bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Autonomic Multimedia and Information Service Gateway for Mobile Devices
Authors: Li Yuhong , Pan Shuwen , He Na , Zhao Yi , Su Huichun , Yu Kuifei , Ma Jian 
Published: January 2009

With the increase of the networking functions of the mobile handheld devices, today there is a strong need for receiving multimedia through mobile handheld devices. However, the current streaming technologies cannot well satisfy the users' need due to the large network bandwidth requirement and high price. And the infrastructure of broadcasting oriented for a mobile handheld device, such as DVB-H, are not yet popular in the daily life. Based on these considerations, a new multimedia and information service gateway is proposed, where novel multimedia and information services can be well provided to users with mobile devices. The gateway can connect DVB network, Internet, IPTV etc. media and content provisioning networks with the local area networks such as WLAN and LAN, as well as 3G cellular networks and WiMax which provide access to mobile and portable devices. The gateway aggregates media and Internet information and then distributes them via different access networks to mobile users. The most important feature of the gateway is that it has introduced the idea of the autonomic communications to solve the key problems for providing multimedia services like the video quality and the heterogeneity of mobile devices. Two control loops are designed in the gateway, based on which the autonomic source media transcoding and the dual-driven autonomic channel transcoding techniques are realized. Hence, the gateway system can adapt itself to the varying environments and can therefore provide better multimedia services to users. In general, the gateway can realize the following functions: sending multimedia to individual mobile devices with suitable format, size, and resolution multicasting multimedia to a group of mobile devices broadcasting multimedia to the mobile devices in the local area providing various information services to users through “push” or “pull” Especially, the gateway has the following three autonomic features: autonomic user management: i.e., it can obtain the users context information automatically and deal with users' subscription of the services autonomic source media transcoding: i.e., it can adapt the format of the multimedia data received from the media provisioning network according to the capability of the receivers' devices autonomic channel coding: i.e., it can adapt the coding parameters for the video transmission within WLAN by monitoring the status of the network and the receivers Simulation and test results show that the proposed service gateway can provide a new solution for multimedia and information service provisioning.
Clinical Practice Guidelines for the Management Candidiasis: 2009 Update by the Infectious Diseases Society of America
Authors: Pappas Peter G. , Kauffman Carol A. , Andes David , Benjamin Daniel K. , Calandra Thierry F. , Edwards John E. , Filler Scott G. , Fisher John F. , Kullberg Bart-Jan , Zeichner Luis Ostrosky , Reboli Annette C. , Rex John H. , Walsh Thomas J. , Sobe Jack D. 
Published: January 2009

AbstractGuidelines for the management of patients with invasive candidiasis and mucosal candidiasis were prepared by an Expert Panel of the Infectious Diseases Society of America. These updated guidelines replace the previous guidelines published in the 15 January 2004 issue of Clinical Infectious Diseases and are intended for use by health care providers who care for patients who either have or are at risk of these infections. Since 2004, several new antifungal agents have become available, and several new studies have been published relating to the treatment of candidemia, other forms of invasive candidiasis, and mucosal disease, including oropharyngeal and esophageal candidiasis. There are also recent prospective data on the prevention of invasive candidiasis in high-risk neonates and adults and on the empiric treatment of suspected invasive candidiasis in adults. This new information is incorporated into this revised document.
Genome-wide association analysis by lasso penalized logistic regression
Authors: Wu Tong Tong , Chen Yi Fang , Hastie Trevor , Sobel Eric , Lange Kenneth 
Published: January 2009

AbstractMotivation: In ordinary regression, imposition of a lasso penalty makes continuous model selection straightforward. Lasso penalized regression is particularly advantageous when the number of predictors far exceeds the number of observations.Method: The present article evaluates the performance of lasso penalized logistic regression in case–control disease gene mapping with a large number of SNPs (single nucleotide polymorphisms) predictors. The strength of the lasso penalty can be tuned to select a predetermined number of the most relevant SNPs and other predictors. For a given value of the tuning constant, the penalized likelihood is quickly maximized by cyclic coordinate ascent. Once the most potent marginal predictors are identified, their two-way and higher order interactions can also be examined by lasso penalized logistic regression.Results: This strategy is tested on both simulated and real data. Our findings on coeliac disease replicate the previous SNP results and shed light on possible interactions among the SNPs.Availability: The software discussed is available in Mendel 9.0 at the UCLA Human Genetics web site.Contact: klange@ucla.eduSupplementary information: Supplementary data are available at Bioinformatics online.
QMSim: a large-scale genome simulator for livestock
Authors: Sargolzaei Mehdi , Schenkel Flavio S 
Published: January 2009

