Miracle-dz/UniFAR-FTUs huggingface dataset:
Word Sense Disambiguation with Spreading Activation Networks Generated from Thesauri

Most word sense disambiguation (WSD) methods require large quantities of manually annotated training data and/or do not exploit fully the semantic relations of thesauri. We propose a new unsupervised WSD algorithm, which is based on generating Spreading Activation Networks (SANs) from the senses of a thesaurus and the relations between them. A new method of assigning weights to the networks' links is also proposed. Experiments show that the algorithm outperforms previous unsupervised approaches to WSD.
Anthracycline Cardiotoxicity: Prevalence, Pathogenesis and Treatment

Anthracyclines, such as doxorubicin and idarubicin, remain an important class of chemotherapeutic agents. Unfortunately, their efficacy in treating cancer is limited by a cumulative dose-dependent cardiotoxicity, which can cause irreversible heart failure. In this review, we discuss the pathogenesis and incidence of anthracycline-induced cardiotoxicity as well as methods to detect, prevent and treat the condition.
Efficient data reduction with EASE

A variety of mining and analysis problems --- ranging from association-rule discovery to contingency table analysis to materialization of certain approximate datacubes --- involve the extraction of knowledge from a set of categorical count data. Such data can be viewed as a collection of "transactions," where a transaction is a fixed-length vector of counts. Classical algorithms for solving count-data problems require one or more computationally intensive passes over the entire database and can be prohibitively slow. One effective method for dealing with this ever-worsening scalability problem is to run the algorithms on a small sample of the data. We present a new data-reduction algorithm, called EASE, for producing such a sample. Like the FAST algorithm introduced by Chen et al., EASE is especially designed for count data applications. Both EASE and FAST take a relatively large initial random sample and then deterministically produce a subsample whose "distance" --- appropriately defined --- from the complete database is minimal. Unlike FAST, which obtains the final subsample by quasi-greedy descent, EASE uses epsilon-approximation methods to obtain the final subsample by a process of repeated halving. Experiments both in the context of association rule mining and classical χ2 contingency-table analysis show that EASE outperforms both FAST and simple random sampling, sometimes dramatically.
Inverse compilation feasibility

The feasibility of the use of techniques of inverse compilation (decompilation) for the solution of Software Transport problems depends to a great extent upon the level of adaptability of software systems designed to automate the decompilation process. The attainment of a sufficiently high level of adaptability requires the development of very general and <u>efficient</u> techniques of program structure and variable usage analysis. However, while such techniques are necessary for the development of adaptable decompilation software, they are not by themselves sufficient. What is further needed is a highly sophisticated medium of program description that 1) is comparatively easy to map to and from assembly languages for a wide variety of machines, 2) is suitable for direct input to a program analyzer, and 3) is easily produced by a high-level language compiler.
Multifinger Indium Phosphide Double-Heterostructure Transistor Circuit Technology With Integrated Diamond Heat Sink Layer

The RF power output of scaled subterahertz and terahertz indium phosphide double-heterostructure bipolar transistors (InP DHBTs) is limited by the thermal device resistance, which increases with the geometrical frequency scaling of these devices. We present a diamond thin-film heat sink process aimed at the efficient removal of the heat generated in submicrometer InP HBTs. The thin-film diamond is integrated in a wafer bond process. Vertical connections are facilitated by plasma-processed contact holes through the diamond layer, metallized with electroplated gold. The process is suitable for monolithic circuit integration, amenable to the realization of high-power analog circuits in the millimeter-wave region and beyond. The thermal resistance of double-finger transistors with a 0.8-μm emitter width could be reduced to 0.7 K/mW, while reaching the gain cutoff frequencies of fT = 360 GHz and fmax = 350 GHz. An integrated two-stage power amplifier with four-way power combining fabricated in this technology exhibited 20-dBm power output at 90 GHz with a bandwidth of 10 GHz.
LEACH enhancements for wireless sensor networks based on energy model

