Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptional Regulation of Proteoglycans and Glycosaminoglycan Chain-synthesizing Glycosyltransferases by UV Irradiation in Cultured Human Dermal Fibroblasts

Various kinds of glycosaminoglycans (GAGs) and proteoglycans (PGs) have been known to be involved in structural and space-filling functions, as well as many physiological regulations in skin. To investigate ultraviolet (UV) radiation-mediated regulation of GAGs and PGs in cultured human dermal fibroblasts, transcriptional changes of many types of PGs and GAG chain-synthesizing enzymes at 18 hr after 75 mJ/cm2 of UV irradiation were examined using quantitative real-time polymerase chain reaction methods. Hyaluronic acid synthase (HAS)-1, -2, and -3 and hyaluronidase-2 mRNA expressions were significantly increased by UV irradiation. Expressions of lumican, fibromodulin, osteoglycin, syndecan-2, perlecan, agrin, versican, decorin, and biglycan were significantly decreased by UV irradiation, while syndecan-1 was increased. Expressions of GAG chain-synthesizing glycosyltransferases, xylosyltransferase-1, β1,3-glucuronyltransferase-1, β1,4-galactosyltransferase-2, -4, exostosin-1, chondroitin polymerizing factor, and chondroitin sulfate synthase-3 were significantly reduced, whereas those of β1,3-galactosyltransferase-6, β1,4-galactosyltransferase-3, -7, β-1,3-N-acetylglucosaminyltran sferase-2, and -7 were increased by UV irradiation. Heparanase-1 mRNA expression was increased, but that of heparanase-2 was reduced by UV irradiation. Time-course investigation of representative genes showed consistent results. In conclusion, UV irradiation may increase hyaluronic acid production through HAS induction, and decrease other GAG productions through downregulation of PG core proteins and GAG chain-synthesizing glycosyltransferases in cultured human dermal fibroblasts.
Investigating characteristics of a concentrated-winding interior permanent magnet synchronous machine for sensorless direct torque control

This paper investigates characteristics of a fractional-slot, concentrated-winding (FSCW) Interior Permanent Magnet Synchronous Machines (IPMSM) under sensorless Direct Torque Control (DTC). The FSCW IPMSM is being developed vigorously in recent years because of its high-power density, high efficiency, wide field-weakening capability, and high fault tolerance compared to the distributed-wound IPMSMs. The major disadvantage of concentrated winding is often cited to be its non-sinusoidal stator MMF. However, using appropriate combination of slots and poles, nearly sinusoidal EMF and very low cogging torque can be achieved. Although steady-state performance such as efficiency and constant power speed range of this type of PM machines have recently been published, dynamic performances have yet not been reported. The sensorless DTC schemes, which rely on the machine model, were applied to a prototype a 14-pole/ 18-slot, double layer concentrated-wound IPM machine. The model for distributed wound IPMSM was used for the control. This paper investigates the appropriate stationary reference frame of the FSCW IPMSM motors which should be appropriately shifted because of the harmonic and sub-harmonic components in the stator mmf of the concentrated winding machine compared with the distributed windings (DW) machine. The experimental results on the concentrated winding IPM machine confirmed the effectiveness of the proposed adjustment of the stationary reference frame according to the investigation of the difference between concentrated and distributed windings of an IPMSM.
Higher-order modules and the phase distinction

In earlier work, we used a typed function calculus, XML, with dependent types to analyze several aspects of the Standard ML type system. In this paper, we introduce a refinement of XML with a clear compile-time/run-time phase distinction, and a direct compile-time type checking algorithm. The calculus uses a finer separation of types into universes than XML and enforces the phase distinction using a nonstandard equational theory for module and signature expressions. While unusual from a type-theoretic point of view, the nonstandard equational theory arises naturally from the well-known Grothendieck construction on an indexed category.
Long-term Sequelae of Childhood Bacterial Meningitis: An Underappreciated Problem

