bluuebunny/crossref_metadata_2025_split huggingface dataset:
Melody Valve Implantation Into the Branch Pulmonary Arteries for Treatment of Pulmonary Insufficiency in an Ovine Model of Right Ventricular Outflow Tract Dysfunction Following Tetralogy of Fallot Repair
Authors: Robb J. Daniel , Harris Matthew A. , Minakawa Masahito , Rodriguez Evelio , Koomalsingh Kevin J. , Shuto Takashi , Shin David C. , Dori Yoav , Glatz Andrew C. , Rome Jonathan J. , Gorman Robert C. , Gorman Joseph H. , Gillespie Matthew J. 
Published: January 2011

Background—
Transannular patch (TAP) repair of tetralogy of Fallot often results in significant right ventricular outflow tract (RVOT) dilation and distortion. We hypothesized that insertion of Melody valves into the proximal right and left branch pulmonary arteries (PAs) would reduce pulmonary regurgitation fraction (PRF) in an ovine model of pulmonary insufficiency and dilated RVOT.

Methods and Results—
Ten sheep underwent baseline cardiac catheterization, surgical pulmonary valvectomy, and TAP placement. A subset (n=5) had Melody valves (2 devices per animal) inserted into the proximal right and left PAs during the surgical procedure. Melody valves were placed distal to the right-upper-lobe (RUL) artery branch, leaving the RUL “unprotected.” Preoperative MRIs (n=5) were used to determine baseline RV ejection fraction (RVEF) and left ventricular (LV) EF. All surviving animals (n=9) underwent MRI and catheterization 6 weeks postsurgery.

Mean PRF was lower in the Melody valve group (15±6% versus 37±3%;
P
=0.014). The unprotected RUL was responsible for 64% of the PRF measured in the Melody valve group. In the non-Melody group, the RVEF was lower than baseline (
P
=0.003) and than in the Melody group (
P
=0.05). The LVEF was also lower in the non-Melody group versus baseline (
P
=0.004) and versus Melody (
P
=0.01).

Conclusions—
Bilateral branch PA Melody valve implantation significantly reduced PRF and altered RV and LV function favorably in a model of TAP for tetralogy of Fallot. This novel intervention may offer potential benefit in treating patients with anatomically heterogeneous disease of the RVOT.
A multiplex real-time PCR assay for the simultaneous quantification of the major plant-parasitic nematodes in Japan
Authors: Min Yu Yu , Goto Keita , Toyota Koki , Sato Erika 
Published: January 2011

AbstractMultiplex real-time PCR assays were developed to quantify multiple species of Meloidogyne incognita, Pratylenchus penetrans, Globodera rostochiensis and Heterodera glycines in soil. The probes specific for P. penetrans and H. glycines are labelled with a fluorescence molecule, FAM, and those for M. incognita and G. rostochiensis with ROX. The primers and probes are species-specific to P. penetrans, but group-specific to the other species. DNA was extracted from suspensions containing each nematode and multiplex Cycleave® PCR assays were done for pairs of P. penetrans and M. incognita, P. penetrans and G. rostochiensis, or G. rostochiensis and H. glycines. The results revealed that the target nematode, except for H. glycines, was quantified in the presence of less than 100 times that of the other nematode (competitor), but underestimated in the presence of 1000 times the competitor. Such underestimation was solved by the use of SYBR Green I real time PCR assays targeting a single species. Multiplex PCR assay for P. penetrans and M. incognita was done using environmental DNA (eDNA) extracted from a soil naturally infested with the nematodes. Results quantified both species. Multiplex assay using eDNA may enable a sensitive and simultaneous detection of P. penetrans and M. incognita or P. penetrans and G. rostochiensis in soil although caution is needed in case the existing ratio is biased to one of the species.
Numerical Simulations of Lateral Dispersion by the Relaxation of Diapycnal Mixing Events
Authors: Sundermeyer Miles A. , Lelong M-Pascale 
Published: January 2011