The low-energy adaptive clustering hierarchy (LEACH) protocol is one of the most adaptive protocols used in the wireless sensor networks (WSNs). LEACH is a hierarchical model that provides a powerful strategy for energy balancing, using head rotations. However, the original LEACH protocol suffers from many drawbacks and many researchers proposed new methods to mitigate them. In this paper, we propose two approaches based on an energy model to enhance cluster heads (CHs) selection method through not only minimizing the power consumption of network nodes, but also minimizing the number of CHs. The first proposed approach effectively selects a cluster head that has the lowest power consumption when communicating with other nodes. In addition to what is proposed in the first approach, the idea of incorporating the shortest distance has been considered in the second proposed approach. This significantly decreases the energy consumption and increases the lifetime of associated nodes.
Cholangiocarcinoma: A cancer in search of the right classification

The recent flurry of exciting reports on the potential antifibrotic benefit of pentoxifylline (PTX) in nonalcoholic steatohepatitis (NASH) has encouraged me to write this letter to the Editor of HEPATOLOGY to include some earlier reports in this area of hepatology research. We were the first to report that plateletderived growth factor (PDGF) played a role in experimental hepatic fibrosis and describe its role in human fibrosis. PTX blocked fibrosis via an effect on PDGF, by inhibiting phosphorylation of c-Jun on serine 73. Our results in NASH and hepatitis C virus (HCV) showed that ribavirin, but not interferon, inhibited fibrosis, and that this effect was mediated by the block of phosphorylation of c-Jun on serine 73, resulting in decreased synthesis of collagen and decreased hepatic stellate cell proliferation. PTX decreased NASH sera-stimulated Fibrogenic Stimulation Index (FSI; our patented diagnostic test) and c-Jun phosphorylation as assessed by H-thymidine incorporation and Western analysis, respectively. Our recent data indicate that PTX decreased the FSI, and that the FSI correlates well with the METAVIR fibrosis score in HCV patients and may be predictive of fibrosis in this cohort.
Robust Learning of Chaotic Attractors

A fundamental problem with the modeling of chaotic time series data is that minimizing short-term prediction errors does not guarantee a match between the reconstructed attractors of model and experiments. We introduce a modeling paradigm that simultaneously learns to short-term predict and to locate the outlines of the attractor by a new way of nonlinear principal component analysis. Closed-loop predictions are constrained to stay within these outlines, to prevent divergence from the attractor. Learning is exceptionally fast: parameter estimation for the 1000 sample laser data from the 1991 Santa Fe time series competition took less than a minute on a 166 MHz Pentium PC.
Increasing prevalence and dissemination of NDM-1 metallo-β-lactamase in India: data from the SMART study (2009).

OBJECTIVES To investigate the β-lactamase background of ertapenem non-susceptible isolates for the presence of the most commonly detected carbapenemase genes, bla(KPC), bla(OXA-48) and bla(VIM), and the newly described bla(NDM-1). METHODS Two hundred and thirty-five ertapenem-non-susceptible (MIC ≥ 0.5 mg/L) isolates of Enterobacteriaceae from the worldwide Study for Monitoring Antimicrobial Resistance Trends (SMART) 2009 programme were screened using a multiplex PCR for the presence of bla(KPC), bla(OXA-48), bla(VIM) and bla(NDM-1) genes. Extended-spectrum β-lactamase (ESBL) and AmpC genes (bla(ESBL) and bla(AmpC)) were identified using the Check-MDR CT101 microarray. DNA sequencing was performed to identify the bla(ESBL), bla(KPC) and bla(NDM-1) genes. Molecular typing was also performed to genetically characterize these isolates. RESULTS Sixty-six isolates (28%) had a carbapenemase gene, with bla(NDM-1) identified in 33 isolates including 2 isolates carrying both bla(NDM-1) and bla(OXA-48); other carbapenemase genes found included bla(KPC) (n = 23), bla(VIM) (n = 7) and bla(OXA-48) (n = 3). All bla(NDM-1)-carrying isolates were from patients in India and comprised five different species. With the exception of one isolate carrying only bla(NDM-1), all bla(NDM-1) carbapenemase-possessing isolates carried additional β-lactamases in various combinations: bla(ESBL) and bla(AmpC) (n = 18); bla(ESBL) (n = 10); bla(ESBL), bla(AmpC) and bla(OXA-48) (n = 2); and bla(AmpC) (n = 2). Except for bla(OXA-48)-carrying isolates, novel multilocus sequence types or enterobacterial repetitive intergenic consensus PCR patterns were observed along with clonal dissemination within and among sites. CONCLUSIONS A range of carbapenemase genes, associated with diverse ESBLs and/or AmpC backgrounds, were found among Enterobacteriaceae isolated during the study. Many of these ertapenem non-susceptible strains were clonally related and carried various combinations of β-lactamases.
Isolation and Characterization of Bacteria Capable of Tolerating the Extreme Conditions of Clean Room Environments

