bluuebunny/crossref_metadata_2025_split huggingface dataset:
Potential pathways of indole acetic acid (IAA) biosynthesis in Euphorbia abyssinica
Authors: Aerts Raf , Prinsen Els , Muys Bart 
Published: August 2008

AbstractDesert candle (Euphorbia abyssinica J.F. Gmel.) (further referred to as EAG) is a succulent tree of dry deciduous and evergreen montane forest, woodland and shrub savanna. It occurs widely throughout dryland Africa, where it is appreciated as a live fence because it is easily propagated from untreated mature branch cuttings.Earlier we argued that the ability of large EAG branches to regenerate with ease in dry soil may be related to the natural plant growth regulator hormone indole acetic acid (IAA) contained in the latex of the plant. EAG latex samples from northern Ethiopia (n = 3) that were chemically analyzed contained on average 0.06 mg/l latex, as well as the IAA metabolites indole lactate (ILA) and indole ethanol (IEt). One sample also contained IAA conjugated to amino-acids and to glucose. Here we present a schematic overview of the potential pathways of IAA biosynthesis in EAG and suggest that auxin biosynthesis in EAG is tryptophane (Trp) dependent.
Phantom-calibrated versus automatic coronary artery mass quantification with multidetector-row computed tomography: in vitro and in vivo study
Authors: Serafin Z. , Lasek W. , Laskowska K. 
Published: August 2008

Background: Coronary artery calcium scoring is used as a method for cardiovascular risk stratification and monitoring of coronary heart disease. Automatic software-based calcium mass calculation has been proposed to improve the performance of the procedure. Purpose: To compare two algorithms of calcium mass measurement, automatic and phantom calibrated, with respect to correlation, measurement error, and accuracy in vitro and in vivo. Material and Methods: A cardiac phantom with calcium cylinder inserts was scanned with sequential non-overlapping collimation 4×2.5 mm, at 120 kV and 165 mAs. Fifty adults (37 men; mean age 46.2 years) were examined with the same settings using prospective electrocardiographic triggering to detect and quantify coronary artery calcifications. Calculations were performed with two methods: software-based automatic calcium mass measurement (ACM) and phantom-calibrated calcium mass measurement (CCM). Results: The total phantom calcium masses measured with ACM and CCM were 175.0±13.8 mg and 163.0±4.4 mg, respectively ( P<0.0001), and ACM produced a higher mean error (4.5 vs. 3.2; P<0.05). Results of ACM and CCM were strongly correlated to each other ( R=0.73–0.96; P<0.0001). Mean image noise in the patient study was 8.72±1.68 HU. Results of patient calcium scoring with ACM and CCM were significantly different (median 70.3 mg and 59.7 mg, respectively; P<0.0001), with a mean systematic error of 17.5% (limit of agreement between 14.6% and 20.4%). The use of ACM resulted in an altered quartile classification for 14% of patients, as compared to CCM; all of these patients were classified into a higher category. Conclusion: Our data indicate that multidetector-row computed tomography coronary calcium mass determination based on dedicated phantom calibration shows lower measurement error than an automatic software-based calculation method. The tested automatic software does not yet seem to be a reliable option for calcium mass measurement.
Recurrence after percutaneous ethanol ablation of simple hepatic, renal, and splenic cysts: is it true recurrence requiring an additional treatment?
Authors: Hahn S. T. , Han S. Y. , Yun E. H. , Park S. H. , Lee S. H. , Lee H. J. , Hahn H. J. , Hahn H. M. 
Published: August 2008