Abstract
In this second of two companion papers, numerical simulations of lateral dispersion by small-scale geostrophic motions, or vortical modes, generated by the adjustment of mixed patches following diapycnal mixing events are examined. A three-dimensional model was used to solve the Navier–Stokes equations and an advection/diffusion equation for a passive tracer. Model results were compared with theoretical predictions for vortical mode stirring with results from dye release experiments conducted over the New England continental shelf. For “weakly nonlinear” cases in which adjustment events were isolated in space and time, lateral dispersion in the model was consistent to within a constant scale factor with the parameter dependencepredicted by Sundermeyer et al., where h and L are the vertical and horizontal scales of the mixed patches, ΔN 2 is the change in stratification associated with the mixed patches, f is the Coriolis parameter, ϕ is the frequency of diapycnal mixing events, and νB is the background viscosity. The associated scale factor, assumed to be of order 1, had an actual value of about 7, although this value will depend, in an unknown way, on the assumed horizontal scale of the mixed patches, which was here held constant at close to the deformation radius. A second more energetic parameter regime was also identified in which vortical mode stirring became strongly nonlinear and the effective lateral dispersion was larger. Estimates of the relevant parameters over the New England shelf suggest that this strongly nonlinear regime is more relevant to the real ocean than the weakly nonlinear regime, at least under late summer conditions. This suggests that stirring by small-scale geostrophic motion may, under certain conditions, contribute significantly to lateral dispersion on scales of 1–10 km in the ocean.
Sex, Contagion, Control: Prison Officers vs Condoms in New South Wales Gaols
Authors: Cregar Jan , Kippax Susan , Crawford June 
Published: January 2011

Since the beginning of the HIV/AIDS epidemic, public health experts have identified prison populations as a target for preventive strategies in order to minimise transmission of HIV among the general community. Public opinion favours supplying condoms to prisoners, but this was successfully resisted by prison officers in New South Wales for eight years. This paper examines expert and community opinions, HIV/AIDS and prison policies, public and correctional discourse, and statements made by prison officers' union representatives. It offers an account of the prison officers' success in blocking condom distribution, based on three major discursive themes emerging from the analysis.
Evaluation of Immunohistochemical Fine Sectioning for Sentinel Lymph Node Biopsy in Oral Squamous Cell Carcinoma
Authors: Jefferson Gina D. , Sollaccio David , Gomez‐Fernandez Carmen R. , Civantos Francisco 
Published: January 2011

ObjectiveTo determine the level of sentinel lymph node sectioning necessary to accurately detect nodal micrometastasis.Study DesignCross‐sectional.SettingTertiary care university medical center.Subjects and MethodsFine sections of oral squamous cell carcinoma sentinel lymph nodes previously sectioned at 2‐mm intervals in a prospective clinical trial were reexamined. The results yielded from prior hematoxylin and eosin and immunohistochemical staining were compared with results following exhaustive serial sectioning at 150‐µm intervals using identical staining methods. These experimental findings were compared with pathologic results of immediate completion selective neck dissection, previously recorded prospectively.ResultsReexamination of 35 sentinel nodes at 150‐µm intervals has not revealed any missed micrometastatic disease at 2‐mm intervals used initially. Both comparisons of 150‐µm sectioning analysis to the original 2‐mm section samples and to the neck dissection pathology reports demonstrate a 100% negative predictive value.ConclusionThese data suggest that sentinel lymph node sectioning at 2‐mm intervals for oral carcinoma using hematoxylin and eosin staining and then immunohistochemical analysis maximizes efficiency, accuracy, and expenditure for the detection of micrometastasis.
Aberrant interferon-signaling is associated with aggressive chronic lymphocytic leukemia
Authors: Tomic Jelena , Lichty Brian , Spaner David E. 
Published: January 2011

