bluuebunny/crossref_metadata_2025_split huggingface dataset:
Geochemical constraints on the origin of enigmatic cemented chalks, Norfolk, UK
Authors: WOOLHOUSE G. , ANDREWS J. E. , MARCA-BELL A. , DENNIS P. F. 
Published: September 2008

AbstractVery hard cemented chalk stacks and crusts found locally in the upper part of the Cretaceous Chalk of north Norfolk, UK, are related to solution features. The solution features, mainly pipes and caves, formed after deposition of the overlying Middle Pleistocene Wroxham Crag, probably by routing of sub-glacial, or glacial, melt-waters derived from late Pleistocene glaciers. New geochemical (particularly stable isotope) data shows that cementation of the chalks, although related spatially to the solution features, was not caused by glacier-derived waters. The carbon isotope composition of the chalk cements is typically around −9.5‰, indicative of biologically active soils. Moreover, the oxygen isotope compositions of the cements, around −5‰, are incompatible with water δ18O values much below −9 to −10‰ (which probably precludes isotopically negative glacier-derived water), as resulting palaeo-temperatures are below zero. Taken together, the isotope data suggest chalk cementation occurred under interglacial conditions similar to the present. Dissolved calcium carbonate for cementation came from dissolution of reworked chalk in overlying MIS 12 glacial tills.
Dehydration, melting and related garnet growth in the deep root of the Amalaoulaou Neoproterozoic magmatic arc (Gourma, NE Mali)
Authors: BERGER JULIEN , CABY RENAUD , LIÉGEOIS JEAN-PAUL , MERCIER JEAN-CLAUDE C. , DEMAIFFE DANIEL 
Published: September 2008

AbstractThe Amalaoulaou Neoproterozoic island-arc massif belongs to the Gourma belt in Mali. The metagabbros and pyroxenites forming the main body of this arc root show the pervasive development of garnet. In the pyroxenites, the latter has grown by reaction between pyroxene and spinel during isobaric cooling. By contrast, in the metagabbros, garnet textures and relations to felsic veins exclude an origin through solid-state reactions only. It is proposed that garnet has grown following dehydration and localized melting of amphibole-bearing gabbros at the base of the arc. The plagioclase-saturated melts represented by anorthositic veins in the metagabbros and by trondhjemites in the upper part of the massif provide evidence for melting in the deep arc crust, which locally generated high-density garnet–clinopyroxene–rutile residues. Garnet growth and melting began around 850 °C at 10 kbar and the tonalitic melts were most probably generated around 1050 °C at P ≥ 10 kbar. This HT granulitic imprint can be related to arc maturation, leading to a P–T increase in the deep arc root and dehydration and/or dehydration-melting of amphibole-bearing gabbros. Observation of such features in the root of this Neoproterozoic island arc has important consequences, as it provides a link to models concerning the early generation of continental crust.
Sentinel lymph node biopsy in node-negative squamous cell carcinoma of the oral cavity and oropharynx
Authors: Burns P , Foster A , Walshe P , O'Dwyer T 
Published: September 2008

AbstractObjectives:Considerable controversy exists regarding the merits of elective neck dissection in patients with early stage oral cavity and oropharyngeal squamous cell carcinoma. It is highly desirable to have a method of identifying those patients who would benefit from further treatment of the neck when they are clinically node-negative. The purpose of the present study was to examine the use of sentinel lymph node biopsy in identifying occult neck disease in a cohort of patients with node-negative oral cavity and oropharyngeal squamous cell carcinoma.Design:We evaluated a total of 13 patients with oral cavity and oropharyngeal cancer who were clinically and radiologically node-negative.Results:A sentinel lymph node was found in all 13 patients, revealing metastatic disease in five patients, four of whom had one or more positive sentinel lymph nodes. There was one false negative result, in which the sentinel lymph node was negative for tumour whereas histological examination of the neck dissection specimen showed occult disease.Conclusion:In view of these findings, we would recommend the use of sentinel lymph node biopsy in cases of oral cavity and oropharyngeal squamous cell carcinoma, in order to aid the differentiation of those patients whose necks are harbouring occult disease and who require further treatment.
The septal body revisited
Authors: Elwany S , Salam S A , Soliman A , Medanni A , Talaat E 
Published: September 2008

