise multiple regression analysis showed that doing reflexology can explain the 7.5% of anxiety reduction which made a significant model. Conclusions: Reflexology can decrease the anxiety level before coronary angiography. Therefore, reflexology before coronary angiography is recommended.
Overlapping functions of Cdx1, Cdx2, and Cdx4 in the development of the amphibian Xenopus tropicalis

Using Xenopus tropicalis, we present the first analysis of the developmental effects that result from knocking down the function of the three Cdx genes present in the typical vertebrate genome. Knockdowns of individual Cdx genes lead to a similar range of posterior defects; compound Cdx knockdowns result in increasingly severe posterior truncations, accompanied by posterior shifts and reduction of 5′ Hox gene expression. We provide evidence that Cdx and Wnt3A genes are components of a positive feedback loop operating in the posterior axis. We show that Cdx function is required during later, but not early stages of development, for correct regional specification of the endoderm and morphogenesis of the gut. Our results support the hypothesis that during amphibian development the overall landscape of Cdx activity in the embryo is more important than the specific function of individual Cdx proteins. Developmental Dynamics 238:835–852, 2009. © 2009 Wiley‐Liss, Inc.
Shape parameters of Galactic open clusters

Context. There are only a few tens of open clusters for which ellipticities have been determined in the past. Aims. In this paper we derive observed and modelled shape parameters (apparent ellipticity and orientation of the ellipse) of 650 Galactic open clusters identified in the ASCC-2.5 catalogue. Methods. We provide the observed shape parameters of Galactic open clusters, computed with the help of a multi- component analysis. For the vast majority of clusters these parameters are determined for the first time. High resolution ("star by star") N-body simulations are carried out with the specially developedGRAPE code providing models of clusters of different initial masses, Galactocentric distances and rotation velocities. Results. The comparison of models and observations of about 150 clusters reveals ellipticities of observed clusters which are too low (0.2 vs. 0.3), and offers the basis to find the main reason for this discrepancy. The models predict that after � 50 Myr clusters reach an oblate shape with an axes ratio of 1.65 : 1.35 : 1, and with the major axis tilted by an angle of qXY � 30 ◦ with respect to the Galactocentric radius due to differential rotation of the Galaxy. Conclusions. Unbiased estimates of cluster shape parameters requires reliable membership determination in large cluster areas up to 2-3 tidal radii where the density of cluster stars is considerably lower than the background. Although dynamically bound stars outside the tidal radius contribute insignificantly to the cluster mass, their distribution is essential for a correct determination of cluster shape parameters. In contrast, a restricted mass range of cluster stars does not play such a dramatic role, though deep surveys allow to identify more cluster members and, therefore, to increase the accuracy of the observed shape parameters.
Learning to re-rank web search results with multiple pairwise features

Web search ranking functions are typically learned to rank search results based on features of individual documents, i.e., pointwise features. Hence, the rich relationships among documents, which contain multiple types of useful information, are either totally ignored or just explored very limitedly. In this paper, we propose to explore multiple pairwise relationships between documents in a learning setting to rerank search results. In particular, we use a set of pairwise features to capture various kinds of pairwise relationships and design two machine learned re-ranking methods to effectively combine these features with a base ranking function: a pairwise comparison method and a pairwise function decomposition method. Furthermore, we propose several schemes to estimate the potential gains of our re-ranking methods on each query and selectively apply them to queries with high confidence. Our experiments on a large scale commercial search engine editorial data set show that considering multiple pairwise relationships is quite beneficial and our proposed methods can achieve significant gain over methods which only consider pointwise features or a single type of pairwise relationship.
Multilingual acoustic modeling for speech recognition based on subspace Gaussian Mixture Models

Although research has previously been done on multilingual speech recognition, it has been found to be very difficult to improve over separately trained systems. The usual approach has been to use some kind of “universal phone set” that covers multiple languages. We report experiments on a different approach to multilingual speech recognition, in which the phone sets are entirely distinct but the model has parameters not tied to specific states that are shared across languages. We use a model called a “Subspace Gaussian Mixture Model” where states' distributions are Gaussian Mixture Models with a common structure, constrained to lie in a subspace of the total parameter space. The parameters that define this subspace can be shared across languages. We obtain substantial WER improvements with this approach, especially with very small amounts of in-language training data.
Perceptually Grounded Word Meaning Acquisition: A Computational Model

