bluuebunny/crossref_metadata_2025_split huggingface dataset:
A distribution free summarization method for Affymetrix GeneChip® arrays
Authors: Chen Zhongxue , McGee Monnie , Liu Qingzhong , Scheuermann Richard H. 
Published: December 2006

AbstractMotivation: Affymetrix GeneChip arrays require summarization in order to combine the probe-level intensities into one value representing the expression level of a gene. However, probe intensity measurements are expected to be affected by different levels of non-specific- and cross-hybridization to non-specific transcripts. Here, we present a new summarization technique, the Distribution Free Weighted method (DFW), which uses information about the variability in probe behavior to estimate the extent of non-specific and cross-hybridization for each probe. The contribution of the probe is weighted accordingly during summarization, without making any distributional assumptions for the probe-level data.Results: We compare DFW with several popular summarization methods on spike-in datasets, via both our own calculations and the ‘Affycomp II’ competition. The results show that DFW outperforms other methods when sensitivity and specificity are considered simultaneously. With the Affycomp spike-in datasets, the area under the receiver operating characteristic curve for DFW is nearly 1.0 (a perfect value), indicating that DFW can identify all differentially expressed genes with a few false positives. The approach used is also computationally faster than most other methods in current use.Availability: The R code for DFW is available upon request.Contact: mmcgee@smu.eduSupplementary information: Supplementary data are available at Bioinformatics online.
The automation of Nested Clade Phylogeographic Analysis
Authors: Panchal Mahesh 
Published: December 2006

AbstractSummary: ANeCA is a fully automated implementation of Nested Clade Phylogeographic Analysis. This was originally developed by Templeton and colleagues, and has been used to infer, from the pattern of gene sequence polymorphisms in a geographically structured population, the historical demographic processes that have shaped its evolution. Until now it has been necessary to perform large parts of the procedure manually. We provide a program that will take data in Nexus sequential format, and directly output a set of inferences. The software also includes TCS v1.18 and GeoDis v2.2 as part of automation.Availability: The software is available free of charge from . The program is written in Java and requires the Java 1.4 Runtime Environment (or later) to run. The source code is included in the package, and includes the source from TCS and GeoDis. ANeCA, TCS and GeoDis are released under the GNU General Public License.Contact: m.panchal@rdg.ac.uk
Exploiting large scale computing to construct high resolution linkage disequilibrium maps of the human genome
Authors: Lau Winston , Kuo Tai-Yue , Tapper William , Cox Simon , Collins Andrew 
Published: December 2006

AbstractSummary: Linkage disequilibrium (LD) maps increase power and precision in association mapping, define optimal marker spacing and identify recombination hot-spots and regions influenced by natural selection. Phase II of HapMap provides ∼2.8-fold more single nucleotide polymorphisms (SNPs) than phase I for constructing higher resolution maps. LDMAP-cluster, is a parallel program for rapid map construction in a Linux environment used here to construct genome-wide LD maps with &gt;8.2 million SNPs from the phase II data.Availability: The LD maps, LDMAP-cluster and documentation are available from:Contact: arc@soton.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online.
RelEx—Relation extraction using dependency parse trees
Authors: Fundel Katrin , Küffner Robert , Zimmer Ralf 
Published: December 2006

AbstractMotivation: The discovery of regulatory pathways, signal cascades, metabolic processes or disease models requires knowledge on individual relations like e.g. physical or regulatory interactions between genes and proteins. Most interactions mentioned in the free text of biomedical publications are not yet contained in structured databases.Results: We developed RelEx, an approach for relation extraction from free text. It is based on natural language preprocessing producing dependency parse trees and applying a small number of simple rules to these trees. We applied RelEx on a comprehensive set of one million MEDLINE abstracts dealing with gene and protein relations and extracted ~150 000 relations with an estimated perfomance of both 80% precision and 80% recall.Availability: The used natural language preprocessing tools are free for use for academic research. Test sets and relation term lists are available from our website ().Contact: katrin.fundel@bio.ifi.lmu.de
Genomic sweeping for hypermethylated genes
Authors: Goh Liang , Murphy Susan K. , Muhkerjee Sayan , Furey Terrence S. 
Published: December 2006

