Miracle-dz/UniFAR-FTUs huggingface dataset:
A Role of CREB in BRCA1 Constitutive Promoter Activity and Aromatase Basal Expression

Aromatase is the rate-limiting enzyme in estrogen biosynthesis and a key target in breast cancer treatment. Its ovary-specific promoter, pII, is induced in response to protein kinase A (PKA) activation. It has been proposed that breast cancer susceptibility gene 1, BRCA1, is involved in negative regulation of aromatase pII activity. Surprisingly, inhibition of PKA pathway by inhibitor H89 elevates basal aromatase expression while abolishes cAMP-mediated aromatase induction in an ovarian granulosa cell line, KGN. In this report, we decipher the mechanism by which the PKA pathway negatively regulates aromatase basal expression. We show that PKA pathway plays a positive role in the expression of BRCA1. H89 effectively reduces endogenous BRCA1 mRNA levels as well as reporter gene expression from a BRCA1 promoter. Mutation of a cAMP-responsive element (CRE) in the BRCA1 promoter reduces BRCA1 expression. Chromatin immunoprecipitation (ChIP) shows that CRE-binding protein, CREB, binds to the BRCA1 promoter. Furthermore, knockdown of CREB in KGN cells leads to decreased BRCA1 level as well as elevated basal aromatase mRNA expression. These data demonstrate that both the CRE site in the BRCA1 promoter and CREB are required for BRCA1 constitutive expression. Our study suggests that PKA pathway exerts its negative impact on basal aromatase expression indirectly by contributing to the constitutive expression of BRCA1.
Electrothermal analysis and optimization techniques for nanoscale integrated circuits

With technology scaling, on-chip power densities are growing steadily, leading to the point where temperature has become an important consideration in the design of electrical circuits. This paper overviews several methods for the analysis and optimization of thermal effects in integrated circuits. Thermal analysis may be carried out efficiently through the use of finite difference methods, finite element methods, or Green function based methods, each of which provides different accuracy-computation tradeoffs, and the paper begins by surveying these. Next, we overview a restricted set of thermal optimization methods, specifically, placement techniques for thermal heat-spreading, and then we conclude by summarizing a set of future directions in electrothermal design
Localized Surface Plasmon Resonance Biosensing: Current Challenges and Approaches

Localized surface plasmon resonance (LSPR) has emerged as a leader among label-free biosensing techniques in that it offers sensitive, robust, and facile detection. Traditional LSPR-based biosensing utilizes the sensitivity of the plasmon frequency to changes in local index of refraction at the nanoparticle surface. Although surface plasmon resonance technologies are now widely used to measure biomolecular interactions, several challenges remain. In this article, we have categorized these challenges into four categories: improving sensitivity and limit of detection, selectivity in complex biological solutions, sensitive detection of membrane-associated species, and the adaptation of sensing elements for point-of-care diagnostic devices. The first section of this article will involve a conceptual discussion of surface plasmon resonance and the factors affecting changes in optical signal detected. The following sections will discuss applications of LSPR biosensing with an emphasis on recent advances and approaches to overcome the four limitations mentioned above. First, improvements in limit of detection through various amplification strategies will be highlighted. The second section will involve advances to improve selectivity in complex media through self-assembled monolayers, “plasmon ruler” devices involving plasmonic coupling, and shape complementarity on the nanoparticle surface. The following section will describe various LSPR platforms designed for the sensitive detection of membrane-associated species. Finally, recent advances towards multiplexed and microfluidic LSPR-based devices for inexpensive, rapid, point-of-care diagnostics will be discussed.
Mesh Forging: Editing of 3D-Meshes Using Implicitly Defined Occluders

In recent years the ease of use and the flexibility in the editing process shifted into focus in modelling and animation applications. In this spirit we present a 3D mesh editing method that is similar to the simple constrained deformation (scodef) method9. We extend this method to the so-called mesh forging paradigm by adding an occluder to the editing environment. Our method resembles and was in fact motivated by the forging process where an anvil is used to give the manipulated object the desired shape. While users perform the editing operation by directly manipulating the 3D-mesh, the occluder is defined implicitly. To enable fine detail edits even in sparsely triangulated areas, we propose an adaptive refinement method that also allows the creation of sharp features where desired. The functionality and ease of use of our editing approach is shown by several examples.
A Fuzzy Logic Controller with Adaptive Dynamic Programming Optimization for Traffic Signals

