bluuebunny/crossref_metadata_2025_split huggingface dataset:
Puma Deletion Delays Cardiac Dysfunction in Murine Heart Failure Models Through Attenuation of Apoptosis
Authors: Mandl Adel , Huong Pham Ly , Toth Kalman , Zambetti Gerald , Erhardt Peter 
Published: June 2011

Background—

Puma (p53-upregulated modulator of apoptosis) is a proapoptotic Bcl-2 family protein that serves as a general sensor in response to pathological apoptotic stimuli. In previous work, we demonstrated that
puma
ablation protects the heart from reperfusion injury in a Langendorff setting. Consistent with this, downregulation of Puma in isolated cardiac myocytes prevented apoptosis induced by different proapoptotic agents. Here, we extended our research to investigate the role of Puma, a downstream mediator of p53, in the development of heart failure using
Puma
−/−
mice.

Methods and Results—

Mice underwent transverse aortic constriction, and the characteristics of cardiac remodeling were analyzed by echocardiography, histology, and gene expression at multiple time points after surgery. Four weeks after the operation,
puma
deletion attenuated pressure overload–induced apoptosis and fibrosis; however, it did not affect hypertrophy and angiogenesis and maintained functional performance (fractional shortening, 39% versus 25.2% in
Puma
−/−
versus WT mice, respectively). Even at 12 weeks after transverse aortic constriction,
Puma
−/−
mice displayed only slightly reduced contractility. In addition, transverse aortic constriction induced
puma
expression in a partially p53-dependent manner. To corroborate these findings, we studied another heart failure model in which heart-specific
mdm4
deletion leads to p53 activation and dilated cardiomyopathy. In these mice, Puma was upregulated and its deletion rescued the cardiomyopathy phenotype.

Conclusions—
Our data indicate that Puma might be a critical component of the apoptotic signaling pathways that contribute to ventricular remodeling and heart failure. Therefore, Puma inactivation may serve as a preferential target to prevent heart failure induced by cellular stress.
The ‘Tractate’ of Conversion—BT Yeb. 46‐48 and the Evolution of Conversion Procedure
Authors: Lavee Moshe 
Published: June 2011

AbstractTractate Yebamoth of the Babylonian Talmud contains a long unit devoted to the procedure of conversion (Yeb 46a‐48b). Form analysis of the unit reveals its design as a ‘tractate within a tractate.’ The unit is a collection of discussions on baraitas. It follows various literary conventions, such as placing a full description of the procedure towards the end and concluding with haggadic material and a verse of comfort. A variety of methods are applied in order to identify the unique Babylonian tendencies documented in this unit. Synoptic comparison to tannaitic parallels demonstrates the growing stringency and institutionalization of the rabbinic conversion procedure. A common structural feature of each discussion is the ending with an amoraic statement that reassure the halakhic validation of the stringent views. Stammaitic comments and the overall literary structure of the unit also seem to confirm this tendency.This unit demonstrates Babylonian efforts to further reinforce the boundaries of Jewish identity. The traditions as preserved in this unit show that Babylonian proclivities were gradually attributed to earlier Palestinian authorities. The most prominent example is the institution of the court for conversion. This is a Babylonian construct, systematically presented in places where it is missing in Palestinian rabbinic sources. In our unit it is also attributed to early Palestinain amora’im, and even to a tanna. Not only did the Babylonian sages change the model of conversion from witnessed circumcision (and later immersion) to court controlled procedure, they also projected their innovations onto earlier generations.
One or Three? Exploring the Scholarly Conflict over the Question of Triple riple Talāq (Divorce) in Islamic Law with Particular Emphasis on Oman
Authors: al-Azri Khalid 
Published: June 2011