AbstractThe type I interferons (IFNs) normally suppress tumor growth by phosphorylating and activating the signal transducer and activator of transcription 1 (STAT1), but also briefly activate STAT3, which promotes cell growth. In chronic lymphocytic leukemia (CLL) cells, the duration of IFN-mediated STAT3 phosphorylation was found to exhibit significant interpatient variability and was prolonged in cells with high risk features, such as 11q− and 17p− deletions involving ataxia telangiectasia mutated (ATM) and p53. This aberrant signaling pattern was associated with a paradoxical increase in cell size and number in response to IFN and similar alterations in IFN-signaling and responses were seen in cell lines that developed in the absence of p53 or ATM. However, direct inhibition of p53 or ATM failed to cause these changes, and CLL cells with aggressive clinical features were found to also express high levels of reactive oxygen species (ROS), which decrease tyrosine phosphatase activity. Prolonged IFN-mediated STAT3 phosphorylation and lowered phosphatase activity could be reversed by antioxidants. These findings suggest that increased ROS levels may corrupt IFN-signaling processes in aggressive CLL cells, causing IFN to be used as a growth factor rather than a tumor suppressor. Antioxidants or STAT3 kinase inhibitors might improve the outcome of IFN therapy in CLL by restoring normal signaling.
Systemic perturbation of cytokine and chemokine networks in Erdheim-Chester disease: a single-center series of 37 patients
Authors: Arnaud Laurent , Gorochov Guy , Charlotte Frédéric , Lvovschi Virginie , Parizot Christophe , Larsen Martin , Ghillani-Dalbin Pascale , Hervier Baptiste , Kahn Jean-Emmanuel , Deback Claire , Musset Lucile , Amoura Zahir , Haroche Julien 
Published: January 2011

AbstractImmunopathogenesis of Erdheim-Chester disease (ECD), a rare non–Langerhans cell histiocytosis, is poorly known. In previous studies, various cytokines were detected in ECD lesions, presumably orchestrating lesional histiocyte recruitment. Because ECD lesions are frequently associated with systemic symptoms, we postulated that underlying global immune perturbations might also be revealed. We quantitatively analyzed 23 cytokines in serum samples obtained from a large single-center cohort of 37 patients with ECD, and studied the impact of treatment on cytokine production. IL-6, IL-12, interferon-α (IFN-α), and monocyte chemotactic protein-1 (MCP-1) levels were significantly higher in untreated patients than in controls, whereas interferon-γ (IFN-γ) inducible protein 10, IL-12, MCP-1, and IL-1 receptor antagonist were found significantly increased in IFN-α–treated patients. A biomathematical approach was used to rationalize multiparameter data, to generate new hypotheses, and identify global control pathways. Interestingly, cytokine profiles proved to be particularly stable at the individual level, and an “ECD signature” further distinguished patients from controls, based on their production of IFN-α, IL-12, MCP-1, IL-4, and IL-7. Altogether, our data underline the systemic immune Th-1–oriented perturbation associated with this condition and provide clues for the choice of more focused therapeutic agents in this rare disease with noncodified therapeutic management.
Genetic diversity of selected genes that are potentially economically important in feral sheep of New Zealand
Authors: McKenzie Grant W , Abbott Johanna , Zhou Huitong , Fang Qian , Merrick Norma , Forrest Rachel H , Sedcole J Richard , Hickford Jonathan G 
Published: January 2011

Abstract

Background
Feral sheep are considered to be a source of genetic variation that has been lost from their domestic counterparts through selection.

Methods
This study investigates variation in the genes KRTAP1-1, KRT33, ADRB3 and DQA2 in Merino-like feral sheep populations from New Zealand and its offshore islands. These genes have previously been shown to influence wool, lamb survival and animal health.

Results
All the genes were polymorphic, but no new allele was identified in the feral populations. In some of these populations, allele frequencies differed from those observed in commercial Merino sheep and other breeds found in New Zealand. Heterozygosity levels were comparable to those observed in other studies on feral sheep. Our results suggest that some of the feral populations may have been either inbred or outbred over the duration of their apparent isolation.

