Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptional Regulation of Human CYP2A13 Expression in the Respiratory Tract by CCAAT/Enhancer Binding Protein and Epigenetic Modulation

CYP2A13, which is highly active in the metabolic activation of tobacco-specific nitrosamines, is selectively expressed in the respiratory tract, in which it is believed to play an important role in chemical carcinogenesis. The aim of this study was to determine the basis for tissue-specific regulation of CYP2A13 gene expression. We have shown that expression of CYP2A3, the rat homolog of CYP2A13, is regulated by nuclear factor I (NFI) in a tissue-specific manner. In the present study, we found that the transcriptional regulation of human CYP2A13 gene involves CCAAT/enhancer binding protein (C/EBP) transcription factors instead of NFI. DNase I footprinting and gel-shift assays with human lung nuclear extract identified two DNA elements bound by C/EBP. Reporter gene assays using a 216-base pair CYP2A13 promoter fragment confirmed the activation of CYP2A13 by transfected C/EBP factors, and results from chromatin immunoprecipitation assays indicated that C/EBP is associated with CYP2A13 promoter in vivo in the olfactory mucosa of CYP2A13-transgenic mice. In NCI-H441 human lung cancer cells, we discovered that CYP2A13 expression can be induced by a combined treatment with 5-aza-2′-deoxycytosine, a DNA demethylation agent, and trichostatin, a histone deacetylation inhibitor. In 5-aza-2′-deoxycytosine/trichostatin-treated NCI-H441 cells, overexpression of C/EBPδ, a lung-enriched C/EBP, led to additional increases in CYP2A13 expression, whereas C/EBPδ knockdown by small interference RNA suppressed CYP2A13 expression, findings that confirm a role for C/EBP in CYP2A13 regulation. Our findings pave the way for further studies of the regulation of the CYP2A13 gene, particularly the gene's potential suppression by airway inflammation, and the role of epigenetic modulation in the gene's tissue-selective expression.
Remendable Polymeric Materials Using Reversible Covalent Bonds

Abstract : Materials that can recover mechanical properties following failure offer increased safety and service life. Moreover, successful development of such systems would reduce factors of safety required in design thus reducing weight. Two approaches for healing polymer networks have captured much attention. In one method, polymer networks are made to self-heal by adding particles filled with uncured resin. The resin held within the particles is released upon crack formation and cures to mend the damage. The other mechanism for healing relies on inherent reversibility of bonds found designed into polymer networks. Our approach to design self-healing composites combines advantages of healing via encapsulation and healing via reversible bonds. Incorporation of a healing agent allows for crack healing while maintaining the desirable physical and mechanical properties of the base thermoset. Reversible bonding of the healing agent provides the ability to crack heal cracks multiple times. We report on the development of two healing systems for epoxy-amine thermosets based on the thermoreversible Diels-Alder reaction of furan and maleimide. Both phenomena occur at room temperature and minimal pressure and significant load recovery is possible multiple times in a given location.
Clonal analysis of Streptococcus pneumoniae nonsusceptible to penicillin at day-care centers with index cases, in a region with low incidence of resistance: emergence of an invasive type 35B clone among carriers.

