bluuebunny/crossref_metadata_2025_split huggingface dataset:
Why are some ectopic pregnancies characterized as pregnancies of unknown location at the initial transvaginal ultrasound examination?
Authors: KIRK EMMA , DAEMEN ANNELEEN , PAPAGEORGHIOU ARIS T. , BOTTOMLEY CECILIA , CONDOUS GEORGE , DE MOOR BART , TIMMERMAN DIRK , BOURNE TOM 
Published: October 2008

AbstractObjective. To compare the appearance and behavior of ectopic pregnancies (EPs) initially classified as pregnancies of unknown location (PULs) to those visualized on the initial transvaginal ultrasound scan (TVS). Methods. An observational study over a four‐year period on women undergoing a TVS prior to diagnosis of a tubal EP. Demographic details, presenting symptoms, TVS findings, serum hCG and progesterone levels were recorded at the time of the initial TVS and at the time of diagnosis of the EP in those initially classified as a PUL. Results. 411 women with a tubal EP underwent a TVS prior to treatment. In 85.9% (353/411) the EP was visualized on the initial TVS while 14.1%(58/411) were initially classified as PULs. Those initially classified as PULs had significantly lower mean gestational age and mean initial human chorionic gonadotrophin (hCG) levels, and significantly higher mean progesterone level at presentation than those where the EP was visualized on the initial TVS. Of those with a PUL, 60.3% (35/58) had the EP subsequently visualized on TVS. At the time of diagnosis these EPs were significantly smaller (p<0.0001); the appearance of the EPs, serum hCG and progesterone levels at the time of visualization on TVS were not significantly different from those visualized on the initial TVS. Conclusion. In women with EPs who are initially classified as PULs, failure of visualization of the EP on the initial TVS is likely to be due to the fact that they are too small and probably too early in the disease process.
Reduced adaptation of the pancreatic B cells during pregnancy is the major causal factor for gestational diabetes: Current knowledge and metabolic effects on the offspring
Authors: DEVLIEGER ROLAND , CASTEELS KRISTINA , VAN ASSCHE FRANS A. 
Published: October 2008

AbstractThis commentary summarizes current knowledge on the pathophysiology of gestational diabetes, focusing on the role of the endocrine pancreas and the β‐cells, their adaptation in normal pregnancy, and recent insights in the molecular basis for deficient adaptation in diabetes occurring during pregnancy. Additionally, the effects of disturbed maternal glucose metabolism during pregnancy on the glucose metabolism of the offspring are discussed.
Treatment of deep venous thrombosis in pregnant women
Authors: LYKKE JACOB A. , GRØNLYKKE THOR , LANGHOFF‐ROOS JENS 
Published: October 2008

AbstractThe recommended dosage of tinzaparin in the treatment of thromboembolism during pregnancy is 175 IU/kg/day, as for non‐pregnant subjects. In clinical practice, we have experienced a need for a higher dosage, especially in the initial phase of the treatment of deep vein thrombosis, based on four‐hour post‐dose measurements of anti‐Xa activity.Twenty‐two pregnant patients with a confirmed deep venous thrombosis were treated with tinzaparin either in a once‐ or twice‐daily regimen. Four‐hour post‐dosage plasma anti‐Xa activity was measured in 357 sequential blood samples during treatment. An higher dosage than recommended, was required to maintain anti‐Xa activity in the target range. We suggest that the starting dosage should be 250 IU/kg/day in a twice‐daily regimen, and that the dose in the initial phase be adjusted by daily monitoring of anti‐Xa.
Measurement of lower-leg volume change by quantitative computed tomography
Authors: Angelhed J.-E. , Strid L. , Bergelin E. , Fagerberg B. 
Published: October 2008

