bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mechanisms of Poleward Propagating, Intraseasonal Convective Anomalies in Cloud System–Resolving Models
Authors: Boos William R. , Kuang Zhiming 
Published: November 2010

Abstract
An envelope of convection that propagates both poleward and eastward accounts for the largest fraction of intraseasonal variance of the tropical atmosphere during boreal summer. Here the mechanisms of poleward propagating convective anomalies are examined in a nonhydrostatic model with zonally symmetric boundary conditions, integrated on a beta plane at resolutions high enough to explicitly represent moist convection. When the domain has a narrow zonal dimension of 100 km or less, the model produces a quasisteady intertropical convergence zone (ITCZ). Meridionally propagating transients are produced for some prescribed sea surface temperature distributions, but these transients are shallow, vanish at finer resolutions, and have a structure that bears little resemblance to that of observed poleward propagating anomalies. This is in sharp contrast to previous studies that obtained robust poleward propagating anomalies in axisymmetric models using parameterized moist convection, and it suggests that the anomalies seen in those models may be caused by deficient representations of dynamics or subgrid-scale physics.
Robust poleward propagating anomalies are obtained when the high-resolution, nonhydrostatic model is integrated in a wider domain with a zonal dimension near 1000 km. Diagnostics suggest that poleward propagation in this wide domain results from the convectively coupled beta drift of low-level vorticity anomalies. Deep near-equatorial ascent produces low-level cyclones that migrate poleward through the process of beta drift; Ekman pumping in these drifting cyclones then humidifies the free troposphere ahead of the initial deep ascent, shifting the convection poleward. The moist static energy budget and model sensitivity tests suggest that these anomalies can be viewed as moisture modes destabilized through a moisture–radiation feedback. Wind–evaporation feedback also seems to contribute to the instability of these anomalies, but because it enhances surface fluxes on the equatorward side of the anomalies, it also reduces their propagation speed. These results suggest a novel mechanism for the poleward propagation of intraseasonal convective anomalies and illustrate the need to evaluate theoretical models that use parameterized convection against cloud system–resolving models.
Parallel Low-Storage Runge—Kutta Solvers for ODE Systems with Limited Access Distance
Authors: Korch Matthias , Rauber Thomas 
Published: November 2010

We consider the solution of initial value problems (IVPs) of large systems of ordinary differential equations (ODEs) for which memory space requirements determine the choice of the integration method. In particular, we discuss the space-efficient sequential and parallel implementation of embedded Runge—Kutta (RK) methods. Our focus is on the exploitation of a special structure of commonly appearing ODE systems, referred to as ‘‘limited access distance,’’ to improve scalability and memory usage. Such systems may arise, for example, from the semi-discretization of partial differential equations (PDEs). The storage space required by classical RK methods is directly proportional to the dimension n of the ODE system and the number of stages s of the method. We propose an implementation strategy based on a pipelined processing of the stages of the RK method and show how the memory usage of this computation scheme can be reduced to less than three storage registers by an overlapping of vectors without compromising the choice of method coefficients or the potential for efficient stepsize control. We analyze and compare the scalability of different parallel implementation strategies in detailed runtime experiments on different modern parallel architectures.
Achievement of VGPR to induction therapy is an important prognostic factor for longer PFS in the IFM 2005-01 trial
Authors: Moreau Philippe , Attal Michel , Pégourié Brigitte , Planche Lucie , Hulin Cyrille , Facon Thierry , Stoppa Anne-Marie , Fuzibet Jean-Gabriel , Grosbois Bernard , Doyen Chantal , Ketterer Nicolas , Sebban Catherine , Kolb Brigitte , Chaleteix Carine , Dib Mamoun , Voillat Laurent , Fontan Jean , Garderet Laurent , Jaubert Jérôme , Mathiot Claire , Esseltine Dixie , Avet-Loiseau Hervé , Harousseau Jean-Luc ,   for the IFM 2005-01 study investigators*
Published: November 2010