Background: Numerous sequelae have been noted in survivors of bacterial meningitis; however, few studies document sequelae for several years following a childhood episode of bacterial meningitis. In addition, studies generally focus on the more commonly found sequelae. To review the known information and highlight this gap, this article presents a comprehensive literature review of the long-term (≥5 years of follow-up) sequelae of childhood bacterial meningitis. Methods: A systematic literature search was conducted between December 2009 and February 2010. English-language articles published between January 1970 and January 2010 were selected for screening. Articles were included if the subjects were between the ages of 1 month and <18 years at the time of diagnoses of meningitis. Results: A total of 1433 children who were survivors of childhood bacterial meningitis were evaluated for sequelae after the time of discharge. Of these children, 705 (49.2%) were reported to have 1 or more long-term sequelae. A majority of reported sequelae were behavioral and/or intellectual disorders (n = 455, 45.0%). Hearing changes accounted for 6.7% (n = 68) of sequelae and gross neurologic deficits accounted for 14.3% (n = 145). Discussion: A majority of childhood bacterial meningitis survivors with long-term sequelae that are documented in the literature have academic and behavioral limitations. While neurologic deficits may resolve over time, subtle behavioral deficits may not be appreciated initially and may continue to affect survivors for many years. Further studies are needed to quantify the true societal and economic burden of long-term sequelae as well as fully understand the breadth of types of sequelae that survivors experience.
Comparison of Risk-scoring Systems in Predicting Symptomatic Intracerebral Hemorrhage After Intravenous Thrombolysis

Background and Purpose— Various risk score models have been developed to predict symptomatic intracerebral hemorrhage (SICH) after intravenous thrombolysis for acute ischemic stroke. In this study, we aimed to determine the prediction performance of these risk scores in a Taiwanese population Methods— Prospectively collected data from 4 hospitals were used to calculate probability of SICH with the scores developed by Cucchiara et al, the Hemorrhage After Thrombolysis (HAT) score, the Safe Implementation of Thrombolysis in Stroke-SICH risk score, the Glucose Race Age Sex Pressure Stroke Severity score, and the Stroke Prognostication using Age and National Institutes of Health Stroke Scale-100 index. We used logistic regression to evaluate the effectiveness of each risk model in predicting SICH and the c statistic to assess performance. Results— A total of 548 patients were included. The rates of SICH were 7.3% by the National Institute of Neurological Diseases and Stroke definition, 5.3% by the European-Australasian Cooperative Acute Stroke Study II definition, and 3.5% by the Safe Implementation of Thrombolysis in Stroke-Monitoring Study definition. The Cucchiara score, the HAT score, and the Safe Implementation of Thrombolysis in Stroke-SICH risk score were significant predictors of SICH for all 3 definitions, whereas the Glucose Race Age Sex Pressure Stroke Severity score and the Stroke Prognostication using Age and National Institutes of Health Stroke Scale-100 index predicted well only for 1 or 2 definitions of SICH. The c statistic was highest for the HAT score (range, 0.69–0.73) across the definitions of SICH. Conclusions— The Cucchiara score, the HAT score, and the Safe Implementation of Thrombolysis in Stroke-SICH risk score predicted SICH reasonably well regardless of which SICH definition was used. However, only the HAT score had an acceptable discriminatory ability.
Endothelial cell–Matrix interactions

Dynamic interactions between endothelial cells and components of their surrounding extracellular matrix are necessary for the invasion, migration, and survival of endothelial cells during angiogenesis. These interactions are mediated by matrix receptors that initiate intracellular signaling cascades in response to binding to specific extracellular matrix molecules. The interactions between endothelial cells and their environment are also modulated by enzymes that degrade different matrix components and thus enable endothelial invasion. Recent reports on gene targeting in mice have confirmed the role of two classes of matrix receptors, integrins and cell surface heparan sulfate proteoglycans, and a group of matrix degrading proteolytic enzymes, matrix metalloproteinases, in angiogenesis. The significance of endothelial cell–matrix interactions is further supported by several ongoing clinical trials that analyze the effects of drugs blocking this interaction on angiogenesis‐dependent growth of human tumors. Microsc. Res. Tech. 60:13–22, 2003. © 2002 Wiley‐Liss, Inc.
A General Phase Transition Model for Vehicular Traffic

