Miracle-dz/UniFAR-FTUs huggingface dataset:
A Novel In Vitro Model for Microvasculature Reveals Regulation of Circumferential ECM Organization by Curvature

In microvascular vessels, endothelial cells are aligned longitudinally whereas several components of the extracellular matrix (ECM) are organized circumferentially. While current three-dimensional (3D) in vitro models for microvasculature have allowed the study of ECM-regulated tubulogenesis, they have limited control over topographical cues presented by the ECM and impart a barrier for the high-resolution and dynamic study of multicellular and extracellular organization. Here we exploit a 3D fibrin microfiber scaffold to develop a novel in vitro model of the microvasculature that recapitulates endothelial alignment and ECM deposition in a setting that also allows the sequential co-culture of mural cells. We show that the microfibers' nanotopography induces longitudinal adhesion and alignment of endothelial colony-forming cells (ECFCs), and that these deposit circumferentially organized ECM. We found that ECM wrapping on the microfibers is independent of ECFCs' actin and microtubule organization, but it is dependent on the curvature of the microfiber. Microfibers with smaller diameters (100–400 µm) guided circumferential ECM deposition, whereas microfibers with larger diameters (450 µm) failed to support wrapping ECM. Finally, we demonstrate that vascular smooth muscle cells attached on ECFC-seeded microfibers, depositing collagen I and elastin. Collectively, we establish a novel in vitro model for the sequential control and study of microvasculature development and reveal the unprecedented role of the endothelium in organized ECM deposition regulated by the microfiber curvature.
Curcumin Inhibition of the Functional Interaction between Integrin α6β4 and the Epidermal Growth Factor Receptor

The functional interaction between integrin α6β4 and growth factor receptors has been implicated in key signaling pathways important for cancer cell function. However, few attempts have been made to selectively target this interaction for therapeutic intervention. Previous studies showed that curcumin, a yellow pigment isolated from turmeric, inhibits integrin α6β4 signaling important for breast carcinoma cell motility and invasion, but the mechanism is not currently known. To address this issue, we tested the hypothesis that curcumin inhibits the functional interaction between α6β4 and the epidermal growth factor receptor (EGFR). In this study, we found that curcumin disrupts functional and physical interactions between α6β4 and EGFR, and blocks α6β4/EGFR-dependent functions of carcinoma cells expressing the signaling competent form of α6β4. We further showed that curcumin inhibits EGF-dependent mobilization of α6β4 from hemidesmosomes to the leading edges of migrating cells such as lammelipodia and filopodia, and thereby prevents α6β4 distribution to lipid rafts where functional interactions between α6β4 and EGFR occur. These data suggest a novel paradigm in which curcumin inhibits α6β4 signaling and functions by altering intracellular localization of α6β4, thus preventing its association with signaling receptors such as EGFR. Mol Cancer Ther; 10(5); 883–91. ©2011 AACR.
A Growth Curve Model with Fractional Polynomials for Analysing Incomplete Time-Course Data in Microarray Gene Expression Studies

Identifying the various gene expression response patterns is a challenging issue in expression microarray time-course experiments. Due to heterogeneity in the regulatory reaction among thousands of genes tested, it is impossible to manually characterize a parametric form for each of the time-course pattern in a gene by gene manner. We introduce a growth curve model with fractional polynomials to automatically capture the various time-dependent expression patterns and meanwhile efficiently handle missing values due to incomplete observations. For each gene, our procedure compares the performances among fractional polynomial models with power terms from a set of fixed values that offer a wide range of curve shapes and suggests a best fitting model. After a limited simulation study, the model has been applied to our human in vivo irritated epidermis data with missing observations to investigate time-dependent transcriptional responses to a chemical irritant. Our method was able to identify the various nonlinear time-course expression trajectories. The integration of growth curves with fractional polynomials provides a flexible way to model different time-course patterns together with model selection and significant gene identification strategies that can be applied in microarray-based time-course gene expression experiments with missing observations.
Automatic detection of ocular movements during sleep with an application to a sleep-disorders study