This article explores
Talāq
, which refers to the right of men in Islam to divorce their wives, with particular emphasis upon triple
Talāq
. This article seeks to answer the question of how triple
Talāq
at one time is applied in modern-day Muslim societies, in light of contemporary socio-economic conditions. The historical events surrounding the emergence of triple
Talāq
in Islam demonstrates the possibility of its renewal in Islamic law. This is significant because it demonstrates that, contrary to the teaching of many Muslim scholars including contemporary Ibadī scholars in Oman, change and renewal are not inimical to Islam but rather intrinsic to it. I argue here that the inflexibility of Ibadī scholars regarding triple
Talāq
at one time promotes gender inequality and discriminatory practices in Oman, especially towards women. This article begins by exploring the different methods of
Talāq
in Islamic law. It then focuses on triple
Talāq
at one time (in one event). The discussion of triple
Talāq
at one time aims to explore the interaction between legal, economic and social factors, on one hand, and how these factors have affected the law of triple
Talāq
during both pre-modern and contemporary Muslim societies. Subsequently, the article will examine how contemporary Muslim scholars react to the new social and economic factors associated with triple
Talāq
at one time.
Conceptualizing Economic Diplomacy:The Crossroads of International Relations, Economics, IPE and Diplomatic Studies
Authors: Okano-Heijmans Maaike 
Published: June 2011

AbstractThis article introduces both a conceptual and an analytical framework of economic diplomacy so as to contribute to sounder understanding of economic diplomacy’s activities, tools and goals. While the state is not regarded as the only player, or as a coherent entity, it is assumed that the state is the primary actor in economic diplomacy. The conceptual framework discerns five strands of economic diplomacy, which involve tools and purposes that are relatively more commercial/economic or political in character and are thereby closer to the ‘business end’ or ‘power-play end’ of economic diplomacy. The analytical framework identifies four essential dimensions of economic diplomacy within which historically contingent change may occur: the context; tools; theatres; and processes. Interaction between these dimensions takes place in multiple ways. Building on the insights provided by these frameworks, the article analyses the foci, assumptions and methodologies of the research fields that are concerned with economic diplomacy, and discusses the strategic and ideological considerations that underpin it.
Reappraising the Effects of Language Contact in the Torres Strait
Authors: Round Erich , Hunter Jessica , Bowern Claire 
Published: June 2011

Abstract
The contact history of the languages of the Eastern and Western Torres Strait has been claimed (e.g. by Dixon 2002, Wurm 1972, and others) to have been sufficiently intense as to obscure the genetic relationship of the Western Torres Strait language. Some have argued that it is an Australian (Pama-Nyungan) language, though with considerable influence from the Papuan language Meryam Mir (the Eastern Torres Strait language). Others have claimed that the Western Torres language is, in fact, a genetically Papuan language, though with substantial Australian substrate or adstrate influence. Much has been made of phonological structures which have been viewed as unusual for Australian languages. In this paper we examine the evidence for contact claims in the region. We review aspects of the phonology, morphology, syntax and lexicon of the Eastern and Western Torres Strait languages with an eye to identifying areal influence. This larger data pool shows that the case for intense contact has been vastly overstated. Beyond some phonological features and some loan words, there is no linguistic evidence for intense contact; moreover, the phonological features adduced to be evidence of contact are also found to be not specifically Papuan, but part of a wider set of features in Australian languages.
The Effect of Hawai’i’s Big Island on Track and Structure of Tropical Cyclones Passing to the South and West*
Authors: Chambers Christopher R. S. , Li Tim 
Published: June 2011

Abstract
The effect of the Big Island of Hawai’i on tropical cyclone (TC) track and structure is investigated using the Weather Research and Forecasting (WRF) model. The high (~4000 m) mountains of the Big Island modulate lower-tropospheric flow in such a way that it can influence TCs hundreds of kilometers away from the island. When a TC approaches from the east, the blocking of lower-tropospheric flow leads to a slowing of the TC’s movement. As a TC passes close to the south side of the Big Island, it deviates southward. The TC core convection and winds can become axisymmetric because of the blocking of the stronger northeasterly flow to the north of the storm. The authors hypothesize that this axisymmetrization led to the unexpected eye formation of Hurricane Flossie (2007) just southeast of the Big Island. As a TC moves into the lee (southwest side) of the Big Island, the flow associated with the island wake leads to a track deviated to the right. The Hurricane Dot (1959) simulations suggest that this effect contributed to an observed deviation to the north, which led to eventual Kauai landfall. A greater TC intensity is found in the lee of the Big Island compared to the case without the island, which is primarily attributed to a weakened vertical wind shear associated with the island blocking.
Arrow behaviour in free flight
Authors: Park J L 
Published: June 2011

