Miracle-dz/UniFAR-FTUs huggingface dataset:
Mast cells modulate transport of CD23/IgE/antigen complex across human intestinal epithelial barrier

Background: Food allergy and chronic intestinal inflammation are common in western countries. The complex of antigen/IgE is taken up into the body from the gut lumen with the aid of epithelial cell-derived CD23 (low affinity IgE receptor II) that plays an important role in the pathogenesis of intestinal allergy. This study aimed to elucidate the role of mast cell on modulation of antigen/IgE complex transport across intestinal epithelial barrier. Methods: Human intestinal epithelial cell line HT29 cell monolayer was used as a study platform. Transepithelial electric resistance (TER) and permeability to ovalbumin (OVA) were used as the markers of intestinal epithelial barrier function that were recorded in response to the stimulation of mast cell-derived chemical mediators. Results: Conditioned media from naïve mast cell line HMC-1 cells or monocyte cell line THP-1 cells significantly upregulated the expression of CD23 and increased the antigen transport across the epithelium. Treatment with stem cell factor (SCF), nerve growth factor (NGF), retinoic acid (RA) or dimethyl sulphoxide (DMSO) enhanced CD23 expression in HT29 cells. Conditioned media from SCF, NGF or RA-treated HMC-1 cells, and SCF, NGF, DMSO or RA-treated THP-1 cells enhanced immune complex transport via enhancing the expression of the CD23 in HT29 cells and the release of inflammatory mediator TNF-α. Nuclear factor kappa B inhibitor, tryptase and TNF-α inhibited the increase in CD23 in HT29 cells and prevents the enhancement of epithelial barrier permeability. Conclusions: Mast cells play an important role in modulating the intestinal CD23 expression and the transport of antigen/IgE/CD23 complex across epithelial barrier. (Tu YH, Oluwole C, Struiksma S, Perdue MH, Yang PC. Mast cells modulate transport of CD23/IgE/antigen complex across human intestinal epithelial barrier.
Genetic modifiers of folate, vitamin B-12, and homocysteine status in a cross-sectional study of the Canadian population.

BACKGROUND Genetic variation can cause variable responses to environmental stimuli. A number of single-nucleotide polymorphisms (SNPs) have been associated with B vitamin status or chronic diseases related to vitamin B-12 and folate metabolism. OBJECTIVE Our objective was to identify associations between common SNPs in genes related to folate and vitamin B-12 metabolism or associated with B vitamin-related chronic diseases and biomarkers of nutrient status in a population exposed to folic acid fortification. DESIGN A panel of 116 SNPs was sequenced by using the Sequenom iPLEX Gold platform in a sample of 3114 adults aged 20-79 y from the Canadian Health Measures Survey, cycle 1. Associations between these SNPs and red blood cell (RBC) folate, serum vitamin B-12, and plasma total homocysteine were determined. RESULTS Twenty-one SNPs and 6 haplotype blocks were associated with RBC folate, serum vitamin B-12, and/or plasma homocysteine concentrations. Vitamin status was associated mainly with SNPs in genes directly involved in vitamin absorption/uptake (CUBN, CD320), transport (TCN1, TCN2), or metabolism (BHMT2, CBS, MTHFR, MUT, SHMT1). Other SNPs included those in the DNMT2, DPEP1, FUT2, NOX4, and PON1 genes. CONCLUSIONS We identified novel associations between SNPs in CD320 and DNMT2, which had been previously associated with neural tube defects, and vitamin B-12 status, as well as between SNPs in SHMT1, which had been previously associated with colorectal cancer and cardiovascular disease risk, and RBC folate status. These novel associations provide a plausible metabolic rationale for the association of these SNPs with B vitamin-related diseases. We also observed a novel association between an SNP in CUBN with RBC folate and confirmed the association of a number of SNPs with B vitamin status in this large cross-sectional study.
Engaging in cultural activities compensates for educational differences in cognitive abilities