We present a computational model for the incremental acquisition of word meanings. Inspired by Complementary Learning Systems theory the model comprises different components which are specifically tailored to satisfy the contradictory needs of (1) rapid memorization of word-scene associations and (2) statistical feature extraction to reveal word meanings. Both components are recurrently coupled to achieve a memory consolidation. This process reflects itself in a gradual transfer of the knowledge about a word’s meaning into the extracted features. Thereby, the internal representation of a word becomes more efficient and robust. We present simulation results for a visual scene description task in which words describing the relations between objects have been trained. This includes relations in size, color, and position. The results demonstrate our model’s capability to acquire word meanings from few training exemplars. We further show that the model correctly extracts word meaning-relevant features and therefore perceptually grounds the words.
On the Convergence of Stochastic Gradient MCMC Algorithms with High-Order Integrators

Recent advances in Bayesian learning with large-scale data have witnessed emergence of stochastic gradient MCMC algorithms (SG-MCMC), such as stochastic gradient Langevin dynamics (SGLD), stochastic gradient Hamiltonian MCMC (SGHMC), and the stochastic gradient thermostat. While finite-time convergence properties of the SGLD with a 1st-order Euler integrator have recently been studied, corresponding theory for general SG-MCMCs has not been explored. In this paper we consider general SG-MCMCs with high-order integrators, and develop theory to analyze finite-time convergence properties and their asymptotic invariant measures. Our theoretical results show faster convergence rates and more accurate invariant measures for SG-MCMCs with higher-order integrators. For example, with the proposed efficient 2nd-order symmetric splitting integrator, the mean square error (MSE) of the posterior average for the SGHMC achieves an optimal convergence rate of L-4/5 at L iterations, compared to L-2/3 for the SGHMC and SGLD with 1st-order Euler integrators. Furthermore, convergence results of decreasing-step-size SG-MCMCs are also developed, with the same convergence rates as their fixed-step-size counterparts for a specific decreasing sequence. Experiments on both synthetic and real datasets verify our theory, and show advantages of the proposed method in two large-scale real applications.
Effects of Fructooligosaccharides on Intestinal Flora and Human Health

A study was made of the effects of fructooligosaccharides , which exist widely in plants such as onion, edible burdock, wheat etc., on the human and animal intestinal flora . Fructooligosaccharides are produced from sucrose with the aid of ƒÀ-fructofuranosidase from Aspergillus niger on a commercial scale by Meiji Seika Kaisha , Ltd. (Neosugar, Meioligo(R) . It has been found that they are not hydrolyzed by any digestive enzymes of humans and animals. Moreover utilization by various kinds of intestinal bacteria indicated that Bifidobacterium spp. , the Bacteroides fragilis group , Peptostreptococcus spp. and Klebsiella pneumoniae can utilize these saccharides, but Clostridium perfringens , Escherichia coli and others cannot. The fructooligosaccharides are selectively utilized , particularly by bifidobacteria. The clinical studies showed that fructooligosaccharides administration improved the intestinal flora , with subsequent relief of constipation, improved blood lipids in hyperlipidemia , and suppressed the production of intestinal putrefactive substances.
Intestinal Parasite Prevalence in an Area of Ethiopia after Implementing the SAFE Strategy, Enhanced Outreach Services, and Health Extension Program

Background The SAFE strategy aims to reduce transmission of Chlamydia trachomatis through antibiotics, improved hygiene, and sanitation. We integrated assessment of intestinal parasites into large-scale trachoma impact surveys to determine whether documented environmental improvements promoted by a trachoma program had collateral impact on intestinal parasites. Methodology We surveyed 99 communities for both trachoma and intestinal parasites (soil-transmitted helminths, Schistosoma mansoni, and intestinal protozoa) in South Gondar, Ethiopia. One child aged 2–15 years per household was randomly selected to provide a stool sample of which about 1 g was fixed in sodium acetate-acetic acid-formalin, concentrated with ether, and examined under a microscope by experienced laboratory technicians. Principal Findings A total of 2,338 stool specimens were provided, processed, and linked to survey data from 2,657 randomly selected children (88% response). The zonal-level prevalence of Ascaris lumbricoides, hookworm, and Trichuris trichiura was 9.9% (95% confidence interval (CI) 7.2–12.7%), 9.7% (5.9–13.4%), and 2.6% (1.6–3.7%), respectively. The prevalence of S. mansoni was 2.9% (95% CI 0.2–5.5%) but infection was highly focal (range by community from 0–52.4%). The prevalence of any of these helminth infections was 24.2% (95% CI 17.6–30.9%) compared to 48.5% as found in a previous study in 1995 using the Kato-Katz technique. The pathogenic intestinal protozoa Giardia intestinalis and Entamoeba histolytica/E. dispar were found in 23.0% (95% CI 20.3–25.6%) and 11.1% (95% CI 8.9–13.2%) of the surveyed children, respectively. We found statistically significant increases in household latrine ownership, use of an improved water source, access to water, and face washing behavior over the past 7 years. Conclusions Improvements in hygiene and sanitation promoted both by the SAFE strategy for trachoma and health extension program combined with preventive chemotherapy during enhanced outreach services are plausible explanations for the changing patterns of intestinal parasite prevalence. The extent of intestinal protozoa infections suggests poor water quality or unsanitary water collection and storage practices and warrants targeted intervention.
Sure independence screening in generalized linear models with NP-dimensionality

