bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intrapartum translabial ultrasound (ITU): sonographic landmarks and correlation with successful vacuum extraction
Authors: Henrich W. , Dudenhausen J. , Fuchs I. , Kämena A. , Tutschek B. 
Published: October 2006

AbstractObjectiveHaving studied intrapartum translabial ultrasound (ITU) to define easily obtainable sonographic criteria during maternal pushing, we used it dynamically immediately before vacuum extraction to determine its use in predicting successful operative vaginal delivery.MethodsIn a pilot study, maternal and fetal landmarks were determined sonographically during maternal pushing from a mid‐sagittal translabial insonation using a curved array transducer in women delivering singleton fetuses in cephalic presentation spontaneously. With this transducer placed infrapubically (‘infrapubic plane’), easily obtainable landmarks and signs were: (i) the ‘infrapubic line’, perpendicular to the long axis of the pubic joint and extending dorsally from its inferior margin in a mid‐sagittal plane, (ii) the widest fetal head diameter and its movement with regard to the infrapubic line during pushing, and (iii) the ‘head direction’ with respect to the long axis of the symphysis. A three‐dimensional reconstruction from a computed tomographic (CT) dataset of a normal female pelvis was then used to quantify accurately the spatial relationship between the infrapubic line and the anatomical landmarks. Finally, 20 pregnant women in spontaneous term labor with normal singleton fetuses in cephalic presentation and clinical indication for vacuum extraction were studied by ITU immediately before operative vaginal delivery.ResultsCT reconstruction demonstrated the infrapubic line to be 3 cm cranial to the parallel interspinous plane. Eleven of the 20 vacuum deliveries with the ‘head‐up’ sign (head pointing ventrally) and objective descent of the fetal head below the infrapubic line, both noted at the height of pushing, resulted in successful (‘simple’ or ‘moderately difficult’) operative delivery. Lack of descent or lack of passage below the infrapubic line and horizontal or downward head direction were poor prognostic signs.ConclusionsITU provides objective information on the dynamics of the second stage of labor, head station and head direction. ITU may be used to assess the prognosis for operative vaginal delivery. Copyright © 2006 ISUOG. Published by John Wiley & Sons, Ltd.
Minimizing the effect of deafness and hidden terminal problem in wireless ad hoc networks using directional antennas
Authors: Gossain Hrishikesh , Cordeiro Carlos , Agrawal Dharma P. 
Published: October 2006

AbstractIn this work we address the issue of deafness and hidden terminal problem in mobile ad hoc networks (MANETs) using directional antennas. To minimize these effects, we propose a MAC protocol for directional Antennas (MDA) which employs a novel enhanced directional network allocation vector (EDNAV) scheme and an efficient technique of diametrically opposite directions (DOD) transmission of RTS and CTS packets. We compare MDA with IEEE 802.11 and two recently proposed directional MAC (DMAC) schemes and results show that MDA outperforms these protocols in the majority of scenarios investigated. We also point out that the performance does depend on the network topology and the traffic pattern. A shorter version of this has appeared in Globecom 2005.
Copyright © 2006 John Wiley & Sons, Ltd.
Variant maple syrup urine disease (MSUD)—The entire spectrum
Authors: Simon E. , Flaschker N. , Schadewaldt P. , Langenbeck U. , Wendel U. 
Published: October 2006

SummaryBackground: In the rare inborn autosomal recessive disorder maple syrup urine disease (MSUD) the accumulation of the branched‐chain amino acids (BCAAs) and their metabolic products results in acute and chronic brain dysfunction. About 20% of the patients suffer from non‐classic variant forms of MSUD of different clinical severity. Aim: Up to now variant cases have mostly been published as individual case reports; the aim of this study was to give a comparative description of 16 individuals (aged 6–30 years) with different forms of variant MSUD. Methods: Laboratory data, information on clinical course and treatment as well as aspects of developmental, intellectual and social outcome were obtained retrospectively. Data from in vitro and in vivo methods measuring the degree of enzyme deficiency were included. Results: In addition to a mild phenotype, which fits well into the so‐called intermittent variant, and a more severe phenotype with a wider range from a mild variant to an almost classic form, which fits well into the so‐called intermediate variant, we assume the existence of an asymptomatic, non‐disease variant of MSUD. These clinical phenotypes are not unambiguously differentiable on the basis of biochemical parameters. Conclusion: A continuum of clinical severity from asymptomatic to very severe (border to classic) exists in variant MSUD. Apart from newborns with classic MSUD, also those with variant forms benefit from early diagnosis and start of adequate treatment.
Evaluation of quality of life and psychiatric morbidity in patients with malignant tumours of the skull base
Authors: Martinez-Devesa P , Barnes M L , Alcock C J , Kerr R S C , Milford C A 
Published: October 2006