ABSTRACT The goal of the current project was to examine whether engagement in intellectual/cultural activities explains the long-term effects of education on cognitive abilities throughout adulthood, and whether it compensates for educational differences in cognitive abilities throughout adulthood. Participants between 18 and 96 years of age completed a comprehensive questionnaire about intellectual/cultural activities that they participated in and performed a wide variety of cognitive tests. There were no mediation effects of engagement in intellectual/cultural activities on the relationship between education and cognitive functioning. In contrast, engagement in intellectual/cultural activities was found to moderate the relations between education and the level of fluid ability, working memory, speed of processing, and episodic memory. Findings suggest that the risk of cognitive decline in people with less education can be reduced via engagement in intellectual and cultural activities throughout adulthood.
Video data management and information retrieval

In this chapter, we present a basic introduction to two very important areas of research in the domain of Information Technology, namely, video data management and video information retrieval. Both of these areas need additional research efforts to seek solutions to many unresolved problems for efficient data management and information retrieval. We discuss those issues and relevant works done so far in these two fields. INTRODUCTION An enormous amount of video data is being generated these days all over the world. This requires efficient and effective mechanisms to store, access, and retrieve these data. But the technology developed to date to handle those issues is far from the level of maturity required. Video data, as we know, would contain image, audio, graphical and textual data. The first problem is the efficient organization of raw video data available from various sources. There has to be proper consistency in data in the sense that data are to be stored in a standard format for access and retrieval. Then comes the issue of compressing the data to reduce the storage space required, since the data could be really voluminous. Also, various features of video data have to be extracted from low-level features like shape, color, texture, and spatial relations and stored efficiently for access. 701 E. Chocolate Avenue, Suite 200, Hershey PA 17033-1240, USA Tel: 717/533-8845; Fax 717/533-8661; URL-http://www.irm-press.com IRM PRESS This chapter appears in the book, Video Data Management and Information Retrieval by Sagarmay Deb. Copyright © 2005, IRM Press, an imprint of Idea Group Inc. Copying or distributing in print or electronic forms without written permission of Idea Group Inc. is prohibited.
White matter degeneration profile in the cognitive cortico‐subcortical tracts in Parkinson's disease

Background: In Parkinson's disease cognitive impairment is an early nonmotor feature, but it is still unclear why some patients are able to maintain their cognitive performance at normal levels, as quantified by neuropsychological tests, whereas others cannot. The objectives of this study were to perform a cross‐sectional study and analyze the white matter changes in the cognitive and motor bundles in patients with Parkinson's disease.
On the mobility and manipulability of general multiple limb robots

In this paper, the analysis of the differential kinematics and manipulability measures of robotic systems comprised of multiple cooperating limbs is considered. The goals of this study can be articulated in four points: 1) to enumerate the degrees of freedom of the manipulation system; 2) to describe analytically all possible first-order differential motions of the system at a given configuration; 3) to evaluate in the velocity domain the functionality of a manipulation system, with respect to the task it is required to perform; and 4) to calculate the bounds for the velocities achievable by the system, given bounds on the capabilities of joint actuators. The assumptions made on the robotic system are quite general, so that many complex devices (e.g., dextrous hands, legged vehicles, whole-arm manipulators, etc.) can be dealt with in a unified and convenient framework. >
Lumican is increased in experimental and clinical heart failure, and its production by cardiac fibroblasts is induced by mechanical and proinflammatory stimuli