An algorithm for automatic detection of ocular movements (OMs) during sleep is described. Typical EOG recordings were transformed into the time-frequency plane using a wavelet transform. This kind of representation was helpful to localize preciselythe OMs activity in the frequency domain, making thedesign of two digital filters (FEOG1 and FEOG2) possible. The EOG signal was filtered off-line using FEOG1 and FEOG2. Then 2 context-dependent thresholds were computed to perform OMs detection. Chin EMG recordings were processed simultaneously in order to reject movements due to artefacts. The automatic detection was applied to a pharmacological study aimed at measuring the action of 2 pharmacological compounds on sleep disorders.
A new method for separation of speech signals in convolutive mixtures

In this paper, the performance of the gradient method based on Score Function Difference (SFD) in the separation of i.i. d. and periodic signals will be investigated. We will see that this algorithm will separate periodic signals better than i.i. d. ones. By using this experimental result and the fact that voiced frames of speech signals are approximately periodic, a modified algorithm named VDGaradient has been proposed for separation of speech signals in synthetic convolutive mixtures. In this method, voiced frames of speech signal will be used as the input to the gradient method, then the resulting separating system will be applied to separate sources completely.
Atmospheric oxygen level affects growth trajectory, cardiopulmonary allometry and metabolic rate in the American alligator (Alligator mississippiensis)

SUMMARY Recent palaeoatmospheric models suggest large-scale fluctuations in ambient oxygen level over the past 550 million years. To better understand how global hypoxia and hyperoxia might have affected the growth and physiology of contemporary vertebrates, we incubated eggs and raised hatchlings of the American alligator. Crocodilians are one of few vertebrate taxa that survived these global changes with distinctly conservative morphology. We maintained animals at 30°C under chronic hypoxia (12% O2), normoxia (21% O2) or hyperoxia (30% O2). At hatching, hypoxic animals were significantly smaller than their normoxic and hyperoxic siblings. Over the course of 3 months, post-hatching growth was fastest under hyperoxia and slowest under hypoxia. Hypoxia, but not hyperoxia, caused distinct scaling of major visceral organs–reduction of liver mass, enlargement of the heart and accelerated growth of lungs. When absorptive and post-absorptive metabolic rates were measured in juvenile alligators, the increase in oxygen consumption rate due to digestion/absorption of food was greatest in hyperoxic alligators and smallest in hypoxic ones. Hyperoxic alligators exhibited the lowest breathing rate and highest oxygen consumption per breath. We suggest that, despite compensatory cardiopulmonary remodelling, growth of hypoxic alligators is constrained by low atmospheric oxygen supply, which may limit their food utilisation capacity. Conversely, the combination of elevated metabolism and low cost of breathing in hyperoxic alligators allows for a greater proportion of metabolised energy to be available for growth. This suggests that growth and metabolic patterns of extinct vertebrates would have been significantly affected by changes in the atmospheric oxygen level.
Invariant Gaussian Process Latent Variable Models and Application in Causal Discovery

In nonlinear latent variable models or dynamic models, if we consider the latent variables as confounders (common causes), the noise dependencies imply further relations between the observed variables. Such models are then closely related to causal discovery in the presence of nonlinear confounders, which is a challenging problem. However, generally in such models the observation noise is assumed to be independent across data dimensions, and consequently the noise dependencies are ignored. In this paper we focus on the Gaussian process latent variable model (GPLVM), from which we develop an extended model called invariant GPLVM (IG-PLVM), which can adapt to arbitrary noise covariances. With the Gaussian process prior put on a particular transformation of the latent nonlinear functions, instead of the original ones, the algorithm for IGPLVM involves almost the same computational loads as that for the original GPLVM. Besides its potential application in causal discovery, IGPLVM has the advantage that its estimated latent nonlinear manifold is invariant to any nonsingular linear transformation of the data. Experimental results on both synthetic and real-world data show its encouraging performance in nonlinear manifold learning and causal discovery.
The Correlation between the Frequency of Oral Lesions and the Amount of Smokeless Tobacco Usage in Patients Referred to Oral Medicine Department of Zahedan Dental School

