bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gravity Current Dynamics and Entrainment—A Process Study Based on Observations in the Arkona Basin
Authors: Arneborg Lars , Fiekas Volker , Umlauf Lars , Burchard Hans 
Published: September 2007

Abstract
A 19-h time series of dissipation, stratification, and horizontal velocities has been obtained for a dense gravity current flowing into the Arkona Basin in the western Baltic Sea. The observations are compared with one-dimensional, quasi-steady theory, in which the gravity component in the flow direction is balanced by bottom friction, while that in the cross-flow direction is balanced by the Coriolis force. The observations deviate from the theory in that the bottom shear stress is more than 2 times as large as that required to balance the gravity. Several reasons for this discrepancy are discussed. A 1D turbulence model is also compared with the observations. Profiles of velocity, stratification, and dissipation rates generally show similar variations with depth as the observations, although the observed dissipation rates are somewhat larger than the modeled and the modeled transverse velocities are much larger than the observed. Subsequently, the model is used to investigate the variation of the entrainment parameter for a large range of Ekman and Froude numbers. Within the modeled parameter space, the entrainment parameter can be collapsed onto a curve that is an increasing function of both the Froude and the Ekman numbers. There is one puzzling result of the observations that differs from the model results and earlier observations: the observed entrainment rate increases dramatically during the observation period, where the Froude number decreases slightly. Some reasons for this increase are discussed.
Thermodynamic Analysis of Ocean Circulation
Authors: Nycander J. , Nilsson J. , Döös K. , Broström G. 
Published: September 2007

Abstract
Calculating a streamfunction as function of depth and density is proposed as a new way of analyzing the thermodynamic character of the overturning circulation in the global ocean. The sign of an overturning cell in this streamfunction directly shows whether it is driven mechanically by large-scale wind stress or thermally by heat conduction and small-scale mixing. It is also shown that the integral of this streamfunction gives the thermodynamic work performed by the fluid. The analysis is also valid for the Boussinesq equations, although formally there is no thermodynamic work in an incompressible fluid. The proposed method is applied both to an idealized coarse-resolution three-dimensional numerical ocean model, and to the realistic high-resolution Ocean Circulation and Climate Advanced Model (OCCAM). It is shown that the overturning circulation in OCCAM between the 200- and 1000-m depth is dominated by a thermally indirect cell of 24 Sverdrups (1 Sv ≡ 106 m3 s−1), forced by Ekman pumping. In the densest and deepest waters there is a thermally direct cell of 18 Sv, which requires a forcing by around 100 GW of parameterized small-scale mixing.
Management of platinum-based chemotherapy-induced acute nausea and vomiting: is there a superior serotonin receptor antagonist?
Authors: Hamadani Mehdi , Chaudhary Lubna , Awan Farrukh T. , Khan Jawad K. , Kojouri Kiarash , Ozer Howard , Tfayli Arafat 
Published: September 2007

