bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Fuzzy Logic Algorithm for the Separation of Precipitating from Nonprecipitating Echoes Using Polarimetric Radar Observations
Authors: Gourley Jonathan J. , Tabary Pierre , Parent du Chatelet Jacques 
Published: August 2007

Abstract
A fuzzy logic algorithm has been developed for the purpose of segregating precipitating from nonprecipitating echoes using polarimetric radar observations at C band. Adequate polarimetric descriptions for each type of scatterer are required for the algorithm to be effective. An observations-based approach is presented in this study to derive membership functions and objectively weight them so that they apply directly to conditions experienced at the radar site and to the radar wavelength. Three case studies are examined and show that the algorithm successfully removes nonprecipitating echoes from rainfall accumulation maps.
Impact of Accurate Geoid Fields on Estimates of the Ocean Circulation
Authors: Stammer Detlef , Köhl Armin , Wunsch Carl 
Published: August 2007

Abstract
The impact of new geoid height models on estimates of the ocean circulation, now available from the Gravity Recovery and Climate Experiment (GRACE) spacecraft, is assessed, and the implications of far more accurate geoids, anticipated from the European Space Agency’s (ESA) Gravity and Ocean Circulation Explorer (GOCE) mission, are explored. The study is based on several circulation estimates obtained over the period 1992–2002 by combining most of the available ocean datasets with a global general circulation model on a 1° horizontal grid and by exchanging only the EGM96 geoid model with two different geoid models available from GRACE. As compared to the EGM96-based solution, the GRACE geoid leads to an estimate of the ocean circulation that is more consistent with the Levitus temperature and salinity climatology. While not a formal proof, this finding supports the inference of a substantially improved GRACE geoid skill. However, oceanographic implications of the GRACE model are only modest compared to what can be obtained from ocean observations alone. To understand the extent to which this is merely a consequence of a not-optimally converged solution or if a much more accurate geoid field could in principle play a profound role in the ocean estimation procedure, an additional experiment was performed in which the geoid error was artificially reduced relative to all other datasets. Adjustments occur then in all elements of the ocean circulation, including 10% changes in the meridional overturning circulation and the corresponding meridional heat transport in the Atlantic. For an optimal use of new geoid fields, improved error information is required. The error budget of existing time-mean dynamic topography estimates may now be dominated by residual errors in time-mean altimetric corrections. Both these and the model errors need to be better understood before improved geoid estimates can be fully exploited. As is commonly found, the Southern Ocean is of particular concern.
Lidar-Based Characterization of the Geometry and Structure of Water Clouds
Authors: Bissonnette Luc R. , Roy Gilles , Tremblay Grégoire 
Published: August 2007

Abstract
Lidar remote sensing measurements of low-level water clouds in the form of vertical soundings and instantaneous (∼1 min) azimuth-over-elevation scans are reported. Retrievals are made of the liquid water content and effective droplet diameter at the same range, time, and angular resolutions as those of the measurements. The results are presented as time–height plots and two-dimensional horizontal maps of the retrieved parameters. The cloud structure is resolved by calculating histograms, spatial autocorrelation functions, and power spectra. The distribution of the horizontal inhomogeneities is characterized over the size range from 10 to ∼1000 m. The Kolmogorov −5/3 power-law dependence is verified in all cases, but the −5/3 regime is broken into two subregimes that are separated by a sudden increase in the energy density level. The results illustrate how lidars can contribute meaningful information on cloud structure at high spatial and temporal resolutions, in near–real time, and over extended periods of time.
Combined Proximal and Distal Realignment Procedures to Treat the Habitual Dislocation of the Patella in Adults
Authors: Shen Hsain-Chung , Chao Kuo-Hua , Huang Guo-Shu , Pan Ru-Yu , Lee Chian-Her 
Published: August 2007