Background: Recurrence after percutaneous ethanol ablation (PEA) of benign hepatic and renal cysts has been common, resulting in re-treatment or additional surgery. However, in recent years, a few cases of spontaneous regression of recurrent cysts following PEA have been experienced, which led to the design of this study to evaluate cyst recurrence after PEA and the necessity of additional treatment. Purpose: To evaluate whether the initial recurrence after PEA of benign hepatic, renal, and splenic cysts is true recurrence, and to decide whether additional treatment is needed. Material and Methods: Thirty-nine benign cysts (21 hepatic, 17 renal, and one splenic) were treated with PEA. PEA was performed with injection of 13–900 ml (40–50% of the volume of aspirated fluid) of absolute ethanol into the cysts. For cysts larger than 100 ml, two or more PEAs were given in one session. Ultrasonography was then performed during a period of 12 months with 1–2-month intervals. Results: Two months after PEA, eight cysts (20.5%) regressed completely; another 31 cysts recurred with decreased size. After 6 months, 10 of the recurrent cysts had regressed spontaneously. Another four recurrent cysts regressed after 8 months, and three regressed after 12 months. Hence, 25 out of 39 (64.1%) cysts regressed within 12 months after PEA. The mean regression time of the 25 recurrent cysts was 6.3 months. All recurrent cysts, including the 14 that were lost to complete follow-up, showed gradual decrease overtime. There were no major complications associated with PEA. Conclusion: Initial relapse of a cyst following PEA does not signify true recurrence, but transient, reactive, or inflammatory fluid collections which eventually disappear within several months, and thus does not necessitate additional treatment.
A piglet model for detection of hypoxic-ischemic brain injury with magnetic resonance imaging
Authors: Munkeby B. H. , De Lange C. , Emblem K. E. , Bjørnerud A. , Kro G. A. B. , Andresen J. , Winther-Larssen E. H. , Løberg E. M. , Hald J. K. 
Published: August 2008

Background: Early detection of hypoxic-ischemic (HI) injury in the asphyxic newborn is important because present prognostic factors are inadequate. Furthermore, therapeutic interventions may have additional benefit if initiated in time. Purpose: To assess whether the use of a combined protocol including conventional magnetic resonance imaging (MRI), diffusion-weighted imaging (DWI), diffusion tensor imaging (DTI), and proton MR spectroscopy (MRS) could detect pathological findings in a piglet model 7 hours after HI. Material and Methods: Ten piglets were submitted to HI for 30 min followed by reoxygenation with 21% O2 for 7 hours. MRI at 1.5T was done prior to and 7 hours after the HI. Single-voxel proton MRS was performed, and apparent diffusion coefficient (ADC) and fractional anisotropy (FA) were measured in the basal ganglia. MRS identified N-acetylaspartate (NAA), choline (Cho), creatine (Cr), and lactate (Lac). Histology and microtubule-associated protein 2 (MAP-2) staining was performed in the basal ganglia at the end of the experiment. Results: Compared to baseline, ADC, NAA/Cho, and NAA/Cr were significantly reduced after 7 hours ( P<0.001, P=0.01, and P=0.05, respectively) and FA values were increased ( P<0.025). The ratios of Lac/Cho and Lac/NAA were significantly higher after 7 hours compared to baseline ( P<0.001). Presence of necrosis correlated well with reduced ADC ( RS=0.91) and presence of Lac ( RS=0.80). Histology and MAP-2 staining showed more than 90% necrosis in eight piglets, 60% in one piglet, and no necrosis in one piglet. Conclusion: Diffusion MRI and proton MRS can detect HI injury in the piglet brain 7 hours after hypoxia. DWI and MRS can be used to give useful prognostic information. This piglet model may potentially be used to mimic clinical situations and is suitable for further research investigating HI injury.
An unsupervised conditional random fields approach for clustering gene expression time series
Authors: Li Chang-Tsun , Yuan Yinyin , Wilson Roland 
Published: August 2008

Abstract
Motivation: There is a growing interest in extracting statistical patterns from gene expression time-series data, in which a key challenge is the development of stable and accurate probabilistic models. Currently popular models, however, would be computationally prohibitive unless some independence assumptions are made to describe large-scale data. We propose an unsupervised conditional random fields (CRF) model to overcome this problem by progressively infusing information into the labelling process through a small variable voting pool.
Results: An unsupervised CRF model is proposed for efficient analysis of gene expression time series and is successfully applied to gene class discovery and class prediction. The proposed model treats each time series as a random field and assigns an optimal cluster label to each time series, so as to partition the time series into clusters without a priori knowledge about the number of clusters and the initial centroids. Another advantage of the proposed method is the relaxation of independence assumptions.
Contact: ctli@dcs.warwick.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Multi-dimensional classification of biomedical text: Toward automated, practical provision of high-utility text to diverse users
Authors: Shatkay Hagit , Pan Fengxia , Rzhetsky Andrey , Wilbur W. John 
Published: August 2008