This paper proposes a fuzzy logic signal controller with adaptive dynamic programming optimizing for traffic intersection. Because fuzzy logic has a clear advantage that it is able to use expert knowledge well, we adopt it in our controller. As adaptive dynamic programming is an advanced technology which is suitable for solving non-linear stochastic system optimizing problems, we use it to optimize our fuzzy logic controller. We set up an isolated intersection model of two-way roads with both left and right turns, and test the controller with ADP optimization under both constant and variable traffic flow rates. The simulation results show that this controller has a good performance.
An Antioxidant Extract of the Insectivorous Plant Drosera burmannii Vahl. Alleviates Iron-Induced Oxidative Stress and Hepatic Injury in Mice

Free iron typically leads to the formation of excess free radicals, and additional iron deposition in the liver contributes to the oxidative pathologic processes of liver disease. Many pharmacological properties of the insectivorous plant Drosera burmannii Vahl. have been reported in previous studies; however, there is no evidence of its antioxidant or hepatoprotective potential against iron overload. The antioxidant activity of 70% methanolic extract of D. burmannii (DBME) was evaluated. DBME showed excellent DPPH, hydroxyl, hypochlorous, superoxide, singlet oxygen, nitric oxide, peroxynitrite radical and hydrogen peroxide scavenging activity. A substantial iron chelation (IC50 = 40.90 ± 0.31 μg/ml) and supercoiled DNA protection ([P]50 = 50.41 ± 0.55 μg) were observed. DBME also displayed excellent in vivo hepatoprotective activity in iron-overloaded Swiss albino mice compared to the standard desirox treatment. Administration of DBME significantly normalized serum enzyme levels and restored liver antioxidant enzymes levels. DBME lowered the raised levels of liver damage parameters, also reflected from the morphological analysis of the liver sections. DBME also reduced liver iron content by 115.90% which is also seen by Perls’ staining. A phytochemical analysis of DBME confirms the presence of various phytoconstituents, including phenols, flavonoids, carbohydrates, tannins, alkaloids and ascorbic acid. Alkaloids, phenols and flavonoids were abundantly found in DBME. An HPLC analysis of DBME revealed the presence of purpurin, catechin, tannic acid, reserpine, methyl gallate and rutin. Purpurin, tannic acid, methyl gallate and rutin displayed excellent iron chelation but exhibited cytotoxicity toward normal (WI-38) cells; while DBME found to be non-toxic to the normal cells. These findings suggest that the constituents present in DBME contributed to its iron chelation activity. Additional studies are needed to determine if DBME can be used as a treatment for iron overload diseases.
Coarse-to-Fine , Cost-Sensitive Classification of E-Mail

In many real-world scenarios, it is necessary to make judgments at differing levels of granularity due to computational constraints. Particularly when there are a large number of classifications that must be done in a real-time streaming setting and there is a significant difference in the time required to acquire different subsets of features, it is important to have an intelligent strategy for optimizing classification accuracy versus computational costs. Accurate and timely email classification requires trading off the classification granularity with the feature acquisition costs. To solve this problem, we introduce a Granular Cost-Sensitive Classifier (GCSC) which modulates the cost of feature acquisition with the granularity of the classification, allowing inexpensive classification at a coarse level and more costly classification at finer levels of granularity. Our approach can classify messages with greater accuracy while incurring a lower feature acquisition cost relative to baseline classifiers that do not make use of cost information.
Quantitative Surface-Enhanced Raman Spectroscopy Based Analysis of MicroRNA Mixtures