Background Habitual dislocation of the patella (HDP) is a rare condition. Many surgical procedures using proximal realignment have been reported to treat HDP in children, with around 80% satisfactory results. However, few articles have addressed the treatment of HDP associated with high-grade patellofemoral chondromalacia in adults. Hypothesis A combination of proximal and distal realignment procedures of the patella will reduce pain and increase function in adult patients with HDP. Study Design Case series; Level of evidence, 4. Methods Twelve patients with 13 symptomatic cases of HDP of the knee underwent surgical treatment that included lateral release, medial retinaculum advancement, and the anteromedial tibial tubercle transfer procedure. The average period between dislocation and surgery was 10.8 years. One patient had an additional procedure, an open-wedge varus corrective osteotomy of the distal femur, because of a 20° valgus deformity of the knee. The patellofemoral morphology study included routine and Merchant views of the knee and a computed tomography scan at full extension and at 30° flexion of the knee, before the operation and at follow-up. Any associated intra-articular pathologic findings during the surgical procedure were addressed. Patellofemoral function was evaluated with the Kujala functional score before surgery and at the time of the final follow-up. Results Chondromalacia of the patella over the medial facet and central ridge was grade III in 8 knees and grade IV in 5 knees. Corresponding chondral erosion of the lateral femoral condyle was noted in every knee. All patients were followed for an average period of 67.3 months (range, 25-103 months). The average preoperative Kujala functional score was 43.9 and the average postoperative score was 88.9 (P < .05). Radiographically, there was a statistically significant improvement in the congruence angle from 62.1° ± 15.0° preoperatively to —2.7° ± 9.8° postoperatively (P < .01) and in the lateral patellofemoral angle from —40.2° ± 9.3° preoperatively to 1.4° ± 7.0° postoperatively (P < .01). No patient has reported an episode of patellar dislocation after the surgical procedures. Conclusion Combined proximal and distal realignments of the patella effectively treat HDP in adults with associated high-grade patellofemoral chondromalacia.
Exploring conversational shadowing
Authors: Murphey Tim 
Published: August 2007

The background literature on the repeating of a conversation partner’s words, here called conversational shadowing, shows it to be naturally occurring in L1 acquisition and adult use. This study was motivated by the question ‘What happens when second language learners and native speakers actively shadow each other in conversation?’ I look closely at conversational shadowing through transcripts of recorded conversations between two Japanese learners of English talking with two English native speakers in mixed dyads in which they were instructed to shadow each other. First, it was found that the different sets of data emerging from the two Japanese students reveal that there may be a variety of effective types of shadowing, from those which may lengthen auditory short-term memory to more interactive and naturally selective shadowing that includes commenting and questioning. Secondly, it was found that interactive conversational shadowing gives rise to the types of conversational adjustments and negotiations that are thought to positively affect language acquisition (Long, 1983) through their impact on negotiation, noticing, intake, and uptake. Thirdly, the data highlights different learning advantages for the non-native speakers (NNSs) when shadowing native speakers (NSs) and when being shadowed by NSs. Finally, I attempt to place shadowing developmentally within Vygotskian socio-cultural theory with reference to Bakhtin’s ventriloquation and to outline a generative action research agenda.
Cooperation of the proapoptotic receptor agonist rhApo2L/TRAIL with the CD20 antibody rituximab against non-Hodgkin lymphoma xenografts
Authors: Daniel Dylan , Yang Becky , Lawrence David A. , Totpal Klara , Balter Inessa , Lee Wyne P. , Gogineni Alvin , Cole Mary J. , Yee Sharon Fong , Ross Sarajane , Ashkenazi Avi 
Published: August 2007

AbstractRecombinant human rhApo2L/TRAIL selectively stimulates apoptosis in various cancer cells through its receptors DR4 and DR5, and is currently in clinical trials. Preclinical studies have established antitumor activity of rhApo2L/TRAIL in models of epithelial cancers; however, efficacy in non-Hodgkin lymphoma (NHL) models is not well studied. Of 7 NHL cell lines tested in vitro, rhApo2L/TRAIL stimulated apoptosis in BJAB, Ramos RA1, and DoHH-2 cells. Rituximab, a CD20 antibody used to treat certain types of NHL, augmented rhApo2L/TRAIL-induced caspase activation in Ramos RA1 and DoHH2 but not BJAB or SC-1 cells, through modulation of intrinsic rather than extrinsic apoptosis signaling. In vivo, rhApo2L/TRAIL and rituximab cooperated to attenuate or reverse growth of tumor xenografts of all 4 of these cell lines. Depletion of natural killer (NK) cells or serum complement substantially reduced combined efficacy against Ramos RA1 tumors, suggesting involvement of antibodydependent cell- and complement-mediated cytotoxicity. Both agents exhibited greater activity against disseminated than subcutaneous BJAB xenografts, and worked together to inhibit or abolish disseminated tumors and increase survival. Moreover, rhApo2L/TRAIL helped circumvent acquired rituximab resistance of a Ramos variant. These findings provide a strong rationale for clinical investigation of rhApo2L/TRAIL in combination with rituximab as a novel strategy for NHL therapy.
Extracellular calcium sensing promotes human B-cell activation and function
Authors: Hammond Caitlin M. , White Dionne , Tomic Jelena , Shi Yonghong , Spaner David E. 
Published: August 2007