Objective. The last decade has witnessed the great impact of 5-hydroxytryptamine-3 receptor (5-HT3) antagonists in revolutionizing the management of platinum-based chemotherapy–induced acute nausea and vomiting (CINV). However, despite the availability of a variety of 5-HT3 antagonists, little data is published to support superiority of one drug over another, leaving the choice of serotonin receptor antagonist largely empirical. The National Comprehensive Cancer Network and American Society of Clinical Oncology guidelines for management of chemotherapy-associated nausea and vomiting clearly endorse the use of serotonin receptor antagonist; however, no single agent is preferred over the rest. Methods. Data for patients (n¼159) receiving platinum-based chemotherapy regimens were retrospectively collected. Patients getting 5-HT3 antagonists without steroids or those with known history of brain metastasis, gastroparesis, and intestinal obstruction were not eligible for the study. Patient characteristics including age, gender, primary diagnosis, history of heavy alcohol intake, chemotherapy regimen administered, number of cycles, and Eastern Cooperative Oncology Group performance status at the start of therapy were noted. Primary outcome was the complete control of platinum-induced acute nausea and vomiting. Secondary outcome measures included control of >grade 1 nausea or vomiting, comparison of two doses of dexamethasone, and antiemetic efficacy among various platinum drugs. National Cancer Institute Common Toxicity Criteria version 2.0 was used to assess toxicity. Results. A total of 126 patients received 369 cycles of platinum-based therapy. Dolasetron (n¼157), granisetron (n¼81), and ondansetron (n¼131) achieved complete control of vomiting in 89.8, 95.5, and 92.3% (p¼0.67) of cycles, respectively. Respectively, complete nausea control was observed in 68.1, 75.3 and, 69.4% (p¼0.50). Dexamethasone 20 mg was not superior to 10 mg in complete control of nausea and vomiting (p¼0.15 and p¼0.63, respectively). However, complete nausea control was significantly better in the subgroup of patients getting cisplatin-compared with carboplatin-based regimens (78.8% vs. 67.7%, p50.05). Conclusion. No significant difference exists in the antiemetic efficacy of the three 5-HT3 antagonists studied in controlling CINV when administered in combination with dexamethasone. Choice of antiemetic regimen should therefore be based on drug cost.
Dose-banding of carboplatin: rationale and proposed banding scheme
Authors: Kaestner Sabine , Sewell Graham 
Published: September 2007

Background. In dose-banding (DB) prescribed doses of cancer chemotherapy are fitted to doseranges or ‘bands’ and standard doses for each band are provided using a selection of pre-filled infusions or syringes, either singly or in combination. DB is used for several drugs where dose is based on body surface area. No DB-scheme has been reported for carboplatin, which, in clinical practice, is routinely dosed according to renal function. Study objective. To assess the rationale for DB of carboplatin with regards to factors that influence dosing accuracy, develop a DB scheme, and discuss its potential use and limitations. Methods. Prospective evaluations of carboplatin area under the plasma concentration – time curve (AUC) following application of the Calvert-formula were identified by a literature search. A relevant carboplatin dose range for construction of a DB-scheme with Calvert-formula based doses was obtained from published glomerular filtration rate distributions for patients receiving carboplatin. Results. A DB-scheme was developed for individually calculated carboplatin doses of 358–1232 mg, with 35 mg increments between each standard dose and a maximum deviation of 4.7% from prescribed dose. The proposed DB-scheme covers the GFR-ranges 47–221 mL/min and 26–151 mL/min for patients receiving doses based on the target AUCs of 5 and 7 mg/mL/min, respectively. Conclusion. There is a strong scientific rationale to support DB of carboplatin. The proposed banding scheme could introduce benefits to patients and healthcare staff but, as with other DB schemes, should be validated with prospective clinical and pharmacokinetic studies to confirm safety and efficacy.
A sequential temperature cycling study for the investigation of carboplatin infusion stability to facilitate `dose-banding'
Authors: Kaestner Sabine , Sewell Graham 
Published: September 2007

Study objective. To determine the physical and chemical stability of carboplatin infusion for dosebanding, with cycling between refrigerated storage and room temperature in-use conditions. Design. A sequential study design was selected to closely simulate the temperatures and conditions experienced by drug infusions in pharmaceutical storage and in clinical use. Carboplatin infusions, 0.70 and 2.15 mg/mL, were stored refrigerated for up to 84 days, followed by incubation at 258C for 24 h. The infusions were also returned to refrigerated storage for 3 and 7 days, to replicate a situation in which returned, unused infusions are kept for re-issuing. On pre-determined time-points, infusion chemical and physical stability were determined by HLPC, sub-visual particulatecounts, pH-measurement, and weighing of infusions. Results. Light protected carboplatin infusions at both study concentrations were chemically and physically stable following refrigerated storage for 84 days, followed by a further 24 h under ‘in-use’ conditions at 258C. Additionally, the infusions were stable following return to refrigerated storage again for at least 7 days. Conclusion. This study has demonstrated extended stability of carboplatin infusions which enables batch-scale preparation of standard infusions for dose- J Oncol Pharm Practice (2007) 13: 119–126.
The Coming Son of Man Revisited
Authors: Kazen Thomas 
Published: September 2007