ABSTRACT In assessing the bacterial populations present in spacecraft assembly, spacecraft test, and launch preparation facilities, extremophilic bacteria (requiring severe conditions for growth) and extremotolerant bacteria (tolerant to extreme conditions) were isolated. Several cultivation approaches were employed to select for and identify bacteria that not only survive the nutrient-limiting conditions of clean room environments but can also withstand even more inhospitable environmental stresses. Due to their proximity to spacefaring objects, these bacteria pose a considerable risk for forward contamination of extraterrestrial sites. Samples collected from four geographically distinct National Aeronautics and Space Administration clean rooms were challenged with UV-C irradiation, 5% hydrogen peroxide, heat shock, pH extremes (pH 3.0 and 11.0), temperature extremes (4°C to 65°C), and hypersalinity (25% NaCl) prior to and/or during cultivation as a means of selecting for extremotolerant bacteria. Culture-independent approaches were employed to measure viable microbial (ATP-based) and total bacterial (quantitative PCR-based) burdens. Intracellular ATP concentrations suggested a viable microbial presence ranging from below detection limits to 106 cells/m2. However, only 0.1 to 55% of these viable cells were able to grow on defined culture medium. Isolated members of the Bacillaceae family were more physiologically diverse than those reported in previous studies, including thermophiles (Geobacillus), obligate anaerobes (Paenibacillus), and halotolerant, alkalophilic species (Oceanobacillus and Exiguobacterium). Non-spore-forming microbes (α- and β-proteobacteria and actinobacteria) exhibiting tolerance to the selected stresses were also encountered. The multiassay cultivation approach employed herein enhances the current understanding of the physiological diversity of bacteria housed in these clean rooms and leads us to ponder the origin and means of translocation of thermophiles, anaerobes, and halotolerant alkalophiles into these environments.
Crystal Structure of the tRNA Processing Enzyme RNase PH from Aquifex aeolicus*

RNase PH is one of the exoribonucleases that catalyze the 3′ end processing of tRNA in bacteria. RNase PH removes nucleotides following the CCA sequence of tRNA precursors by phosphorolysis and generates mature tRNAs with amino acid acceptor activity. In this study, we determined the crystal structure of Aquifex aeolicus RNase PH bound with a phosphate, a co-substrate, in the active site at 2.3-Å resolution. RNase PH has the typical α/β fold, which forms a hexameric ring structure as a trimer of dimers. This ring structure resembles that of the polynucleotide phosphorylase core domain homotrimer, another phosphorolytic exoribonuclease. Four amino acid residues, Arg-86, Gly-124, Thr-125, and Arg-126, of RNase PH are involved in the phosphate-binding site. Mutational analyses of these residues showed their importance in the phosphorolysis reaction. A docking model with the tRNA acceptor stem suggests how RNase PH accommodates substrate RNAs.
Cyclic nucleotide gated channel gene family in tomato: genome-wide identification and functional analyses in disease resistance