We have developed a rapid, sensitive, and quantitative method for identification of microRNA (miRNA) sequences in multicomponent mixtures using surface-enhanced Raman spectroscopy (SERS). The method uses Ag nanorod array substrates prepared by oblique angle vapor deposition as the SERS platform. We show that Ag nanorod-based SERS spectra are uniquely characteristic for each miRNA sequence studied, and that the spectral reproducibility is sufficient for quantitative analysis of miRNA profiles in multicomponent mixtures using partial least squares (PLS) regression analysis. This method was applied to individual sample mixtures consisting of two, three, and five miRNAs. Separate PLS models were generated for the two-, three-, and five-component mixtures from >150 calibration spectra covering a concentration range of 6 to 150 μM for each miRNA. The PLS models were externally validated with independent test samples resulting in root mean square errors of prediction (RMSEP) of 7.4, <7.4, and <10 μM for the two-, three-, and five-component models, respectively. These results demonstrate the applicability of SERS for quantitative detection and profiling of miRNAs and suggest that SERS may prove to be a novel, label-free method for identification of disease biomarkers.
Feasibility and practicality of MR imaging of stroke in the management of hyperacute cerebral ischemia.

BACKGROUND AND PURPOSE Neuroimaging techniques such as diffusion- and perfusion-weighted MR imaging have been proposed as tools for advanced diagnosis in hyperacute ischemic stroke. There is, however, substantial doubt regarding the feasibility and practicality of applying MR imaging for the diagnosis of stroke on a routine basis, especially with respect to possible delay for specific treatment such as thrombolysis. In this study, we tested whether MR imaging of stroke is safe, fast, and accurate, and whether the gain in additional information can be used in the daily routine without a loss of time and a risk of suboptimal treatment for the patient with stroke. METHODS Between September 1997 and August 1999, 64 patients with acute ischemic stroke were recruited for MR imaging (ie, diffusion-weighted imaging, perfusion-weighted imaging, MR angiography, T2-weighted imaging) after a baseline CT was performed. We evaluated practicality and feasibility of MR imaging of stroke by analyzing the intervals between symptom onset, arrival, CT, and MR imaging. RESULTS Sixty-four patients (mean age, 60.9 years) underwent routine CT and MR imaging within 12 hours after stroke onset (n=25, < or =3 hr; n=26, 3-6 hr; n=13, 6-12 hr). Median times to arrival, start of CT, MR imaging, and between CT and MR imaging were 1.625 hours, 2 hours, 3.875 hours, and 1 hour, respectively. Intervals between symptom onset and MR imaging (P<.005), arrival and MR imaging (P<.002), and CT and MR imaging (P=.0007) differed significantly between the early phase of the study and after November 1998, whereas the intervals between symptom onset and arrival, symptom onset and CT, and arrival and CT did not. Hemorrhage could be excluded in all; a perfusion/diffusion match or mismatch could be shown in 63 of 64 patients. CONCLUSION Practice and experience with MR imaging in a stroke team significantly reduce the time and effort required to perform this technique and thus make 24-hour availability for MR imaging of stroke practical. Assessment of patients with hyperacute stroke is rapid and comprehensive. Image quality can be substantially improved by head immobilization and by mild sedation, if necessary.
A New Methodology for Multiscale Myocardial Deformation and Strain Analysis Based on Tagging MRI

Myocardial deformation and strain can be investigated using suitably encoded cine MRI that admits disambiguation of material motion. Practical limitations currently restrict the analysis to in-plane motion in cross-sections of the heart (2D + time), but the proposed method readily generalizes to 3D + time. We propose a new, promising methodology, which departs from a multiscale algorithm that exploits local scale selection so as to obtain a robust estimate for the velocity gradient tensor field. Time evolution of the deformation tensor is governed by a first-order ordinary differential equation, which is completely determined by this velocity gradient tensor field. We solve this matrix-ODE analytically and present results obtained from healthy volunteers as well as from patient data. The proposed method requires only off-the-shelf algorithms and is readily applicable to planar or volumetric tagging MRI sampled on arbitrary coordinate grids.
From keywords to links: an automatic approach