Abstract
Summary: QMSim was designed to simulate large-scale genotyping data in multiple and complex livestock pedigrees. The simulation is basically carried out in two steps. In the first step, a historical population is simulated to establish mutation-drift equilibrium, and in the second step, recent population structures are generated, which can be very complex. A wide variety of genome architectures, ranging from infinitesimal model to single-locus model, can be simulated. The program is efficient in terms of computing time and memory requirements.
Availability: Executable versions of QMSim for Windows and Linux are freely available at http://www.aps.uoguelph.ca/~msargol/qmsim/.
Contact: msargol@uoguelph.ca
Retention time alignment algorithms for LC/MS data must consider non-linear shifts
Authors: Podwojski Katharina , Fritsch Arno , Chamrad Daniel C. , Paul Wolfgang , Sitek Barbara , Stühler Kai , Mutzel Petra , Stephan Christian , Meyer Helmut E. , Urfer Wolfgang , Ickstadt Katja , Rahnenführer Jörg 
Published: January 2009

Abstract
Motivation: Proteomics has particularly evolved to become of high interest for the field of biomarker discovery and drug development. Especially the combination of liquid chromatography and mass spectrometry (LC/MS) has proven to be a powerful technique for analyzing protein mixtures. Clinically orientated proteomic studies will have to compare hundreds of LC/MS runs at a time. In order to compare different runs, sophisticated preprocessing steps have to be performed. An important step is the retention time (rt) alignment of LC/MS runs. Especially non-linear shifts in the rt between pairs of LC/MS runs make this a crucial and non-trivial problem.
Results: For the purpose of demonstrating the particular importance of correcting non-linear rt shifts, we evaluate and compare different alignment algorithms. We present and analyze two versions of a new algorithm that is based on regression techniques, once assuming and estimating only linear shifts and once also allowing for the estimation of non-linear shifts. As an example for another type of alignment method we use an established alignment algorithm based on shifting vectors that we adapted to allow for correcting non-linear shifts also. In a simulation study, we show that rt alignment procedures that can estimate non-linear shifts yield clearly better alignments. This is even true under mild non-linear deviations.
Availability: R code for the regression-based alignment methods and simulated datasets are available at http://www.statistik.tu-dortmund.de/genetik-publikationen-alignment.html
Contact: katharina.podwojski@tu-dortmund.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Testing significance relative to a fold-change threshold is a TREAT
Authors: McCarthy Davis J. , Smyth Gordon K. 
Published: January 2009

AbstractMotivation: Statistical methods are used to test for the differential expression of genes in microarray experiments. The most widely used methods successfully test whether the true differential expression is different from zero, but give no assurance that the differences found are large enough to be biologically meaningful.Results: We present a method, t-tests relative to a threshold (TREAT), that allows researchers to test formally the hypothesis (with associated p-values) that the differential expression in a microarray experiment is greater than a given (biologically meaningful) threshold. We have evaluated the method using simulated data, a dataset from a quality control experiment for microarrays and data from a biological experiment investigating histone deacetylase inhibitors. When the magnitude of differential expression is taken into account, TREAT improves upon the false discovery rate of existing methods and identifies more biologically relevant genes.Availability: R code implementing our methods is contributed to the software package limma available at http://www.bioconductor.org.Contact: smyth@wehi.edu.au
Fast computation of neighbor seeds
Authors: Ilie Lucian , Ilie Silvana 
Published: January 2009