As an arrow exits a bow, it may have a non-zero angle of attack in both the vertical and the horizontal planes. It might also have a non-zero angular rotation about its centre of mass and will probably be flexing longitudinally. In this paper, the arrow behaviour in free flight in the horizontal plane and without wind has been analysed. A finite difference method was used to solve the equations of motion. This was compared with the measured behaviour for arrows shot from a compound archery bow (although the results are also applicable for recurve bows). Given typical initial conditions, the arrow oscillates longitudinally about its centre of mass, with the period and damping largely determined by the fletch area, and gains a lateral velocity component and lateral displacement. For normal fletch sizes the oscillation will be under-damped. In the absence of archer technique error, the longitudinal oscillation was found to have minimal effect on the accuracy.
The experimental study of a miniature high-speed gas-bearing expansion turbine
Authors: Chen R G , Liu Y , Hou Y , Xi G 
Published: June 2011

The miniature high-speed gas-bearing turbomachinery is one of the research focuses in the fields of energy and cryogenic engineering in recent years. In this article, a new miniature static gas-bearing expansion turbine with a shaft diameter of 6 mm, turbine impeller diameter of 9 mm, and designed rotational speed of 300 000 r/min was developed. The developed prototype of this miniature expansion turbine is comprehensively introduced and the structure characteristics are presented. Then the preliminary mechanical and thermodynamic performances for the developed prototype are experimentally measured. Research results show that this developed expansion turbine has some noticeable features, such as stable operation with small vibration. It can reach 15 per cent over-speed and provide a quick temperature drop. Experimental verification demonstrates that both mechanical and thermodynamic performances agree with expected requirements. Hence, a strong base has been established in China to further develop miniature high-speed gas-bearing expansion turbines.
Xenografts of highly resistant leukemia recapitulate the clonal composition of the leukemogenic compartment
Authors: Schmitz Maike , Breithaupt Petra , Scheidegger Nastassja , Cario Gunnar , Bonapace Laura , Meissner Barbara , Mirkowska Paulina , Tchinda Joelle , Niggli Felix K. , Stanulla Martin , Schrappe Martin , Schrauder Andre , Bornhauser Beat C. , Bourquin Jean-Pierre 
Published: June 2011

Abstract
Clonal evolution of the leukemogenic compartment may contribute to alter the therapeutic response in acute lymphoblastic leukemia (ALL). Using xenotransplantation of primary leukemia cells, we evaluated the phenotypic and genetic composition of de novo resistant very high risk precursor B-cell ALL, a subgroup defined by the persistence of minimal residual disease despite intensive chemotherapy. Analysis of copy number alterations (CNAs) showed that the xenografted leukemia, even when reconstituted from 100 cells, remained highly related to the diagnostic sample, with minor changes in CNAs, mostly deletions, emerging in most cases in the first passage into mice. At the single-cell level, the pattern of monoallelic and biallelic deletions of the CDKN2A locus revealed distinct leukemia subpopulations, which were reproducibly tracked in xenografts. In most very high risk ALL cases, the predominant diagnostic clones were reconstituted in xenografts, as shown by multiplex polymerase chain reaction analysis of immunoglobulin and T-cell receptor loci. In other cases, the pattern in CNAs and immunoglobulin and T-cell receptor rearrangement was less concordant in xenografts, suggesting the outgrowth of subclones. These results unequivocally demonstrate the existence of clonally closely related but distinct subsets of leukemia initiating cells in ALL, which has important implications for drug development and preclinical disease modeling.
Thalidomide for previously untreated elderly patients with multiple myeloma: meta-analysis of 1685 individual patient data from 6 randomized clinical trials
Authors: Fayers Peter M. , Palumbo Antonio , Hulin Cyrille , Waage Anders , Wijermans Pierre , Beksaç Meral , Bringhen Sara , Mary Jean-Yves , Gimsing Peter , Termorshuizen Fabian , Haznedar Rauf , Caravita Tommaso , Moreau Philippe , Turesson Ingemar , Musto Pellegrino , Benboubker Lotfi , Schaafsma Martijn , Sonneveld Pieter , Facon Thierry ,   on behalf of the Nordic Myeloma Study Group, Italian Multiple Myeloma Network, Turkish Myeloma Study Group, Hemato-Oncologie voor Volwassenen Nederland, Intergroupe Francophone du Myélome, and European Myeloma Network
Published: June 2011