This study explores using keywords to automatically generate hyperlinks for large sets of reference materials. A content analysis was performed and the results indicate that keywords seem to be closely associated with manually generated hyperlinks. Two prototypes were developed, differing in whether the keywords were manually generated by the author, or mechanically extracted by an automatic process. In both prototypes, different types of intra-document and inter-document links were generated. A preliminary evaluation on the first prototype (which was based on manually identified keywords) shows that this prototype system holds promise for further exploration. In the second prototype, keywords were automatically extracted with Oracle Text gist/theme generation tools. Although the automatically extracted keywords were different from those identified by authors, there was a significant overlap between the set of links generated by each prototype. The next step will be testing the usefulness of this automatic approach with a thorough user evaluation.
Cytoplasmic Compartmentalization of the Fetal piRNA Pathway in Mice

Derepression of transposable elements (TEs) in the course of epigenetic reprogramming of the mouse embryonic germline necessitates the existence of a robust defense that is comprised of PIWI/piRNA pathway and de novo DNA methylation machinery. To gain further insight into biogenesis and function of piRNAs, we studied the intracellular localization of piRNA pathway components and used the combination of genetic, molecular, and cell biological approaches to examine the performance of the piRNA pathway in germ cells of mice lacking Maelstrom (MAEL), an evolutionarily conserved protein implicated in transposon silencing in fruit flies and mice. Here we show that principal components of the fetal piRNA pathway, MILI and MIWI2 proteins, localize to two distinct types of germinal cytoplasmic granules and exhibit differential association with components of the mRNA degradation/translational repression machinery. The first type of granules, pi-bodies, contains the MILI-TDRD1 module of the piRNA pathway and is likely equivalent to the enigmatic “cementing material” first described in electron micrographs of rat gonocytes over 35 years ago. The second type of granules, piP-bodies, harbors the MIWI2-TDRD9-MAEL module of the piRNA pathway and signature components of P-bodies, GW182, DCP1a, DDX6/p54, and XRN1 proteins. piP-bodies are found predominantly in the proximity of pi-bodies and the two frequently share mouse VASA homolog (MVH) protein, an RNA helicase. In Mael-mutant gonocytes, MIWI2, TDRD9, and MVH are lost from piP-bodies, whereas no effects on pi-body composition are observed. Further analysis revealed that MAEL appears to specifically facilitate MIWI2-dependent aspects of the piRNA pathway including biogenesis of secondary piRNAs, de novo DNA methylation, and efficient downregulation of TEs. Cumulatively, our data reveal elaborate cytoplasmic compartmentalization of the fetal piRNA pathway that relies on MAEL function.
Modeling Impact-induced Failure of Polysilicon MEMS: A Multi-scale Approach

Failure of packaged polysilicon micro-electro-mechanical systems (MEMS) subjected to impacts involves phenomena occurring at several length-scales. In this paper we present a multi-scale finite element approach to properly allow for: (i) the propagation of stress waves inside the package; (ii) the dynamics of the whole MEMS; (iii) the spreading of micro-cracking in the failing part(s) of the sensor. Through Monte Carlo simulations, some effects of polysilicon micro-structure on the failure mode are elucidated.
ERGDB: Estrogen Responsive Genes Database

ERGDB is an integrated knowledge database dedicated to genes responsive to estrogen. Genes included in ERGDB are those whose expression levels are experimentally proven to be either up-regulated or down-regulated by estrogen. Genes included are identified based on publications from the PubMed database and each record has been manually examined, evaluated and selected for inclusion by biologists. ERGDB aims to be a unified gateway to store, search, retrieve and update information about estrogen responsive genes. Each record contains links to relevant databases, such as GenBank, LocusLink, Refseq, PubMed and ATCC. The unique feature of ERGDB is that it contains information on the dependence of gene reactions on experimental conditions. In addition to basic information about the genes, information for each record includes gene functional description, experimental methods used, tissue or cell type, gene reaction, estrogen exposure time and the summary of putative estrogen response elements if the gene's promoter sequence was available. Through a web interface at http://sdmc.i2r. a-star.edu. sg/ergdb/ cgi-bin/explore.pl users can either browse or query ERGDB. Access is free for academic and non-profit users.
Phase II study of gemcitabine in children with relapsed acute lymphoblastic leukemia or acute myelogenous leukemia (ADVL0022): A Children's Oncology Group Report