Background: Lower-leg edema is a common symptom in many diseases. A precise method with low variability for measurement of edema is warranted in order to obtain optimal conditions for investigation of treatment effects. Purpose: To evaluate computed tomography for precise measurement of lower-leg muscle and adipose tissue volumes using a very low level of effective radiation dose. Material and Methods: Eleven volunteers were examined three times during 1 day, either as two consecutive examinations in the morning and one single examination in the afternoon, or as one examination in the morning and two in the afternoon. Eleven scans with computed tomography were made at each examination, and lower-leg volumes were calculated from automatically measured scan areas and interscan distances. Volumes for muscle, adipose tissue, and bone were calculated separately. Minimal radiation dose was used. Results: Mean difference between the repeated examinations was −0.1 ml for total volume, −1.4 ml for muscle, and 1.6 ml for adipose tissue volume. The corresponding 95% confidence intervals were −6.5 to 6.0 ml, −3.5 to 6.5 ml, and −7.0 to 4.0 ml, respectively. The resulting effective dose was 0.5 µSv to one leg. Conclusion: Computed tomography can be used as a precise quantitative method to measure small volume changes of the lower leg as a whole, and separately for muscle and adipose tissue. The results were obtained with a negligible effective dose, lower than that delivered by modern fan-beam dual-energy X-ray absorptiometry whole-body examinations and equal to a few hours of background radiation.
A MODEL FOR THE CHROMOSPHERE/WIND OF 31 CYGNI AND ITS IMPLICATIONS FOR SINGLE STARS
Authors: Eaton Joel A. 
Published: October 2008

ABSTRACT
I develop a detailed empirical model for the chromosphere and wind of 31 Cyg based on a previously published analysis of International Ultraviolet Explorer spectra from the 1993 eclipse and on the thermodynamics of how the wind must be driven. I then use this model to interpret observations of single supergiant stars and to assess the evidence that their winds are fundamentally different from those of supergiants in binary systems. This model naturally predicts a certain level of clumping of the gas to balance the pressure that drives the wind. It also predicts that anisotropic turbulence, such as would result from transverse displacements of Alfven waves directed along radial magnetic flux lines, would not give the roughly Gaussian profiles of emission lines seen in cool giant stars. Furthermore, it implies that C ii] may not tell us much at all about general conditions in chromospheres. Finally, I speculate that chaotic magnetic fields, in dynamical equilibrium with the gas of the wind, are the actual driving mechanism.
A bioinformatics analysis of the cell line nomenclature
Authors: Sarntivijai Sirarat , Ade Alexander S. , Athey Brian D. , States David J. 
Published: October 2008

Abstract
Motivation: Cell lines are used extensively in biomedical research, but the nomenclature describing cell lines has not been standardized. The problems are both linguistic and experimental. Many ambiguous cell line names appear in the published literature. Users of the same cell line may refer to it in different ways, and cell lines may mutate or become contaminated without the knowledge of the user. As a first step towards rationalizing this nomenclature, we created a cell line knowledgebase (CLKB) with a well-structured collection of names and descriptive data for cell lines cultured in vitro. The objectives of this work are: (i) to assist users in extracting useful information from biomedical text and (ii) to highlight the importance of standardizing cell line names in biomedical research. This CLKB contains a broad collection of cell line names compiled from ATCC, Hyper CLDB and MeSH. In addition to names, the knowledgebase specifies relationships between cell lines. We analyze the use of cell line names in biomedical text. Issues include ambiguous names, polymorphisms in the use of names and the fact that some cell line names are also common English words. Linguistic patterns associated with the occurrence of cell line names are analyzed. Applying these patterns to find additional cell line names in the literature identifies only a small number of additional names. Annotation of microarray gene expression studies is used as a test case. The CLKB facilitates data exploration and comparison of different cell lines in support of clinical and experimental research.
Availability: The web ontology file for this cell line collection can be downloaded at http://www.stateslab.org/data/celllineOntology/cellline.zip.
Contact: dstates@umich.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Profile Comparer: a program for scoring and aligning profile hidden Markov models
Authors: Madera Martin 
Published: October 2008

Abstract
Summary: Profile Comparer (PRC) is a stand-alone program for scoring and aligning profile hidden Markov models (HMMs) of protein families. PRC can read models produced by SAM and HMMER, two popular profile HMM packages, as well as PSI-BLAST checkpoint files. This application note provides a brief description of the profile–profile algorithm used by PRC.
Availability: The C source code licensed under the GNU General Public Licence and Linux and Mac OS X binaries can be downloaded from http://supfam.org/PRC.
Contact: martin.madera@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database
Authors: Carver Tim , Berriman Matthew , Tivey Adrian , Patel Chinmay , Böhme Ulrike , Barrell Barclay G. , Parkhill Julian , Rajandream Marie-Adèle 
Published: October 2008