The nasopharyngeal carriage rate of potential respiratory pathogens was studied in 36 index children with a pneumococci nonsusceptible to penicillin (PNSP), in 595 healthy children, and in 123 personnel at 16 day-care centers (DCCs) with index cases in the Stockholm area, an urban area with a low incidence of antibiotic resistant pneumococci, during the winter of 1997-1998. The spread and clonality of PNSP, Haemophilus influenzae and Moraxella catarrhalis, were studied by analyzing antibiotic susceptibility and serotype, and for PSNP also by using pulsed-field electrophoresis (PFGE) and multilocus sequence typing (MLST). In contrast to the low carriage rate found among the adult contacts (2%), 40% of the children harbored pneumococci, of which 20% were PNSP. Nasopharyngeal colonization decreased with age. The 49 PNSP isolates consisted of 20 clones, of which 10 could be identified in more than one child attending the same or different DCCs. In five DCCs, we observed a spread of PNSP from the index case. A novel PNSP clone of type 35B, found to cause invasive disease in several states in the United States, was found to emerge among several carriers at two DCCs . A high proportion of PNSP isolates were multiresistant to antibiotics (34%), which has implications for treatment regimens, even in a country like Sweden where the proportion of PNSP currently is low (3-4%). One PNSP clone of type 9V found among the carriers, has been shown to cause invasive disease in Sweden as well as in other countries, suggesting that one reason for the occurrence of invasive PNSP clones may be their ability to colonize and spread among healthy carriers. Other internationally spread antibiotic resistant pneumococcal clones found were of types 9V, 19F, and 23F.
Exemplar-based pitch contour generation using DOP for syntactic tree decomposition

The generation of a pitch contour from linguistic information has long been recognised as a requirement for natural sounding speech synthesis. This paper investigates the use of an exemplar-based model for pitch contour generation. The main drawbacks of previous unit selection-based approaches for pitch contour generation is determining the size of the unit, and to guarantee that only prosodic and linguistically related units will be selected. The work presented in this paper overcomes these drawbacks by using only prosodic-syntactic correlated data, and a dynamic unit size model using data-oriented parsing. An AB comparison perceptual test showed 58% preference for the exemplar-based model, 25% for a HTS model, and 17% find both the same in terms of naturalness and pitch. In a MOS test, exemplar-based model achieved higher scores than that the HTS model achieved.
Can waist circumference identify children with the metabolic syndrome?

OBJECTIVE To determine in children the association between waist circumference (WC) and insulin resistance determined by homeostasis modeling (HOMA-IR) and proinsulinemia and components of the metabolic syndrome, including lipid profile and blood pressure (BP). METHODS Eighty-four students (40 boys) aged 6 to 13 years and matched for sex and age underwent anthropometric measurements; 40 were obese; 28, overweight; and 16, nonobese. Body mass index (BMI), WC, BP, and Tanner stage were determined. An oral glucose tolerance test, lipid profile, and insulin and proinsulin assays were performed. Children were classified as nonobese (BMI < 85th percentile), overweight (BMI, 85th-94th percentile), and obese (BMI > or = 95th percentile). RESULTS There was univariate association (P < .01) between WC and height (r = 0.73), BMI (r = 0.96), Tanner stage (r = 0.67), age (r = 0.56), systolic BP (r = 0.64), diastolic BP (r = 0.61), high-density lipoprotein cholesterol level (r = 0.45), triglyceride level (r = 0.28), proinsulin level (r = 0.59), and HOMA-IR (r = 0.59). Multiple linear regression analysis using HOMA-IR as the dependent variable showed that WC (beta coefficient = 0.050 [95% confidence interval, 0.028 to 0.073]; P = .001) and systolic BP (beta coefficient = 0.033 [95% confidence interval, 0.004 to 0.062]; P = .004) were significant independent predictors for insulin resistance adjusted for diastolic BP, height, BMI, acanthosis nigricans, and high-density lipoprotein cholesterol level. CONCLUSION Waist circumference is a predictor of insulin resistance syndrome in children and adolescents and could be included in clinical practice as a simple tool to help identify children at risk.
Post-irradiation chemical processing of DNA damage generates double-strand breaks in cells already engaged in repair

