bluuebunny/crossref_metadata_2025_split huggingface dataset:
Core‐shell type dually fluorescent polymer nanoparticles for ratiometric pH‐sensing
Authors: Allard Emmanuel , Larpent Chantal 
Published: August 2008

AbstractThe synthesis and pH‐sensing properties of fluorescent polymer nanoparticles (NPs) in the 20 nm diameter range with a sensitive dye covalently attached to the particle surface and a reference dye entrapped within the particle core are presented. Fluorescein‐functionalized NPs were readily obtained by conjugation of fluorescein isothiocyanate (FITC) to amine‐coated crosslinked polystyrene‐based nanoparticles prepared by microemulsion polymerization followed by postfunctionalization. This all water‐based method gave access to stable aqueous suspensions of pH‐sensing fluorescent NPs. The encapsulation of the insensitive reference fluorescent dye (1,9‐diphenylanthracene, DPA) was then conveniently achieved by soaking leading to dual fluorescent NPs containing about 20 DPA and 55 fluorescein, as deduced from spectroscopic analyses. This core‐shell type architecture maximizes the interactions of the sensing dye with the medium while protecting the reference dye. The variations of the ratio of the fluorescence emission intensities of the sensitive dye (fluorescein) to the reference dye (DPA) with pH show that the dual fluorescent NPs act as a ratiometric pH sensor with a measuring range between pH 4 and pH 8. This pH nanosensor was found to be fast, fully reversible, and robust without any leaching of dye over a long period of time. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 6206–6213, 2008
Poly(hydroxyisobutyrate) by ring‐opening polymerizations of 5,5‐dimethyl‐1,3,2‐dioxithiolan‐4‐one‐2‐oxide
Authors: Kricheldorf Hans R. , Lomadze Nino , Schwarz Gert 
Published: August 2008

Abstractα‐Hydroxyisobutyric acid anhydrosulfate HiBAS (5,5‐dimethyl‐1,3,2‐dioxithiolan‐4‐one‐2‐oxide) was polymerized under various reaction conditions and the solid reaction products were characterized by 1H NMR spectroscopy, MALDI‐TOF mass spectrometry (MT m.s.), fast atom bombardment mass spectrometry (FAB m.s.), viscosity, and SEC measurements. Thermal polymerizations at 100 °C mainly yielded cyclic oligo polyesters presumably resulting from a zwitterionic polymerization. Cycles were also detected when pyridine was used as catalyst at 20 °C. When triethylamine was used as catalyst traces of H2O played the role of initiators. Benzyl alcohol initiated the polymerization of HiBAS at 100 °C and yielded a polyester terminated by one benzylester and one OH endgroup. The SEC measurements indicated that all samples possess relatively low molar masses with number–average molecular weights ≤ 10,000 Da (in contrast to the literature data). © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 6229–6237, 2008
A graphical approach for confidence limits of optimal preventive maintenance cycles
Authors: Halim Tony , Tang Loon‐Ching 
Published: August 2008

AbstractFacilities management (FM) is the management of infrastructure resources and services to support and sustain the operational strategy of an organization over time. Maintenance is often the business process that has not been optimized and is considered as a liability of business operations. Therefore, extensive studies have been done to determine the optimal replacement interval for irreparable parts of repairable systems where typically the time between failures is characterized by lifetime distribution in which the parameters are estimated from failure data. As a result, the optimal preventive maintenance (PM) interval computed is exposed to sampling risk as the repair cost and failure data used for estimation are typically highly censored due to issues related to data collection and unobserved failures. In this paper, we present a graphical approach to obtain the confidence interval for the optimal PM interval that resulted from sampling variations parameter estimates. The proposed methodology is applied in the context of FM as a strategy for opportunistic replacement and for the purpose of validating the cost components in maintenance. Copyright © 2008 John Wiley & Sons, Ltd.
SEM characterization of silicon nanostructures: can we meet the challenge?
Authors: Myhajlenko S. , Luby A. S. , Fischer A. M. , Ponce F. A. , Tracy C. 
Published: August 2008