Statement of Problem: The increasing use of smokeless tobacco in the last 15 years has motivated researchers to evaluate its impact on its user’s health. Purpose: The aim of this study was to determine the frequency of oral lesions related to smokeless tobacco and any possible correlation between the frequency of oral lesions and the amount of usage in patients referred to Zahedan Dental School. Materials and Method: A total of 90 (77 male and 13 female) cases, all snuff consumers, were surveyed in this cross sectional study which was accomplished by employing questionnaires. The questionnaire included demographic information, type and amount of smokeless tobacco used and the location where it was placed in the mouth. The completion of the questionnaires was followed by oral clinical examinations of patients. The location of any lesion found in soft tissue, was recorded in questionnaire. Results: The mean age for men and women was 47.7 and 55.61, respectively. A total of 38 cases (29 males, 9 females) were found to have oral lesions. 26 patients were using the snuff one pack per day. The common site of lesions was lower buccal sulcus. From 38 lesions, 32 lesions were found at the site of snuff placement. Most of the lesions were degree 1 and white in color. After taking biopsy from 32 lesions, 26 cases were detected as hyperkeratotic and 6 cases as epithelial dysplasia. Conclusion: This study showed that use of snuff is very common in Zahedan and usage of this material can produce oral lesions. There is not a significant correlation between the frequency of oral lesions and the amount of usage.
Congenital infection with human herpesvirus 6 variant B associated with neonatal seizures and poor neurological outcome

Human herpesvirus 6 (HHV 6) has neurotropic and neuroinvasive properties. The virus has been found in the cerebrospinal fluid of many children with aseptic meningoencephalitis. Intrauterine transmission has been documented by HHV 6 DNA detection in cord blood specimens of apparently healthy newborns and in fetuses following spontaneous abortions. A patient is described with early neonatal afebrile seizures resulting from a congenital HHV 6 variant B infection disclosed by repeated detection of viral genome by polymerase chain reaction (PCR) in cerebrospinal fluid in the first days of life. At follow‐up, magnetic resonance imaging (MRI) studies disclosed hyperintensities in the periventricular white matter and basal ganglia, associated with cerebral atrophy. Further follow‐up at 18 months revealed poor neurological outcome with mild neurodevelopmental retardation, strabismus and hypertonia of legs. This report provides evidence of neurological involvement after HHV 6 vertical transmission, and the association with neurological sequelae. J. Med. Virol. 70:628–632, 2003. © 2003 Wiley‐Liss, Inc.
Biomass, nutrient content and distribution in a stand of Sitka spruce.

The annual uptake of nitrogen, phosphorus and potassium by an unthinned 33 year old crop of Sitka spruce was estimated by destructive sampling of eight trees. Extrapolation of their nutrient contents to the total crop gave estimates of 81kg N, 4kg P and 15kg K. Although the stemwood and bark accounted for half of the total dry matter production they only contained 17, 14 and 36 per cent of the total quantities of N, P and K present in the crop and forest floor, the main bulk of the nutrients being in the needles and branches.
Seagrass: A Dynamic System

Small herbivorous invertebrates consume algal epiphytes, reducing negative effects (e.g. shading) on seagrass. Much research to date has focused on crustacean grazers, and comparatively little on gastropods. The aim of this research was to 1) examine seasonal and spatial variation in seagrass and associated gastropods in a large, tidal estuary and 2) examine the response of seagrass and epiphytic algae to nutrient enrichment and grazing pressure in a laboratory experiment. Surveys were conducted in summer and winter of 2016 to assess the seasonal fluctuations in the associated gastropods and relationships with seagrass and epiphyte biomass within three sites in the Porirua Harbour. Seagrass, gastropods and epiphytic algae showed seasonal trends, including evidence of a loss of grazer control on epiphytes during winter. Potamopyrgus estuarinus, Notoacmea scapha, Diloma spp. and Micrelenchus spp. were the dominant gastropod grazers in the system in both seasons. The gastropod assemblage and seagrass characteristics differed between sites, likely in response to small scale differences in abiotic factors. Seagrass from Elsdon (a site with elevated nutrient levels) and Browns Bay (a relatively pristine site) were used to investigate the role of select grazers and nutrient enrichment on epiphyte and seagrass growth. Nutrient treatments represented nitrate and phosphate concentrations of Elsdon (High), a 20% increase (High+) and a control (no addition). Little evidence was found for epiphyte regulation by gastropods, nor did epiphyte loads increase with nutrient addition. Seagrass from Browns Bay responded more strongly to High+ treatments than that of Elsdon. The results suggest that seagrass from Elsdon is adapted to the site’s high nutrient loads, where seagrass from Browns Bay is not. The results of this thesis support prior research findings of high variation in seagrass over a small scale, and adds to the currently lacking information on the role of micro-grazers in New Zealand’s seagrass meadows.
Approximate Confidence Interval for Effect Size Base on Bootstrap Resampling Method

