bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diagnosing the Observed Seasonal Cycle of Atlantic Subtropical Mode Water Using Potential Vorticity and Its Attendant Theorems
Authors: Maze Guillaume , Marshall John 
Published: June 2011

Abstract
Analyzed fields of ocean circulation and the flux form of the potential vorticity equation are used to map the creation and subsequent circulation of low potential vorticity waters known as subtropical mode water (STMW) in the North Atlantic. Novel mapping techniques are applied to (i) render the seasonal cycle and annual-mean mixed layer vertical flux of potential vorticity (PV) through outcrops and (ii) visualize the extraction of PV from the mode water layer in winter, over and to the south of the Gulf Stream. Both buoyancy loss and wind forcing contribute to the extraction of PV, but the authors find that the former greatly exceeds the latter. The subsequent path of STMW is also mapped using Bernoulli contours on isopycnal surfaces.
Stratospheric Sudden Warmings as Self-Tuning Resonances. Part II: Vortex Displacement Events
Authors: Esler J. G. , Matthewman N. Joss 
Published: June 2011

Abstract
Vortex displacement stratospheric sudden warmings (SSWs) are studied in an idealized model of a quasigeostrophic columnar vortex in an anelastic atmosphere. Motivated by the fact that observed events occur at a fixed orientation to the earth’s surface and have a strongly baroclinic vertical structure, vortex Rossby waves are forced by a stationary topographic forcing designed to minimize excursions of the vortex from its initial position. Variations in the background stratospheric “climate” are represented by means of an additional flow in solid body rotation. The vortex response is determined numerically as a function of the forcing strength M and the background flow strength Ω.
At moderate M it is found that a large response, with many features resembling observed displacement SSWs, occurs only for a narrow range of Ω. Linear analysis reveals that for this range of Ω the first baroclinic azimuthal wave-1 Rossby wave mode is close to being resonantly excited. A forced nonlinear oscillator equation is proposed to describe the nonlinear behavior, and a method for determining the relevant coefficients numerically, using unforced calculations of steadily propagating vortex “V states,” is adopted. The nonlinear equation predicts some qualitative details of the variation in the response at finite M. However, it is concluded that strongly nonlinear processes, such as wave breaking and filament formation, are necessarily quantitatively important in determining the amplitude of the near-resonant response at finite M.
Market Socialism Is Not Market Capitalism
Authors: DiQuattro Arthur 
Published: June 2011

In his recent work, Robin Hahnel defends a monolithic metric of economic desert: to each according to effort or sacrifice. I criticize from an egalitarian standpoint this meritocratic distributive principle on theoretical, practical, and normative grounds. I also question his argument that in market socialism the allocation of labor cannot accommodate an egalitarian distribution of labor income; his not unfamiliar argument rests on a fatal theoretical error that conflates the allocative and distributive functions of market prices. I treat Hahnel’s work in the context of larger issues about competing concepts of justice and the distributive institutions that might suit them. JEL classification: A13, P1, P2
Towards depth and width in Qualitative Social Work: Aligning interpretative phenomenological analysis with the theory of social domains
Authors: Houston Stan , Mullan-Jensen Christine 
Published: June 2011

Queen's University Belfast, UK In this article the authors argue that qualitative inquiry in social work can gain a clear-sighted awareness of the social world by aligning a methodological approach, Interpretative Phenomenological Analysis, with a sociological theory of agency and structure, the Theory of Social Domains. The authors contend that this alignment equips the researcher with an understanding of both the psychological and sociological dimensions of existence – its ontological depth and width. A case for this alignment is made, first, by setting out the theoretical and methodological foundations of both approaches and then, second, proffering a conceptual bridge between them through their shared interest in social phenomenology. The remaining part of the article goes on to consider how this alignment provides a theoretical and methodological substratum for qualitative investigations into social work where anti-oppressive research practice is to the fore.
A targeted metabolic protocol with D-ribose for off-pump coronary artery bypass procedures: a retrospective analysis
Authors: Perkowski David J. , Wagner Susan , Schneider Joseph R. , St. Cyr J. A. 
Published: June 2011