AbstractThe current semiconductor technology road map for device scaling champions a 4.5 nm gate length in production by 2022. The scanning electron microscope (SEM) as applied to critical dimensions (CD) metrology and associated characterization modes such as electron beam‐induced current and cathodoluminescence (CL) has proved to be a workhorse for the semiconductor industry during the microelectronics era. We review some of the challenges facing these techniques in light of the silicon nanotechnology road map. We present some new results using voltage contrast imaging and CL spectroscopy of top‐down fabricated silicon nanopillar/nanowires (<100 nm diameter), which highlight the visualization challenge. However, both techniques offer the promise of providing process characterization on the 10–20 nm scale with existing technology. Visualization at the 1 nm scale with these techniques may have to wait for aberration‐corrected SEM to become more widely available. Basic secondary electron imaging and CD applications may be separately addressed by the He‐ion microscope. SCANNING 30: 310–316, 2008. © 2008 Wiley Periodicals, Inc.
Midlife Neuroticism and the age of onset of Alzheimer's disease
Authors: Archer N. , Brown R. G. , Reeves S. , Nicholas H. , Boothby H. , Lovestone S. 
Published: August 2008

BackgroundThere may be important public health implications of increasing our knowledge of factors associated with age of dementia onset. The pre-morbid personality domain of Neuroticism constituted an interesting and theoretically plausible, yet uninvestigated, candidate for such an association. We aimed to examine whether midlife Neuroticism was associated with earlier age of onset of Alzheimer's disease (AD).MethodThis was a case–comparison study of 213 patients with probable AD. Detailed clinical information was collected for all patients including age of onset of dementia symptoms. One or two knowledgeable informants rated each patient's midlife personality retrospectively using the Neuroticism, Extraversion, Openness Five-Factor Inventory (NEO-FFI) questionnaire. The relationship between midlife Neuroticism and age of dementia onset was evaluated using both correlational analysis and backward linear regression analysis.ResultsMidlife Neuroticism predicted younger age of dementia onset in females but not in males. The association found in females was independent of pre-morbid history of affective disorder.ConclusionsThis finding and its potential mechanism warrant further investigation.
Depression and Type D personality represent different forms of distress in the Myocardial INfarction and Depression – Intervention Trial (MIND-IT)
Authors: Denollet J. , de Jonge P. , Kuyper A. , Schene A. H. , van Melle J. P. , Ormel J. , Honig A. 
Published: August 2008

BackgroundWe investigated whether depressive disorder and Type D personality refer to different forms of distress in the Myocardial INfarction and Depression – Intervention Trial (MIND-IT).MethodA total of 1205 myocardial infarction (MI) patients were screened at 3, 6, 9 and 12 months post-MI; those with a Beck Depression Inventory (BDI) score ⩾10 underwent the World Health Organization (WHO) Composite International Diagnostic Interview (CIDI). Patients completed the DS14 measure of Type D personality at 12 months and were stratified to one of four subgroups: depressed/Type D, depressed/non-Type D, non-depressed/Type D, or non-distressed.ResultsTwo hundred and six (17%) patients were diagnosed with depression and 224 (19%) with Type D. Only 7% (n=90) had both forms of distress, and 60% of Type D patients were free of depression in the first year post-MI. Type D moderated the relationship between depressive and cardiac disorder. Depressed patients without Type D had the worst clinical status (left ventricular dysfunction, heart failure, Killip class ⩾2) as compared to other patients, whereas depressed patients with a Type D personality did not differ in clinical status from non-distressed patients. Contrasting ‘pure’ Type D and depression subgroups showed that Type D patients without depression were less likely to have left ventricular dysfunction [odds ratio (OR) 0.47, 95% confidence interval (CI) 0.35–0.65, p<0.0001] than depressed patients without Type D.ConclusionsDepression and Type D refer to different forms of distress in post-MI patients; most Type D patients display non-psychiatric levels of distress and Type D moderates the relationship between depressive and cardiac disorder. Different depression/Type D subgroups may be involved in the prediction of cardiac prognosis.
Re-examining vocalic variation in Scottish English: a Cognitive Grammar approach
Authors: Clark Lynn 
Published: August 2008