In general, patients with malignant tumours of the skull base have a poor prognosis. Treatment may have a disfiguring physical and disabling mental effect on patients.To evaluate the effect of treatment on physical and mental quality of life in patients with skull base malignancy, we conducted a cross-sectional patient survey of 18 patients treated for such tumours, using the University of Washington (version 4) quality of life questionnaire and the hospital anxiety and depression scale.The total quality of life score (median value) was 980 (550–1125). Patients with anterior skull base malignancy scored lower than those with lateral skull base malignancy (p=0.003).In general, the worst individual domain scores were: mood (64 per cent); activity (69 per cent); and, specifically for patients with anterior skull base malignancy, taste (54 per cent, p=0.004) and anxiety (60 per cent, p=0.034).One-third of skull base cancer patients were at risk of suffering from mental distress and psychiatric morbidity (indicated as a score of more than seven on the hospital anxiety and depression scale).
Should FDG-PET scanning be routinely used for patients with an unknown head and neck squamous primary?
Authors: Silva P , Hulse P , Sykes A J , Carrington B , Julyan P J , Homer J J , Hastings D L , Slevin N J 
Published: October 2006

Background: Between 1 and 2 per cent of head and neck squamous cell carcinoma patients will reveal no evidence of a primary malignancy. The management of this group poses many problems, including the morbidity associated with wide field irradiation as well as the difficulty in treatment when a primary does emerge. The aim of this study was to assess the use of fluoro-deoxy-glucose positron emission tomography (FDG-PET) imaging in patients presenting with an unknown head and neck primary and to consider its routine use in such patients.Methods: We enrolled 25 patients into our study over a four year period. They all presented with a histologically proven, metastatic, squamous cell carcinoma of the neck for which no primary could be found despite full clinical, endoscopic and radiological evaluation with computed tomography (CT) and/or magnetic resonance imaging (MRI). Additionally, all the patients underwent imaging using FDG-PET. The images were interpreted by two radiologists experienced in PET imaging.Results: A primary was identified in nine of the 25 patients (42 per cent); however, of these patients, six had false positive results and only three patients were true positives with supportive histology. In the remaining 16 patients, no abnormality was identified on CT, MRI or PET. Of these 16 patients, two eventually displayed a primary carcinoma, the other 14 patients remaining without evidence of any primary.Conclusion: Despite the high number of positive PET scans, the actual true positive rate was 3/9 (33 per cent); conversely, the true negative rate was 14/16 (88 per cent). We conclude from this study that there is a role for FDG-PET in the patient with an unknown head and neck primary, particularly in the context of a negative PET scan.
Family cluster of cholesteatoma
Authors: Homøe P , Rosborg J 
Published: October 2006

Objective: We report an extremely rare case of family clustering of cholesteatoma.Method: Case reports and a review of the world literature concerning cholesteatoma and heredity are presented.Results: The family consists of parents and seven siblings of whom the mother and three sons have been surgically treated for cholesteatoma. All cholesteatomas in the family are acquired and all have a history of otitis media. Cholesteatomas occur with an incidence of 5/100 000 in Greenland, corresponding to two to three new cholesteatoma patients per year among the 57 000 inhabitants of Greenland. The family is very exceptional and interesting for further research concerning heredity in the pathogenesis of acquired cholesteatoma.Conclusion: To our knowledge this is the first report in the world literature of family clustering of acquired cholesteatoma. This case indicates that hereditary factors interplay with other factors in the pathogenesis of cholesteatoma.
Helix Interaction Tool (HIT): a web-based tool for analysis of helix-helix interactions in proteins
Authors: Burba Anne E. Counterman , Lehnert Ursula , Yu Eric Z. , Gerstein Mark 
Published: October 2006