Objectives: Coronary revascularization using cardiopulmonary bypass is an effective surgical procedure for ischemic coronary artery disease. Complications associated with cardiopulmonary bypass have included cerebral vascular accidents, neurocognitive disorders, renal dysfunction, and acute systemic inflammatory responses. Within the last two decades off-pump coronary artery bypass has emerged as an approach to reduce the incidence of these complications, as well as shorten hospital stays and recovery times. Many patients with coronary artery disease have insulin resistance and altered energy metabolism, which can exacerbate around the time of coronary revascularization. D-ribose has been shown to enhance the recovery of high-energy phosphates following myocardial ischemia. We hypothesized that patient outcomes could improve using a perioperative metabolic protocol with D-ribose. Methods: A perioperative metabolic protocol was used in 366 patients undergoing off-pump coronary artery bypass during 2004–2008. D-ribose was added in 308 of these 366 patients. Data were collected prospectively as part of the Society of Thoracic Surgeons database and retrospectively analyzed. Results: D-ribose patients were generally similar to those who did not receive D-ribose. There was one death, two patients suffered strokes and renal failure requiring dialysis occurred in two patients postoperatively among the entire group of patients. D-ribose patients enjoyed a greater improvement in cardiac index postrevascularization compared with non-D-ribose patients (37% vs. 17%, respectively, p < 0.001). Conclusions: This metabolic protocol was associated with very low mortality and morbidity with a significant early postoperative improvement in cardiac index using D-ribose supplementation. These preliminary results support a prospective randomized trial using this protocol and D-ribose.
GABP transcription factor is required for myeloid differentiation, in part, through its control of Gfi-1 expression
Authors: Yang Zhong-Fa , Drumea Karen , Cormier James , Wang Junling , Zhu Xuejun , Rosmarin Alan G. 
Published: June 2011

Abstract
GABP is an ets transcription factor that regulates genes that are required for myeloid differentiation. The tetrameric GABP complex includes GABPα, which binds DNA via its ets domain, and GABPβ, which contains the transcription activation domain. To examine the role of GABP in myeloid differentiation, we generated mice in which Gabpa can be conditionally deleted in hematopoietic tissues. Gabpa knockout mice rapidly lost myeloid cells, and residual myeloid cells were dysplastic and immunophenotypically abnormal. Bone marrow transplantation demonstrated that Gabpα null cells could not contribute to the myeloid compartment because of cell intrinsic defects. Disruption of Gabpa was associated with a marked reduction in myeloid progenitor cells, and Gabpα null myeloid cells express reduced levels of the transcriptional repressor, Gfi-1. Gabp bound and activated the Gfi1 promoter, and transduction of Gabpa knockout bone marrow with Gfi1 partially rescued defects in myeloid colony formation and myeloid differentiation. We conclude that Gabp is required for myeloid differentiation due, in part, to its regulation of the tran-scriptional repressor Gfi-1.
Maintenance and break of immune tolerance against human factor VIII in a new transgenic hemophilic mouse model
Authors: van Helden Pauline M. , Unterthurner Sabine , Hermann Corinna , Schuster Maria , Ahmad Rafi U. , Schiviz Alexandra N. , Weiller Markus , Antoine Gerhard , Turecek Peter L. , Muchitsch Eva M. , Schwarz Hans Peter , Reipert Birgit M. 
Published: June 2011

AbstractReplacement of the missing factor VIII (FVIII) is the current standard of care for patients with hemophilia A. However, the short half-life of FVIII makes frequent treatment necessary. Current efforts focus on the development of longer-acting FVIII concentrates by introducing chemical and genetic modifications to the protein. Any modification of the FVIII protein, however, risks increasing its immunogenic potential to induce neutralizing antibodies (FVIII inhibitors), and this is one of the major complications in current therapy. It would be highly desirable to identify candidates with a high risk for increased immunogenicity before entering clinical development to minimize the risk of exposing patients to such altered FVIII proteins. In the present study, we describe a transgenic mouse line that expresses a human F8 cDNA. This mouse is immunologically tolerant to therapeutic doses of native human FVIII but is able to mount an antibody response when challenged with a modified FVIII protein that possesses altered immunogenic properties. In this situation, immunologic tolerance breaks down and antibodies develop that recognize both the modified and the native human FVIII. The applicability of this new model for preclinical immunogenicity assessment of new FVIII molecules and its potential use for basic research are discussed.
Kill one bird with two stones: potential efficacy of BCR-ABL and autophagy inhibition in CML
Authors: Helgason G. Vignir , Karvela Maria , Holyoake Tessa L. 
Published: June 2011