Ultrahigh dimensional variable selection plays an increasingly important role in contemporary scientific discoveries and statistical research. Among others, Fan and Lv (2008) propose an independent screening framework by ranking the marginal correlations. They showed that the correlation ranking procedure possesses a sure independence screening property within the context of the linear model with Gaussian covariates and responses. In this paper, we propose a more general version of the independent learning with ranking the maximum marginal likelihood estimates or the maximum marginal likelihood itself in generalized linear models. We show that the proposed methods, with Fan and Lv (2008) as a very special case, also possess the sure screening property with vanishing false selection rate. The conditions under which that the independence learning possesses a sure screening is surprisingly simple. This justifies the applicability of such a simple method in a wide spectrum. We quantify explicitly the extent to which the dimensionality can be reduced by independence screening, which depends on the interactions of the covariance matrix of covariates and true parameters. Simulation studies are used to illustrate the utility of the proposed approaches. In addition, we � Supported in part by Grant NSF grants DMS-0714554 and DMS-0704337. The bulk of the work was conducted when Rui Song was a postdoctoral research fellow at Princeton University. The authors would like to thank the associate editor and two referees for their constructive comments that improve the presentation and the results of the paper. AMS 2000 subject classifications: Primary 68Q32, 62J12; secondary 62E99, 60F10
Measuring Acetabular Cup Orientation on Antero-Posterior Radiographs of the Hip after Total Hip Arthroplasty with a Vector Arithmetic Radiological Method. Is It Valid and Verified for Daily Clinical Practice?

Abstract Purpose: The aim of this prospective study is to validate a vector arithmetic method for measuring acetabular cup orientation after total hip arthroplasty (THA) and to verify the clinical practice. Materials and Methods: We measured cup anteversion and inclination of 123 patients after cementless primary THA twice by two examiners on AP pelvic radiographs with a vector arithmetic method and compared with a 3D-CT based reconstruction model within the same radiographic coronal plane. Results: The mean difference between the radiographic and the 3D-CT measurements was – 1.4° ± 3.9° for inclination and 0.8°± 7.9° for anteversion with excellent correlation for inclination (r = 0.81, p < 0.001) and moderate correlation for anteversion (r = 0.65, p < 0.001). The intraclass correlation coefficient for measurements on radiographs ranged from 0.98 (95 %-CI: 0.98; 0.99) for the first observer to 0.94 (95 %-CI: 0.92; 0.96) for the second observer. The interrater reliability was 0.96 (95 %-CI: 0.93; 0.98) for inclination and 0.93 (95 %-CI: 0.85; 0.96) for anteversion. Conclusion: The largest errors in measurements were associated with an extraordinary pelvic tilt. In order to get a valuable measurement for measuring cup position after THA on pelvic radiographs by this vector arithmetic method, there is a need for a correct postoperative ap view, with special regards to the pelvic tilt for the future. Key points: • Measuring acetabular cup orientation on anteroposterior radiographs of the hip after THA is a helpful procedure in everyday clinical practice as a first-line imaging modality • CT remains the golden standard to accurately determine acetabular cup position. • Future measuring on radiographs for cup orientation after THA should account for integration of the pelvic tilt in order to maximize the measurement accuracy. Citation Format: • Craiovan B, Weber M, Worlicek M et al. Measuring Acetabular Cup Orientation on Antero-Posterior Radiographs of the Hip after Total Hip Arthroplasty with a Vector Arithmetic Radiological Method. Is It Valid and Verified for Daily Clinical Practice? Fortschr Röntgenstr 2016; 188: 574 – 581
Multiclass spectral clustering