Conclusion
The variation described here allows us to draw some conclusions about the likely genetic origin of the populations and selective pressures that may have acted upon them, but they do not appear to be a source of new genetic material, at least for these four genes.
The complexity of gene expression dynamics revealed by permutation entropy
Authors: Sun Xiaoliang , Zou Yong , Nikiforova Victoria , Kurths Jürgen , Walther Dirk 
Published: January 2011

AbstractBackgroundHigh complexity is considered a hallmark of living systems. Here we investigate the complexity of temporal gene expression patterns using the concept of Permutation Entropy (PE) first introduced in dynamical systems theory. The analysis of gene expression data has so far focused primarily on the identification of differentially expressed genes, or on the elucidation of pathway and regulatory relationships. We aim to study gene expression time series data from the viewpoint of complexity.ResultsApplying the PE complexity metric to abiotic stress response time series data in Arabidopsis thaliana, genes involved in stress response and signaling were found to be associated with the highest complexity not only under stress, but surprisingly, also under reference, non-stress conditions. Genes with house-keeping functions exhibited lower PE complexity. Compared to reference conditions, the PE of temporal gene expression patterns generally increased upon stress exposure. High-complexity genes were found to have longer upstream intergenic regions and more cis-regulatory motifs in their promoter regions indicative of a more complex regulatory apparatus needed to orchestrate their expression, and to be associated with higher correlation network connectivity degree. Arabidopsis genes also present in other plant species were observed to exhibit decreased PE complexity compared to Arabidopsis specific genes.ConclusionsWe show that Permutation Entropy is a simple yet robust and powerful approach to identify temporal gene expression profiles of varying complexity that is equally applicable to other types of molecular profile data.
MBAT: A scalable informatics system for unifying digital atlasing workflows
Authors: Lee Daren , Ruffins Seth , Ng Queenie , Sane Nikhil , Anderson Steve , Toga Arthur 
Published: January 2011

Abstract

Background
Digital atlases provide a common semantic and spatial coordinate system that can be leveraged to compare, contrast, and correlate data from disparate sources. As the quality and amount of biological data continues to advance and grow, searching, referencing, and comparing this data with a researcher's own data is essential. However, the integration process is cumbersome and time-consuming due to misaligned data, implicitly defined associations, and incompatible data sources. This work addressing these challenges by providing a unified and adaptable environment to accelerate the workflow to gather, align, and analyze the data.

Results
The MouseBIRN Atlasing Toolkit (MBAT) project was developed as a cross-platform, free open-source application that unifies and accelerates the digital atlas workflow. A tiered, plug-in architecture was designed for the neuroinformatics and genomics goals of the project to provide a modular and extensible design. MBAT provides the ability to use a single query to search and retrieve data from multiple data sources, align image data using the user's preferred registration method, composite data from multiple sources in a common space, and link relevant informatics information to the current view of the data or atlas. The workspaces leverage tool plug-ins to extend and allow future extensions of the basic workspace functionality. A wide variety of tool plug-ins were developed that integrate pre-existing as well as newly created technology into each workspace. Novel atlasing features were also developed, such as supporting multiple label sets, dynamic selection and grouping of labels, and synchronized, context-driven display of ontological data.

Conclusions
MBAT empowers researchers to discover correlations among disparate data by providing a unified environment for bringing together distributed reference resources, a user's image data, and biological atlases into the same spatial or semantic context. Through its extensible tiered plug-in architecture, MBAT allows researchers to customize all platform components to quickly achieve personalized workflows.
Galaxy CloudMan: delivering cloud compute clusters
Authors: Afgan Enis , Baker Dannon , Coraor Nate , Chapman Brad , Nekrutenko Anton , Taylor James 
Published: January 2011

Abstract

Background
Widespread adoption of high-throughput sequencing has greatly increased the scale and sophistication of computational infrastructure needed to perform genomic research. An alternative to building and maintaining local infrastructure is “cloud computing”, which, in principle, offers on demand access to flexible computational infrastructure. However, cloud computing resources are not yet suitable for immediate “as is” use by experimental biologists.

Results
We present a cloud resource management system that makes it possible for individual researchers to compose and control an arbitrarily sized compute cluster on Amazon’s EC2 cloud infrastructure without any informatics requirements. Within this system, an entire suite of biological tools packaged by the NERC Bio-Linux team (http://nebc.nerc.ac.uk/tools/bio-linux) is available for immediate consumption. The provided solution makes it possible, using only a web browser, to create a completely configured compute cluster ready to perform analysis in less than five minutes. Moreover, we provide an automated method for building custom deployments of cloud resources. This approach promotes reproducibility of results and, if desired, allows individuals and labs to add or customize an otherwise available cloud system to better meet their needs.