Abstract
Motivation: Much current research in biomedical text mining is concerned with serving biologists by extracting certain information from scientific text. We note that there is no ‘average biologist’ client; different users have distinct needs. For instance, as noted in past evaluation efforts (BioCreative, TREC, KDD) database curators are often interested in sentences showing experimental evidence and methods. Conversely, lab scientists searching for known information about a protein may seek facts, typically stated with high confidence. Text-mining systems can target specific end-users and become more effective, if the system can first identify text regions rich in the type of scientific content that is of interest to the user, retrieve documents that have many such regions, and focus on fact extraction from these regions. Here, we study the ability to characterize and classify such text automatically. We have recently introduced a multi-dimensional categorization and annotation scheme, developed to be applicable to a wide variety of biomedical documents and scientific statements, while intended to support specific biomedical retrieval and extraction tasks.
Results: The annotation scheme was applied to a large corpus in a controlled effort by eight independent annotators, where three individual annotators independently tagged each sentence. We then trained and tested machine learning classifiers to automatically categorize sentence fragments based on the annotation. We discuss here the issues involved in this task, and present an overview of the results. The latter strongly suggest that automatic annotation along most of the dimensions is highly feasible, and that this new framework for scientific sentence categorization is applicable in practice.
Contact: shatkay@cs.queensu.ca
Local coherence in genetic interaction patterns reveals prevalent functional versatility
Authors: Pu Shuye , Ronen Karen , Vlasblom James , Greenblatt Jack , Wodak Shoshana J. 
Published: August 2008

Abstract
Motivation: Epistatic or genetic interactions, representing the effects of mutating one gene on the phenotypes caused by mutations in one or moredistinct genes, can be very helpful for uncovering functional relationships between genes. Recently, the epistatic miniarray profiles (E-MAP) method has emerged as a powerful approach for identifying such interactions systematically. For E-MAP data analysis, hierarchical clustering is used to partition genes into groups on the basis of the similarity between their global interaction profiles, and the resulting descriptions assign each gene to only one group, thereby ignoring the multifunctional roles played by most genes.
Results: Here, we present the original local coherence detection (LCD) algorithm for identifying groups of functionally related genes from E-MAP data in a manner that allows individual genes to be assigned to more than one functional group. This enables investigation of the pleiotropic nature of gene function. The performance of our algorithm is illustrated by applying it to two E-MAP datasets and an E-MAP-like in silico dataset for the yeast Saccharomyces cerevisiae. In addition to recapitulating the majority of the functional modules and many protein complexes reported previously, our algorithm uncovers many recently documented and novel multifunctional relationships between genes and gene groups. Our algorithm hence represents a valuable tool for uncovering new roles for genes with annotated functions and for mapping groups of genes and proteins into pathways.
Availability: A Java implementation of the LCD algorithm is available at URL http://genepro.ccb.sickkids.ca/biclustering.html
Contact: shuyepu@sickkids.ca
Supplementary information: Supplementary data are available at Bioinformatics online.
siDRM: an effective and generally applicable online siRNA design tool
Authors: Gong Wuming , Ren Yongliang , Zhou Haiyan , Wang Yejun , Kang Shuli , Li Tongbin 
Published: August 2008

Abstract
Summary: Small interfering RNAs (siRNAs) have become an indispensable tool for the investigation of gene functions. Most existing siRNA design tools were trained on datasets assembled from confined origins, incompatible with the diverse siRNA laboratory practice to which these tools will ultimately be applied. We have performed an updated analysis using the disjunctive rule merging (DRM) approach on a large and diverse dataset compiled from siRecords, and implemented the resulting rule sets in siDRM, a new online siRNA design tool. siDRM also implements a few high-sensitivity rule sets and fast rule sets, links to siRecords, and uses several filters to check unwanted detrimental effects, including innate immune responses, cell toxic effects and off-target activities in selecting siRNAs. A performance comparison using an independent dataset indicated that siDRM outperforms 19 existing siRNA design tools in identifying effective siRNAs.
Availability: siDRM can be accessed at http://siRecords.umn.edu/siDRM/.
Contact: toli@biocompute.umn.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Seeder: discriminative seeding DNA motif discovery
Authors: Fauteux François , Blanchette Mathieu , Strömvik Martina V. 
Published: August 2008

