bluuebunny/crossref_metadata_2025_split huggingface dataset:
History and the Philosophy of Art
Authors: Carroll Noël 
Published: December 2011

Abstract
In this essay I trace the role of history in the philosophy of art from the early twentieth century to the present, beginning with the rejection of history by formalists like Clive Bell. I then attempt to show how the arguments of people like Morris Weitz and Arthur Danto led to a re-appreciation of history by philosophers of art such as Richard Wollheim, Jerrold Levinson, Robert Stecker and others.
Four Species of Reflexivity and History of Economics in Economic Policy Science
Authors: Schliesser Eric 
Published: December 2011

Abstract
This paper argues that history of economics has a fruitful, underappreciated role to play in the development of economics, especially when understood as a policy science. This goes against the grain of the last half century during which economics, which has undergone a formal revolution, has distanced itself from its ‘literary’ past and practices precisely with the aim to be a more successful policy science.
The paper motivates the thesis by identifying and distinguishing four kinds of reflexivity in economics. The main thesis of this paper is that because these forms of reflexivity are not eliminable, the history of economics must play a constitutive role in economics (and graduate education within economics). An assumption that I clarify in this paper is that the history of economics ought to be part of the subject matter studied by economics when they are interested in policy science. Even if one does not accept the conclusion, the fourfold classification of reflexivity might hold independent interest.
The paper is divided in two parts. First, by reflecting on the writings of George Stigler, Paul Samuelson, George and Milton Friedman, I offer a stylized historical introduction to and conceptualization of the themes of this paper. In particular, I identify various historically influential arguments and strategies that reduced the role of history of economics within the economics discipline. In it I also canvass six arguments that try to capture the cost to economics (understood as a science) for sidelining the history of economics from within the discipline. A sub-text of the introduction is that for contingent reasons, post World War II economics evolved into a policy science. Second, by drawing on the work of Kenneth Boulding, in particular, George Soros, Thomas Merton, Gordon Tullock, I distinguish between four species of reflexivity. These are used to then strengthen the argument for the constitutive role of the history of economics within the economics profession. In particular, I argue that so-called Kuhn-losses are especially pernicious when faced with policy choices under so-called Knightian uncertainty.
Seven Mystical Poems on the Hebrew Vowels as Interpreted by Yosef Giqaṭilla and Mordekhay Dato
Authors: Martini Annett 
Published: December 2011

Abstract
One of the most original facets of Yosef Giqaṭilla’s mystical concept is his approach to the symbolical meaning of the Hebrew vowels. Throughout his life, he wrote several treatises about this subject, which deal with the Hebrew vowels as fundamental elements within Creation and the structure of the cosmos. About three hundred years later, the Italian kabbalist Mordekhay Dato wrote a commentary on the Secrets of the Vowels which actually is an interpretation of the poems written by Giqaṭilla in order to condense his theses about the Hebrew vowels. The present paper explores the following questions: (1) From where did Dato derive the seven poems, which, on the one hand, are part of Giqaṭilla’s discussion about the vowels, but on the other, have been transmitted separately? (2) Did Dato know their original context? (3) In what way does his interpretation of these verses differ from Giqaṭilla’s?
“The qebla of Jāmi is None Other than Tabriz”: ʿAbd al-Rahmān Jāmi and Naqshbandi Sufism at the Aq Qoyunlu Royal Court
Authors: Lingwood Chad G. 
Published: December 2011