AbstractCalcium is a second messenger for many signaling pathways in B cells, but its role as a receptor ligand has not been well characterized. However, pulses of free calcium were found to cause the rapid release of internal calcium stores in normal human B cells. This response appeared to be mediated by a cell surface protein with receptor properties as it could be blocked by pretreatment with trypsin and with kinase and phospholipase Cγ inhibitors. The calcium receptor on B cells was not the conventional calcium-sensing receptor (CaSR) since B cells did not express CaSR and calcium-induced responses could not be blocked by specific CaSR inhibitors. B-cell responses to extracellular calcium activated phosphoinositide-3 kinase/AKT, calcineurin, extracellular signal regulated kinase, p38 mitogen-activated protein kinase, protein kinase C, Ca2+/calmodulin kinase II, and nuclear factor-κB signaling pathways, and resulted in transcription of the early response gene, CD83. This extracellular calcium sensor enhanced B-cell responses to Toll-like receptor, B-cell receptor, and cytokine receptor agonists. These findings suggest a means by which B cells prepare to engage in immune responses by responding to calcium fluctuations in their environment.
Analysis of the role of retrotransposition in gene evolution in vertebrates
Authors: Yu Zhan , Morais David , Ivanga Mahine , Harrison Paul M 
Published: August 2007

Abstract

Background
The dynamics of gene evolution are influenced by several genomic processes. One such process is retrotransposition, where an mRNA transcript is reverse-transcribed and reintegrated into the genomic DNA.

Results
We have surveyed eight vertebrate genomes (human, chimp, dog, cow, rat, mouse, chicken and the puffer-fish T. nigriviridis), for putatively retrotransposed copies of genes. To gain a complete picture of the role of retrotransposition, a robust strategy to identify putative retrogenes (PRs) was derived, in tandem with an adaptation of previous procedures to annotate processed pseudogenes, also called retropseudogenes (RψGs). Mammalian genomes are estimated to contain 400–800 PRs (corresponding to ~3% of genes), with fewer PRs and RψGs in the non-mammalian vertebrates. Focussing on human and mouse, we aged the PRs, analysed for evidence of transcription and selection pressures, and assigned functional categories. The PRs have significantly less transcription evidence mappable to them, are significantly less likely to arise from alternatively-spliced genes, and are statistically overrepresented for ribosomal-protein genes, when compared to the proteome in general. We find evidence for spurts of gene retrotransposition in human and mouse, since the lineage of either species split from the dog lineage, with >200 PRs formed in mouse since its divergence from rat. To examine for selection, we calculated: (i) Ka/Ks values (ratios of non-synonymous and synonymous substitutions in codons), and (ii) the significance of conservation of reading frames in PRs. We found >50 PRs in both human and mouse formed since divergence from dog, that are under pressure to maintain the integrity of their coding sequences. For different subsets of PRs formed at different stages of mammalian evolution, we find some evidence for non-neutral evolution, despite significantly less expression evidence for these sequences.

Conclusion
These results indicate that retrotranspositions are a significant source of novel coding sequences in mammalian gene evolution.
Integrated network reconstruction, visualization and analysis using YANAsquare
Authors: Schwarz Roland , Liang Chunguang , Kaleta Christoph , Kühnel Mark , Hoffmann Eik , Kuznetsov Sergei , Hecker Michael , Griffiths Gareth , Schuster Stefan , Dandekar Thomas 
Published: August 2007

Abstract

Background
Modeling of metabolic networks includes tasks such as network assembly, network overview, calculation of metabolic fluxes and testing the robustness of the network.