In cells exposed to ionizing radiation (IR), double-strand breaks (DSBs) form within clustered-damage sites from lesions disrupting the DNA sugar–phosphate backbone. It is commonly assumed that these DSBs form promptly and are immediately detected and processed by the cellular DNA damage response (DDR) apparatus. This assumption is questioned by the observation that after irradiation of naked DNA, a fraction of DSBs forms minutes to hours after exposure as a result of temperature dependent, chemical processing of labile sugar lesions. Excess DSBs also form when IR-exposed cells are processed at 50°C, but have been hitherto considered method-related artifact. Thus, it remains unknown whether DSBs actually develop in cells after IR exposure from chemically labile damage. Here, we show that irradiation of ‘naked’ or chromatin-organized mammalian DNA produces lesions, which evolve to DSBs and add to those promptly induced, after 8–24 h in vitro incubation at 37°C or 50°C. The conversion is more efficient in chromatin-associated DNA, completed within 1 h in cells and delayed in a reducing environment. We conclude that IR generates sugar lesions within clustered-damage sites contributing to DSB formation only after chemical processing, which occurs efficiently at 37°C. This subset of delayed DSBs may challenge DDR, may affect the perceived repair kinetics and requires further characterization.
Wetland Classification Using Multi-Source and Multi-Temporal Optical Remote Sensing Data in Newfoundland and Labrador, Canada

ABSTRACT Newfoundland and Labrador (NL) is the only province in Atlantic Canada that does not have a wetland inventory system. As a consequence, both classifying and monitoring wetland areas are necessary for wetland conservation and human services in the province. In this study, wetlands in 5 pilot sites, distributed across NL, were classified using multi-source and multi-temporal optical remote sensing images. The procedures involved the application of an object-based method to segment and classify the images. To classify the areas, 5 different machine learning algorithms were examined. The results showed that the Random Forest (RF) algorithm in combination with an object-based approach was the most accurate method to classify wetlands. The average producer and user accuracies of wetland classes considering all pilot sites were 68% and 73%, respectively. The overall classification accuracies, which considered the accuracy of all wetland and non-wetland classes varied from 86% to 96% across all pilot sites confirming the robustness of the methodology despite the biological, ecological, and geographical differences among the study areas. Additionally, we assessed the effects of the tuning parameters on the accuracy of results, as well as the difference between pixel-based and object-based methods for wetland classification in this study.
Using the Extensible Model Checker XTL to Verify StAC Business Specifications

StAC is a business specification language that has been developed as part of a partnership program between IBM UK Labs. and the University of Southampton. It is highly desirable for Business specification languages like StAC to have a way to explore the correctness of specifications. We provide some details about how XTL can provide model checking capabilities for StAC and why it proved to be more successful than SPIN and STeP in that sense.
Higher-Dimensional Segmentation by Minimum-cut Algorithm

It is important in many applications of 3D and higher dimensional segmentation that the resulting segments of voxels are not required to have only one connected component, as in some of extant methods. Indeed, it is generally necessary to be able to automatically determine the appropriate number of connected components. More generally, for a larger class of applications, the segments should have no topological restrictions at all. For instance, each connected component should be allowed to have as many holes as appropriate to fit the data. We propose a method based on a graph algorithm to automatically segment 3D and higher-dimensional images into two segments without user intervention, with no topological restriction on the solution, and in such a way that the solution is optimal under a precisely defined optimization criterion.
Benchmarking Big Data Systems: State-of-the-Art and Future Directions

The great prosperity of big data systems such as Hadoop in recent years makes the benchmarking of these systems become crucial for both research and industry communities. The complexity, diversity, and rapid evolution of big data systems gives rise to various new challenges about how we design generators to produce data with the 4V properties (i.e. volume, velocity, variety and veracity), as well as implement application-specific but still comprehensive workloads. However, most of the existing big data benchmarks can be described as attempts to solve specific problems in benchmarking systems. This article investigates the state-of-the-art in benchmarking big data systems along with the future challenges to be addressed to realize a successful and efficient benchmark.
Shallow Creep Along the 1999 Izmit Earthquake Rupture (Turkey) From GPS and High Temporal Resolution Interferometric Synthetic Aperture Radar Data (2011–2017)