The cyclic nucleotide gated channel (CNGC) is suggested to be one of the important calcium conducting channels. Nevertheless, genome-wide identification and systemic functional analysis of CNGC gene family in crop plant species have not yet been conducted. In this study, we performed genome-wide identification of CNGC gene family in the economically important crop tomato (Solanum lycopersicum L.) and analyzed function of the group IVb SlCNGC genes in disease resistance. Eighteen CNGC genes were identified in tomato genome, and four CNGC loci that were misannotated at database were corrected by cloning and sequencing. Detailed bioinformatics analyses on gene structure, domain composition and phylogenetic relationship of the SlCNGC gene family were conducted and the group-specific feature was revealed. Comprehensive expression analyses demonstrated that SlCNGC genes were highly, widely but differently responsive to diverse stimuli. Pharmacological assays showed that the putative CNGC activators cGMP and cAMP enhanced resistance against Sclerotinia sclerotiorum. Silencing of group IVb SlCNGC genes significantly enhanced resistance to fungal pathogens Pythium aphanidermatum and S. sclerotiorum, strongly reduced resistance to viral pathogen Tobacco rattle virus, while attenuated PAMP- and DAMP-triggered immunity as shown by obvious decrease of the flg22- and AtPep1-elicited hydrogen peroxide accumulation in SlCNGC-silenced plants. Additionally, silencing of these SlCNGC genes significantly altered expression of a set of Ca2+ signaling genes including SlCaMs, SlCDPKs, and SlCAMTA3. Collectively, our results reveal that group IV SlCNGC genes regulate a wide range of resistance in tomato probably by affecting Ca2+ signaling.
Shear localization in viscoplastic solids

An outstanding problem in mechanics is the modeling of the phenomenon of initiation and development of localized shear bands in materials whose inelastic deformation behavior is inherently ratedependent. Clifton (1980) and Bai (1982) have presented a onedimensional linear perturbation stability analysis for the initiation of shear bands in viscoplaatic solids deforming in simple shear. Although this one-dimensional analysis provides much insight into the phenomenon of shear localization, the results are not directly applicable to the practically more interesting problems in two and three dimensions. Accordingly, here, a three-dimensional generalization of this linear perturbatiou stability analysis is presented for a J2 flow theory of plasticity which exhibits isotropic strain hardening or softening, strain rate hardening, and thermal softening. The results are then specialized to the simpler case of plane motions and the limiting cases of quasi-static isothermal deformations and dynamic adiabatic deformations are thoroughly analyzed. An inherent limitation of this linear perturbation analyses is that it provides only (a) the necessary conditions for the initiation of shear bands, and (b) the orientatiorrs and the incipient rate of growth of the emergent shear bands. It does not provide any information regarding the more interesting stages of localization when the strain, strain rate, and temperature in the shear bands becomes much larger than elsewhere. To predict the beginning stages of significant flow localization a new criterion has been developed for adiabatic flow localization. A history dependent dimensionless parameter X which represents the integral in time of the ratio of the rate of flow softening to the rate of strain-rate hardening is identified as a possible flow localization parameter, and the attainment of a critically large value Xc of X is suggested as a simple criterion for monitoring the beginning of severe adiabatic fiow localization. Fully two dimensional large deformation finite element simulations of plane strain compression, tension and U-notch bending tests on a class of thermo-elasto-viscoplastic materials under adiabatic conditions have been performed and the initiation and growth of naturally appearing band-like regions of localization is followed from slow early growth to severe localization. By simultaneo~isly monitoring level contours of X it is demonstrated that the time when there appeara a zone of noticeable size in which X > Xc within the specimen correlates very well with the beginning of significant shear localization. Thesis Supervisor: Lallit Anand Title: Aasociate Professor of Mechanical Engineering
Visualization of very Large Datasets Improving progressive view-dependent isosurface propagation

Recently, we proposed a new isosurface extraction algorithm that extracts portions of the isosurface in a viewdependent manner by ray casting and propagation. The algorithm casts rays through a volume to find visible active cells as seeds and then propagates their polygonal isosurface into the neighboring cells. Small pieces of the isosurface are generated by distance-limited propagation and joined together to form the final surface. This paper presents our evaluation of several design choices of the algorithm. We have implemented these design choices and showed that by making right design decisions, we can substantially reduce the time to obtain most (such as 99.9%) of the isosurface. r 2002 Elsevier Science Ltd. All rights reserved.
Study on Al2O3 Film in Anhydrous HF Vapor