AbstractMotivation: Genes silenced by the aberrent methylation of nearby CpG islands can contribute to the onset or progression of cancer and represent potential biomarkers for diagnosis and prognosis. Relatively few have thus far been validated as hypermethylated in cancer among over 14 000 candidates with promoter region CpG islands. A descriptive set of genes known to be unmethylated in cancer does not exist. This lack of a negative set and a large number of candidates necessitated the development of a new approach to identify novel genes hypermethylated in cancer.Results: We developed a general method, cluster_boost, that in an imbalanced data setting predicts new minority class members given limited known samples and a large set of unlabeled samples. Synthetic datasets modeled after the hypermethylated genes data show that cluster_boost can successfully identify minority samples within unlabeled data. Using genome sequence features, cluster_boost predicted candidate hypermethylated genes among 14 000 genes of unknown status. In primary ovarian cancers, we determined the methylation status for 15 genes with different levels of support for being hypermethlyated. Results indicate cluster_boost can accurately identify novel genes hypermethylated in cancer.Availability: Software and datasets are freely available atContact: tsfurey@duke.eduSupplementary information: Supplementary data are available at Bioinformatics online.
The use of nitrous oxide in paediatric anaesthetic practice in the United Kingdom: a questionnaire survey*
Authors: Sheraton T. E. , Gildersleve C. D. , Hall J. E. 
Published: December 2006

SummaryNitrous oxide pollution is common in paediatric anaesthetic practice. A questionnaire was sent to all UK members of the Association of Paediatric Anaesthetists requesting details of three areas of their paediatric practice relating to nitrous oxide: attitudes to its use; current usage; and availability of alternatives. Replies were received from 296 (68%) consultants. Of these, 169 (57%) stated that their use of nitrous oxide had decreased over the last 5 years. One hundred and fifty‐eight (54%) considered theatre pollution a problem in paediatric anaesthesia. One hundred and sixty‐nine (57%) reported that in normal circumstances potential deleterious effects on patients influenced their use of nitrous oxide, whilst only 70 (24%) felt potential effects on staff influenced usage. Fifty‐five (18%) felt there should be some restriction in the availability of nitrous oxide.
The attitudes and beliefs of healthcare professionals on the causes and reporting of medication errors in a UK Intensive care unit
Authors: Sanghera I. S. , Franklin B. D. , Dhillon S. 
Published: December 2006

SummaryOur aim was to explore the attitudes and beliefs of healthcare professionals relating to the causes and reporting of medication errors in a UK intensive care unit. Medication errors were identified by the unit pharmacist and semi‐structured qualitative interviews conducted with 13 members of staff involved with 12 errors. Interviews were analysed using a model of human error theory. Staff identified many contributing factors, including poor communication and frequent interruptions. Organisational factors included lack of clarity on the responsibility of the second nurse's check for medication administration, lack of feedback on medication errors, and a common and accepted practice of administering medication without a complete medication order. Barriers to reporting included administrative paperwork and lack of encouragement by management. Greater feedback on medication errors seems essential to improve current practice and increase reporting.
Treatment of the first known case of king cobra envenomation in the United Kingdom, complicated by severe anaphylaxis
Authors: Veto T. , Price R. , Silsby J. F. , Carter J. A. 
Published: December 2006

SummaryWe report the first known case of envenomation following snake bite by a king cobra in the UK. The patient required tracheal intubation and ventilation. Treatment with king cobra antivenom resulted in anaphylaxis (bronchospasm and hypotension), requiring adrenaline infusion. The patient's trachea was extubated 11 h after administration of antivenom.
Neurocardiogenic syncope in the obstetric patient
Authors: Saqr L. , Kumar M. M. 
Published: December 2006

SummaryWe report two patients who presented to our obstetric unit with a diagnosis of neurocardiogenic syncope. The first patient presented to the obstetricians in the second trimester having had two episodes of syncope during her pregnancy. The second patient had a pacemaker fitted prior to conceiving. We present the peri‐partum management of both these patients.
Tumour lysis syndrome developing during an operation
Authors: Lee M. H. , Cheng K. I. , Jang R. C. , Hsu J. H. , Dai Z. K. , Wu J. R. 
Published: December 2006