AbstractThe interpretation of the synoptic Son of Man is still a formidable swamp with no consensus emerging. Unfortunately, one of the most interesting suggestions, the collective interpretation of Manson, Moule and Gaston, has been somehow left by the wayside. It has certain advantages, however, in respecting both the basic `generic' sense of an underlying Semitic expression and the Danielic kingdom imagery, without denying this expression for the historical Jesus. The present article focuses on the coming Son of Man sayings and demonstrates the plausibility of applying a collective interpretation to them. The result is an eschatology, focusing not on an individual redeemer figure, but on the manifestation of the Kingdom in community practice. Some suggestions are offered for how such an eschatology, based on a collective interpretation of the coming Son of Man, could `mutate' so quickly into the idea of a second coming of Christ.
Support Vector Machine-based method for predicting subcellular localization of mycobacterial proteins using evolutionary information and motifs
Authors: Rashid Mamoon , Saha Sudipto , Raghava Gajendra PS 
Published: September 2007

Abstract

Background
In past number of methods have been developed for predicting subcellular location of eukaryotic, prokaryotic (Gram-negative and Gram-positive bacteria) and human proteins but no method has been developed for mycobacterial proteins which may represent repertoire of potent immunogens of this dreaded pathogen. In this study, attempt has been made to develop method for predicting subcellular location of mycobacterial proteins.

Results
The models were trained and tested on 852 mycobacterial proteins and evaluated using five-fold cross-validation technique. First SVM (Support Vector Machine) model was developed using amino acid composition and overall accuracy of 82.51% was achieved with average accuracy (mean of class-wise accuracy) of 68.47%. In order to utilize evolutionary information, a SVM model was developed using PSSM (Position-Specific Scoring Matrix) profiles obtained from PSI-BLAST (Position-Specific Iterated BLAST) and overall accuracy achieved was of 86.62% with average accuracy of 73.71%. In addition, HMM (Hidden Markov Model), MEME/MAST (Multiple Em for Motif Elicitation/Motif Alignment and Search Tool) and hybrid model that combined two or more models were also developed. We achieved maximum overall accuracy of 86.8% with average accuracy of 89.00% using combination of PSSM based SVM model and MEME/MAST. Performance of our method was compared with that of the existing methods developed for predicting subcellular locations of Gram-positive bacterial proteins.

Conclusion
A highly accurate method has been developed for predicting subcellular location of mycobacterial proteins. This method also predicts very important class of proteins that is membrane-attached proteins. This method will be useful in annotating newly sequenced or hypothetical mycobacterial proteins. Based on above study, a freely accessible web server TBpred http://www.imtech.res.in/raghava/tbpred/ has been developed.
The extracellular Leucine-Rich Repeat superfamily; a comparative survey and analysis of evolutionary relationships and expression patterns
Authors: Dolan Jackie , Walshe Karen , Alsbury Samantha , Hokamp Karsten , O'Keeffe Sean , Okafuji Tatsuya , Miller Suzanne FC , Tear Guy , Mitchell Kevin J 
Published: September 2007

Abstract

Background
Leucine-rich repeats (LRRs) are highly versatile and evolvable protein-ligand interaction motifs found in a large number of proteins with diverse functions, including innate immunity and nervous system development. Here we catalogue all of the extracellular LRR (eLRR) proteins in worms, flies, mice and humans. We use convergent evidence from several transmembrane-prediction and motif-detection programs, including a customised algorithm, LRRscan, to identify eLRR proteins, and a hierarchical clustering method based on TribeMCL to establish their evolutionary relationships.