ABSTRACTThe existing literature on vocalic variation in Scottish English has shown that variation tends to pattern according to the age, gender, and socioeconomic class of the speaker. However, studies that employ these gross social categories are unable to explain the variation that exists within these categories. This article therefore presents an alternative approach. Based on data from 16 adolescents who form a community of practice in west Fife, Scotland, this article attempts to consider both social and cognitive motivations for linguistic variation. The theoretical framework of Cognitive Grammar is particularly well-suited to incorporating sociolinguistic variation, and this article illustrates how an exploration of frequency effects and schematic organization can lead to a more insightful understanding of the patterning of two vocalic variables in a community. This article also explores the implications of these findings for our understanding of the place of sociolinguistics in cognitive theories of linguistics.
The Effects of Auditory–Visual Vowel Identification Training on Speech Recognition Under Difficult Listening Conditions
Authors: Richie Carolyn , Kewley-Port Diane 
Published: August 2008

Purpose
The effective use of visual cues to speech provides benefit for adults with normal hearing in noisy environments and for adults with hearing loss in everyday communication. The purpose of this study was to examine the effects of a computer-based, auditory–visual vowel identification training program on sentence recognition under difficult listening conditions.

Method
Normal-hearing adults were trained and tested under auditory–visual conditions, in noise designed to simulate the effects of a hearing loss. After initial tests of vowel, word, and sentence recognition, 1 group of participants received training on identification of 10 American English vowels in CVC context. Another group of participants received no training. All participants were then retested on vowel, word, and sentence recognition.

Results
Improvements were seen for trained compared with untrained participants, in auditory–visual speech recognition under difficult listening conditions, for vowels in monosyllables and key words in sentences.

Conclusions
Results from this study suggest benefit may be gained from this computer-based, auditory–visual vowel identification training method.
Effects of the SpeechEasy on Objective and Perceived Aspects of Stuttering: A 6-Month, Phase I Clinical Trial in Naturalistic Environments
Authors: Pollard Ryan , Ellis John B. , Finan Don , Ramig Peter R. 
Published: August 2008

Purpose
Effects of the SpeechEasy when used under extraclinical conditions over several months were investigated. Primary purposes were to help establish Phase I level information about the therapeutic utility of the SpeechEasy and to compare those results with previous findings obtained in laboratory and clinical settings.

Method
Eleven adults who stutter participated. A nonrandomized ABA group design was utilized. Speech samples were collected every 2 weeks in extraclinical environments. Qualitative data were collected through weekly written logs and an exit questionnaire.

Results
Group analyses revealed a statistically significant effect of the SpeechEasy immediately postfitting but no treatment effect across 4 months' time. Individual responses varied greatly with regard to stuttering frequency and subjective impressions. Relatively more stuttering reduction occurred during oral reading than during formulated speech.

Conclusions
Based on this protocol, Phase II trials are not indicated. However, positive individual responses and self-reports suggest some clinical utility for the SpeechEasy. The use of more challenging sampling procedures strengthened external validity and captured more modest altered auditory feedback effects compared with those previously reported in laboratory settings. Device use coincided more so with positive subjective impressions than with measurable fluency improvement, highlighting challenges facing clinicians when implementing principles of evidence-based practice, including client-based preferences.
Aerodynamic and Acoustic Effects of Abrupt Frequency Changes in Excised Larynges
Authors: Alipour Fariborz , Finnegan Eileen M. , Scherer Ronald C. 
Published: August 2008

Purpose
To determine the aerodynamic and acoustic effects due to a sudden change from chest to falsetto register or vice versa. It was hypothesized that the continuous change in subglottal pressure and flow rate alone (pressure-flow sweep [PFS]) can trigger a mode change in the canine larynx.

Method
Ten canine larynges were each mounted over a tapered tube that supplied pressurized, heated, and humidified air. Glottographic signals were recorded during each PFS experiment, during which airflow was increased in a gradual manner for a period of 20–30 s.