Abstract
In the 2005-01 trial, we have demonstrated that bortezomib-dexamethasone as induction therapy before autologous stem cell transplantation was superior to vincristine-adriamycin-dexamethasone. We conducted a post-hoc analysis to assess the prognostic impact of initial characteristics as well as response to therapy in patients enrolled in this study. Multivariate analysis showed that ISS stages 2 and 3 and achievement of response less than very good partial response (VGPR) both after induction therapy and after autologous stem cell transplantation were adverse prognostic factors for progression-free survival, the most important one being achievement of response less than VGPR after induction. Progression-free survival was significantly improved with bortezomib-dexamethasone induction therapy in patients with poor-risk cytogenetics and ISS stages 2 and 3 compared with vincristine-adriamycin-dexamethasone. In these 2 groups of patients, achievement of at least VGPR after induction was of major importance. This study is registered with EudraCT (https://eudract.ema.europa.eu; EUDRACT 2005-000537-38) and http://clinicaltrials.gov (NCT00200681).
Bovine proteins containing poly-glutamine repeats are often polymorphic and enriched for components of transcriptional regulatory complexes
Authors: Whan Vicki , Hobbs Matthew , McWilliam Sean , Lynn David J , Lutzow Ylva Strandberg , Khatkar Mehar , Barendse William , Raadsma Herman , Tellam Ross L 
Published: November 2010

Abstract

Background
About forty human diseases are caused by repeat instability mutations. A distinct subset of these diseases is the result of extreme expansions of polymorphic trinucleotide repeats; typically CAG repeats encoding poly-glutamine (poly-Q) tracts in proteins. Polymorphic repeat length variation is also apparent in human poly-Q encoding genes from normal individuals. As these coding sequence repeats are subject to selection in mammals, it has been suggested that normal variations in some of these typically highly conserved genes are implicated in morphological differences between species and phenotypic variations within species. At present, poly-Q encoding genes in non-human mammalian species are poorly documented, as are their functions and propensities for polymorphic variation.

Results
The current investigation identified 178 bovine poly-Q encoding genes (Q ≥ 5) and within this group, 26 genes with orthologs in both human and mouse that did not contain poly-Q repeats. The bovine poly-Q encoding genes typically had ubiquitous expression patterns although there was bias towards expression in epithelia, brain and testes. They were also characterised by unusually large sizes. Analysis of gene ontology terms revealed that the encoded proteins were strongly enriched for functions associated with transcriptional regulation and many contributed to physical interaction networks in the nucleus where they presumably act cooperatively in transcriptional regulatory complexes. In addition, the coding sequence CAG repeats in some bovine genes impacted mRNA splicing thereby generating unusual transcriptional diversity, which in at least one instance was tissue-specific. The poly-Q encoding genes were prioritised using multiple criteria for their likelihood of being polymorphic and then the highest ranking group was experimentally tested for polymorphic variation within a cattle diversity panel. Extensive and meiotically stable variation was identified.

Conclusions
Transcriptional diversity can potentially be generated in poly-Q encoding genes by the impact of CAG repeat tracts on mRNA alternative splicing. This effect, combined with the physical interactions of the encoded proteins in large transcriptional regulatory complexes suggests that polymorphic variations of proteins in these complexes have strong potential to affect phenotype.
Developing high throughput genotyped chromosome segment substitution lines based on population whole-genome re-sequencing in rice (Oryza sativa L.)
Authors: Xu Jianjun , Zhao Qiang , Du Peina , Xu Chenwu , Wang Baohe , Feng Qi , Liu Qiaoquan , Tang Shuzhu , Gu Minghong , Han Bin , Liang Guohua 
Published: November 2010

Abstract

Background
Genetic populations provide the basis for a wide range of genetic and genomic studies and have been widely used in genetic mapping, gene discovery and genomics-assisted breeding. Chromosome segment substitution lines (CSSLs) are the most powerful tools for the detection and precise mapping of quantitative trait loci (QTLs), for the analysis of complex traits in plant molecular genetics.