AbstractIntroduction:The term septal body refers to a thickened area of the nasal septum which is located superior to the inferior turbinate and anterior to the middle turbinate. Despite its important role in changing nasal airflow resistance, it has received little attention. Clinically, a well developed septal body may be misdiagnosed as high septal deviation.Aim:The aim of the present study was to reassess the histological characteristics of the septal body mucosa and the morphometric differences between it and the adjacent septal mucosa. This information was then used to determine the exact location and surface area of the septal body.Materials and methods:The study was performed on 30 cadaveric specimens (60 sides). Serial numbered sections of the whole septal mucosa were stained with haematoxylin and eosin as well as periodic acid Schiff – Alcian blue. Morphometric analysis was performed to determine the histological differences between the septal body mucosa, the anterior septal mucosa and the inferior septal mucosa. The precise boundaries of the septal body area were then defined in a manner similar to the Mohs micrographic surgical technique.Results:The histological characteristics of the septal body mucosa included thick (more than 60 µm), pseudostratified, ciliated respiratory epithelium with goblet cells, abundant seromucinous glands and many blood sinusoids. Morphometric analysis showed that the septal body mucosa had thicker epithelium and more glandular acini and blood sinusoids than the rest of the septal mucosa. Mapping of the septal body area showed that its anterior end was 2.2 ± 0.3 cm (mean ± standard deviation) behind the caudal edge of the septal cartilage, and its inferior border was 1.1 ± 0.2 cm above the floor of the nose. The mean horizontal diameter of the septal body was 2.0 ± 0.15 cm, and the mean vertical diameter was 1.5 ± 0.11 cm.Conclusions:The present study determined the morphometric characteristics of the septal body as well as its location and surface area. The intimate relationship of the septal body to the internal nasal valve and the histological characteristics of its mucosa should stimulate research into its potential role in modifying nasal airflow pattern and resistance, and its role in changing the humidity and temperature of the inspiratory air stream.
Development of cavernous haemangioma following radical chemo-radiotherapy for nasopharyngeal carcinoma
Authors: Ellenbogen J R , Joshi S M , Kitchen N 
Published: September 2008

AbstractObjective:We report an adult case of nasopharyngeal carcinoma treated with radical chemo-radiotherapy, with subsequent development of a histologically proved temporal cavernous haemangioma within the radiation field.Method:Case report and review of the current literature concerning radiation-induced, secondary, space-occupying lesions.Conclusion:The increasing role of radiotherapy in nasopharyngeal carcinoma treatment, together with improved patient survival, is likely to lead to radiation-induced, secondary, space-occupying lesions being encountered more frequently. We emphasise the need to be vigilant for this important but relatively rare complication, which has significant associated morbidity.
Avian influenza viruses detected by surveillance of waterfowl in Ireland during 2003–2007
Authors: RALEIGH P. J. , FLYNN O. , O'CONNOR M. , O'DONOVAN T. , PURCELL B. , DE BURCA M. , REGAZZOLI V. , MINIHAN D. , CONNELL J. , MARKEY B. K. , SAMMIN D. J. 
Published: September 2008

SUMMARYSpecimens for the detection of avian influenza virus (AIV) were collected from 1937 waterfowl on the Wexford Sloblands, a major wetland reserve in southeast Ireland, between January 2003 and September 2007. During the same period, 1404 waterfowl were sampled at other locations in Ireland. Specimens were tested either by virus isolation or real-time reverse transcriptase polymerase chain reaction (rtRT–PCR). A total of 32 isolates of AIV, comprising nine subtypes, was obtained from specimens from the Sloblands compared with just one isolate from elsewhere in Ireland. Samples from nine other waterfowl, five of which were from the Sloblands, tested positive for AIV by rtRT–PCR. Ecological factors are likely to have contributed to the higher detection rate of AIV at the Sloblands compared with the rest of Ireland. It was concluded that targeted surveillance at such sites is a cost-effective means of monitoring the circulation of new AIVs in waterfowl, whereas widespread opportunistic sampling is unproductive and wasteful of resources.
Repair of aortic coarctation using temporary ascending to descending aortic bypass in children with poor collateral circulation
Authors: Christenson Jan T. , Sierra Jorge , Didier Dominique , Beghetti Maurice , Kalangos Afksendiyos 
Published: September 2008