Abstract
The introduction of imatinib in the treatment of chronic myeloid leukemia (CML) represents the most successful example of targeted therapy in human cancer. However, leukemic stem cells are insensitive to tyrosine kinase inhibitors (TKIs) and contribute to the persistence of disease by representing a reservoir of selfrenewing cells that replenish the disease after drug discontinuation. This finding has refocused the interest of scientists toward drug combinations, ie, treating with TKIs and simultaneously targeting alternative survival mechanisms. One candidate target mechanism is autophagy, a cellular recycling process that acts as a cytoprotective shield in CML cells in response to TKI-induced stress and in other cancer cells surviving in an inhospitable microenvironment. On that basis, inhibition of autophagy has now become an exciting option for combination treatment in cancer, and clinical trials have been initiated in solid and hemopoietic tumors such as CML, chronic lymphocytic leukemia, and multiple myeloma. This review describes the biology of CML and elucidates how the molecular driver BCR-ABL led to the development of TKIs. We then discuss the molecular regulation of autophagy and the potential for autophagy inhibition as the next step in our attempt to tackle the problem of CML persistence to offer a curative option.
α4 integrin levels on mobilized peripheral blood stem cells predict rapidity of engraftment in patients receiving autologous stem cell transplantation
Authors: Hartz Bernd , Volkmann Thorsten , Irle Sebastian , Loechelt Cordula , Neubauer Andreas , Brendel Cornelia 
Published: June 2011

Abstract
Rapidness of leukocyte engraftment in patients receiving peripheral blood stem cell transplantation is clinically important because the risk of fatal opportunistic infections increases with time to engraftment. Adhesion receptor molecules on hematopoietic stem cells (HSCs) have been shown to modulate homing and engraftment of HSCs. Therefore, we correlated expression levels of α4 (CD49d) and α6 (CD49f) integrins in the CD34+ HSC compartment with time to engraftment. Leukapheresis products from 103 patients were retrospectively analyzed for CD34, CD38, CD3, CD49f, and CD49d surface molecules by multiparameter flow cytometry. High expression levels of α4 integrin, but not α6 integrin on CD34+ cells, were associated with regular engraftment of leukocytes (days 8-19), whereas low surface expression correlated with delayed recovery (> 19 days; P < .0005). We show that α4 integrin expression levels on HSCs in leukapheresis products predict the engraftment capacity of mobilized peripheral blood stem cells in peripheral blood stem cell transplantation patients.
Plasmacytoid dendritic cells are recruited to the colorectum and contribute to immune activation during pathogenic SIV infection in rhesus macaques
Authors: Kwa Suefen , Kannanganat Sunil , Nigam Pragati , Siddiqui Mariam , Shetty Ravi Dyavar , Armstrong Wendy , Ansari Aftab , Bosinger Steven E. , Silvestri Guido , Amara Rama Rao 
Published: June 2011