HF vapor etching using thin Al2O3 film as etch stop material was studied. It was found that behavior of Al2O3 film in HF vapor can not be predicted from the blanket film studies only but it is important to use samples that resemble closely real process conditions instead. Resistivity of Al2O3 against HF vapor depends on whether a SiO2 was etched on top of it or not. Other affecting factors are the thickness of the Al2O3 film, HF vapor process, stress of the oxide on top of it as well as topography under it. Even very thin 3 nm Al2O3 film resist HF vapor if no SiO2 film is etched on top of it and etch process is slow enough.
CYP-dependent metabolism of PF9601N, a new monoamine oxidase-B inhibitor, by C57BL/6 mouse and human liver microsomes.

PURPOSE The selective monoamine oxidase-B (MAO-B) inhibitor, l-deprenyl, is still used for treating Parkinson's patients, however, a disadvantage of its use lies in the formation of l-amphetamine and l-methamphetamine. Subsequently, this has promoted the design of a novel, more potent, MAO-B inhibitor PF9601N, which also has neuroprotective and antioxidant properties. The aim of this work was to investigate the effect of treatment with PF9601N on its own phase I hepatic metabolism. Kinetic parameters of PF9601N CYP-dependent N-dealkylation reaction was also studied and compared with those of l-deprenyl. METHODS C57BL/6 mice were treated with PF9601N for 4 days. After CYP content and related monooxygenase activities were assayed in liver microsomes of control and treated animals. RESULTS CYP activities, cytochrome b5 content, NADPH-cytochrome P450 reductase and various monooxygenase activities were unaffected by in vivo PF9601N treatment. With microsomes from both control and treated mice, the PF9601N-dealkylation product, FA72, was the only detected metabolite with its formation rate following an hyperbolic, Michaelis-Menten curve. Among various inhibitors, only ketoconazole inhibited the FA72 formation rate, indicating a major involvement for CYP3A. Apparent Km and Vmax values generated by human liver microsomes were similar to those found with mouse microsomes. Ketoconazole inhibition indicates that CYP3A is one of the major enzymes involved in PF9601N metabolism also by human liver microsomes. In mouse liver microsomes, the intrinsic clearance of PF9601N was significantly lower than that of l-deprenyl suggestive of an improved bioavailability for the former. CONCLUSION The observed favourable metabolic profile may suggest suitability of PF9601N for clinical use.
Synthesis of gold nanoparticles for application as biosensors in engineering

This paper presents the synthesis of gold nanoparticles (AuNPs) suitable to the construction of engineering biosensors. The phenomenon of Localized Surface Plasmons Resonance (LSPR) and Surface Plasmon Polarization are explored in these sensors. AuNPs allow developing nanoscale devices that interacts with chemical and biological systems. The LSPR is the main operation principle explored in these nanosystems that promote electromagnetic wave oscillation on such small metallic structures. Our results have shown that the resonance is directly linked to the size of the nanoparticles, the nature of the dielectric material and support environment where the device is being studied, previously reported for Zhao et al. [1]. Nanoparticles with size of 56 to 88 nm was obtained this work. The Turkevich method was to used to make AuNP’s with spherical morphology, this system is it possible to application in biosensor because your strong interation with light and environment.
A quick primer on brain development

Neuroscience is a relatively new discipline encompassing neurology, psychology and biology. It has made great strides in the last 100 years, during which many aspects of the physiology, biochemistry, pharmacology and structure of the vertebrate brain have been understood. Understanding of some of the basic perceptual, cognitive, attentional, emotional and mnemonic functions is also making progress, particularly since the advent of the cognitive neurosciences, which focus specifically on understanding higher level processes of cognition via imaging technology. Neuroimaging has enabled scientists to study the human brain at work in vivo, deepening our understanding of the very complex processes underpinning speech and language, thinking and reasoning, reading and mathematics. It seems timely, therefore, to consider how we might implement our increased understanding of brain development and brain function to explore educational questions.