During progression to heart failure (HF), myocardial extracellular matrix (ECM) alterations and tissue inflammation are central. Lumican is an ECM‐localized proteoglycan associated with inflammatory conditions and known to bind collagens. We hypothesized that lumican plays a role in the dynamic alterations in cardiac ECM during development of HF. Thus, we examined left ventricular cardiac lumican in a mouse model of pressure overload and in HF patients, and investigated expression, regulation and effects of increased lumican in cardiac fibroblasts. After 4 weeks of aortic banding, mice were divided into groups of hypertrophy (AB) and HF (ABHF) based on lung weight and left atrial diameter. Sham‐operated mice were used as controls. Accordingly, cardiac lumican mRNA and protein levels were increased in mice with ABHF. Similarly, cardiac biopsies from patients with end‐stage HF revealed increased lumican mRNA and protein levels compared with control hearts. In vitro, mechanical stretch and the proinflammatory cytokine interleukin‐1β increased lumican mRNA as well as secreted lumican protein from cardiac fibroblasts. Stimulation with recombinant glycosylated lumican increased collagen type I alpha 2, lysyl oxidase and transforming growth factor‐β1 mRNA, which was attenuated by costimulation with an inhibitor of the proinflammatory transcription factor NFκB. Furthermore, lumican increased the levels of the dimeric form of collagen type I, decreased the activity of the collagen‐degrading enzyme matrix metalloproteinase‐9 and increased the phosphorylation of fibrosis‐inducing SMAD3. In conclusion, cardiac lumican is increased in experimental and clinical HF. Inflammation and mechanical stimuli induce lumican production by cardiac fibroblasts and increased lumican altered molecules important for cardiac remodeling and fibrosis in cardiac fibroblasts, indicating a role in HF development.
Self-determination theory and motivational interviewing interventions for type 2 diabetes prevention and treatment: A systematic review

Treatment of those with obesity, prediabetes, and type 2 diabetes often yields initial health improvements, but gains erode over time. A systematic search of self-determination theory and motivational interviewing papers for the above populations was conducted, yielding 54 publications and 42 independent samples. Interventions to treat overweight and obesity (n = 15), prediabetes (n = 4), and type 2 diabetes (n = 23) are summarized and evaluated using the Quality Rating Scale. While the results of these studies are mixed, the majority of the interventions resulted in health benefits. Suggestions for future research are discussed.
Agraph convolution-based classification model for identifying anticancer metabolites from traditional vietnamese herbal medicine database

Vietnam has been well known as a source of abundantly diverse herbal medicines for thousands of years, which serves a variety of purposes in drug development in attempts to address health issues, such as cancer. As claimed by a chemoinformatics-related principle that structurally similar chemical compounds will very likely have similar biological activity, this study employs molecular graph convolution, a machine learning architecture for extracting features from small molecules as undirected graphs, to predict anticancer ability of Vietnamese herbal medicines based on their metabolites' structures. In addition to molecular graph convolution, extended connectivity fingerprint (ECFP), a traditional featurizer for exploiting details of molecules, is also performed in order to make performance comparison. Finally, we successfully constructed a graph convolution-based neural network with high predictive accuracy on both training and validation set, suggesting that the model is reliable in detecting anticancer activity.
Sketch Based Image Deformation

We present an image editing tool that allows to deform and composite image regions using an intuitive sketch-based interface. Users simply draw the outline of the source image region and sketch a new boundary shape onto the location where this region is to be pasted. The deformation optimizes a shape distortion energy, and we use Poisson cloning for subsequent compositing. Since the correspondence between the source and target boundary curves is not known a priori, we propose an alternating optimization process that interleaves minimization of the deformation energy w.r. t. the image region interior and the mapping between the boundary curves, thus automatically determining the boundary correspondence and deforming the image at the same time. Thanks to the particular design of the deformation energy, its gradient can be efficiently computed, making the entire image editing framework interactive and convenient for practical use.
Rigorous simulation of EUV mask pellicle

Pellicles that satisfy transmission, emission, thermal, and mechanical requirements are highly desired for EUV high volume manufacturing. We present here the capability of integrating pellicles in the full flow of rigorous EUV lithography simulations. This platform allows us to investigate new coherence effects in EUV lithography when pellicle is used. Critical dimension uniformity and throughput loss due to pellicle defects and add-on particles are also analyzed. Our study provides theoretical insights into pellicle development and facilitates pellicle insertion in EUV lithography.
A Brief Comparison of Community Detection Algorithms over Semantic Web Data