We propose a principled account on multiclass spectral clustering. Given a discrete clustering formulation, we first solve a relaxed continuous optimization problem by eigen-decomposition. We clarify the role of eigenvectors as a generator of all optimal solutions through orthonormal transforms. We then solve an optimal discretization problem, which seeks a discrete solution closest to the continuous optima. The discretization is efficiently computed in an iterative fashion using singular value decomposition and nonmaximum suppression. The resulting discrete solutions are nearly global-optimal. Our method is robust to random initialization and converges faster than other clustering methods. Experiments on real image segmentation are reported.
Mind the gaps: the evolution of regional inequalities in the UK, 1982-1997

In this paper we apply earnings equations for UK regions over 1982-1997. We find strong evidence of rapid convergence across regions regarding the determinants of individual wages (ie regional fixed-effects, gender gaps and returns to education and experience). Data on average regional earnings, by contrast, point at a worsening of UK regional inequalities and a rise in the North-South gap. Education accounts for most of the discrepancy between aggregate divergence and disaggregated convergence. First, London gained because its workforce became relatively more educated over the period. Second, returns to education increased nation-wide, which favoured the most educated regions (ie London). Third, returns to education were initially lower in London but they (partially) caught up with the rest of the country. Had returns to education and their distribution across UK regions remained stable over the period, the UK North-South divide would have decreased.
Spatial and Spectral Characterization of Human Retinal Pigment Epithelium Fluorophore Families by Ex Vivo Hyperspectral Autofluorescence Imaging

Purpose Discovery of candidate spectra for abundant fluorophore families in human retinal pigment epithelium (RPE) by ex vivo hyperspectral imaging. Methods Hyperspectral autofluorescence emission images were captured between 420 and 720 nm (10-nm intervals), at two excitation bands (436–460, 480–510 nm), from three locations (fovea, perifovea, near-periphery) in 20 normal RPE/Bruch's membrane (BrM) flatmounts. Mathematical factorization extracted a BrM spectrum (S0) and abundant lipofuscin/melanolipofuscin (LF/ML) spectra of RPE origin (S1, S2, S3) from each tissue. Results Smooth spectra S1 to S3, with perinuclear localization consistent with LF/ML at all three retinal locations and both excitations in 14 eyes (84 datasets), were included in the analysis. The mean peak emissions of S0, S1, and S2 at λex 436 nm were, respectively, 495 ± 14, 535 ± 17, and 576 ± 20 nm. S3 was generally trimodal, with peaks at either 580, 620, or 650 nm (peak mode, 650 nm). At λex 480 nm, S0, S1, and S2 were red-shifted to 526 ± 9, 553 ± 10, and 588 ± 23 nm, and S3 was again trimodal (peak mode, 620 nm). S1 often split into two spectra, S1A and S1B. S3 strongly colocalized with melanin. There were no significant differences across age, sex, or retinal location. Conclusions There appear to be at least three families of abundant RPE fluorophores that are ubiquitous across age, retinal location, and sex in this sample of healthy eyes. Further molecular characterization by imaging mass spectrometry and localization via super-resolution microscopy should elucidate normal and abnormal RPE physiology involving fluorophores. Translational Relevance Our results help establish hyperspectral autofluorescence imaging of the human retinal pigment epithelium as a useful tool for investigating retinal health and disease.
Feature and classifier fusion for 12-lead ECG classification

Two methodologies, feature and classifier fusion, for the problem of computerized 12-lead electrocardiogram classification, are investigated. Firstly, the entire classification problem is subdivided into a number of smaller bi-dimensional ones. By employing bi-group Neural Network classifiers, independent feature vectors for each diagnostic class are examined individually and the output from each classifier are fused together to produce one single result. Secondly, two classifiers, namely the aforementioned and a decision tree, are fused together through a novel approach of a Specificity Matrix. This methodology addresses the problem of unresolved conflict during fusion of classifiers and aims to exploit the merits of each classifier and suppress their weaknesses. 290 validated 12-lead electrocardiogram recordings, comprising six diagnostic classes, were used to train, validate and test both methodologies. The framework of bi-group classifiers enhanced the overall performance by 12.0% in comparison with conventional approaches. In the second instance, the fusion of the two classifiers produced a performance level of 81.3%; superior to either classifier in isolation. This approach offers a viable solution to the unresolved problem of conflict between classifiers during fusion and can be extended readily to accommodate any number of diagnostic classes and classifiers.
The PROSITE database, its status in 1999

The PROSITE database (http://www.expasy.ch/sprot/prosite.htm l) consists of biologically significant patterns and profiles formulated in such a way that with appropriate computational tools it can help to determine to which known family of protein (if any) a new sequence belongs, or which known domain(s) it contains.