Results
YANAsquare provides a software framework for rapid network assembly (flexible pathway browser with local or remote operation mode), network overview (visualization routine and YANAsquare editor) and network performance analysis (calculation of flux modes as well as target and robustness tests). YANAsquare comes as an easy-to-setup program package in Java. It is fully compatible and integrates the programs YANA (translation of gene expression values into flux distributions, metabolite network dissection) and Metatool (elementary mode calculation). As application examples we set-up and model the phospholipid network in the phagosome and genome-scale metabolic maps of S.aureus, S.epidermidis and S.saprophyticus as well as test their robustness against enzyme impairment.

Conclusion
YANAsquare is an application software for rapid setup, visualization and analysis of small, larger and genome-scale metabolic networks.
Translational machinery of the chaetognath Spadella cephaloptera: a transcriptomic approach to the analysis of cytosolic ribosomal protein genes and their expression
Authors: Barthélémy Roxane M , Chenuil Anne , Blanquart Samuel , Casanova Jean-Paul , Faure Eric 
Published: August 2007

Abstract

Background
Chaetognaths, or arrow worms, are small marine, bilaterally symmetrical metazoans. The objective of this study was to analyse ribosomal protein (RP) coding sequences from a published collection of expressed sequence tags (ESTs) from a chaetognath (Spadella cephaloptera) and to use them in phylogenetic studies.

Results
This analysis has allowed us to determine the complete primary structures of 23 out of 32 RPs from the small ribosomal subunit (SSU) and 32 out of 47 RPs from the large ribosomal subunit (LSU). Ten proteins are partially determined and 14 proteins are missing. Phylogenetic analyses of concatenated RPs from six animals (chaetognath, echinoderm, mammalian, insect, mollusc and sponge) and one fungal taxa do not resolve the chaetognath phylogenetic position, although each mega-sequence comprises approximately 5,000 amino acid residues. This is probably due to the extremely biased base composition and to the high evolutionary rates in chaetognaths. However, the analysis of chaetognath RP genes revealed three unique features in the animal Kingdom. First, whereas generally in animals one RP appeared to have a single type of mRNA, two or more genes are generally transcribed for one RP type in chaetognath. Second, cDNAs with complete 5'-ends encoding a given protein sequence can be divided in two sub-groups according to a short region in their 5'-ends: two novel and highly conserved elements have been identified (5'-TAATTGAGTAGTTT-3' and 5'-TATTAAGTACTAC-3') which could correspond to different transcription factor binding sites on paralog RP genes. And, third, the overall number of deduced paralogous RPs is very high compared to those published for other animals.

Conclusion
These results suggest that in chaetognaths the deleterious effects of the presence of paralogous RPs, such as apoptosis or cancer are avoided, and also that in each protein family, some of the members could have tissue-specific and extra-ribosomal functions. These results are congruent with the hypotheses of an allopolyploid origin of this phylum and of a ribosome heterogeneity.
Thioredoxin reductase is a key factor in the oxidative stress response of Lactobacillus plantarum WCFS1
Authors: Serrano L Mariela , Molenaar Douwe , Wels Michiel , Teusink Bas , Bron Peter A , de Vos Willem M , Smid Eddy J 
Published: August 2007

Abstract

Background
Thioredoxin (TRX) is a powerful disulfide oxido-reductase that catalyzes a wide spectrum of redox reactions in the cell. The aim of this study is to elucidate the role of the TRX system in the oxidative stress response in Lactobacillus plantarum WCFS1.

Results
We have identified the trxB1-encoded thioredoxin reductase (TR) as a key enzyme in the oxidative stress response of Lactobacillus plantarum WCFS1.
Overexpression of the trxB1 gene resulted in a 3-fold higher TR activity in comparison to the wild-type strain. Subsequently, higher TR activity was associated with an increased resistance towards oxidative stress. We further determined the global transcriptional response to hydrogen peroxide stress in the trxB1-overexpression and wild-type strains grown in continuous cultures. Hydrogen peroxide stress and overproduction of TR collectively resulted in the up-regulation of 267 genes. Additionally, gene expression profiling showed significant differential expression of 27 genes in the trxB1-overexpression strain. Over expression of trxB1 was found to activate genes associated with DNA repair and stress mechanisms as well as genes associated with the activity of biosynthetic pathways for purine and sulfur-containing amino acids. A total of 16 genes showed a response to both TR overproduction and hydrogen peroxide stress. These genes are involved in the purine metabolism, energy metabolism (gapB) as well as in stress-response (groEL, npr2), and manganese transport (mntH2).