Community detection is a task responsible for categorizing nodes of a graph into groups that share similar features or properties (e.g. topological structure or node attributes). This is an important task in fields such as social network analysis or pattern recognition that span a large and varied amount of information hiding relations with knowledge. In this sense, an initiative that seeks to extract knowledge from data is the Semantic Web, whose primary goal is to represent Web data into a graph in order to discover facts and relations. In this paper, we developed a strategy to apply community detection algorithms over Semantic Web data graphs. For this purpose, five algorithms were tested to identify groups from a dataset retrieved from the DBpedia knowledge base containing more than 45 thousand nodes and almost 500 thousand edges in the domain of movies. Clustering quality was evaluated by using the modularity measure and the features of the best communities were analyzed.
The Q2 Mitochondrial Haplogroup in Oceania

Many details surrounding the origins of the peoples of Oceania remain to be resolved, and as a step towards this we report seven new complete mitochondrial genomes from the Q2a haplogroup, from Papua New Guinea, Fiji and Kiribati. This brings the total to eleven Q2 genomes now available. The Q haplogroup (that includes Q2) is an old and diverse lineage in Near Oceania, and is reasonably common; within our sample set of 430, 97 are of the Q haplogroup. However, only 8 are Q2, and we report 7 here. The tree with all complete Q genomes is proven to be minimal. The dating estimate for the origin of Q2 (around 35 Kya) reinforces the understanding that humans have been in Near Oceania for tens of thousands of years; nevertheless the Polynesian maternal haplogroups remain distinctive. A major focus now, with regard to Polynesian ancestry, is to address the differences and timing of the ‘Melanesian’ contribution to the maternal and paternal lineages as people moved further and further into Remote Oceania. Input from other fields such as anthropology, history and linguistics is required for a better understanding and interpretation of the genetic data.
Cross-cultural adaptation and content and semantic validation of the Difficult Intravenous Access Score for pediatric use in Brazil 1

ABSTRACT Objective: present the cross-cultural adaptation and content and semantic validation of the Difficult Intravenous Access Score for current use in Brazil. Method: cross-cultural adaptation and validation study, structured in six phases: initial translation, synthesis of translations, back-translation, assessment of documents by expert committee of specialized judges, pretest and presentation of the documents to the expert judges and to the author of the original instrument. Twenty health professionals were randomly recruited from a public hospital in the South of Brazil, working in pediatrics, in order to assess the agreement level with the variables in the instrument. In addition, a convenience sample of 30 pediatric patients was selected for the face validation of the same instrument. Cronbach’s alpha coefficient, simple and percentage frequencies, the Shapiro-Wilk and Fisher’s exact tests were used for the data analysis and reliability measures. Results: the cross-cultural adaptation phases were executed with totally clear translated variables, demonstrating satisfactory results in the content and semantic validation process. Conclusions: the Difficult Intravenous Access Score was adapted and its content and semantics were validated. External clinical validity, measuring equivalence and reproducibility analyses are needed.
Ambiguous genitalia: two decades of experience

Background and Objectives: Ambiguous genitalia is a complex, medical and social emergency. The aim of this study is to present our experience over two decades, focusing on the pattern and clinical presentation. Design and Setting: A retrospective study conducted in the pediatric endocrine clinic at a university hospital Saudi Arabia during the period 1989-2008. Patients and Methods: Medical records of children with ambiguous genitalia were reviewed and the genitalia described. Results: Of the 81 children with ambiguous genitalia, 53 (65.4%) patients were genetically females (46XX), with congenital adrenal hyperplasia being the common cause in 51 (96.5%) patients. Hyperpigmentation, variable degrees of salt wasting and a family history of a similar problem helped in diagnosis. Male genetic sex (46XY) was present in only 28 (34.6%) patients with a diversity of causes; multiple congenital anomalies in 9 (32.1%), local anorectal anomalies in 2 (7.1%), congenital adrenal hyperplasia (3-β-hydroxysteroid dehydrogenase deficiency) in 2 (7.14%), 5-α-reductase deficiency in 4 (14.28%), partial androgen insensitivity in 3 (10.7%), complete androgen insensitivity in 4 (14.28%), and hypogonadotrophin deficiency in 4 (14.3%). Twenty-five (47.2%) of females were wrongly assigned as males, where only two (7.1%) males were wrongly assigned as females. Conclusion: Ambiguous genitalia, currently termed disorders of sex development (DSD), is not uncommon in our community. Increased awareness, a detailed history, and a careful physical examination, coupled with appropriate laboratory and radiological investigations aid in early diagnosis and avoid serious sequelae.
Distribution Map