Results
In this study, a wide population consisting of 128 CSSLs was developed, derived from the crossing and back-crossing of two sequenced rice cultivars: 9311, an elite indica cultivar as the recipient and Nipponbare, a japonica cultivar as the donor. First, a physical map of the 128 CSSLs was constructed on the basis of estimates of the lengths and locations of the substituted chromosome segments using 254 PCR-based molecular markers. From this map, the total size of the 142 substituted segments in the population was 882.2 Mb, was 2.37 times that of the rice genome. Second, every CSSL underwent high-throughput genotyping by whole-genome re-sequencing with a 0.13× genome sequence, and an ultrahigh-quality physical map was constructed. This sequencing-based physical map indicated that 117 new segments were detected; almost all were shorter than 3 Mb and were not apparent in the molecular marker map. Furthermore, relative to the molecular marker-based map, the sequencing-based map yielded more precise recombination breakpoint determination and greater accuracy of the lengths of the substituted segments, and provided more accurate background information. Third, using the 128 CSSLs combined with the bin-map converted from the sequencing-based physical map, a multiple linear regression QTL analysis mapped nine QTLs, which explained 89.50% of the phenotypic variance for culm length. A large-effect QTL was located in a 791,655 bp region that contained the rice 'green revolution' gene.

Conclusions
The present results demonstrated that high throughput genotyped CSSLs combine the advantages of an ultrahigh-quality physical map with high mapping accuracy, thus being of great potential value for gene discovery and genetic mapping. These CSSLs may provide powerful tools for future whole genome large-scale gene discovery in rice and offer foundations enabling the development of superior rice varieties.
Common and distinct organ and stress responsive transcriptomic patterns in Oryza sativa and Arabidopsis thaliana
Authors: Narsai Reena , Castleden Ian , Whelan James 
Published: November 2010

AbstractBackgroundArabidopsis thalianais clearly established as the model plant species. Given the ever-growing demand for food, there is a need to translate the knowledge learned in Arabidopsis to agronomically important species, such as rice (Oryza sativa). To gain a comparative insight into the similarities and differences into how organs are built and how plants respond to stress, the transcriptomes of Arabidopsis and rice were compared at the level of gene orthology and functional categorisation.ResultsOrgan specific transcripts in rice and Arabidopsis display less overlap in terms of gene orthology compared to the orthology observed between both genomes. Although greater overlap in terms of functional classification was observed between root specific transcripts in rice and Arabidopsis, this did not extend to flower, leaf or seed specific transcripts. In contrast, the overall abiotic stress response transcriptome displayed a significantly greater overlap in terms of gene orthology compared to the orthology observed between both genomes. However, ~50% or less of these orthologues responded in a similar manner in both species. In fact, under cold and heat treatments as many or more orthologous genes responded in an opposite manner or were unchanged in one species compared to the other. Examples of transcripts that responded oppositely include several genes encoding proteins involved in stress and redox responses and non-symbiotic hemoglobins that play central roles in stress signalling pathways. The differences observed in the abiotic transcriptomes were mirrored in the presence ofcis-acting regulatory elements in the promoter regions of stress responsive genes and the transcription factors that potentially bind these regulatory elements. Thus, both the abiotic transcriptome and its regulation differ between rice and Arabidopsis.ConclusionsThese results reveal significant divergence between Arabidopsis and rice, in terms of the abiotic stress response and its regulation. Both plants are shown to employ unique combinations of genes to achieve growth and stress responses. Comparison of these networks provides a more rational approach to translational studies that is based on the response observed in these two diverse plant models.
Development and psychometric properties of a belief-based Physical Activity Questionnaire for Diabetic Patients (PAQ-DP)
Authors: Ghazanfari Zeinab , Niknami Shamsaddin , Ghofranipour Fazlollah , Hajizadeh Ebrahim , Montazeri Ali 
Published: November 2010