To determine the response rate and toxicity to gemcitabine administered as 10 mg/m2/min × 360 min weekly for 3 weeks in children with relapsed acute lymphoblastic leukemia (ALL) or acute myelogenous leukemia (AML). Gemcitabine is a deoxycytidine analog that inhibits DNA synthesis and repair and has a broad spectrum of antitumor activity.
DOMINANT β-THALASSEMIA DUE TO A NEWLY IDENTIFIED FRAMESHIFT MUTATION IN EXON 3 (CODON 113, GTG → TG)

Provincial Hemoglobinopathy DNA Diagnostic Laboratory, Hamilton Regional Laboratory Medicine Program, Hamilton, Ontario L8N 3Z5, Canada Department of Pathology and Molecular Medicine, McMaster University Medical Centre, Room 3N17, McMaster University Faculty of Health Sciences, 1200 Main Street West, Hamilton, Ontario L8N 3Z5, Canada St. Joseph’s Hospital, Hamilton, Ontario L8N 4A6, Canada Division of Medical Genetics, Department of Pediatrics, University of Saskatchewan and Royal University Hospital, Saskatoon Saskatchewan S7N 0W8, Canada
What makes readers laugh?: value of sensing laughter for humor webtoon

Webtoon is a popular content in South Korea that has more fun techniques by using both IT and cartoon elements. However, the rating system for webtoon is still unsatisfying which have limitations on comprehending users' unconscious behavior. In this paper, we explore the value of using users' laughter reaction data for humor webtoons. Users' laughter reaction data and the rating scores were extracted simultaneously in user observation. As a result, the laughter reaction significantly correlates with the manual rating score. Also, we elicited each participants' flow of laughter which enabled to understand their laughter behavior and scenes that were attractive. With those data, ideation was conducted to generate ideas on how laughter reaction data can be used in new ways for humor webtoons. Thus, we proposed the potential values that suggest viable solutions of capturing laughter reactions for humor webtoons.
Molecular Diagnosis of an Ocular Toxocariasis Patient in Vietnam

An ocular Toxocara canis infection is reported for the first time in Vietnam. A 34-year-old man residing in a village of Son La Province, North Vietnam, visited the National Eye Hospital (NEH) in August 2011. He felt a bulge-sticking pain in his left eye and loss of vision occurred over 3 months before visiting the hospital. The eye examination in the hospital showed damage of the left eye, red eye, retinal fibrosis, retinal detachment, inflammation of the eye tissues, retinal granulomas, and a parasitic cyst inside. A larva of Toxocara was collected with the cyst by a medical doctor by surgery. Comparison of 264 nucleotides of internal transcribed spacer 2 (ITS2) of ribosomal DNA was done between our Vietnamese Toxocara canis and other Toxocara geographical isolates, including Chinese T. canis, Japanese T. canis, Sri Lankan T. canis, and Iranian T. canis. The nucleotide homology was 97-99%, when our T. canis was compared with geographical isolates. Identification of a T. canis infection in the eye by a molecular method was performed for the first time in Vietnam.
A Study on Test Coverage in Software Testing

Test Coverage is an important indicator of software quality and an essential part of software maintenance. It helps in evaluating the effectiveness of testing by providing data on different coverage items. Although much research effort has been put on how to get coverage information by either code based testing or requirement based testing, not much has been paid to measure and analyze the coverage by covering maximum number of coverage items. This paper provides a study of the current test coverage researches conducted by other researchers for test coverage in software testing. By looking at the existing approaches; gaps and uncovered measurement of Test Coverage can be explored further.
Agglomeration and Innovation

This chapter reviews academic research on the connections between agglomeration and innovation. We first describe the conceptual distinctions between invention and innovation. We then describe how these factors are frequently measured in the data and some resulting empirical regularities. Innovative activity tends to be more concentrated than industrial activity, and we discuss important findings from the literature about why this is so. We highlight the traits of cities (e.g., size, industrial diversity) that theoretical and empirical work link to innovation, and we discuss factors that help sustain these features (e.g., the localization of entrepreneurial finance).