Abstract
The role of thalidomide for previously untreated elderly patients with multiple myeloma remains unclear. Six randomized controlled trials, launched in or after 2000, compared melphalan and prednisone alone (MP) and with thalidomide (MPT). The effect on overall survival (OS) varied across trials. We carried out a meta-analysis of the 1685 individual patients in these trials. The primary endpoint was OS, and progression-free survival (PFS) and 1-year response rates were secondary endpoints. There was a highly significant benefit to OS from adding thalidomide to MP (hazard ratio = 0.83; 95% confidence interval 0.73-0.94, P = .004), representing increased median OS time of 6.6 months, from 32.7 months (MP) to 39.3 months (MPT). The thalidomide regimen was also associated with superior PFS (hazard ratio = 0.68, 95% confidence interval 0.61-0.76, P < .0001) and better 1-year response rates (partial response or better was 59% on MPT and 37% on MP). Although the trials differed in terms of patient baseline characteristics and thalidomide regimens, there was no evidence that treatment affected OS differently according to levels of the prognostic factors. We conclude that thalidomide added to MP improves OS and PFS in previously untreated elderly patients with multiple myeloma, extending the median survival time by on average 20%.
Efficient alignment of pyrosequencing reads for re-sequencing applications
Authors: Fernandes Francisco , da Fonseca Paulo GS , Russo Luis MS , Oliveira Arlindo L , Freitas Ana T 
Published: June 2011

Abstract

Background
Over the past few years, new massively parallel DNA sequencing technologies have emerged. These platforms generate massive amounts of data per run, greatly reducing the cost of DNA sequencing. However, these techniques also raise important computational difficulties mostly due to the huge volume of data produced, but also because of some of their specific characteristics such as read length and sequencing errors. Among the most critical problems is that of efficiently and accurately mapping reads to a reference genome in the context of re-sequencing projects.

Results
We present an efficient method for the local alignment of pyrosequencing reads produced by the GS FLX (454) system against a reference sequence. Our approach explores the characteristics of the data in these re-sequencing applications and uses state of the art indexing techniques combined with a flexible seed-based approach, leading to a fast and accurate algorithm which needs very little user parameterization. An evaluation performed using real and simulated data shows that our proposed method outperforms a number of mainstream tools on the quantity and quality of successful alignments, as well as on the execution time.

Conclusions
The proposed methodology was implemented in a software tool called TAPyR--Tool for the Alignment of Pyrosequencing Reads--which is publicly available from http://www.tapyr.net.
Global analysis of gene expression in mineralizing fish vertebra-derived cell lines: new insights into anti-mineralogenic effect of vanadate
Authors: Tiago Daniel M , Laizé Vincent , Bargelloni Luca , Ferraresso Serena , Romualdi Chiara , Cancela M Leonor 
Published: June 2011

Abstract

Background
Fish has been deemed suitable to study the complex mechanisms of vertebrate skeletogenesis and gilthead seabream (Sparus aurata), a marine teleost with acellular bone, has been successfully used in recent years to study the function and regulation of bone and cartilage related genes during development and in adult animals. Tools recently developed for gilthead seabream, e.g. mineralogenic cell lines and a 4 × 44K Agilent oligo-array, were used to identify molecular determinants of in vitro mineralization and genes involved in anti-mineralogenic action of vanadate.

Results
Global analysis of gene expression identified 4,223 and 4,147 genes differentially expressed (fold change - FC > 1.5) during in vitro mineralization of VSa13 (pre-chondrocyte) and VSa16 (pre-osteoblast) cells, respectively. Comparative analysis indicated that nearly 45% of these genes are common to both cell lines and gene ontology (GO) classification is also similar for both cell types. Up-regulated genes (FC > 10) were mainly associated with transport, matrix/membrane, metabolism and signaling, while down-regulated genes were mainly associated with metabolism, calcium binding, transport and signaling. Analysis of gene expression in proliferative and mineralizing cells exposed to vanadate revealed 1,779 and 1,136 differentially expressed genes, respectively. Of these genes, 67 exhibited reverse patterns of expression upon vanadate treatment during proliferation or mineralization.