AbstractIn SIV/HIV infection, the gastrointestinal tissue dominates as an important site because of the impact of massive mucosal CD4 depletion and immune activation-induced tissue pathology. Unlike AIDS-susceptible rhesus macaques, natural hosts do not progress to AIDS and resolve immune activation earlier. Here, we examine the role of dendritic cells (DCs) in mediating immune activation and disease progression. We demonstrate that plasmacytoid DCs (pDCs) in the blood up-regulate β7-integrin and are rapidly recruited to the colorectum after a pathogenic SIV infection in rhesus macaques. These pDCs were capable of producing proinflammatory cytokines and primed a T cytotoxic 1 response in vitro. Consistent with the up-regulation of β7-integrin on pDCs, in vivo blockade of α4β7-integrin dampened pDC recruitment to the colorectum and resulted in reduced immune activation. The up-regulation of β7-integrin expression on pDCs in the blood also was observed in HIV-infected humans but not in chronically SIV-infected sooty mangabeys that show low levels of immune activation. Our results uncover a new mechanism by which pDCs influence immune activation in colorectal tissue after pathogenic immunodeficiency virus infections.
The munc13-4–rab27 complex is specifically required for tethering secretory lysosomes at the plasma membrane
Authors: Elstak Edo D. , Neeft Maaike , Nehme Nadine T. , Voortman Jarno , Cheung Marc , Goodarzifard Monireh , Gerritsen Hans C. , van Bergen en Henegouwen Paul M. P. , Callebaut Isabelle , de Saint Basile Geneviève , van der Sluijs Peter 
Published: June 2011

AbstractCytotoxic T lymphocytes (CTLs) kill target cells through the polarized release of lytic molecules from secretory lysosomes. Loss of munc13-4 function inhibits this process and causes familial hemophagocytic lymphohistiocytosis type 3 (FHL3). munc13-4 binds rab27a, but the necessity of the complex remains enigmatic, because studies in knockout models suggest separate functions. In the present study, we describe a noncanonical rab27a-binding motif in the N-terminus of munc13-4. Point mutants in this sequence have severely impaired rab27a binding, allowing dissection of rab27a requirements in munc13-4 function. The munc13-4–rab27a complex is not needed for secretory lysosome maturation, as shown by complementation in CTLs from FHL3 patients and in a mast cell line silenced for munc13-4. In contrast, fusion of secretory lysosomes with, and content release at the plasma membrane during degranulation, strictly required the munc13-4–rab27a complex. Total internal reflection fluorescence microscopy imaging revealed that the complex corrals motile secretory lysosomes beneath the plasma membrane during degranulation and controls their docking. The propensity to stall motility of secretory lysosomes is lost in cells expressing munc13-4 point mutants that do not bind rab27. In summary, these results uncovered a mechanism for tethering secretory lysosomes to the plasma membrane that is essential for degranulation in immune cells.
Response of ETV6-FLT3–positive myeloid/lymphoid neoplasm with eosinophilia to inhibitors of FMS-like tyrosine kinase 3
Authors: Walz Christoph , Erben Philipp , Ritter Michael , Bloor Adrian , Metzgeroth Georgia , Telford Nick , Haferlach Claudia , Haferlach Torsten , Gesk Stefan , Score Joannah , Hofmann Wolf-Karsten , Hochhaus Andreas , Cross Nicholas C. P. , Reiter Andreas 
Published: June 2011

Abstract
Imatinib-resistant tyrosine kinase (TK) fusions involving FGFR1, JAK2, or FLT3 are rare but recurrent in patients with eosinophilia-associated neoplasms. We report here 2 male patients with ETV6-FLT3+ myeloid/lymphoid neoplasms with eosinophilia who were treated with the multitargeted TK inhibitors sunitinib and sorafenib. Patient 1 achieved rapid complete hematologic response and complete cytogenetic response after 3 months of taking sunitinib. A secondary blast phase caused by clonal evolution was diagnosed after 6 months. He achieved a second complete hematologic response after taking sorafenib but relapsed 2 months later. An N841K point mutation within the TK domain of FLT3, previously reported in acute myeloid leukemia and potentially conferring resistance to sorafenib, was subsequently identified. Patient 2 was heavily pretreated according to the initial diagnosis of T-lymphoblastic lymphoma and died in sunitinib-induced pancytopenia. This report highlights the importance of a careful diagnostic workup for eosinophilia-associated neoplasms to evaluate the possibility of TK inhibitor therapy.
Computable visually observed phenotype ontological framework for plants
Authors: Harnsomburana Jaturon , Green Jason M , Barb Adrian S , Schaeffer Mary , Vincent Leszek , Shyu Chi-Ren 
Published: June 2011

Abstract

Background
The ability to search for and precisely compare similar phenotypic appearances within and across species has vast potential in plant science and genetic research. The difficulty in doing so lies in the fact that many visual phenotypic data, especially visually observed phenotypes that often times cannot be directly measured quantitatively, are in the form of text annotations, and these descriptions are plagued by semantic ambiguity, heterogeneity, and low granularity. Though several bio-ontologies have been developed to standardize phenotypic (and genotypic) information and permit comparisons across species, these semantic issues persist and prevent precise analysis and retrieval of information. A framework suitable for the modeling and analysis of precise computable representations of such phenotypic appearances is needed.