Abstract
Motivation: In many proteins, helix–helix interactions can be critical to establishing protein conformation (folding) and dynamics, as well as determining associations between protein units. However, the determination of a set of rules that guide helix–helix interaction has been elusive. In order to gain further insight into the helix–helix interface, we have developed a comprehensive package of tools for analyzing helix–helix packing in proteins. These tools are available at . They include quantitative measures of the helix interaction surface area and helix crossing angle, as well as several methods for visualizing the helical interaction. These methods can be used for analysis of individual protein conformations or to gain insight into dynamic changes in helix interactions. For the latter purpose, a direct interface from entries in the Molecular Motions Database to the HIT site has been provided.
Contact: Mark.Gerstein@yale.edu
An algorithm for modularity analysis of directed and weighted biological networks based on edge-betweenness centrality
Authors: Yoon Jeongah , Blumer Anselm , Lee Kyongbum 
Published: October 2006

Abstract
Motivation: Modularity analysis is a powerful tool for studying the design of biological networks, offering potential clues for relating the biochemical function(s) of a network with the ‘wiring’ of its components. Relatively little work has been done to examine whether the modularity of a network depends on the physiological perturbations that influence its biochemical state. Here, we present a novel modularity analysis algorithm based on edge-betweenness centrality, which facilitates the use of directional information and measurable biochemical data.
Contact: kyongbum.lee@tufts.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Prediction of oxidoreductase-catalyzed reactions based on atomic properties of metabolites
Authors: Mu Fangping , Unkefer Pat J. , Unkefer Clifford J. , Hlavacek William S. 
Published: October 2006

Abstract
Motivation: Our knowledge of metabolism is far from complete, and the gaps in our knowledge are being revealed by metabolomic detection of small-molecules not previously known to exist in cells. An important challenge is to determine the reactions in which these compounds participate, which can lead to the identification of gene products responsible for novel metabolic pathways. To address this challenge, we investigate how machine learning can be used to predict potential substrates and products of oxidoreductase-catalyzed reactions.
Results: We examined 1956 oxidation/reduction reactions in the KEGG database. The vast majority of these reactions (1626) can be divided into 12 subclasses, each of which is marked by a particular type of functional group transformation. For a given transformation, the local structures of reaction centers in substrates and products can be characterized by patterns. These patterns are not unique to reactants but are widely distributed among KEGG metabolites. To distinguish reactants from non-reactants, we trained classifiers (linear-kernel Support Vector Machines) using negative and positive examples. The input to a classifier is a set of atomic features that can be determined from the 2D chemical structure of a compound. Depending on the subclass of reaction, the accuracy of prediction for positives (negatives) is 64 to 93% (44 to 92%) when asking if a compound is a substrate and 71 to 98% (50 to 92%) when asking if a compound is a product. Sensitivity analysis reveals that this performance is robust to variations of the training data. Our results suggest that metabolic connectivity can be predicted with reasonable accuracy from the presence or absence of local structural motifs in compounds and their readily calculated atomic features.
Availability: Classifiers reported here can be used freely for noncommercial purposes via a Java program available upon request.
Contact: wish@lanl.gov
Supplementary information: Supplementary data are available at Bioinformatics online.
Linkage analysis using sex-specific recombination fractions with GENEHUNTER-MODSCORE
Authors: Dietter Johannes , Mattheisen Manuel , Fürst Robert , Rüschendorf Franz , Wienker Thomas F. , Strauch Konstantin 
Published: October 2006