Results

Abrupt changes in fundamental frequency (F
0
) and mode of vibration occurred during the PFS in the passive larynx without any change in adduction or elongation. The lower frequency mode of oscillation of the vocal folds, perceptually identified as the chest register, had relatively large amplitude oscillation, significant vocal fold contact, a rich spectral content, and a relatively loud audio signal. The higher frequency mode of oscillation, perceptually identified as falsetto, had little or no vocal fold contact and a dominant first partial. Relatively abrupt F
0
changes also occurred for gradual adduction changes, with the chest register corresponding to greater adduction, falsetto to less adduction.
Coping with racism in Hebrew literary translation
Authors: Weissbrod Rachel 
Published: August 2008

This article examines the treatment of racism in Hebrew literary translation. It relies on culture theorists such as Foucault, Said, Fanon and Bhabha who have analyzed the relations of a society with individuals and groups whom it regards as “others”. The texts discussed have been selected because they can illustrate critical arguments made by these theorists. They include texts which are openly racist (Henryk Sienkiewicz’s W pustyni i w puszczy [In Desert and Wilderness], Margaret Mitchell’s Gone with the Wind, Edgar Wallace’s The People of the River) and others that criticize racism but fall into the trap against which they warn (Mark Twain’s Adventures of Huckleberry Finn, Harriet Beecher Stowe’s Uncle Tom’s Cabin). The article also refers to “Geschichte von den schwarzen Buben” (in English, “The Story of the Inky Boys”), one of the stories included in Heinrich Hoffmann’s Struwwelpeter (The Slovenly Peter). In the latter, the Hebrew translations (rather than the German source) make use of racist stereotypes.
Inspired by translation researchers who regard translation as the meeting place of a culture with “others” (Venuti, Tymoczco, Cronin), the article also makes use of the concept of norms as elaborated by Toury. In line with his theoretical approach, it is assumed that the treatment of racism in translation depends not only on the overall attitude to racism in the receiving culture but also on its translation norms.
Fusing time series expression data through hybrid aggregation and hierarchical merge
Authors: Tsiporkova Elena , Boeva Veselka 
Published: August 2008

Abstract
Summary: A novel integration approach targeting the combination of multi-experiment time series expression data is proposed. A recursive hybrid aggregation algorithm is initially employed to extract a set of genes, which are eventually of interest for the biological phenomenon under study. Next, a hierarchical merge procedure is specifically developed for the purpose of fusing together the multiple-experiment expression profiles of the selected genes. This employs dynamic time warping alignment techniques in order to account adequately for the potential phase shift between the different experiments. We subsequently demonstrate that the resulting gene expression profiles consistently reflect the behavior of the original expression profiles in the different experiments.
Contact: vboeva@tu-plovdiv.bg
Supplementary information: Supplementary data are available at http://www.tu-plovdiv.bg/Container/bi/DataIntegration/
A fast and flexible method for the segmentation of aCGH data
Authors: Ben-Yaacov Erez , Eldar Yonina C. 
Published: August 2008

AbstractMotivation: Array Comparative Genomic Hybridization (aCGH) is used to scan the entire genome for variations in DNA copy number. A central task in the analysis of aCGH data is the segmentation into groups of probes sharing the same DNA copy number. Some well known segmentation methods suffer from very long running times, preventing interactive data analysis.Results: We suggest a new segmentation method based on wavelet decomposition and thresholding, which detects significant breakpoints in the data. Our algorithm is over 1000 times faster than leading approaches, with similar performance. Another key advantage of the proposed method is its simplicity and flexibility. Due to its intuitive structure, it can be easily generalized to incorporate several types of side information. Here, we consider two extensions which include side information indicating the reliability of each measurement, and compensating for a changing variability in the measurement noise. The resulting algorithm outperforms existing methods, both in terms of speed and performance, when applied on real high density CGH data.Availability: Implementation is available under software tab at: http://www.ee.technion.ac.il/Sites/People/YoninaEldar/Contact: yonina@ee.technion.ac.il
Automatic decomposition of kinetic models of signaling networks minimizing the retroactivity among modules
Authors: Saez-Rodriguez Julio , Gayer Stefan , Ginkel Martin , Gilles Ernst Dieter 
Published: August 2008