Abstract
Motivation: The computational identification of transcription factor binding sites is a major challenge in bioinformatics and an important complement to experimental approaches.
Results: We describe a novel, exact discriminative seeding DNA motif discovery algorithm designed for fast and reliable prediction of cis-regulatory elements in eukaryotic promoters. The algorithm is tested on biological benchmark data and shown to perform equally or better than other motif discovery tools. The algorithm is applied to the analysis of plant tissue-specific promoter sequences and successfully identifies key regulatory elements.
Availability: The Seeder Perl distribution includes four modules. It is available for download on the Comprehensive Perl Archive Network (CPAN) at http://www.cpan.org.
Contact: martina.stromvik@mcgill.ca
Supplementary information: Supplementary data are available at Bioinformatics online.
Analyzing gene perturbation screens with nested effects models in R and bioconductor
Authors: Fröhlich Holger , Beißbarth Tim , Tresch Achim , Kostka Dennis , Jacob Juby , Spang Rainer , Markowetz F. 
Published: August 2008

Abstract
Summary: Nested effects models (NEMs) are a class of probabilistic models introduced to analyze the effects of gene perturbation screens visible in high-dimensional phenotypes like microarrays or cell morphology. NEMs reverse engineer upstream/downstream relations of cellular signaling cascades. NEMs take as input a set of candidate pathway genes and phenotypic profiles of perturbing these genes. NEMs return a pathway structure explaining the observed perturbation effects. Here, we describe the package nem, an open-source software to efficiently infer NEMs from data. Our software implements several search algorithms for model fitting and is applicable to a wide range of different data types and representations. The methods we present summarize the current state-of-the-art in NEMs.
Availability: Our software is written in the R language and freely avail-able via the Bioconductor project at http://www.bioconductor.org.
Contact: rainer.spang@klinik.uni-regensburg.de
An electron diffraction and Monte Carlo simulation study of diffuse scattering in Pb(Zr,Ti)O3
Authors: Baba-Kishi K. Z. , Welberry T. R. , Withers R. L. 
Published: August 2008

Transverse polarized diffuse streaks have been recordedviatransmission electron microscopy for a range of Pb(Zr1−xTix)O3ceramics spanning the entire phase diagram from the rhombohedral phase (x= 0.3), through the monoclinic morphotropic phase boundary region (MPB;x= 0.48) to the tetragonal phase (x = 0.7). Although the same type of streaks are observed over the whole composition range, they are strongest and most distinct in the rhombohedral phase and diminish in clarity as the MPB is approached. The streaks have been shown to correspond to diffuse planes of scattering in three dimensions and are oriented normal to the (cubic) 〈111〉cdirections. A Monte Carlo computer simulation model has been developed that convincingly reproduces the observed diffraction patterns in the rhombohedral phase. In this model the displacements of Pb ions in chains running along each of the 〈111〉cdirections are directed along the chain and are strongly correlated from cell to cell. There is no evidence of lateral correlation, indicating that neighbouring chains are essentially independent.
The subcellular Sox11 distribution pattern identifies subsets of mantle cell lymphoma: correlation to overall survival
Authors: Wang Xiao , Asplund A. Charlotta , Porwit Anna , Flygare Jenny , Smith C. I. Edvard , Christensson Birger , Sander Birgitta 
Published: August 2008

SummaryGene expression analysis demonstrated high expression of the neuronal transcription factor SOX11 in mantle cell lymphoma (MCL). In contrast to follicular lymphoma, small lymphocytic lymphoma and reactive lymphoid tissue, most MCLs tested (48/53 patients) expressed sox11 protein in the nucleus. Therefore nuclear sox11 expression represents a new tumour marker for a subset of MCL. However, 5/53 MCL cases expressed sox11 only in the cytoplasm; these MCL patients had a shorter survival compared to MCL with nuclear sox11 expression. These results suggest sox11 expression as a new diagnostic marker in MCL that could be related to the clinical and biological behaviour of MCL.
Practical blood dendritic cell vaccination for immunotherapy of multiple myeloma
Authors: Vari F. , Munster D. J. , Hsu J. L. , Rossetti T. R. , Mahler S. M. , Gray P. P. , Turtle C. J. , Prue R. L. , Hart D. N. J. 
Published: August 2008