Understanding large software systems is a challenging task, and to support it many approaches have been developed. Often, the result of these approaches categorize existing entities into new groups or associates them with mutually exclusive properties. In this paper we present the distribution map as a generic technique to visualize and analyze this type of result. Our technique is based on the notion of focus, which shows whether a property is well-encapsulated or cross-cutting, and the notion of spread, which shows whether the property is present in several parts of the system. We present a basic visualization and complement it with measurements that quantify focus and spread. To validate our technique we show evidence of applying it on the result sets of different analysis approaches. As a conclusion we propose that the distribution map technique should belong to any reverse engineering toolkit
Coverage estimation for symbolic model checking

Although model checking is an exhaustive formal verification method, a bug can still escape detection if the erroneous behavior does not violate any verified property. We propose a coverage metric to estimate the "completeness" of a set of properties verified by model checking. A symbolic algorithm is presented to compute this metric for a subset of the CTL property specification language. It has the same order of computational complexity as a model checking algorithm. Our coverage estimator has been applied in the course of some real-world model checking projects. We uncovered several coverage holes including one that eventually led to the discovery of a bug that escaped the initial model checking effort.
Identification of the Chromophores Involved in Aggregation-dependent Energy Quenching of the Monomeric Photosystem II Antenna Protein Lhcb5*

Non-photochemical quenching (NPQ) of excess absorbed light energy is a fundamental process that regulates photosynthetic light harvesting in higher plants. Among several proposed NPQ mechanisms, aggregation-dependent quenching (ADQ) and charge transfer quenching have received the most attention. In vitro spectroscopic features of both mechanisms correlate with very similar signals detected in more intact systems and in vivo, where full NPQ can be observed. A major difference between the models is the proposed quenching site, which is predominantly the major trimeric light-harvesting complex II in ADQ and exclusively monomeric Lhcb proteins in charge transfer quenching. Here, we studied ADQ in both monomeric and trimeric Lhcb proteins, investigating the activities of each antenna subunit and their dependence on zeaxanthin, a major modulator of NPQ in vivo. We found that monomeric Lhcb proteins undergo stronger quenching than light-harvesting complex II during aggregation and that this is enhanced by binding to zeaxanthin, as occurs during NPQ in vivo. Finally, the analysis of Lhcb5 mutants showed that chlorophyll 612 and 613, in close contact with lutein bound at site L1, are important facilitators of ADQ.
Biodegradable, polymer encapsulated, metal oxide particles for MRI‐based cell tracking

Metallic particles have shaped the use of magnetic resonance imaging (MRI) for molecular and cellular imaging. Although these particles have generally been developed for extracellular residence, either as blood pool contrast agents or targeted contrast agents, the coopted use of these particles for intracellular labeling has grown over the last 20 years. Coincident with this growth has been the development of metal oxide particles specifically intended for intracellular residence, and innovations in the nature of the metallic core. One promising nanoparticle construct for MRI‐based cell tracking is polymer encapsulated metal oxide nanoparticles. Rather than a polymer coated metal oxide nanocrystal of the core: shell type, polymer encapsulated metal oxide nanoparticles cluster many nanocrystals within a polymer matrix. This nanoparticle composite more efficiently packages inorganic nanocrystals, affording the ability to label cells with more inorganic material. Further, for magnetic nanocrystals, the clustering of multiple magnetic nanocrystals within a single nanoparticle enhances r2 and r2* relaxivity. Methods for fabricating polymer encapsulated metal oxide nanoparticles are facile, yielding both varied compositions and synthetic approaches. This review presents a brief history into the use of metal oxide particles for MRI‐based cell tracking and details the development and use of biodegradable, polymer encapsulated, metal oxide nanoparticles and microparticles for MRI‐based cell tracking. Magn Reson Med 73:376–389, 2015. © 2014 Wiley Periodicals, Inc.