Characterizing the spatiotemporal evolution of creep is essential to constrain fault slip budget and understand creep mechanism. Studies based on interferometric synthetic aperture radar and Global Positioning System (GPS) satellite observations until 2012 have shown that the central segment of the 17 August 1999 Mw 7.4 Izmit earthquake on the North Anatolian Fault began slipping aseismically following the event. In the present study, we combine new interferometric synthetic aperture radar time series, based on TerraSAR‐X and Sentinel 1A/B radar images acquired over the period 2011–2017, with near‐field GPS measurement campaigns performed every 6 months from 2014 to 2016. The mean velocity fields reveal that creep on the central segment of the 1999 Izmit fault rupture continues to decay, more than 19 years after the earthquake, in overall agreement with models of postseismic afterslip decaying logarithmically with time for a long period of time. Along the fault section that experienced supershear velocity rupture during the Izmit earthquake creep continues with a rate up to ~ 8 mm/year. A significant transient accelerating creep is detected in December 2016 on the Sentinel‐1 time series, near the maximum creep rate location, associated with a total surface slip of 10 mm released in 1 month only. Additional analyses of the vertical velocity fields show a persistent subsidence on the hanging wall block of the Golcuk normal fault that also ruptured during the Izmit earthquake. Our results demonstrate that afterslip processes along the North Anatolian Fault east‐southeast of Istanbul are more complex than previously proposed as they vary spatiotemporally along the fault.
UvA-DARE (Digital Academic Repository) Applications of Physiotope Mapping in the Cuesta Landscape of Luxembourg

Digital physiotope maps combine multi-source abiotic information, and can be used to assess derived characteristics such as natural hazards and type of forest community. Physiotopes are spatially explicit functional landscape units that stratify landscapes into distinct units, resulting from the interplay between geological, geomorphological and soil processes. Boundaries of the physiotopes in the cuesta landscape of Luxembourg are based on geological boundaries, geomorphological processes boundaries and key indicators of soil forming processes which are supplemented by quantitative topographic land surface parameters such as slope angle. A physiotope map is presented for an area near the village of Bigelbach, which re ﬂ ects the resource potential of the landscape. We present three derived applications of the physiotope map: a hazard zonation map, a forest community map and a soil erosion vulnerability map. The hazard zonation map is based on weighting and ranking of attributes of the physiotopes, such as process activity, materials, slope angle and forest cover. The derived forest community map strongly re ﬂ ects the spatial distribution of geological substrate and soils of the main physiotope units along the cuesta. The soil erosion vulnerability map implements the Revised Universal Soil Loss Equation in combination with the physiotope map. The physiotope map content can be extended and updated and its derived products may support landscape conservation and restoration programs, and can be used to monitor temporal changes within a landscape.
Storage of correlated patterns in a perceptron

We calculate the storage capacity of a perceptron for correlated Gaussian patterns. We find that the storage capacity alpha c can be less than 2 if similar patterns are mapped onto different outputs and vice versa. As long as the patterns are in a general position we obtain, in contrast to previous works, that alpha c>or=1 in agreement with Cover's theorem. Numerical simulations confirm the results.
On the complexity of propositional knowledge base revision, updates, and counterfactuals

We study the complexity of several recently proposed methods for updating or revising propositional knowledge bases. In particular, we derive complexity results for the following problem: given a knowledge base T, an update p, and a formula q, decide whether q is derivable from Top, the updated (or revised) knowledge base. This problem amounts to evaluating the counterfactual p > q over T. Besides the general case, also subcases are considered, in particular where T is a conjunction of Horn clauses, or where the size of p is bounded by a constant.
Hierarchical direct appearance model for elastic labeled graph localization

In this paper a new algorithm to locate the Elastic Labeled Graph is proposed for the face recognition approach based on Gabor wavelet jets. We extend Direct Appearance Model (DAM) to a hierarchical organization, which performs faster and more remote compared with the traditional graph localization method used in Elastic Bunch Graph Matching. A tracking recognition scheme is further discussed through employing the hierarchical DAM in a video sequence. Experimental results demonstrate the effectiveness of the method in locating and tracking the elastic graph.
Population Genetics and Sociobiology: Conflicting Views of Evolution