Results
This yields a total of 369 proteins (29 in worm, 66 in fly, 135 in mouse and 139 in human), many of them of unknown function. We group eLRR proteins into several classes: those with only LRRs, those that cluster with Toll-like receptors (Tlrs), those with immunoglobulin or fibronectin-type 3 (FN3) domains and those with some other domain. These groups show differential patterns of expansion and diversification across species. Our analyses reveal several clusters of novel genes, including two Elfn genes, encoding transmembrane proteins with eL RRs and an FN 3 domain, and six genes encoding transmembrane proteins with eLR Rs on ly (the Elron cluster). Many of these are expressed in discrete patterns in the developing mouse brain, notably in the thalamus and cortex. We have also identified a number of novel fly eLRR proteins with discrete expression in the embryonic nervous system.

Conclusion
This study provides the necessary foundation for a systematic analysis of the functions of this class of genes, which are likely to include prominently innate immunity, inflammation and neural development, especially the specification of neuronal connectivity.
Molecular characterization and temporal expression profiling of presenilins in the developing porcine brain
Authors: Madsen Lone B , Thomsen Bo , Larsen Knud , Bendixen Christian , Holm Ida E , Fredholm Merete , Jørgensen Arne L , Nielsen Anders L 
Published: September 2007

Abstract

Background
The transmembrane presenilin (PSEN) proteins, PSEN1 and PSEN2, have been proposed to be the catalytic components of the γ-secretase protein complex, which is an intramembranous multimeric protease involved in development, cell regulatory processes, and neurodegeneration in Alzheimer's disease. Here we describe the sequencing, chromosomal mapping, and polymorphism analysis of PSEN1 and PSEN2 in the domestic pig (Sus scrofa domesticus).

Results
The porcine presenilin proteins showed a high degree of homology over their entire sequences to the PSENs from mouse, bovine, and human. PSEN1 and PSEN2 transcription was examined during prenatal development of the brain stem, hippocampus, cortex, basal ganglia, and cerebellum at embryonic days 60, 80, 100, and 114, which revealed distinct temporal- and tissue-specific expression profiles. Furthermore, immunohistochemical analysis of PSEN1 and PSEN2 showed similar localization of the proteins predominantly in neuronal cells in all examined brain areas.

Conclusion
The data provide evidence for structural and functional conservation of PSENs in mammalian lineages, and may suggest that the high sequence similarity and colocalization of PSEN1 and PSEN2 in brain tissue reflect a certain degree of functional redundancy. The data show that pigs may provide a new animal model for detailed analysis of the developmental functions of the PSENs.
Differential regulation of iron chelator-induced IL-8 synthesis via MAP kinase and NF-κB in immortalized and malignant oral keratinocytes
Authors: Lee Hwa-Jeong , Lee Jun , Lee Sun-Kyung , Lee Suk-Keun , Kim Eun-Cheol 
Published: September 2007

AbstractBackgroundInterleukin-8 (IL-8) is a cytokine that plays an important role in tumor progression in a variety of cancer types; however, its regulation is not well understood in oral cancer cells. In the present study, we examined the expression and mechanism of IL-8 in which it is involved by treating immortalized (IHOK) and malignant human oral keratinocytes (HN12) cells with deferoxamine (DFO).MethodsIL-8 production was measured by an enzyme-linked immunoabsorbent assay and reverse transcriptase-polymerase chain reaction (RT-PCR) analysis. Electrophoretic mobility shift assays was used to determine NF-κB binding activity. Phosphorylation and degradation of the I-κB were analyized by Western blot.ResultsIHOK cells incubated with DFO showed increased expression of IL-8 mRNA, as well as higher release of the IL-8 protein. The up-regulation of DFO-induced IL-8 expression was higher in IHOK cells than in HN12 cells and was concentration-dependent. DFO acted additively with IL-1β to strongly up-regulate IL-8 in IHOK cells but not in HN12 cells. Accordingly, selective p38 and ERK1/2 inhibitors for both kinases abolished DFO-induced IL-8 expression in both IHOK and HN12 cells. Furthermore, DFO induced the degradation and phosphorylation of IκB, and activation of NF-κB. The IL-8 inducing effects of DFO were mediated by a nitric oxide donor (S-nitrosoglutathione), and by pyrrolidine dithiocarbamate, an inhibitor of NF-κB, as well as by wortmannin, which inhibits the phosphatidylinositol 3-kinase-dependent activation of NAD(P)H oxidase.ConclusionThis results demonstrate that DFO-induced IL-8 acts via multiple signaling pathways in immortalized and malignant oral keratinocytes, and that the control of IL-8 may be an important target for immunotheraphy against human oral premalignant lesions.
A conserved gene family encodes transmembrane proteins with fibronectin, immunoglobulin and leucine-rich repeat domains (FIGLER)
Authors: Munfus Delicia L , Haga Christopher L , Burrows Peter D , Cooper Max D 
Published: September 2007