Abstract
Motivation: Artemis and Artemis Comparison Tool (ACT) have become mainstream tools for viewing and annotating sequence data, particularly for microbial genomes. Since its first release, Artemis has been continuously developed and supported with additional functionality for editing and analysing sequences based on feedback from an active user community of laboratory biologists and professional annotators. Nevertheless, its utility has been somewhat restricted by its limitation to reading and writing from flat files. Therefore, a new version of Artemis has been developed, which reads from and writes to a relational database schema, and allows users to annotate more complex, often large and fragmented, genome sequences.
Results: Artemis and ACT have now been extended to read and write directly to the Generic Model Organism Database (GMOD, http://www.gmod.org) Chado relational database schema. In addition, a Gene Builder tool has been developed to provide structured forms and tables to edit coordinates of gene models and edit functional annotation, based on standard ontologies, controlled vocabularies and free text.
Availability: Artemis and ACT are freely available (under a GPL licence) for download (for MacOSX, UNIX and Windows) at the Wellcome Trust Sanger Institute web sites: http://www.sanger.ac.uk/Software/Artemis/http://www.sanger.ac.uk/Software/ACT/
Contact: artemis@sanger.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Impact of dimeric organization of enzyme on its function: the case of photosynthetic water splitting
Authors: Jablonsky Jiri , Susila Petr , Lazar Dusan 
Published: October 2008

Abstract
Motivation: It is a question of whether the supramolecular organization of the protein complex has an impact on its function, or not. In the case of the photosystem II (PSII), water splitting might be influenced by cooperation of the PSIIs. Since PSII is the source of the atmospheric oxygen and because better understanding of the water splitting may contribute to the effective use of water as an alternative energy source, possible cooperation should be analyzed and discussed.
Results: We suggest that the dimeric organization of the PSII induces cooperation in the water splitting. We show that the model of monomeric PSII is unable to produce the oxygen after the second short flash (associated with the double turnover of the PSII), in contrast to the experimental data and model of dimeric PSII with considered cooperation. On the basis of this fact and partially from the support from other studies, we concluded that the double turnover of the PSII induced by short flashes might be caused by the cooperation in the water splitting. We further discuss a possibility that the known pathway of the electron transport through the PSII might be incomplete and besides D1-Y161, other cofactor which is able to oxidize the special chlorophyll pair (P680) must be considered in the monomeric PSII to explain the oxygen production after the second short flash.
Availability: Commented SBML codes (.XML files) of the monomeric and dimeric PSII models will be available (at the time of publication) in the BioModels database (www.ebi.ac.uk/biomodels).
Contact: lazard@seznam.cz
Supplementary information: Supplementary data are available at Bioinformatics online.
Addendum. Cytoprophet: aCytoscapeplug-in for protein and domain interaction networks inference
Authors: Morcos Faruck , Lamanna Charles , Sikora Marcin , Izaguirre Jesús 
Published: October 2008

AbstractAn additional reference is needed in the article Cytoprophet: a Cytoscape plug-in for protein and domain interaction networks inference. We include this reference as a matter of addendum.Contact: cytoprophet@cse.nd.edu
Factors Affecting Quality of Life of Children and Adolescents With Anorectal Malformations or Hirschsprung Disease
Authors: Hartman Esther E , Oort Frans J , Sprangers Mirjam AG , Hanneman Marianne JG , van Heurn LW Ernest , de Langen Zacharias J , Madern Gerard C , Rieu Paul NMA , van der Zee David C , Looyaard Nic , van Silfhout‐Bezemer Marina , Aronson Daniel C 
Published: October 2008