Aortic coarctation can now be repaired surgically with excellent results. Even though rare, injury to the spinal cord resulting in paraplegia remains a major concern. Preoperative evaluation showing the absence of collateral circulation is valuable in order to introduce protective actions. This report describes our experience using a temporary bypass from the ascending to the descending aorta bypass in children undergoing surgical correction of aortic coarctation in the setting of poorly developed collateral circulation.Between 1990 and 2002, we undertook direct surgical repair in 56 patients with isolated aortic coarctation, 20 as neonates, 11 as infants, and 25 during childhood. From 1998 onwards, we introduced preoperative evaluation of the collateral circulation with magnetic resonance imaging. From that time, we placed a temporary bypass from the ascending to the descending aorta, using a polytetrafluoroethylene tube of 4 to 8 mm diameter, whenever distal pressures were shown to be 25 mmHg or less after test clamping, or when magnetic resonance imaging revealed absence of collateral circulation.We found excellent correlations between the direct intra-operative measurements of distal pressure and the findings at magnetic resonance imaging. Following introduction of the temporary bypass, we observed no neurological complications, nor were there any complications related to bypass. Freedom from restenosis was 96%.Preoperative magnetic resonance imaging, therefore, can accurately visualize poor collateral circulation in children with aortic coarctation. The use of a temporary bypass can possibly eliminate the risk of neurological sequels following direct repair of coarctation in children with poorly developed collateral circulation. The temporary bypass is both easy to apply and safe.
Resection of a cardiac aneurysm in an infant with anomalous origin of the left coronary artery from the pulmonary trunk
Authors: Grotenhuis Heynric B. , Backx Ad , Nijveld Aagje 
Published: September 2008

We describe an infant with an anomalous left coronary artery arising from the pulmonary trunk leading to myocardial ischaemia and development of an apical aneurysm of the left ventricle.Clinical presentation in general is based on myocardial hypoperfusion resulting in ischaemia and infarction. When presenting in infancy, however, then the features, as in our patient, may be tachypnea, dyspnea, failure to thrive and irritability, especially during feeding. Then, again as in our patient, it is possible to miss the definitive diagnosis, which is made by echocardiography and cardiac catheterization. Reimplantation of the anomalous left coronary artery into the aorta usually results in improvement of left ventricular function over time. In our patient, the myocardial infarction was complicated by formation of an aneurysm, and reimplantation alone was not sufficient to restore cardiac function. Resection of the aneurysm greatly improved the hemodynamics.
Who Really Failed New Orleans?
Authors: Barrow Thomas D. 
Published: September 2008

I read with unusual interest the Forum “Earth Scientists and Public Policy: Have We Failed New Orleans?” in the 4 March issue of Eos (89(10), 2008). As an Earth scientist who lived in New Orleans during most of the early 1960s, I believe strongly that Earth scientists did not fail to recognize infrastructure problems. Further, they tried to communicate these problems and potential dangers to civic leaders in New Orleans and to government officials in Baton Rouge and Washington.When I first moved to New Orleans in 1959, I studied existing topographic information carefully. After numerous conversations about the levee system with a cousin who worked for the U.S. Army Corps of Engineers, I concentrated my house search in the uptown section southwest of Tulane University, which was clearly the highest part of town. I bought a raised cottage (these are fairly common) after determining that the first floor above the ground‐level basement was 2 feet higher than the top of the levee. I reasoned that even if a levee break did occur, my house would be slightly above flood level.
Organic Carbon in the Ocean's Twilight Zone: Controls on Organic Carbon Export and Twilight Zone Remineralization; Brussels, Belgium, 28–30 May 2008
Authors: Dehairs Frank , de Brauwere Anouk , Elskens Marc 
Published: September 2008