Abstract

Background

In mouse the cytokine interleukin-7 (IL-7) is required for generation of B lymphocytes, but human IL-7 does not appear to have this function. A bioinformatics approach was therefore used to identify IL-7 receptor related genes in the hope of identifying the elusive human cytokine.

Results

Our database search identified a family of nine gene candidates, which we have provisionally named fibronectin immunoglobulin leucine-rich repeat (FIGLER). The FIGLER 1–9 genes are predicted to encode type I transmembrane glycoproteins with 6–12 leucine-rich repeats (LRR), a C2 type Ig domain, a fibronectin type III domain, a hydrophobic transmembrane domain, and a cytoplasmic domain containing one to four tyrosine residues. Members of this multichromosomal gene family possess 20–47% overall amino acid identity and are differentially expressed in cell lines and primary hematopoietic lineage cells. Genes for FIGLER homologs were identified in macaque, orangutan, chimpanzee, mouse, rat, dog, chicken, toad, and puffer fish databases. The non-human FIGLER homologs share 38–99% overall amino acid identity with their human counterpart.

Conclusion

The extracellular domain structure and absence of recognizable cytoplasmic signaling motifs in members of the highly conserved FIGLER gene family suggest a trophic or cell adhesion function for these molecules.
Susceptibility of schizophrenia and affective disorder not associated with loci on chromosome 6q in Han Chinese population
Authors: Wang Zuowei , Fang Yiru , Yu Shunying , Yuan Chengmei , Hong Wu , Yi Zhenghui , Jiang Sanduo , John R Kelsoe , Wang Zucheng 
Published: September 2007

Abstract

Background
Several linkage studies across multiple population groups provide convergent support for susceptibility loci for schizophrenia – and, more recently, for affective disorder – on chromosome 6q. We explore whether schizophrenia and affective disorder have common susceptibility gene on 6q in Han Chinese population.

Methods
In the present study, we genotyped 45 family trios from Han Chinese population with mixed family history of schizophrenia and affective disorder. Twelve short tandem repeat (STRs) markers were selected, which covered 102.19 cM on chromosome 6q with average spacing 9.29 cM and heterozygosity 0.78. The transmission disequilibrium test (TDT) was performed to search for susceptibility loci to schizophrenia and affective disorder.

Results
The results showed STRs D6S257, D6S460, D6S1021, D6S292 and D6S1581 were associated with susceptibility to psychotic disorders. When families were grouped into schizophrenia and affective disorder group, D6S257, D6S460 and D6S1021, which map closely to the centromere of chromosome 6q, were associated with susceptibility to schizophrenia. Meanwhile, D6S1581, which maps closely to the telomere, was associated with susceptibility to affective disorder. But after correction of multiple test, all above association were changed into no significance (P > 0.05).

Conclusion
These results suggest that susceptibility of schizophrenia and affective disorder not associated with loci on chromosome 6q in Han Chinese population.
DetectiV: visualization, normalization and significance testing for pathogen-detection microarray data
Authors: Watson Michael , Dukes Juliet , Abu-Median Abu-Bakr , King Donald P , Britton Paul 
Published: September 2007

AbstractDNA microarrays offer the possibility of testing for the presence of thousands of micro-organisms in a single experiment. However, there is a lack of reliable bioinformatics tools for the analysis of such data. We have developed DetectiV, a package for the statistical software R. DetectiV offers powerful yet simple visualization, normalization and significance testing tools. We show that DetectiV performs better than previously published software on a large, publicly available dataset.