Abstract
Motivation: The modularity of biochemical networks in general, and signaling networks in particular, has been extensively studied over the past few years. It has been proposed to be a useful property to analyze signaling networks: by decomposing the network into subsystems, more manageable units are obtained that are easier to analyze. While many powerful algorithms are available to identify modules in protein interaction networks, less attention has been paid to signaling networks defined as chemical systems. Such a decomposition would be very useful as most quantitative models are defined using the latter, more detailed formalism.
Results: Here, we introduce a novel method to decompose biochemical networks into modules so that the bidirectional (retroactive) couplings among the modules are minimized. Our approach adapts a method to detect community structures, and applies it to the so-called retroactivity matrix that characterizes the couplings of the network. Only the structure of the network, e.g. in SBML format, is required. Furthermore, the modularized models can be loaded into ProMoT, a modeling tool which supports modular modeling. This allows visualization of the models, exploiting their modularity and easy generation of models of one or several modules for further analysis. The method is applied to several relevant cases, including an entangled model of the EGF-induced MAPK cascade and a comprehensive model of EGF signaling, demonstrating its ability to uncover meaningful modules. Our approach can thus help to analyze large networks, especially when little a priori knowledge on the structure of the network is available.
Availability: The decomposition algorithms implemented in MATLAB (Mathworks, Inc.) are freely available upon request. ProMoT is freely available at http://www.mpi-magdeburg.mpg.de/projects/promot
Contact: gayers@mpi-magdeburg.mpg.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Poisson adjacency distributions in genome comparison: multichromosomal, circular, signed and unsigned cases
Authors: Xu Wei , Alain Benoît , Sankoff David 
Published: August 2008

Abstract
The number of common adjacencies of genetic markers, as a measure of the similarity of two genomes, has been widely used as indicator of evolutionary relatedness and as the basis for inferring phylogenetic relationships. Its probability distribution enables statistical tests in detecting whether significant evolutionary signal remains in the marker order. In this article, we derive the probability distributions of the number of adjacencies for a number of types of genome—signed or unsigned, circular or linear, single-chromosome or multichromosomal. Generating functions are found for singlechromosome cases, from which exact counts can be calculated. Probability approaches are adopted for multichromosomal cases, where we find the exact values for expectations and variances. In both cases, the limiting distributions are derived in term of numbers of adjacencies. For all unsigned cases, the limiting distribution is Poisson with parameter 2; for all signed cases, the limiting distribution is Poisson with parameter ½.
Contact: wxu060@uottawa.ca
Connect the dots: exposing hidden protein family connections from the entire sequence tree
Authors: Loewenstein Yaniv , Linial Michal 
Published: August 2008

Abstract
Motivation: Mapping of remote evolutionary links is a classic computational problem of much interest. Relating protein families allows for functional and structural inference on uncharacterized families. Since sequences have diverged beyond reliable alignment, these are too remote to identify by conventional methods.
Approach: We present a method to systematically identify remote evolutionary relations between protein families, leveraging a novel evolutionary-driven tree of all protein sequences and families. A global approach which considers the entire volume of similarities while clustering sequences, leads to a robust tree that allows tracing of very faint evolutionary links. The method systematically scans the tree for clusters which partition exceptionally well into extant protein families, thus suggesting an evolutionary breakpoint in a putative ancient superfamily. Our method does not require family profiles (or HMMs), or multiple alignment.
Results: Considering the entire Pfam database, we are able to suggest 710 links between protein families, 125 of which are confirmed by existence of Pfam clans. The quality of our predictions is also validated by structural assignments. We further provide an intrinsic characterization of the validity of our results and provide examples for new biological findings, from our systematic scan. For example, we are able to relate several bacterial pore-forming toxin families, and then link them with a novel family of eukaryotic toxins expressed in plants,.sh venom and notably also uncharacterized proteins from human pathogens.
Availability: A detailed list of putative homologous superfamilies, including 210 families of unknown function, has been made available online: http://www.protonet.cs.huji.ac.il/dots
Contact: lonshy@cs.huji.ac.il