Today, the key role played by oceans in the Earth's carbon cycle is widely recognized. The important boundary to consider is not the ocean‐atmosphere interface, across which the carbon dioxide (CO2) concentration gradient is small, but the seasonal and permanent thermoclines, whose positions range from about 20 to 300 meters in depth. Once CO2 is delivered to depths beyond these thermoclines, the sequestration efficiency for CO2 is increased.Both physical and biological pumps act to increase the amount of carbon stored in the deep sea. For the latter process, more than 90% of the organic carbon exported (10–12 gigatons per year) to the deeper mesopelagic waters (i.e., the region below the upper mixed layer down to about 1000 meters, also called the twilight zone) is again respired to form CO2. Only a very small fraction of this organic carbon (<1%) eventually reaches the seafloor, where it is sequestered on longer timescales. The mechanisms controlling carbon export and its fate are still insufficiently understood to allow an informed assessment of its variability.
Mushroom-bodies regulate habit formation in Drosophila
Authors: Brembs Björn 
Published: September 2008

AbstractOur past experience is one of the primary sources of information when faced with a choice. We ask ourselves: "what will happen if I do this?"Accurately predicting the consequences of our actions is usually modeled by operant (instrumental) learning experiments. These types of experiments are often contrasted with classical (Pavlovian) conditioning experiments in a dichotomy. And indeed, different brain circuits mediate the acquisition of skills and habits (via operant/instrumental learning) and the acquisition of facts (via classical/Pavlovian learning). However, realistic learning situations always comprise interactions of skill- and fact-learning components (composite learning). Fixed flying Drosophila melanogaster at the torque meter provide one of the very few systems where the relationship of operant and classical predictors in composite learning can be studied with sufficient rigor. The latest experiments show that the textbook operant/classical dichotomy is misleading and that instead composite learning consists of multiple interacting memory systems. These interactions between predictive stimuli (classical component) and goal-directed actions (operant component) make composite conditioning more effective than the operant and classical components alone (learning-by-doing, generation effect). Rutabaga (rut) mutants are impaired in learning about the (classical) stimuli, but show improved (operant) behavior learning. This is the first evidence that operant and classical conditioning differ not only at the circuit, but also at the molecular level. The interaction between operant and classical components is reciprocal and hierarchical, such that the classical suppresses the operant component. Experiments with transgenic flies demonstrate that this suppression of operant learning is mediated by the mushroom-bodies and serves to ensure that the classical memories can be generalized for access by other behaviors. Extended training can overcome this suppression and transforms goal-directed actions into habitual responses. This interaction leads to efficient learning, enables generalization and prevents premature habit-formation.
GOSLING: a rule-based protein annotator using BLAST and GO
Authors: Jones Craig E. , Schwerdt Julian , Bretag Tessa Arwen , Baumann Ute , Brown Alfred L. 
Published: September 2008

Abstract
Summary: GOSLING is a web-based protein function annotator that uses a decision tree-derived rule set to quickly predict Gene Ontology terms for a protein. A score is assigned to each term prediction that is indicative of the accuracy of the prediction. Due to its speed and accuracy GOSLING is ideally suited for high-throughput annotation tasks.
Availability: https://www.sapac.edu.au/gosling
Contact: craig@cs.adelaide.edu.au
TESE: generating specific protein structure test set ensembles
Authors: Sirocco Francesco , Tosatto Silvio C. E. 
Published: September 2008

Abstract
Summary: TESE is a web server for the generation of test sets of protein sequences and structures fulfilling a number of different criteria. At least three different use cases can be envisaged: (i) benchmarking of novel methods; (ii) test sets tailored for special needs and (iii) extending available datasets. The CATH structure classification is used to control structural/sequence redundancy and a variety of structural quality parameters can be used to interactively select protein subsets with specific characteristics, e.g. all X-ray structures of α-helical repeat proteins with more than 120 residues and resolution &lt;2.0 Å. The output includes FASTA-formatted sequences, PDB files and a clickable HTML index file containing images of the selected proteins. Multiple subsets for cross-validation are also supported.
Availability: The TESE server is available for non-commercial use at URL: http://protein.bio.unipd.it/tese/.
Contact: silvio.tosatto@unipd.it
tCal: transcriptional probability calculator using thermodynamic model
Authors: Zhou Xin , Su Zhen 
Published: September 2008