SummaryWe describe an unusual case of tumour lysis syndrome in a child with a high‐grade lymphoma undergoing a staging laparotomy. The patient presented with a refractory ventricular arrhythmia, which required continuous resuscitation in the operating room and continuous venous‐venous haemodialysis in the intensive care unit. This case report suggests that surgery is a possible trigger for developing tumour lysis syndrome, so anaesthetists should be alert to this possibility during surgery in patients with pre‐existing high tumour burdens.
Anaesthesia services in developing countries: defining the problems
Authors: Hodges S. C. , Mijumbi C. , Okello M. , McCormick B. A. , Walker I. A. , Wilson I. H. 
Published: December 2006

SummaryWe describe the use of a questionnaire to define the difficulties in providing anaesthesia in Uganda. The results show that 23% of anaesthetists have the facilities to deliver safe anaesthesia to an adult, 13% to deliver safe anaesthesia to a child and 6% to deliver safe anaesthesia for a Caesarean section. The questionnaire identified shortages of personnel, drugs, equipment and training that have not been quantified or accurately described before. The method used provides an easy and effective way to gain essential data for any country or national anaesthesia society wishing to investigate anaesthesia services in its hospitals. Solutions require improvements in local management, finance and logistics, and action to ensure that the importance of anaesthesia within acute sector healthcare is fully recognised. Major investment in terms of personnel and equipment is required to modernise and improve the safety of anaesthesia for patients in Uganda.
A Neoproterozoic glacially influenced basin margin succession and ‘atypical’ cap carbonate associated with bedrock palaeovalleys, Mirbat area, southern Oman
Authors: Rieu R. , Allen P.A. , Etienne J.L. , Cozzi A. , Wiechert U. 
Published: December 2006

ABSTRACTThe Ayn Formation of the Neoproterozoic Mirbat Group comprises <400 m of little‐deformed, glacially influenced basin margin deposits. These deposits are preserved in several palaeovalleys eroded in crystalline basement and overlain by a discontinuous cap carbonate. The Ayn Formation and the cap carbonate, which are superbly exposed along a 20 km SW–NE‐striking escarpment in south Oman, provide important insights into the processes operating on a basin margin during a Neoproterozoic glaciation and its demise. The Ayn Formation comprises units of glacimarine rain‐out diamictite and sediment gravity flow deposits, alternated with units of fluvial and deltaic sandstones and conglomerates, which may have formed by proglacial outwash. The stratigraphic evolution of the Ayn Formation indicates a highly active hydrological cycle during a phase of overall (glacio‐eustatic?) low stand when glaciers advanced into and receded upon bedrock valleys. The transgressive cap carbonate was deposited primarily in shallow marine or shallow lacustrine environments over palaeohighs during the deglaciation, and was partly reworked into deeper parts of the basin through sediment gravity flow processes. Locally, the cap carbonate transgresses over crystalline basement containing a network of fissures filled with carbonate originating from the cap. The δ13C isotopic composition of the cap carbonate varies systematically between −3.5 and +5.8‰ Pee Dee Belemnite standard, in common with other older Cryogenian examples.
Miocene extensional basin development in the Betic Cordillera, SE Spain revealed through analysis of the Alhama de Murcia and Crevillente Faults
Authors: Meijninger B. M. L. , Vissers R. L. M. 
Published: December 2006

ABSTRACTThe Alhama de Murcia and Crevillente faults in the Betic Cordillera of southeast Spain form part of a network of prominent faults, bounding several of the late Tertiary and Quaternary intermontane basins. Current tectonic interpretations of these basins vary from late‐orogenic extensional structures to a pull‐apart origin associated with strike–slip movements along these prominent faults. A strike–slip origin of the basins, however, seems at variance both with recent structural studies of the underlying Betic basement and with the overall basin and fault geometry. We studied the structure and kinematics of the Alhama de Murcia and Crevillente faults as well as the internal structure of the late Miocene basin sediments, to elucidate possible relationships between the prominent faults and the adjacent basins. The structural data lead to the inevitable conclusion that the late Miocene basins developed as genuinely extensional basins, presumably associated with the thinning and exhumation of the underlying basement at that time. During the late Miocene, neither the Crevillente fault nor the Alhama de Murcia fault acted as strike–slip faults controlling basin development. Instead, parts of the Alhama de Murcia fault initiated as extensional normal faults, and reactivated as contraction faults during the latest Miocene–early Pliocene in response to continued African–European plate convergence. Both prominent faults presently act as reverse faults with a movement sense towards the southeast, which is clearly at variance with the commonly inferred dextral or sinistral strike–slip motions on these faults. We argue that the prominent faults form part of a larger scale zone of post‐Messinian shortening made up of SSE‐ and NNW‐directed reverse faults and NE to ENE‐trending folds including thrust‐related fault‐bend folds and fault‐propagation folds, transected and displaced by, respectively, WNW‐ and NNE‐trending, dextral and sinistral strike–slip (tear or transfer) faults.
Human Fanconi A cells are susceptible to TRAIL‐induced apoptosis
Authors: Pigullo Simona , Ferretti Elisa , Lanciotti Marina , Bruschi Maurizio , Candiano Giovanni , Svahn Johanna , Haneline Laura , Dufour Carlo , Pistoia Vito , Corcione Anna 
Published: December 2006