Results
We have developed a new framework called the Computable Visually Observed Phenotype Ontological Framework for plants. This work provides a novel quantitative view of descriptions of plant phenotypes that leverages existing bio-ontologies and utilizes a computational approach to capture and represent domain knowledge in a machine-interpretable form. This is accomplished by means of a robust and accurate semantic mapping module that automatically maps high-level semantics to low-level measurements computed from phenotype imagery. The framework was applied to two different plant species with semantic rules mined and an ontology constructed. Rule quality was evaluated and showed high quality rules for most semantics. This framework also facilitates automatic annotation of phenotype images and can be adopted by different plant communities to aid in their research.

Conclusions
The Computable Visually Observed Phenotype Ontological Framework for plants has been developed for more efficient and accurate management of visually observed phenotypes, which play a significant role in plant genomics research. The uniqueness of this framework is its ability to bridge the knowledge of informaticians and plant science researchers by translating descriptions of visually observed phenotypes into standardized, machine-understandable representations, thus enabling the development of advanced information retrieval and phenotype annotation analysis tools for the plant science community.
Evolutionary history of Otophysi (Teleostei), a major clade of the modern freshwater fishes: Pangaean origin and Mesozoic radiation
Authors: Nakatani Masanori , Miya Masaki , Mabuchi Kohji , Saitoh Kenji , Nishida Mutsumi 
Published: June 2011

AbstractBackgroundFreshwater harbors approximately 12,000 fish species accounting for 43% of the diversity of all modern fish. A single ancestral lineage evolved into about two-thirds of this enormous biodiversity (≈ 7900 spp.) and is currently distributed throughout the world's continents except Antarctica. Despite such remarkable species diversity and ubiquity, the evolutionary history of this major freshwater fish clade, Otophysi, remains largely unexplored. To gain insight into the history of otophysan diversification, we constructed a timetree based on whole mitogenome sequences across 110 species representing 55 of the 64 families.ResultsPartitioned maximum likelihood analysis based on unambiguously aligned sequences (9923 bp) confidently recovered the monophyly of Otophysi and the two constituent subgroups (Cypriniformes and Characiphysi). The latter clade comprised three orders (Gymnotiformes, Characiformes, Siluriformes), and Gymnotiformes was sister to the latter two groups. One of the two suborders in Characiformes (Characoidei) was more closely related to Siluriformes than to its own suborder (Citharinoidei), rendering the characiforms paraphyletic. Although this novel relationship did not receive strong statistical support, it was supported by analyzing independent nuclear markers. A relaxed molecular clock Bayesian analysis of the divergence times and reconstruction of ancestral habitats on the timetree suggest a Pangaean origin and Mesozoic radiation of otophysans.ConclusionsThe present timetree demonstrates that survival of the ancestral lineages through the two consecutive mass extinctions on Pangaea, and subsequent radiations during the Jurassic through early Cretaceous shaped the modern familial diversity of otophysans. This evolutionary scenario is consistent with recent arguments based on biogeographic inferences and molecular divergence time estimates. No fossil otophysan, however, has been recorded before the Albian, the early Cretaceous 100-112 Ma, creating an over 100 million year time span without fossil evidence. This formidable ghost range partially reflects a genuine difference between the estimated ages of stem group origin (molecular divergence time) and crown group morphological diversification (fossil divergence time); the ghost range, however, would be filled with discoveries of older fossils that can be used as more reasonable time constraints as well as with developments of more realistic models that capture the rates of molecular sequences accurately.