An extension of the Colombo phase transition model is proposed. The congestion phase is described by a two-dimensional zone defined around an equilibrium flux known as the classical fundamental diagram. General criteria to build such a set-valued fundamental diagram are enumerated, and instantiated on several equilibrium fluxes with different concavity properties. The solution of the Riemann problem in the presence of phase transitions is obtained through the construction of a Riemann solver, which enables the definition of the solution of the Cauchy problem using wavefront tracking. The free-flow phase is described using a Newell-Daganzo fundamental diagram, which allows for a more tractable definition of phase transition compared to the original Colombo phase transition model. The accuracy of the numerical solution obtained by a modified Godunov scheme is assessed on benchmark scenarios for the different flux functions constructed.
Gerotranscendence: Components and Spiritual Roots in the Second Half of Life

According to gerotranscendence theory (Tornstam, 1989), aging persons gradually develop a shift in meta-perspective, from a materialistic and rational vision to a more cosmic and transcendent one. The present study examined the structure of the construct of gerotranscendence, age differences in gerotranscendence, and relations between gerotranscendence and culturally determined meaning in life and death factors, such as levels of spirituality, religious beliefs, moral judgment, and death attitudes. Participants were 467 adults between 17 and 91 years old. Factor analysis of the Gerotranscendence Scale yielded three subscales, Transcendent Connection, Anxiety and Uncertainty, and Active Involvement. Transcendent Connection - the core component of gerotranscendence - was only weakly related to age. However, Transcendent Connection was positively related to spiritual views and practices, relativistic orientation to religious beliefs, moral consistency, higher stages of moral thinking, and negatively related to avoidance of death. Patterns of correlations with the scores on the other two scales were also explored. Together, the findings suggested that individuals' development with regard to issues of spirituality, religiosity, morality, and death attitudes is more fundamental for their development toward "gero"-transcendence than the natural process of aging.
Recursive Feature Selection with Significant Variables of Support Vectors

The development of DNA microarray makes researchers screen thousands of genes simultaneously and it also helps determine high- and low-expression level genes in normal and disease tissues. Selecting relevant genes for cancer classification is an important issue. Most of the gene selection methods use univariate ranking criteria and arbitrarily choose a threshold to choose genes. However, the parameter setting may not be compatible to the selected classification algorithms. In this paper, we propose a new gene selection method (SVM-t) based on the use of t-statistics embedded in support vector machine. We compared the performance to two similar SVM-based methods: SVM recursive feature elimination (SVMRFE) and recursive support vector machine (RSVM). The three methods were compared based on extensive simulation experiments and analyses of two published microarray datasets. In the simulation experiments, we found that the proposed method is more robust in selecting informative genes than SVMRFE and RSVM and capable to attain good classification performance when the variations of informative and noninformative genes are different. In the analysis of two microarray datasets, the proposed method yields better performance in identifying fewer genes with good prediction accuracy, compared to SVMRFE and RSVM.
The Impact of Monetary Policy and Exchange Rate Shocks in Poland: Evidence from a Time-Varying VAR