SummaryTherapeutic vaccination combined with new drugs may cure multiple myeloma (MM). We have developed a bio‐process to purify CMRF‐56 monoclonal antibody (mAb) and a standard operating procedure to immunoselect blood dendritic cells (BDC). Leucopheresed mononuclear cells were cultured overnight, labelled with CMRF‐56 mAb and BDC prepared using a clinical scale immunoselection system. The mean BDC yield from healthy donors was 48% (n = 6, purity 28%). Preparations from MM patients (n = 6, yield 47%, purity 35%) primed cytotoxic T lymphocytes (CTL) to clinically relevant MM antigens. This procedure can be performed readily by clinical cell manufacturing units to facilitate BDC vaccination studies.
MOZ/TIF2‐induced acute myeloid leukaemia in transgenic fish
Authors: Zhuravleva Julia , Paggetti Jérôme , Martin Laurent , Hammann Arlette , Solary Eric , Bastie Jean‐Noël , Delva Laurent 
Published: August 2008

SummaryThe inv(8)(p11q13) chromosomal abnormality, described in acute myeloid leukaemias (AML), fuses the histone acetyl‐transferase (HAT) MYST3 (MOZ) gene with another HAT gene, NCOA2 (TIF2). We generated a transgenic zebrafish in which the MYST3/NCOA2 fusion gene was expressed under control of the spi1 promoter. An AML developed in 2 of 180 MYST3/NCOA2‐EGFP‐expressing embryos, 14 and 26 months after injection of the fusion gene in a one‐cell embryo, respectively. This leukaemia was characterised by an extensive invasion of kidneys by myeloid blast cells. This model, which is the first zebrafish model of AML, demonstrates the oncogenic potency of MYST3/NCOA2 fusion gene.
Influence of ethnicity on IGF‐I and procollagen III peptide (P‐III‐P) in elite athletes and its effect on the ability to detect GH abuse
Authors: Erotokritou‐Mulligan Ioulietta , Bassett E. Eryl , Cowan David A. , Bartlett Christiaan , McHugh Cathy , Sönksen Peter H. , Holt Richard I. G. ,   The GH‐2004 group
Published: August 2008

SummaryContext  A method based on the two GH dependent markers, IGF‐I and procollagen III peptide (P‐III‐P) has been proposed to detect exogenously administered GH. As previous studies involved predominantly white European elite athletes, it is necessary to validate the method in other ethnic groups.Objective  To examine serum IGF‐I and P‐III‐P in elite athletes of different ethnicities within 2 h of competing at national or international events.Design  Cross‐sectional observational study.Setting  National and International sporting events.Subjects  1085 elite athletes of different ethnicities.Intervention  Serum IGF‐I and P‐III‐P were measured and GH‐2000 discriminant function score was calculated. Effect of ethnicity was assessed.Results  In men, IGF‐I was 21·7 ± 2·6% lower in Afro‐Caribbeans than white Europeans (P < 0·0001) but there were no differences between other ethnic groups. In women, IGF‐I was 14·2 ± 5·1% lower in Afro‐Caribbeans (P = 0·005) and 15·6 ± 7·0% higher in Orientals (P = 0·02) compared with white Europeans. P‐III‐P was 15·2 ± 3·5%, 26·6 ± 6·6% and 19·3 ± 5·8% lower in Afro‐Caribbean (P < 0·0001), Indo‐Asian (P < 0·0001) and Oriental men (P = 0·001), respectively, compared with white European men. In women, P‐III‐P was 15·7 ± 4·7% lower in Afro‐Caribbeans compared to white Europeans (P =0·0009) but there were no differences between other ethnicities. Despite these differences, most observations were below the upper 99% prediction limits derived from white European athletes. All GH‐2000 scores lay below the cut‐off limit proposed for doping.Conclusions  The GH‐2000 detection method based on IGF‐I and P‐III‐P would be valid in all ethnic groups.