ABSTRACTObjectives:First, to compare the quality of life (QL) and perceived self‐competence of children and adolescents with anorectal malformations or Hirschsprung disease with that of reference groups. Second, to identify predictors of QL.Patients and Methods:A total of 491 patients with anorectal malformations or Hirschsprung disease were sent a questionnaire, which assessed QL (mental, physical), disease‐specific functioning (defecation‐related), perceived self‐competence (self‐esteem, athletic competencies, school attitude), and demographic characteristics (sex, age). The clinical characteristics (disease severity, presence of congenital anomalies) were extracted from medical records.Results:More than 50% (316, 64%) of patients with anorectal malformations or Hirschsprung disease completed the questionnaire. On average, children and adolescents in both patient groups reported no differences in QL domains compared with the reference groups. However, standard deviations revealed considerable individual variation, indicating the presence of patients with high levels of QL as well as patients with low levels of QL. Children and adolescents in both patient groups reported psychosocial problems in all domains, compared with the reference groups. Females, older patients, and those with a severe form of the disease reported lower levels of perceived self‐competence and global disease‐specific functioning, which in turn predicted QL.Conclusions:Our results should alert clinicians to patients who are at risk for QL problems and may therefore be in need of extra care. Our findings illustrate the importance of both global disease‐specific functioning and perceived psychosocial competencies for enhancing the QL of these patients.
Long‐term Outcome of Colon Interposition After Esophagectomy in Children
Authors: Coopman S , Michaud L , Halna‐Tamine M , Bonnevalle M , Bourgois B , Turck D , Gottrand F 
Published: October 2008

ABSTRACTBackground and Objectives:Tissues derived from the colon, stomach, and jejunum have been used to replace the esophagus in childhood to cure esophageal atresia or stricture secondary to gastroesophageal reflux or the ingestion of corrosive agents. The outcome in adulthood of colon interposition performed at an early age has yet to be satisfactorily assessed. The aim of this single‐center retrospective study was to evaluate the long‐term nutritional, digestive, and respiratory outcome of all patients (n = 32) who underwent colon interposition during childhood in our hospital (1970–2001).Patients and Methods:Medical records of these subjects were reviewed and their nutritional (weight, height, 24‐hour food diary), digestive (questionnaire), and pulmonary function status evaluated.Results:Of the patients, 17 had esophageal atresia (7 males, median age at surgery 11 months, range 0.5–61) and 15 had ingested corrosive substances (10 males, median age at surgery 50 months, range 22–113). Complications occurred less than 1 year postoperatively in 53% and long‐term complications (occurring >1 year after surgery) in 84%. Long‐term complications were common: digestive symptoms were found in 85% (most frequently observed during the first 5 years of follow‐up), abnormal lung function in 7 (58%) of those tested (n = 12), feeding difficulties in 50%, scoliosis in 35%, and nutritional complications in 25%.Conclusions:Our study showed a high rate of sequelae following esophageal replacement. This highlights the need for multidisciplinary long‐term follow‐up into adulthood, and research into alternatives to colon interposition as treatment for esophageal strictures.
Lymphocytic Gastritis and Celiac Disease in Indian Children: Evidence of a Positive Relation
Authors: Prasad Kaushal K , Thapa Babu R , Lal Sadhna , Sharma Arun K , Nain Chander K , Singh Kartar 
Published: October 2008

ABSTRACTObjectives:Lymphocytic gastritis (LG) is characterized by the presence of ≥25 lymphocytes/100 epithelial cells in the gastric surface and pit epithelium. An association of LG with Helicobacter pylori infection or celiac disease (CD) has been suggested. The aim of this study was to verify the relation of LG with CD, with and without H pylori infection, in children.Patients and Methods:A total of 164 children with CD diagnosed between June 2003 and October 2005, in whom gastric and duodenal biopsies were performed simultaneously, were enrolled prospectively. The control group was composed of 164 children without CD, matched for sex and age, who were undergoing upper digestive endoscopy. H pylori was searched for in gastric biopsy specimens sectioned and stained with hematoxylin and eosin, and a modified Giemsa stain for H pylori was performed for confirmation. The Student t test was used to compare quantitative measurements between groups.Results:LG was found in 69 (42.1%) patients with CD. Positive cases had a mean of 43.9 ± 1.5 intraepithelial lymphocytes per 100 surface epithelial cells, compared with a mean of 13.4 ± 0.4 in negative cases and 7.8 ± 0.5 in non‐CD control children (P < 0.0001). Patients not showing LG did, however, show significantly increased gastric intraepithelial lymphocytes compared with the control children. Nine of 164 CD patients, and 4 of 69 patients with LG, had positive results for H pylori.Conclusions:This study supports a pathogenetic relation between CD and LG. CD without LG also showed increased gastric intraepithelial lymphocytes. H pylori infection may be another cause of LG in children.
Combined Esophageal Multichannel Intraluminal Impedance and pH Monitoring After Repair of Esophageal Atresia
Authors: Fröhlich Thorsten , Otto Stephanie , Weber Peter , Pilic Denisa , Schmidt‐Choudhury Anjona , Wenzl Tobias G , Köhler Henrik 
Published: October 2008