: This paper presents the confidence intervals for the effect size base on bootstrap resampling method. The meta-analytic confidence interval for effect size is proposed that are easy to compute. A Monte Carlo simulation study was conducted to compare the performance of the proposed confidence intervals with the existing confidence intervals. The best confidence interval method will have a coverage probability close to 0.95. Simulation results have shown that our proposed confidence intervals perform well in terms of coverage probability and expected length.
Epidemiologic, Experimental, and Clinical Links between Respiratory Syncytial Virus Infection and Asthma

SUMMARY Virtually all children experience respiratory syncytial virus (RSV) infection at least once during the first 2 years of life, but only a few develop bronchiolitis and more severe disease requiring hospitalization, usually in the first 6 months of life. Children who recover from RSV-induced bronchiolitis are at increased risk for the development of recurrent wheeze and asthma in later childhood. Recent studies suggest that there is an association between RSV-induced bronchiolitis and asthma within the first decade of life but that this association is not significant after age 13. Despite the considerable progress made in our understanding of several aspects of respiratory viral infections, further work needs to be done to clarify the molecular mechanisms of early interactions between virus and host cell and the role of host gene products in the infection process. This review provides a critical appraisal of the literature in epidemiology and experimental research which links RSV infection to asthma. Studies to date demonstrate that there is a significant association between RSV infection and childhood asthma and that preventing severe primary RSV infections can decrease the risk of childhood asthma.
New Industrial Product Design and Evaluation Using Multiattribute Value Analysis

Increasingly, the design of successful new industrial products is related to careful market assessment. Traditionally, managers and researchers have studied their markets by examining a small number of product attributes that are common across a range of informed respondents. In many ways, these techniques fail to meet the challenges posed by today's often heterogeneous, highly competitive, fast moving industrial markets. Ralph Keeney and Gary Lilien introduce us to a technique they call multiattribute value analysis, both describing the procedure and describing a comprehensive example. Their approach introduces considerable flexibility to the process of market assessment. Technically, it permits the evaluation of many more attributes, value tradeoffs, and synergies among attributes than do more traditional methods. In addition, it permits nonlinear evaluation functions that may be idiosyncratic to the individual. Practically, their approach, illustrated with a detailed case application, is shown to have significant potential for aiding product design decisions.
Association between three interleukin-10 gene polymorphisms and coronary artery disease risk: a meta-analysis.