Conclusions
The expected knowledge and associated effort with deploying a compute cluster in the Amazon EC2 cloud is not trivial. The solution presented in this paper eliminates these barriers, making it possible for researchers to deploy exactly the amount of computing power they need, combined with a wealth of existing analysis software, to handle the ongoing data deluge.
DNA damage-induced translocation of S100A11 into the nucleus regulates cell proliferation
Authors: Gorsler Theresa , Murzik Ulrike , Ulbricht Tobias , Hentschel Julia , Hemmerich Peter , Melle Christian 
Published: January 2011

Abstract

Background
Proteins are able to react in response to distinct stress stimuli by alteration of their subcellular distribution. The stress-responsive protein S100A11 belongs to the family of multifunctional S100 proteins which have been implicated in several key biological processes. Previously, we have shown that S100A11 is directly involved in DNA repair processes at damaged chromatin in the nucleus. To gain further insight into the underlying mechanism subcellular trafficking of S100A11 in response to DNA damage was analyzed.

Results
We show that DNA damage induces a nucleolin-mediated translocation of S100A11 from the cytoplasm into the nucleus. This translocation is impeded by inhibition of the phosphorylation activity of PKCα. Translocation of S100A11 into the nucleus correlates with an increased cellular p21 protein level. Depletion of nucleolin by siRNA severely impairs translocation of S100A11 into the nucleus resulting in a decreased p21 protein level. Additionally, cells lacking nucleolin showed a reduced colony forming capacity.

Conclusions
These observations suggest that regulation of the subcellular distribution of S100A11 plays an important role in the DNA damage response and p21-mediated cell cycle control.
A sensitive and bright single-cell resolution live imaging reporter of Wnt/ß-catenin signaling in the mouse
Authors: Ferrer-Vaquer Anna , Piliszek Anna , Tian Guangnan , Aho Robert J , Dufort Daniel , Hadjantonakis Anna-Katerina 
Published: January 2011

AbstractBackgroundUnderstanding the dynamic cellular behaviors and underlying molecular mechanisms that drive morphogenesis is an ongoing challenge in biology. Live imaging provides the necessary methodology to unravel the synergistic and stereotypical cell and molecular events that shape the embryo. Genetically-encoded reporters represent an essential tool for live imaging. Reporter strains can be engineered by placingcis-regulatory elements of interest to direct the expression of a desired reporter gene. In the case of canonical Wnt signaling, also referred to as Wnt/β-catenin signaling, since the downstream transcriptional response is well understood, reporters can be designed that reflect sites of active Wnt signaling, as opposed to sites of gene transcription, as is the case with many fluorescent reporters. However, even though several transgenic Wnt/β-catenin reporter strains have been generated, to date, none provides the single-cell resolution favored for live imaging studies.ResultsWe have placed six copies of a TCF/Lef responsive element and anhsp68minimal promoter in front of a fluorescent protein fusion comprising human histone H2B to GFP and used it to generate a strain of mice that would report Wnt/β-catenin signaling activity. Characterization of developmental and adult stages of the resultingTCF/Lef:H2B-GFPstrain revealed discrete and specific expression of the transgene at previously characterized sites of Wnt/β-catenin signaling. In support of the increased sensitivity of theTCF/Lef:H2B-GFPreporter, additional sites of Wnt/β-catenin signaling not documented with other reporters but identified through genetic and embryological analysis were observed. Furthermore, the sub-cellular localization of the reporter minimized reporter perdurance, and allowed visualization and tracking of individual cells within a cohort, so facilitating the detailed analysis of cell behaviors and signaling activity during morphogenesis.ConclusionBy combining the Wnt activity read-out efficiency of multimerized TCF/Lef DNA binding sites, together with the high-resolution imaging afforded by subcellularly-localized fluorescent fusion proteins such as H2B-GFP, we have created a mouse transgenic line that faithfully recapitulates Wnt signaling activity at single-cell resolution. TheTCF/Lef:H2B-GFPreporter represents a unique tool for live imaging thein vivoprocesses triggered by Wnt/β-catenin signaling, and thus should help the formulation of a high-resolution understanding of the serial events that define the morphogenetic process regulated by this signaling pathway.