SummaryTumour necrosis factor (TNF) contributes to the pathogenesis of bone marrow failure in Fanconi anaemia (FA) patients. The sensitivity of haematopoietic cells from FA, complementation group A (FANCA) subjects, who represent the majority of FA patients, to TNF‐related apoptosis‐inducing ligand (TRAIL) is unknown. The human lymphoblastoid FANCA HSC072 cell line and the genetically corrected counterpart HSC072FANCA‐neo were tested for apoptoptic response to TRAIL using flow cytometry and Western blotting. FANCA cells were more sensitive to TRAIL‐induced apoptosis than their corrected counterparts, indicating that TRAIL negatively regulates haematopoietic FANCA cell lines. This effect involved poly(ADP‐ribose) polymerase‐1 cleavage and caspase‐8 activation.
Purified allergens vs. complete extract in the diagnosis of plane tree pollen allergy
Authors: Asturias J. A. , Ibarrola I. , Amat P. , Tella R. , Malet A. , Cisteró‐Bahíma A. , Enrique E. , Malek T. , Martínez A. 
Published: December 2006

SummaryBackground
Plane tree pollen allergy is a clinical disorder affecting human population in cities of Europe, North America, South Africa, and Australia.Objective
To compare IgE‐reactivity of the natural and recombinant forms of two major plane allergens, Pla a 1 and Pla a 2, with the reactivity of Platanus acerifolia pollen extract.Methods
Forty‐seven patients with P. acerifolia allergy, 15 of them monosensitized, and 24 control subjects were included in the study. Natural Pla a 1 and Pla a 2 were purified by standard chromatographic methods and recombinant proteins were expressed in Escherichia coli. Skin prick test and determination of specific IgE were performed with commercial P. acerifolia extract and natural and recombinant purified allergens.Results
Pla a 1 and Pla a 2 were responsible for 79% of the IgE‐binding capacity against P. acerifolia pollen extract. A high correlation has been found between the IgE response to nPla a 1 (R=0.80; P<0.001) or nPla a 2 (R=0.79; P<0.001) vs. P. acerifolia extract as well as between natural and recombinant Pla a 1 (R=0.89; P<0.001). Skin testing showed no significant differences between extract and nPla a 2, whereas a higher reactivity was found with nPla a 1. In contrast, rPla a 1 revealed markedly reduced sensitivity in comparison with extract by skin prick test and specific IgE. The sensitivity of the mix Pla a 1+Pla a 2 was 100% and 87.5% for monosensitized and polysensitized patients, respectively, with no false‐positive reactions detected.Conclusion
Pla a 1 and Pla 2 are sufficient for a reliable diagnosis of P. acerifolia in most patients and induce comparable skin test reactivity as a whole extract.
Analysis of the inducible nitric oxide synthase gene polymorphisms in Czech patients with atopic diseases
Authors: Holla L. I. , Stejskalova A. , Znojil V. , Vasku A. 
Published: December 2006