Abstract
Motivation: Alignment of biological sequences is one of the most frequently performed computer tasks. The current state of the art involves the use of (multiple) spaced seeds for producing high quality alignments. A particular important class is that of neighbor seeds which combine high sensitivity with reduced space requirements. Current algorithms for computing good neighbor seeds are very slow (exponential).
Results: We give a polynomial-time heuristic algorithm that computes better neighbor seeds than previous ones while being several orders of magnitude faster.
Contact: ilie@csd.uwo.ca
Automated procedure for candidate compound selection in GC-MS metabolomics based on prediction of Kovats retention index
Authors: Mihaleva V. V. , Verhoeven H. A. , de Vos R. C. H. , Hall R. D. , van Ham R. C. H. J. 
Published: January 2009

Abstract
Motivation: Matching both the retention index (RI) and the mass spectrum of an unknown compound against a mass spectral reference library provides strong evidence for a correct identification of that compound. Data on retention indices are, however, available for only a small fraction of the compounds in such libraries. We propose a quantitative structure-RI model that enables the ranking and filtering of putative identifications of compounds for which the predicted RI falls outside a predefined window.
Results: We constructed multiple linear regression and support vector regression (SVR) models using a set of descriptors obtained with a genetic algorithm as variable selection method. The SVR model is a significant improvement over previous models built for structurally diverse compounds as it covers a large range (360–4100) of RI values and gives better prediction of isomer compounds. The hit list reduction varied from 41% to 60% and depended on the size of the original hit list. Large hit lists were reduced to a greater extend compared with small hit lists.
Availability: http://appliedbioinformatics.wur.nl/GC-MS
Contact: roeland.vanham@wur.nl
Supplementary information: Supplementary data are available at Bioinformatics online.
A novel comprehensive wave-form MS data processing method
Authors: Chen Shuo , Li Ming , Hong Don , Billheimer Dean , Li Huiming , Xu Baogang J. , Shyr Yu 
Published: January 2009

Abstract
Motivation: Mass spectrometry (MS) can generate high-throughput protein profiles for biomedical research to discover biologically related protein patterns/biomarkers. The noisy functional MS data collected by current technologies, however, require consistent, sensitive and robust data-processing techniques for successful biomedical application. Therefore, it is important to detect features precisely for each spectrum, quantify them well and assign a unique label to features from the same protein/peptide across spectra.
Results: In this article, we propose a new comprehensive MS data preprocessing package, Wave-spec, which includes several novel algorithms. It can overcome several conventional difficulties. Wave-spec can be applied to multiple types of MS data generated with different MS technologies. Results from this new package were evaluated and compared to several existing approaches based on a MALDI-TOF MS dataset.
Availability: An example of MATLAB scripts used to implement the methods described in this article, along with Supplementary Figures, can be found at http://www.vicc.org/biostatistics/supp.php.
Contact: yu.shyr@vanderbilt.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
A flexible rank-based framework for detecting copy number aberrations from array data
Authors: LaFramboise Thomas , Winckler Wendy , Thomas Roman K. 
Published: January 2009

AbstractMotivation: DNA copy number aberration—both inherited and sporadic—is a significant contributor to a variety of human diseases. Copy number characterization is therefore an area of intense research. Probe hybridization-based arrays are important tools used to measure copy number in a high-throughput manner.Results: In this article, we present a simple but powerful nonparametric rank-based approach to detect deletions and gains from raw array copy number measurements. We use three different rank-based statistics to detect three separate molecular phenomena—somatic lesions, germline deletions and germline gains. The approach is robust and rigorously grounded in statistical theory, thereby enabling the meaningful assignment of statistical significance to each putative aberration. We demonstrate the flexibility of our approach by applying it to data from three different array platforms. We show that our method compares favorably with established approaches by applying it to published well-characterized samples. Power simulations demonstrate exquisite sensitivity for array data of reasonable quality.Conclusions: Our flexible rank-based framework is suitable for multiple platforms including single nucleotide polymorphism arrays and array comparative genomic hybridization, and can reliably detect gains or losses of genomic DNA, whether inherited, de novo, or somatic.Availability: An R package RankCopy containing the methods described here, and is freely available from the author's web site (http://mendel.gene.cwru.edu/laframboiselab/).Contact: Thomas.LaFramboise@case.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Seasonality of Birth Month of Children With Celiac Disease Differs From That in the General Population and Between Sexes and Is Linked to Family History and Environmental Factors
Authors: Lewy Hadas , Meirson Hadas , Laron Zvi 
Published: January 2009