AbstractBackgroundThis study carried out to develop a scale for assessing diabetic patients' perceptions about physical activity and to test its psychometric properties (The Physical Activity Questionnaire for Diabetic Patients-PAQ-DP).MethodsAn item pool extracted from the Theory of Planned Behavior literature was generated. Then an expert panel evaluated the items by assessing content validity index and content validity ratio. Consequently exploratory factor analysis (EFA) was performed to indicate the scale constructs. In addition reliability analyses including internal consistency and test-retest analysis were carried out.ResultsIn all a sample of 127 women with diabetes participated in the study. Twenty-two items were initially extracted from the literature. A six-factor solution (containing 19 items) emerged as a result of an exploratory factor analysis namely: instrumental attitude, subjective norm, perceived behavioral control, affective attitude, self-identity, and intention explaining 60.30% of the variance observed. Additional analyses indicated satisfactory results for internal consistency (Cronbach's alpha ranging from 0.54 to 0.8) and intraclass correlation coefficients (ranging from 0.40 to 0.92).ConclusionsThe Physical Activity Questionnaire for Diabetic Patients (PAQ-DP) is the first instrument that applies the Theory of Planned Behavior in its constructs. The findings indicated that the PAQ-DP is a reliable and valid measure for assessing physical activity perceptions and now is available and can be used in future studies.
Localization of uPAR and MMP-9 in lipid rafts is critical for migration, invasion and angiogenesis in human breast cancer cells
Authors: Raghu Hari , Sodadasu Prasanna Kumar , Malla Rama Rao , Gondi Christopher S , Estes Norman , Rao Jasti S 
Published: November 2010

Abstract

Background
uPAR and MMP-9, which play critical roles in tumor cell invasion, migration and angiogenesis, have been shown to be associated with lipid rafts.

Methods
To investigate whether cholesterol could regulate uPAR and MMP-9 in breast carcinoma, we used MβCD (methyl beta cyclodextrin, which extracts cholesterol from lipid rafts) to disrupt lipid rafts and studied its effect on breast cancer cell migration, invasion, angiogenesis and signaling.

Results
Morphological evidence showed the association of uPAR with lipid rafts in breast carcinoma cells. MβCD treatment significantly reduced the colocalization of uPAR and MMP-9 with lipid raft markers and also significantly reduced uPAR and MMP-9 at both the protein and mRNA levels. Spheroid migration and invasion assays showed inhibition of breast carcinoma cell migration and invasion after MβCD treatment. In vitro angiogenesis studies showed a significant decrease in the angiogenic potential of cells pretreated with MβCD. MβCD treatment significantly reduced the levels of MMP-9 and uPAR in raft fractions of MDA-MB-231 and ZR 751 cells. Phosphorylated forms of Src, FAK, Cav, Akt and ERK were significantly inhibited upon MβCD treatment. Increased levels of soluble uPAR were observed upon MβCD treatment. Cholesterol supplementation restored uPAR expression to basal levels in breast carcinoma cell lines. Increased colocalization of uPAR with the lysosomal marker LAMP1 was observed in MβCD-treated cells when compared with untreated cells.

Conclusion
Taken together, our results suggest that cholesterol levels in lipid rafts are critical for the migration, invasion, and angiogenesis of breast carcinoma cells and could be a critical regulatory factor in these cancer cell processes mediated by uPAR and MMP-9.
Investigating dynamic and energetic determinants of protein nucleic acid recognition: analysis of the zinc finger zif268-DNA complexes
Authors: Torella Rubben , Moroni Elisabetta , Caselle Michele , Morra Giulia , Colombo Giorgio 
Published: November 2010

Abstract

Background
Protein-DNA recognition underlies fundamental biological processes ranging from transcription to replication and modification. Herein, we present a computational study of the sequence modulation of internal dynamic properties and of intraprotein networks of aminoacid interactions that determine the stability and specificity of protein-DNA complexes.

Results
To this aim, we apply novel theoretical approaches to analyze the dynamics and energetics of biological systems starting from MD trajectories. As model system, we chose different sequences of Zinc Fingers (ZF) of the Zif268 family bound with different sequences of DNA. The complexes differ for their experimental stability properties, but share the same overall 3 D structure and do not undergo structural modifications during the simulations. The results of our analysis suggest that the energy landscape for DNA binding may be populated by dynamically different states, even in the absence of major conformational changes. Energetic couplings between residues change in response to protein and/or DNA sequence variations thus modulating the selectivity of recognition and the relative importance of different regions for binding.