This paper follows the Bayesian time-varying VAR approach with stochastic volatility developed by Primiceri (2005), to analyse whether the reaction of output and prices to interest rate and exchange rate shocks has changed across time (1996-2012) in the Polish economy. The empirical findings show that: (1) output appears more responsive to an interest rate shock at the beginning of our sample. Since 2000, absorbing this shock has become less costly in terms of output, notwithstanding some reversal since the beginning of the global financial crisis. The exchange rate shock also has a time-varying effect on output. From 1996 to 2000, output seems to decline, whereas for periods between 2000 and 2008 it has a positive significant effect. (2) Consumer prices appear more responsive to an interest rate shock during the first half of our sample, when Poland experienced high inflation. The impact of an exchange rate shock on prices seems to slightly decrease across time.
Towards Recovering the Software Architecture of Microservice-Based Systems

Today the microservice architectural style is being adopted by many key technological players such as Netflix, Amazon, The Guardian. A microservice architecture is composed of a large set of small services, each running in its own process and communicating with lightweight mechanisms (often via REST APIs). If on one side having a large set of independently developed services helps in terms of developer productivity, scalability, maintainability, on the other side it is very difficult to have a clear understanding of the overall architecture of a microservice-based software system, specially when the deployment and operation of the involved microservices evolves at run-time. In this paper we present MicroART, an architecture recovery approach for microservice-based systems. By using Model-Driven Engineering techniques, we leverage a suitably defined domain-specific language for representing the key aspects of the architecture of a microservice-based system and provide a tool-chain for automatically extracting architecture models of the system. The only inputs of MicroART are: (i) a GitHub repository containing the source code of the system and (ii) a reference to the container engine managing it. We validated MicroART on a publicly available benchmark system, with promising results.
Designing an information retrieval system for the STT/SC

The Santa Catarina State Telemedicine and Telehealth System - STT/SC stores well over 2 million examinations and every month about 20 thousand new imaging exams are sent to the system database. As a significant part of the findings associated to these medical data are stored as text documents, the precise extraction of information is a difficult task. In the healthcare domain it is common to find different terms, some of them appearing as composed expressions, used to represent the same concept, whereas the existence of simple modifiers can turn an expression into another, different concept. This work presents an information retrieval architecture developed for the STT/SC. It consists in a module integrated into the STT/SC and was developed in order to support both experienced and inexperienced users to perform queries. Experiments were performed to evaluate the accuracy of the proposed system in real situations. Results show that the search can be performed more much faster and with acceptable precision.
Further tests of the association between schizophrenia and single nucleotide polymorphism markers at the catechol-O-methyltransferase locus in an Askenazi Jewish population using microsatellite markers

Association studies are now primarily being conducted with single nucleotide polymorphisms because they are present everywhere in the genome and can be genotyped in “high throughput” formats. Microsatellite markers have a higher degree of polymorphism than single nucleotide polymorphisms and have been widely used in both linkage and association studies of disease. Polymorphic microsatellite markers with several alleles can readily detect linkage disequilibrium but at any given locus there may be differences between single nucleotide polymorphisms and microsatellites in their power to detect linkage disequilibrium because of the evolutionary history of the locus, especially the rate at which both the single nucleotide polymorphisms and microsatellite polymorphisms have mutated and the number of disease mutations and their history. In the current study, we examined the efficiency of microsatellite markers in association analysis by looking at all existent microsatellite markers in the catechol-O-methyltransferase gene region and by genotyping these microsatellites in a large cohort of schizophrenia patients and healthy controls, a subset of a sample where catechol-O-methyltransferase and schizophrenia were found to be associated. We also estimated the levels of linkage disequilibrium between these microsatellites and the previously reported single nucleotide polymorphisms (within the catechol-O-methyltransferase gene) found to be associated with schizophrenia. A modest allelic association of P=0.041 was found between schizophrenia and the microsatellite marker D22S944, which was not significant, however, when corrected for all microsatellites tested. Nevertheless, significant linkage disequilibrium was found between this marker and the three single nucleotide polymorphisms within the catechol-O-methyltransferase gene that displayed association with the disease in the previously published research on this sample. Significant linkage disequilibrium was also observed between microsatellites up to approximately 300 kb distant from those single nucleotide polymorphisms. Although significant, the extent of linkage disequilibrium in terms of r2 was small (in the order of 0.01).
A Generic Domain Configurable Planner Using Htn For Autonomous Multi-Agent Space System