ABSTRACTObjective:Gastroesophageal reflux disease and impaired esophageal motility is a frequent problem after repair of esophageal atresia (EA). Combined multichannel intraluminal impedance (MII) and pH measurement identifies acidic and weakly acidic esophageal bolus movements. Our aim was to evaluate gastroesophageal reflux and its association with gastrointestinal or extraintestinal symptoms using combined MII‐pH measurement.Patients and Methods:In all, 24 patients (4 months–23 years; 17 male, 7 female) with repaired EA were included in this study. A single catheter with 6 impedance channels and 1 pH channel was used to perform the 24‐hour MII‐pH study. Symptoms were recorded during the study as events and with a standardized questionnaire. In a subgroup of patients, an impedance swallowing test evaluating liquid and viscous bolus movements was performed.Results:We detected a total of 911 episodes of retrograde bolus movement, 379 acidic and 532 weakly acidic bolus movements. In all, 201 symptom events were recorded. Of these events, 42% were associated with retrograde bolus movements. More symptom events were associated with weakly acidic reflux (26%) than with acid reflux episodes (16%). There was a poor correlation between symptoms and MII‐pH study findings. In comparison with patients without esophageal surgery, EA patients showed significantly fewer complete swallows of liquid (42% vs 98%) and viscous material (18% vs 87%).Conclusions:In patients with corrected EA, half of the reflux events could be detected only by MII. We also demonstrated that weakly acidic reflux can be responsible for the patients' symptoms. However, patients may have few or no symptoms despite poor esophageal function and extensive gastroesophageal reflux disease.
Effects of Infliximab and Parenteral Nutrition on Albumin and Fibrinogen Synthesis Rates in Pediatric Crohn Disease
Authors: Steiner Steven J , Pfefferkorn Marian D , Fitzgerald Joseph F , Denne Scott C 
Published: October 2008

ABSTRACTObjectives:Tumor necrosis factor‐α (TNF‐α) may play a significant role in growth disturbance in pediatric Crohn disease. The aim of this study was to determine the effects of anti‐TNF‐α therapy on albumin and fibrinogen synthesis during both fasting and parenteral nutrition infusion in pediatric patients with active Crohn disease.Patients and Methods:Children with active Crohn disease scheduled for their initial dose of infliximab underwent assessment immediately before and 2 weeks following infliximab infusion. Using the stable isotope [d5] phenylalanine, rates of fractional and absolute albumin and fibrinogen synthesis were calculated. Measurements were made in both the fasting and parenterally fed states.Results:Fifteen children (mean age 14.9 ± 0.3) completed the study. The mean serum albumin changed from 3.59 ± 0.08 to 3.66 ± 0.04 g/dL, and the mean fibrinogen level decreased from 230 ± 17 to 187 ± 8 mg/dL (P < 0.05) following infliximab therapy. During fasting, there were no changes in albumin and fibrinogen synthesis rates following infliximab. During parenteral nutrition infusion, the fractional albumin synthesis rate changed from 11.8% to 15.1%/day (P = 0.06), and the absolute albumin synthesis rate increased from 192 to 248 mg · kg−1 · day−1 (P < 0.05), whereas no changes in fibrinogen synthesis rates were observed. Synthesis rates of albumin and fibrinogen were increased during parenteral nutrition infusion compared with the fasting state.Conclusions:Following infliximab therapy, during parenteral nutrition infusion, albumin synthesis increased significantly. Conversely, serum fibrinogen levels decreased following infliximab therapy in the absence of significant change in synthesis rates.