Conclusions
The results show differences in the organization of the intra-protein energy-networks responsible for the stabilization of the protein conformations recognizing and binding DNA. These, in turn, are reflected into different modulation of the ZF's internal dynamics. The results also show a correlation between energetic and dynamic properties of the different proteins and their specificity/selectivity for DNA sequences. Finally, a dynamic and energetic model for the recognition of DNA by Zinc Fingers is proposed.
Tracking hantavirus nucleocapsid protein using intracellular antibodies
Authors: Li Jiandong , Zhang Quanfu , Wang Tao , Li Chuan , Liang Mifang , Li Dexin 
Published: November 2010

Abstract

Background
Hantavirus nucleocapsid (N) protein is a multifunctional viral macromolecule involved in multiple stages of the viral replication cycle. The intracellular trafficking of N protein during virus assembly remains unclear.

Methods
We used N protein-specific intracellular expressed antibodies to track the localization and distribution of Hantaan virus and Seoul virus N protein. The N protein-specific antibody single-chain variable antibody fragments (scFvs), which bind an N-terminal linear epitope (L13F3) and C-terminal conformational domain (H34), were intracellularly expressed in the endoplasmic reticulum (ER) by fusion of the SEKDEL retention signal peptide at the carboxyl terminus, and in the cytoplasm (Cyto) by deletion of the ER membrane target signal peptide. Stable Vero-E6 cell lines expressing intracellular scFvs were either infected with hantavirus or transfected with an N protein expression plasmid; virus replication and N protein intracellular localization were determined.

Result
N protein co-localized with scFvs in the ER and cytoplasm with or without viral membrane glycoproteins. Hantavirus replication was inhibited in both the scFvs-ER- and scFvs-Cyto-expressing stable cell lines.

Conclusion
N protein may be expressed in the ER retention signal peptide of KDEL circulating region (ER/cis-Golgi) without the assistance of G protein, and so expression of N protein in both the cytoplasm and within the ER/cis-Golgi plays an important role in virus replication.
Sensitization of Capsaicin and Icilin Responses in Oxaliplatin Treated Adult Rat DRG Neurons
Authors: Anand Uma , Otto William R , Anand Praveen 
Published: November 2010

Background: Oxaliplatin chemotherapy induced neuropathy is a dose related cumulative toxicity that manifests as tingling, numbness, and chronic pain, compromising the quality of life and leading to discontinued chemotherapy. Patients report marked hypersensitivity to cold stimuli at early stages of treatment, when sensory testing reveals cold and heat hyperalgesia. This study examined the morphological and functional effects of oxaliplatin treatment in cultured adult rat DRG neurons. Results: 48 hour exposure to oxaliplatin resulted in dose related reduction in neurite length, density, and number of neurons compared to vehicle treated controls, using Gap43 immunostaining. Neurons treated acutely with 20 μg/ml oxaliplatin showed significantly higher signal intensity for cyclic AMP immunofluorescence (160.5 ± 13 a.u., n = 3, P < 0.05), compared to controls (120.3 ± 4 a.u.). Calcium imaging showed significantly enhanced capsaicin (TRPV1 agonist), responses after acute 20 μg/ml oxaliplatin treatment where the second of paired capsaicin responses increased from 80.7 ± 0.6% without oxaliplatin, to 171.26 ± 29% with oxaliplatin, (n = 6 paired t test, P < 0.05); this was reduced to 81.42 ± 8.1% (P < 0.05), by pretretreatment with the cannabinoid CB2 receptor agonist GW 833972. Chronic oxaliplatin treatment also resulted in dose related increases in capsaicin responses. Similarly, second responses to icilin (TRPA1/TRPM8 agonist), were enhanced after acute (143.85 ± 7%, P = 0.004, unpaired t test, n = 3), and chronic (119.7 ± 11.8%, P < 0.05, n = 3) oxaliplatin treatment, compared to control (85.3 ± 1.7%). Responses to the selective TRPM8 agonist WS-12 were not affected. Conclusions: Oxaliplatin treatment induces TRP sensitization mediated by increased intracellular cAMP, which may cause neuronal damage. These effects may be mitigated by co-treatment with adenylyl cyclase inhibitors, like CB2 agonists, to alleviate the neurotoxic effects of oxaliplatin.