BACKGROUND Previous studies have investigated the associations between interleukin-10 (IL-10) gene polymorphisms (-592C/A, -819C/T and -1082G/A) and risk of coronary artery disease (CAD). However, the results were inconsistent. The aim of this study was to clarify the relationship between IL-10 polymorphisms and CAD risk by a meta-analysis approach. METHODS The PubMed, Embase, Web of Science, China National Knowledge Infrastructure (CNKI) and Wanfang databases were searched according to predefined criteria for all relevant studies published before June 1, 2015. Pooled odds ratios (ORs) and 95% confidence intervals (95% CIs) were computed to assess the association. RESULTS 24 eligible studies were enrolled including 9736 CAD patients and 8606 controls. We observed a significant decreased risk of CAD for IL-10 -819C/T polymorphism (T allele vs. C allele:OR = 0.91, 95% CI = 0.84-0.99; TT vs. CT + CC:OR = 0.82, 95% CI = 0.69-0.98), especially in Asians (T allele vs. C allele:OR = 0.76, 95% CI = 0.60-0.96; TT vs. CC:OR = 0.51, 95% CI = 0.27-0.96; TT vs. CT + CC:OR = 0.62, 95% CI = 0.44-0.88). Moreover, we found IL-10 -1082G/A polymorphism might contribute to an increased CAD risk in Asians (AA vs. GG:OR = 1.89, 95% CI = 1.36-2.64; AA vs. AG + GG:OR = 1.39, 95% CI = 1.14-1.68) but not in other ethnic groups. However, no significant association between the IL-10 -592C/A polymorphism and CAD risk was observed. CONCLUSIONS Our results indicated that IL-10 -819C/T and IL-10 -1082G/A polymorphisms significantly and race-specifically correlate with CAD risk.
OR Forum - The Next Decade in Operations Research: Comments on the Condor Report

Under the sponsorship of the Systems Theory and Operations Research STOR Program of the National Science Foundation, a Committee on the Next Decade in Operations Research CONDOR held a 3-day workshop in mid-1987. The report of this committee appeared a year later in Operations Research pp. 619-637. In view of the importance of this subject, and because CONDOR had, a fortiori, to limit its considerations to a number of important ones of primary interest to its members, a number of other OR analysts of widely different experience were asked to comment on this report. Four of the responses are presented below.
Abstraction of High Level Concepts from Numerical Values in Databases

A conceptual clustering method is proposed for discovering high level concepts of numerical attribute values from databases. The method considers both frequency and value distributions of data, thus is able to discover relevant concepts from numerical attributes. The discovered knowledge can be used for representing data semantically and for providing approximate answers when exact ones are not available. Our knowledge discovery approach is to partition the data set of one or more attributes into clusters that minimize the relaxation error. An algorithm is developed which finds the best binary partition in O(n) time and generates a concept hierarchy in O(n2) time where n is the number of distinct values of the attribute. The effectiveness of our clustering method is demonstrated by applying it to a large transportation database for approximate query answering.
Spinal Muscular Atrophy: Present State

Spinal muscular atrophy (SMA) is a hereditary neurodegenerative disease caused by homozygous deletions or mutations in the SMN1 gene on Chr.5q13. SMA spans from severe Werdnig‐Hoffmann disease (SMA 1) to relatively benign Kugelberg‐Welander disease (SMA 3). Onset before birth possibly aggravates the clinical course, because immature motoneurons do not show compensatory sprouting and collateral reinnervation, and motor units in SMA 1, in contrast to those in SMA 3, are not enlarged. Genetic evidence indicates that SMN2, a gene 99% identical to SMN1, can attenuate SMA severity: in patients, more SMN2 copies and higher SMN protein levels are correlated with milder SMA. There is evidence that SMN plays a role in motoneuron RNA metabolism, but it has also been linked to apoptosis.
MOHEFT: A multi-objective list-based method for workflow scheduling

Nowadays, scientists and companies are confronted with multiple competing goals such as makespan in high-performance computing and economic cost in Clouds that have to be simultaneously optimized. Multi-objective scheduling of scientific workflows in distributed systems is therefore receiving increasing research attention. Most existing approaches typically aggregate all objectives in a single function, defined a-priori without any knowledge about the problem being solved, which negatively impacts the quality of the solutions. In contrast, Pareto-based approaches having as outcome a set of several (nearly-) optimal solutions that represent a tradeoff among the different objectives, have been scarcely studied. In this paper, we propose a new Pareto-based list scheduling heuristic that provides the user with a set of tradeoff optimal solutions from where the one that better suits the user requirements can be manually selected. We demonstrate the potential of MOHEFT for a bi-objective scheduling problem that optimizes makespan and economic cost in a Cloud-based computing scenario. We compare MOHEFT with two state-of-the-art approaches using different synthetic and real-world workflows: the classical HEFT algorithm used in single-objective scheduling and the SPEA2* genetic algorithm used for multi-objective optimisation problems.