ABSTRACTBackground:Patients with autoimmune diseases, such as type 1 diabetes mellitus, atopic dermatitis, autoimmune thyroid diseases, and multiple sclerosis have a different seasonality of month of birth (MOB) from the general population. This study was undertaken to determine the seasonality of MOB in children with celiac disease (CD), an autoimmune‐mediated enteropathy.Patients and Methods:The medical records of 431 children with CD (239 girls, 192 boys) were included in the study; 138 girls and 81 boys were under the age of 24 months. Data were analyzed by the cosinor method, which, in addition to statistical significance, provides parameters of rhythms. Statistical differences between groups were also analyzed by the χ2 test.Results:Patients with CD showed different patterns from that in the general population, which peaks in September. Boys and girls with CD were found to have a different seasonality of MOB (P < 0.02). Girls whose CD was diagnosed before age 24 months (peak July–August) had a different seasonality of MOB from those whose CD was diagnosed after age 24 months (no rhythm; P < 0.005) and showed a different seasonality from boys whose CD was diagnosed above 24 months (peak July; P < 0.02). In addition, we found a different seasonality of MOB in children with a family history of CD compared with those with no family history (P < 0.001).Conclusions:Girls with the diagnosis of CD and patients of both sexes with a family history of CD have a different pattern of seasonality of birth from the general population. This is suggestive of a perinatal virus infection as a plausible candidate for the primary trigger.
Clinical Evidence for Immunomodulatory Effects of Probiotic Bacteria
Authors: Ruemmele FM , Bier D , Marteau P , Rechkemmer G , Bourdet‐Sicard R , Walker WA , Goulet O 
Published: January 2009

ABSTRACTClose, tightly orchestrated interactions between the intestinal epithelium and the mucosa‐associated immune system are critical for normal intestinal absorptive and immunological functions. Recent data indicate that commensal intestinal microbiota represents a major modulator of intestinal homeostasis. This review analyzes the process of intestinal colonization and the interaction of microbiota with the intestinal epithelium and mucosal immune system, with special reference to the first years of extrauterine life. Dysregulation of the symbiotic interaction between intestinal microbiota and the mucosa may result in a pathological condition with potential clinical repercussions. Based on the concept that there is a beneficial and symbiotic relation between the host and endogenous microbiota, strategies aimed at directly modulating intestinal microbiota with regard to disease prevention or treatment have been developed. One strategy involves administering viable probiotic bacteria. Clinical evidence for the beneficial effect of probiotics in the prevention and/or treatment of necrotizing enterocolitis, infectious and antibiotic‐associated diarrhea, allergic diseases, and inflammatory bowel disorders is reviewed herein.
Anti‐Saccharomyces cerevisiae Antibodies Status Is Associated with Oral Involvement and Disease Severity in Crohn Disease
Authors: Russell RK , Ip B , Aldhous MC , MacDougall M , Drummond HE , Arnott IDR , Gillett PM , McGrogan P , Weaver LT , Bisset WM , Mahdi G , Wilson DC , Satsangi J 
Published: January 2009