This article explores the tension between the population genetics and sociobiological approaches to the study of evolution. Whereas population geneticists, like Stanford's Marc Feldman, insist that the genetic complexities of organisms cannot be overlooked, sociobiologists (many of whom now prefer to call themselves "behavioral ecologists") rely on optimization models that are based on the simplest possible genetics.These optimization approaches have their roots in the classical result known as the fundamental theorem of natural selection, formulated by R. A. Fisher in 1930. From the start there was great uncertainty over the proper interpretation of Fisher's theorem, which became confused with Sewall Wright's immensely influential adaptive landscape concept. In the 1960s, a new generation of mathematical biologists proved that Fisher's theorem did not hold when fitness depended on more than one locus. Similar reasoning was used to attack W. D. Hamilton's inclusive fitness theory. A new theory, known as the theory of long-term evolution, attempts to reconcile the rigorous population genetics approach with the long-standing sociobiological view that natural selection acts to increase the fitness of organisms.
The spatial dimensions of trade: From the geography of uses to the architecture of local economies

© 2014, Istanbul Teknik Universitesi, Faculty of Architecture. All rights reserved. This paper investigates the relationship between urban space and urban economy focusing on the way centralities emerge across scales. A method is presented that combines space syntax theories and an economic model of trade-off that refers to the relation between rent and access. With the argument that economies take place in differences of space, accessibility, therefore, becomes an important matter of scale in order to understand how economic actions are materialised in urban space and how space affects socio-economic interactions at the local design scale of the city. Properties of this relationship are investigated through rent values of different real estate property markets in the city of Cardiff, UK. The method identifes the spatial distribution of activities across scales. Firstly, it is shown that trade-off modelling in the street confguration can be devised as a pattern of use mix profles in the city. Secondly, that trading between cost and access is a local process that can take place in different locations in the city that potentially function as sub-centres. Thirdly, rent and access also encourages people to re-adapt urban spaces for economic benefts, generating the reconversion of uses contained in the same real estate, the commercial-residential building. Finally, the implications of combining space syntax techniques with urban economic models are discussed. It is concluded that while spatial confgurations create possibilities for economic activity, this should also be viewed as the reverse approach of how urban economics requires proximity in distance to be produced –a relationship that has not yet been approached in space syntax research.
Richer concepts are better remembered: number of features effects in free recall

Many models of memory build in a term for encoding variability, the observation that there can be variability in the richness or extensiveness of processing at encoding, and that this variability has consequences for retrieval. In four experiments, we tested the expectation that encoding variability could be driven by the properties of the to-be-remembered item. Specifically, that concepts associated with more semantic features would be better remembered than concepts associated with fewer semantic features. Using feature listing norms we selected sets of items for which people tend to list higher numbers of features (high NoF) and items for which people tend to list lower numbers of features (low NoF). Results showed more accurate free recall for high NoF concepts than for low NoF concepts in expected memory tasks (Experiments 1–3) and also in an unexpected memory task (Experiment 4). This effect was not the result of associative chaining between study items (Experiment 3), and can be attributed to the amount of item-specific processing that occurs at study (Experiment 4). These results provide evidence that stimulus-specific differences in processing at encoding have consequences for explicit memory retrieval.
Sensing Opportunities in UMTS spectrum

The UMTS radio frequency spectrum is a highly expensive commodity. While the UMTS standards make very efficient use of the allocated bands there is however opportunity for further advancements. This paper focuses on opportunistic use of the UMTS spectrum as a means of ensuring that the maximum possible use of this valuable resource is made. In particular we focus on the local detection of UMTS TDD signals through the use of a cyclostationary feature detector. Simulation results for the use of this detector in the presence of multipath propagation and shadowing effects are presented.