Automated planning has been applied to numerous fields such as computer games, industrial robotics and even highprofile missions like planning and scheduling activities for Martian rovers. A current trend among the researchers is to apply automated planning in multiple space systems that work together in a coordinated fashion so as to attain highly complex mission goals. Even though automated planning and scheduling algorithms are mature in industrial scenarios and robotics, little consideration has been given to multiple-agent space applications. In this paper, we describe the development of a domain configurable planner which can be used for different space mission comprising of multiple systems i.e. satellites or rovers. The multiagent planning systems uses agent based modeling techniques, hierarchical task network (HTN) planning and a mixed approach from centralized and distributed planning. The initial results from the prototype planner are also discussed.
Exact universal amplitude ratios for two-dimensional Ising models and a quantum spin chain.

Let f(N) and xi(-1)(N) represent, respectively, the free energy per spin and the inverse spin-spin correlation length of the critical Ising model on a N x infinity lattice, with f(N)-->f(infinity) as N-->infinity. We obtain analytic expressions for a(k) and b(k) in the expansions N( f(N)-f(infinity)) = SUM (k = 1)(infinity)a(k)/N(2k-1) and xi(-1)(N) = SUM (k = 1)(infinity)b(k)/N(2k-1) for square, honeycomb, and plane-triangular lattices, and find that b(k)/a(k) = (2(2k)-1)/(2(2k-1)-1) for all of these lattices, i.e., the amplitude ratio b(k)/a(k) is universal. We also obtain similar results for a critical quantum spin chain and find that such results could be understood from a perturbated conformal field theory.
Identification of Paintings in Camera-Phone Images

This paper presents the algorithm developed, for the EE 368 course project, to identify paintings in query images taken with a camera-phone in the European Gallery of the Cantor Arts Center. The image processing algorithm first extracts the painting of interest, in the center of the photo. It uses edge detection in saturation space, followed by iterative Radon transforms and region removal to find the smallest bounding box enclosing the painting. Using the smallest bounding box, the algorithm computes and performs a projective transform to extract and rectify the painting in the query image. Feature identification is performed on the rectified image using extrema in a difference-of-Gaussians pyramid. At each resulting feature location, feature descriptors are computed using histograms of the gradient distribution among neighboring pixels, without rotation. The resulting features are correlated with a feature database of paintings with aspect ratios similar to that of the painting in the query image. A program to produce the feature database was also developed. This program selects a small set of unique, but repeatable, features from the many available for each painting in the gallery. The image processing algorithm correctly identifies paintings in all 99 training images provided by the EE368 teaching staff. It performs well on the additional 93 test images taken by the group, in difficult configurations, to stress test the algorithm. Details and sensitivities of the algorithm are discussed.
RNApdbee—a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs

In RNA structural biology and bioinformatics an access to correct RNA secondary structure and its proper representation is of crucial importance. This is true especially in the field of secondary and 3D RNA structure prediction. Here, we introduce RNApdbee-a new tool that allows to extract RNA secondary structure from the pdb file, and presents it in both textual and graphical form. RNApdbee supports processing of knotted and unknotted structures of large RNAs, also within protein complexes. The method works not only for first but also for high order pseudoknots, and gives an information about canonical and non-canonical base pairs. A combination of these features is unique among existing applications for RNA structure analysis. Additionally, a function of converting between the text notations, i.e. BPSEQ, CT and extended dot-bracket, is provided. In order to facilitate a more comprehensive study, the webserver integrates the functionality of RNAView, MC-Annotate and 3DNA/DSSR, being the most common tools used for automated identification and classification of RNA base pairs. RNApdbee is implemented as a publicly available webserver with an intuitive interface and can be freely accessed at http://rnapdbee.cs. put.poznan. pl/.