AbstractMotivation: Sex-specific marker maps have become increasingly available. We have implemented the usage of sex-specific recombination frequencies in the GENEHUNTER-MODSCORE program that performs multipoint linkage analysis. Furthermore, we have devised a consistent method to choose the combinations of male and female genetic positions at which linkage scores should be calculated. Marker coordinates can be read automatically from publicly available genetic maps.Results: In a MOD-score analysis of the COGA dataset provided for Genetic Analysis Workshop 14, the highest linkage peak on chromosome 1 further increases when using sex-specific maps, while some smaller peaks are decreased. Simulations confirm that the MOD score can be biased when a sex-averaged instead of the correct sex-specific map is employed. This shows that an adequate modeling of the female:male ratio of genetic distances is important, especially for complex traits.Availability: The new version of GENEHUNTER-MODSCORE can be downloaded from the following website:Contact: dietter@med.uni-marburg.de
SequenceLDhot: detecting recombination hotspots
Authors: Fearnhead Paul 
Published: October 2006

Abstract
Motivation: There is much local variation in recombination rates across the human genome—with the majority of recombination occuring in recombination hotspots—short regions of around ∼2 kb in length that have much higher recombination rates than neighbouring regions. Knowledge of this local variation is important, e.g. in the design and analysis of association studies for disease genes. Population genetic data, such as that generated by the HapMap project, can be used to infer the location of these hotspots. We present a new, efficient and powerful method for detecting recombination hotspots from population data.
Results: We compare our method with four current methods for detecting hotspots. It is orders of magnitude quicker, and has greater power, than two related approaches. It appears to be more powerful than HotspotFisher, though less accurate at inferring the precise positions of the hotspot. It was also more powerful than LDhot in some situations: particularly for weaker hotspots (10–40 times the background rate) when SNP density is lower (&lt; 1/kb).
Availability: Program, data sets, and full details of results are available at:
Contact: p.fearnhead@lancs.ac.uk
A Gibbs sampler for the identification of gene expression and network connectivity consistency
Authors: Brynildsen Mark P. , Tran Linh M. , Liao James C. 
Published: October 2006

Abstract
Motivation: Data from DNA microarrays and ChIP-chip binding assays often form the basis of transcriptional regulatory analyses. However, experimental noise in both data types combined with environmental dependence and uncorrelation between binding and regulation in ChIP-chip binding data complicate analyses that utilize these complimentary data sources. Therefore, to minimize the impact of these inaccuracies on transcription analyses it is desirable to identify instances of gene expression-ChIP-chip agreement, under the premise that inaccuracies are less likely to be present when separate data sources corroborate each other. Current methods for such identification either make key assumptions that limit their applicability and/or yield high false positive and false negative rates. The goal of this work was to develop a method with a minimal amount of assumptions, and thus widely applicable, that can identify agreement between gene expression and ChIP-chip data at a higher confidence level than current methods.
Results: We demonstrate in Saccharomyces cerevisiae that currently available ChIP-chip binding data explain microarray data from a variety of environments only as well as randomized networks with the same connectivity density. This suggests a high degree of inconsistency between the two data types and illustrates the need for a method that can identify consistency between the two data sources. Here we have developed a Gibbs sampling technique to identify genes whose expression and ChIP-chip binding data are mutually consistent. Compared to current methods that could perform the same task, the Gibbs sampling method developed here exceeds their ability at high levels (&gt;50%) of transcription network and gene expression error, while performing similarly at lower levels. Using this technique, we show that on average 73% more gene expression features can be captured per gene as compared to the unfiltered use of gene expression and ChIP-chip-derived network connectivity data. It is important to note that the method described here can be generalized to other transcription connectivity data (e.g. sequence analysis, etc.).
Availability: Our algorithm is available on request from the authors and soon to be posted on the web. See author's homepage for details,
Contact: liaoj@ucla.edu
Supplementary information: Supplementary data are available at Bioinformatics Online.
High-resolution spatial normalization for microarrays containing embedded technical replicates
Authors: Yuan Daniel S. , Irizarry Rafael A. 
Published: October 2006