Conclusion
Based on our findings we propose that overproduction of the trxB1-encoded TR in L. plantarum improves tolerance towards oxidative stress. This response coincides with simultaneous induction of a group of 16 transcripts of genes. Within this group of genes, most are associated with oxidative stress response. The obtained crossover between datasets may explain the phenotype of the trxB1-overexpression strain, which appears to be prepared for encountering oxidative stress. This latter property can be used for engineering robustness towards oxidative stress in industrial strains of L. plantarum.
Microglial activation in the hippocampus of hypercholesterolemic rabbits occurs independent of increased amyloid production
Authors: Xue Qing-Shan , Sparks D Larry , Streit Wolfgang J 
Published: August 2007

AbstractBackgroundRabbits maintained on high-cholesterol diets are known to show increased immunoreactivity for amyloid beta protein in cortex and hippocampus, an effect that is amplified by presence of copper in the drinking water. Hypercholesterolemic rabbits also develop sporadic neuroinflammatory changes. The purpose of this study was to survey microglial activation in rabbits fed cholesterol in the presence or absence of copper or other metal ions, such as zinc and aluminum.MethodsVibratome sections of the rabbit hippocampus and overlying cerebral cortex were examined for microglial activation using histochemistry with isolectin B4fromGriffonia simplicifolia. Animals were scored as showing either focal or diffuse microglial activation with or without presence of rod cells.ResultsApproximately one quarter of all rabbits fed high-cholesterol diets showed evidence of microglial activation, which was always present in the hippocampus and not in the cortex. Microglial activation was not correlated spatially with increased amyloid immunoreactivity or with neurodegenerative changes and was most pronounced in hypercholesterolemic animals whose drinking water had been supplemented with either copper or zinc. Controls maintained on normal chow were largely devoid of neuroinflammatory changes, but revealed minimal microglial activation in one case.ConclusionBecause the increase in intraneuronal amyloid immunoreactivity that results from administration of cholesterol occurs in both cerebral cortex and hippocampus, we deduce that the microglial activation reported here, which is limited to the hippocampus, occurs independent of amyloid accumulation. Furthermore, since neuroinflammation occurred in the absence of detectable neurodegenerative changes, and was also not accompanied by increased astrogliosis, we conclude that microglial activation occurs because of metabolic or biochemical derangements that are influenced by dietary factors.
Fez1/Lzts1 a new mitotic regulator implicated in cancer development
Authors: Vecchione Andrea , Croce Carlo M , Baldassarre Gustavo 
Published: August 2007

Abstract
Considerable evidence has accumulated suggesting that cancer has genetic origin, based on the development of genomic alterations, such as deletions, mutations, and/or methylations in critical genes for homeostasis of cellular functions, including cell survival, DNA replication and cell cycle control. Mechanism controlling the precise timing and sequence of cell cycle events as well as checkpoints insuring fidelity of those events are key targets that when disrupted could result in tumorigenesis. Mitosis is the process by which a cell duplicates its genetic information (DNA), in order to generate two, identical, daughter cells. In addition each daughter cell must receive one centrosome and the appropriate complements of cytoplasm and organelles. This process is conventionally divided in to five distinct stages: prophase, prometaphase, metaphase, anaphase and telophase that correspond to a different morphology of the cell. The entry into mitosis (M) is under the control of the cyclin dependent kinase Cdk1. During G2, the kinases Wee1 and Myt1 phosphorylate Cdk1 at T14/Y15 residues, rendering it inactive. The transition from G2 to M is promoted by the activation of Cdk1 via dephosphorylation by the Cdk1 phosphatase Cdc25C. Activated Cdk1 complexes translocate into the nucleus during prophase where phosphorylate numerous substrates in order to enhance their activation as the cells progresses trough prophase, prometaphase, and metaphase.
Recently we identified a new player: FEZ1/LZTS1 that contributes to the fine-tuning of the molecular events that determine progression through mitosis, and here will review its role in cancer development and in M phase regulation.