Conclusions
Comparative analysis of expression data from fish and data available in the literature for mammalian cell systems (bone-derived cells undergoing differentiation) indicate that the same type of genes, and in some cases the same orthologs, are involved in mechanisms of in vitro mineralization, suggesting their conservation throughout vertebrate evolution and across cell types. Array technology also allowed identification of genes differentially expressed upon exposure of fish cell lines to vanadate and likely involved in its anti-mineralogenic activity. Many were found to be unknown or they were never associated to bone homeostasis previously, thus providing a set of potential candidates whose study will likely bring insights into the complex mechanisms of tissue mineralization and bone formation.
Proteomic analysis of the carotenogenic yeast Xanthophyllomyces dendrorhous
Authors: Martinez-Moya Pilar , Watt Steven Alexander , Niehaus Karsten , Alcaíno Jennifer , Baeza Marcelo , Cifuentes Víctor 
Published: June 2011

Abstract

Background
The yeast Xanthophyllomyces dendrorhous is used for the microbiological production of the antioxidant carotenoid astaxanthin. In this study, we established an optimal protocol for protein extraction and performed the first proteomic analysis of the strain ATCC 24230. Protein profiles before and during the induction of carotenogenesis were determined by two-dimensional polyacrylamide gel electrophoresis and proteins were identified by mass spectrometry.

Results
Among the approximately 600 observed protein spots, 131 non-redundant proteins were identified. Proteomic analyses allowed us to identify 50 differentially expressed proteins that fall into several classes with distinct expression patterns. These analyses demonstrated that enzymes related to acetyl-CoA synthesis were more abundant prior to carotenogenesis. Later, redox- and stress-related proteins were up-regulated during the induction of carotenogenesis. For the carotenoid biosynthetic enzymes mevalonate kinase and phytoene/squalene synthase, we observed higher abundance during induction and/or accumulation of carotenoids. In addition, classical antioxidant enzymes, such as catalase, glutathione peroxidase and the cytosolic superoxide dismutases, were not identified.

Conclusions
Our results provide an overview of potentially important carotenogenesis-related proteins, among which are proteins involved in carbohydrate and lipid biosynthetic pathways as well as several redox- and stress-related proteins. In addition, these results might indicate that X. dendrorhous accumulates astaxanthin under aerobic conditions to scavenge the reactive oxygen species (ROS) generated during metabolism.
MeRy-B: a web knowledgebase for the storage, visualization, analysis and annotation of plant NMR metabolomic profiles
Authors: Ferry-Dumazet Hélène , Gil Laurent , Deborde Catherine , Moing Annick , Bernillon Stéphane , Rolin Dominique , Nikolski Macha , de Daruvar Antoine , Jacob Daniel 
Published: June 2011

AbstractBackgroundImprovements in the techniques for metabolomics analyses and growing interest in metabolomic approaches are resulting in the generation of increasing numbers of metabolomic profiles. Platforms are required for profile management, as a function of experimental design, and for metabolite identification, to facilitate the mining of the corresponding data. Various databases have been created, including organism-specific knowledgebases and analytical technique-specific spectral databases. However, there is currently no platform meeting the requirements for both profile management and metabolite identification for nuclear magnetic resonance (NMR) experiments.DescriptionMeRy-B, the first platform for plant1H-NMR metabolomic profiles, is designed (i) to provide a knowledgebase of curated plant profiles and metabolites obtained by NMR, together with the corresponding experimental and analytical metadata, (ii) for queries and visualization of the data, (iii) to discriminate between profiles with spectrum visualization tools and statistical analysis, (iv) to facilitate compound identification. It contains lists of plant metabolites and unknown compounds, with information about experimental conditions, the factors studied and metabolite concentrations for several plant species, compiled from more than one thousand annotated NMR profiles for various organs or tissues.ConclusionMeRy-B manages all the data generated by NMR-based plant metabolomics experiments, from description of the biological source to identification of the metabolites and determinations of their concentrations. It is the first database allowing the display and overlay of NMR metabolomic profiles selected through queries on data or metadata. MeRy-B is available fromhttp://www.cbib.u-bordeaux2.fr/MERYB/index.php.