Abstract
Summary: Thermodynamic model has been proposed as a realistic model of gene transcriptional regulation in bacteria, in which transcription probability calculation is based on physical interpretation of biological knowledge. We extend the published results in this area, and derive a relatively new model which could serve as a generalized form of previous results. To facilitate the application in gene network modeling studies, we implement our model in a Python module, ‘tCal’. With minimum programming efforts, user can use tCal to build transcription units, and either compute the transcription probabilities, or construct SBML models of regulatory networks.
Availability: tCal module and its online version can be found at: http://bioinformatics.cau.edu.cn/tCal.
Contact: zhensu@cau.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
Specific alignment of structured RNA: stochastic grammars and sequence annealing
Authors: Bradley Robert K. , Pachter Lior , Holmes Ian 
Published: September 2008

Abstract
Motivation: Whole-genome screens suggest that eukaryotic genomes are dense with non-coding RNAs (ncRNAs). We introduce a novel approach to RNA multiple alignment which couples a generative probabilistic model of sequence and structure with an efficient sequence annealing approach for exploring the space of multiple alignments. This leads to a new software program, Stemloc-AMA, that is both accurate and specific in the alignment of multiple related RNA sequences.
Results: When tested on the benchmark datasets BRalibase II and BRalibase 2.1, Stemloc-AMA has comparable sensitivity to and better specificity than the best competing methods. We use a large-scale random sequence experiment to show that while most alignment programs maximize sensitivity at the expense of specificity, even to the point of giving complete alignments of non-homologous sequences, Stemloc-AMA aligns only sequences with detectable homology and leaves unrelated sequences largely unaligned. Such accurate and specific alignments are crucial for comparative-genomics analysis, from inferring phylogeny to estimating substitution rates across different lineages.
Availability: Stemloc-AMA is available from http://biowiki.org/StemLocAMA as part of the dart software package for sequence analysis.
Contact: lpachter@math.berkeley.edu; ihh@berkeley.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
LZF1/SALT TOLERANCE HOMOLOG3, anArabidopsisB-Box Protein Involved in Light-Dependent Development and Gene Expression, Undergoes COP1-Mediated Ubiquitination
Authors: Datta Sourav , Johansson Henrik , Hettiarachchi Chamari , Irigoyen María Luisa , Desai Mintu , Rubio Vicente , Holm Magnus 
Published: September 2008

AbstractB-box containing proteins play an important role in light signaling in plants. Here, we identify LIGHT-REGULATED ZINC FINGER1/SALT TOLERANCE HOMOLOG3 (STH3), a B-box encoding gene that genetically interacts with two key regulators of light signaling, ELONGATED HYPOCOTYL5 (HY5) and CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1). STH3 physically interacts with HY5 in vivo and shows a COP1-dependent localization to nuclear speckles when coexpressed with COP1 in plant cells. A T-DNA insertion mutant, sth3, is hyposensitive to high fluence blue, red, and far-red light and has elongated hypocotyls under short days. Analyses of double mutants between sth3, sth2, and hy5 suggest that they have partially overlapping functions. Interestingly, functional assays in protoplasts suggest that STH3 can activate transcription both independently and together with STH2 through the G-box promoter element. Furthermore, sth3 suppresses the cop1 hypocotyl phenotype in the dark as well as the anthocyanin accumulation in the light. Finally, COP1 ubiquitinates STH3 in vitro, suggesting that STH3 is regulated by COP1. In conclusion, we have identified STH3 as a positive regulator of photomorphogenesis acting in concert with STH2 and HY5, while also being a target of COP1-mediated ubiquitination.