SummaryBackground
Nitric oxide (NO) is an important mediator of physiologic processes in the airways; it plays a significant role in the regulation of the T helper type 1/type 2 balance and contributes to the development of atopic diseases.Objective
We analysed several polymorphisms mainly in the promoter region of the inducible NO synthase (NOS2, iNOS) gene and investigated their associations with asthma and/or atopic phenotypes.Methods
We performed a case–control study in 994 subjects (661 patients with atopic disorders, with subgroups of 304 patients with allergic asthma, and 333 healthy individuals), matched for sex, living in the same geographical area. Screening for polymorphisms was performed by combination of PCR and direct sequencing analysis.Results
We analysed 14 nucleotide sequence variants, seven most common of which were typed in quite large groups of our asthmatic, atopic and control populations. None of these seven frequent polymorphisms was associated with the phenotype bronchial asthma or other atopic diseases. Nevertheless, three from six common promoter polymorphisms showed a significant relation to feather's positivity (P value from 0.01 to 0.03) and the NOS2 608Leu variant was significantly associated with asthma severity [pcorr=0.0005; odds ratio (OR)=5.00, 95% confidence interval (CI): 1.88–13.33]. In haplotype analysis, the most common −2447C/−1659C/−1026G/−0.7del/−277A/Ser608 haplotype was associated with a lower risk of asthma when compared with the common haplotypes with frequency more than 5% (P=0.01, pcorr<0.05; OR=0.65, 95% CI: 0.56–0.77).Conclusion
Our findings suggest that inducible NOS can play a role in atopic disorders, and several polymorphisms in its gene may be important for asthma protection or susceptibility.
Cytokines and soluble CD14 in breast milk in relation with atopic manifestations in mother and infant (KOALA Study)
Authors: Snijders B. E. P. , Damoiseaux J. G. M. C. , Penders J. , Kummeling I. , Stelma F. F. , Van Ree R. , Van Den Brandt P. A. , Thijs C. 
Published: December 2006

SummaryBackground
Conflicting evidence exists concerning the protective role of breastfeeding in allergy and atopic disease aetiology. Breast milk contains biologically active molecules influencing the innate immune system of newborns.Objective
We aim to assess whether cytokines (TGF‐β1, IL‐10 and IL‐12) and soluble CD14 (sCD14) in breast milk are influenced by maternal atopic constitution and modify the development of atopic manifestations in infants.Methods
Milk samples were collected at 1 month post‐partum of 315 lactating mothers participating in the ongoing KOALA Birth Cohort Study. The cytokines and sCD14 were analysed by ELISA in the aqueous fraction. We compared the concentrations of cytokines and sCD14 in breast milk between mothers with and without an allergic history and also with and without allergic sensitization (specific IgE). Associations of cytokines and sCD14 with the development of eczema, wheezing in the first 2 years of life and allergic sensitization of infants at the age of 2 years were analysed by multivariate logistic regression analyses to correct for confounders.Results
We found higher sCD14 levels in mothers with a positive vs. negative allergic history (7.6 vs. 7.0 μg/mL; P=0.04) and in mothers who were sensitized vs. non‐sensitized (7.8 vs. 7.1 μg/mL; P=0.03). None of the studied immune factors were associated with infant's atopic outcomes. IL‐10 was not detected above the detection limit of 0.2 pg/mL.Conclusion
Taking together the results of the present and previous studies, we conclude that there is no convincing evidence for a relation between TGF‐β1, sCD14, IL‐10 or IL‐12 in breast milk and atopic manifestations in infants.
How we do it: A novel approach to the skin–abutment interface of the bone‐anchored hearing aid: use of local skin flaps
Authors: Persaud R.A.P. , Papadimitriou N. , Siva T. , Kothari P. , Quinn J.S. 
Published: December 2006

Keypoints• Various techniques involving skin grafts have been described to obtain thin hairless immobile skin at the abutment interface of the bone‐anchored hearing aid (BAHA), but none are without significant complications such as necrosis and/or infection leading to total graft failure.• A novel technique involving four local thin skin flaps was developed to prevent serious complications.• The procedure essentially involves raising skin flaps at the intradermal level leaving the hair follicles in the subcutaneous tissue, which is subsequently excised.• We have used the skin‐flap approach around 21 BAHAs on 19 patients (two patients had bilateral devices) and the only complications were minor skin loss immediately adjacent to the implants in two patients and mild skin infections, which settled with topical antibiotics, in three patients.• The innovative technique described is simple and straightforward, and does not require any special instrumentation. Furthermore, it may have specific advantages, in terms of morbidity, over contemporary skin grafting methods primarily because of the retained intrinsic blood supply of the skin flaps.