ABSTRACTObjectives:To determine anti‐Saccharomyces cerevisiae antibodies (ASCA) status and its relation to disease phenotype in patients with inflammatory bowel disease (IBD).Patients and Methods:A total of 301 Scottish patients with early‐onset IBD—197 Crohn disease (CD), 76 ulcerative colitis (UC), 28 indeterminate colitis (IC)—and 78 healthy control individuals were studied. ASCA status (IgA, IgG) was determined by enzyme‐linked immunosorbent assay. ASCA status was then analyzed in relation to CD phenotype.Results:Patients with CD had a higher prevalence of ASCA than patients with UC and healthy controls: 82/197 versus 12/76, odds ratio (OR) 3.80 (1.93–7.50) and 82/197 versus 6/78, OR 8.56 (3.55–20.62), respectively. Univariate analysis showed that positive ASCA status was associated with oral CD (17/25 vs 59/153, OR 3.39 [1.38–8.34]), perianal CD (39/77 vs 38/108, OR 1.89 [1.04–3.44]) and the presence of granulomata (63/132 vs 15/52, OR 2.25 [1.13–4.48]) and also with markers of disease severity: raised C‐reactive protein (44/90 vs 12/49, OR 2.95[1.36–6.37]), hypoalbuminemia (44/85 vs 20/74, OR 2.28[1.19–4.37]), and surgery (27/49 vs 54/147, OR 2.11 [1.10–4.06]). From multivariate analysis, the presence of oral disease (adjusted P = 0.001, OR 22.22 [3.41–142.86]) and hypoalbuminemia (adjusted P = 0.01, OR 4.78 [1.40–16.39]) was found to be independently associated with ASCA status. No association was demonstrated between ASCA and IBD candidate genes.Conclusions:Patients with CD had a higher prevalence of ASCA than did other patients with IBD. ASCA status described patients with CD who had a specific phenotype, showing an association with markers of disease severity and oral CD involvement.
The Low-Oxygen-Induced NAC Domain Transcription Factor ANAC102 Affects Viability of Arabidopsis Seeds following Low-Oxygen Treatment
Authors: Christianson Jed A. , Wilson Iain W. , Llewellyn Danny J. , Dennis Elizabeth S. 
Published: January 2009

Abstract
Low-oxygen stress imposed by field waterlogging is a serious impediment to plant germination and growth. Plants respond to waterlogging with a complex set of physiological responses regulated at the transcriptional, cellular, and tissue levels. The Arabidopsis (Arabidopsis thaliana) NAC domain-containing gene ANAC102 was shown to be induced under 0.1% oxygen within 30 min in both roots and shoots as well as in 0.1% oxygen-treated germinating seeds. Overexpression of ANAC102 altered the expression of a number of genes, including many previously identified as being low-oxygen responsive. Decreasing ANAC102 expression had no effect on global gene transcription in plants but did alter expression patterns in low-oxygen-stressed seeds. Increasing or decreasing the expression of ANAC102 did not affect adult plant survival of low-oxygen stress. Decreased ANAC102 expression significantly decreased germination efficiency following a 0.1% oxygen treatment, but increased expression had no effect on germination. This protective role during germination appeared to be specific to low-oxygen stress, implicating ANAC102 as an important regulator of seed germination under flooding.
The Temperature-Sensitive brush Mutant of the Legume Lotus japonicus Reveals a Link between Root Development and Nodule Infection by Rhizobia
Authors: Maekawa-Yoshikawa Makoto , Müller Judith , Takeda Naoya , Maekawa Takaki , Sato Shusei , Tabata Satoshi , Perry Jillian , Wang Trevor L. , Groth Martin , Brachmann Andreas , Parniske Martin 
Published: January 2009

Abstract
The brush mutant of Lotus japonicus exhibits a temperature-dependent impairment in nodule, root, and shoot development. At 26°C, brush formed fewer nodules, most of which were not colonized by rhizobia bacteria. Primary root growth was retarded and the anatomy of the brush root apical meristem revealed distorted cellular organization and reduced cell expansion. Reciprocal grafting of brush with wild-type plants indicated that this genotype only affected the root and that the shoot phenotype was a secondary effect. The root and nodulation phenotype cosegregated as a single Mendelian trait and the BRUSH gene could be mapped to the short arm of chromosome 2. At 18°C, the brush root anatomy was rescued and similar to the wild type, and primary root length, number of infection threads, and nodule formation were partially rescued. Superficially, the brush root phenotype resembled the ethylene-related thick short root syndrome. However, treatment with ethylene inhibitor did not recover the observed phenotypes, although brush primary roots were slightly longer. The defects of brush in root architecture and infection thread development, together with intact nodule architecture and complete absence of symptoms from shoots, suggest that BRUSH affects cellular differentiation in a tissue-dependent way.