Abstract
Motivation: Microarray data are susceptible to a wide-range of artifacts, many of which occur on physical scales comparable to the spatial dimensions of the array. These artifacts introduce biases that are spatially correlated. The ability of current methodologies to detect and correct such biases is limited.
Results: We introduce a new approach for analyzing spatial artifacts, termed ‘conditional residual analysis for microarrays’ (CRAM). CRAM requires a microarray design that contains technical replicates of representative features and a limited number of negative controls, but is free of the assumptions that constrain existing analytical procedures. The key idea is to extract residuals from sets of matched replicates to generate residual images. The residual images reveal spatial artifacts with single-feature resolution. Surprisingly, spatial artifacts were found to coexist independently as additive and multiplicative errors. Efficient procedures for bias estimation were devised to correct the spatial artifacts on both intensity scales. In a survey of 484 published single-channel datasets, variance fell 4- to 12-fold in 5% of the datasets after bias correction. Thus, inclusion of technical replicates in a microarray design affords benefits far beyond what one might expect with a conventional ‘n = 5’ averaging, and should be considered when designing any microarray for which randomization is feasible.
Availability: CRAM is implemented as version 2 of the hoptag software package for R, which is included in the Supplementary information.
Contact: dyuan@jhmi.edu
Supplementary information: Supplementary Data are available at Bioinformatics online.
Mechanisms of action of immune tolerance induction against factor VIII in patients with congenital haemophilia A and factor VIII inhibitors
Authors: Reipert Birgit M. , Van Den Helden Pauline M. W. , Schwarz Hans‐Peter , Hausl Christina 
Published: October 2006

SummaryIn its most severe form, haemophilia A is a life‐threatening haemorrhagic bleeding disorder that is caused by mutations in the factor VIII (FVIII) gene. About 25% of patients who receive replacement therapy with intravenous FVIII products develop neutralising antibodies (FVIII inhibitors) that inhibit the function of substituted FVIII. Long‐term application of high or low doses of FVIII has evolved as an effective strategy for eradicating antibodies and inducing long‐lasting immune tolerance. Despite clinical experience with the therapy, little is known about the immunological mechanisms that cause the downmodulation of FVIII‐specific immune responses or the induction of long‐lasting immune tolerance against FVIII. This review summarises current knowledge of the immunological mechanisms that might be involved in the induction of immune tolerance against FVIII in patients with haemophilia A who have FVIII inhibitors. In addition to data from patients with haemophilia A, data from patients who have had organ transplants or have immune‐related disorders, such as autoimmune diseases, are considered as well as data from animal models.
Differential cell division history between neutrophils and macrophages in their development from granulocyte–macrophage progenitors
Authors: Sugimoto Yuka , Katayama Naoyuki , Masuya Masahiro , Miyata Eri , Ueno Masaya , Ohishi Kohshi , Nishii Kazuhiro , Takakura Nobuyuki , Shiku Hiroshi 
Published: October 2006

SummaryThe appearance of monocytes before neutrophils in the blood during haematopoietic recovery in myelosuppressive patients is commonly observed, thus suggesting a difference in the cell division history between these two lineages in the differentiation from granulocyte–macrophage (GM) progenitors. We investigated the cell division histories of murine GM progenitors. When analysed by the dye dilution method, GM progenitors gave rise to Gr‐1+Fms+ and Gr‐1+Fms− cells that passed through similar rounds of cell division during initial 5 d of culture. The Gr‐1+Fms+ cells showed morphological features of monocytes, while Gr‐1+Fms− cells exhibited an immature morphology of neutrophils. In the subsequent culture, a decline in the number of Gr‐1+Fms+ cells was observed, while Gr‐1+Fms− cells increased. The proliferation of Gr‐1+Fms− cells and no cell division of Gr‐1+Fms+ cells were confirmed by DNA staining, Ki‐67 expression, membrane dye staining and bromodeoxyuridine incorporation. These Gr‐1+Fms− cells acquired mature neutrophil morphology, whereas Gr‐1+Fms+ cells became macrophages. These results demonstrate that GM progenitors generate postmitotic monocytes earlier than mature neutrophils. Our data may also offer one explanation for the rapid recovery of monocytes in comparison with neutrophils in the early phase of haematopoietic regeneration.