AbstractThis article addresses the possibility that members of the Naqshbandi Sufi order exerted a greater influence at the royal court of Yaʿqub b. Uzun Hasan, leader of the Aq Qoyunlu dynasty, than previously acknowledged. In order to substantiate this claim, the article cites contemporary and near-contemporary Persian sources, notably theTārikh-eʿālam-ārā-ye amini, theRowzāt al-jenān va jannāt al-janān, and theRashahāt-e ʿayn al-hayāt, each of which attests to the presence of Naqshbandis in the Aq Qoyunlu capital of Tabriz, and notes that the Naqshbandis most closely associated with Yaʿqub shared the distinction of being protégés of the classical Persian poet ʿAbd al-Rahmān Jāmi. In a related vein, the article suggests that it was Jāmi himself, inSalāmān o Absāl, and in a personal letter sent to Yaʿqub from his residence in Timurid Herat, who may have exerted the most significant Naqshbandi influence over the Aq Qoyunlu. The article therefore concludes that the existing historiography, which emphasizes the involvement of the Khalvati order in Aq Qoyunlu affairs, should be revised in order to recognize the probable influence of members of the Naqshbandi order, particularly Jāmi, at the Aq Qoyunlu court.
A Sidelight on Grotius in Paris
Authors: Toomer Gerald J. 
Published: December 2011

AbstractThis article consists of an annotated edition and translation of a previously unpublished Latin letter to G. J. Vossius from Christianus Ravius, refuting the accusation made by Johann Seyffert in his pamphlet attacking Grotius, Classicum Belli Sacri adversus Hugonem Grotium Papistam ([Amsterdam], 1642), that Grotius, while representative of the Swedish government in Paris, had advised Ravius to convert to Catholicism. The historical introduction outlines the details of and probable reasons for Seyffert's published attacks on Grotius, Grotius's attitude towards those attacks (as expressed in his correspondence), and the implications for his relationship with the Swedish government and Baron von Degenfeld, commander of the German Protestant mercenary soldiers in the service of the French crown. It also recounts what is known of Ravius's stay in Paris during which he met Grotius, and raises the question why Ravius delayed making a response to Seyffert until well after Grotius was dead.
Moist Static Energy Budget of MJO-like Disturbances in the Atmosphere of a Zonally Symmetric Aquaplanet
Authors: Andersen Joseph Allan , Kuang Zhiming 
Published: December 2011

Abstract
A Madden–Julian oscillation (MJO)-like spectral feature is observed in the time–space spectra of precipitation and column-integrated moist static energy (MSE) for a zonally symmetric aquaplanet simulated with Superparameterized Community Atmospheric Model (SPCAM). This disturbance possesses the basic structural and propagation features of the observed MJO.
To explore the processes involved in propagation and maintenance of this disturbance, this study analyzes the MSE budget of the disturbance. The authors observe that the disturbances propagate both eastward and poleward. The column-integrated longwave heating is the only significant source of column-integrated MSE acting to maintain the MJO-like anomaly balanced against the combination of column-integrated horizontal and vertical advection of MSE and latent heat flux. Eastward propagation of the MJO-like disturbance is associated with MSE generated by both column integrated horizontal and vertical advection of MSE, with the column longwave heating generating MSE that retards the propagation.
The contribution to the eastward propagation by the column-integrated horizontal advection of MSE is dominated by synoptic eddies. Further decomposition indicates that the advection contribution to the eastward propagation is dominated by meridional advection of MSE by anomalous synoptic eddies caused by the suppression of eddy activity ahead of the MJO convection. This suppression is linked to the barotropic conversion mechanism, with the gradients of the low-frequency wind experienced by the synoptic eddies within the MJO envelope acting to modulate the eddy kinetic energy. The meridional eddy advection’s contribution to poleward propagation is dominated by the mean state’s (meridionally varying) eddy activity acting on the anomalous MSE gradients associated with the MJO.
CBL mutation in chronic myelomonocytic leukemia secondary to familial platelet disorder with propensity to develop acute myeloid leukemia (FPD/AML)
Authors: Shiba Norio , Hasegawa Daisuke , Park Myoung-ja , Murata Chisato , Sato-Otsubo Aiko , Ogawa Chitose , Manabe Atsushi , Arakawa Hirokazu , Ogawa Seishi , Hayashi Yasuhide 
Published: December 2011

Abstract
Familial platelet disorder with a propensity to develop acute myeloid leukemia (FPD/AML) is a rare autosomal dominant disease characterized by thrombocytopenia, abnormal platelet function, and a propensity to develop myelodysplastic syndrome (MDS) and AML. So far, > 20 affected families have been reported. Recently, a second RUNX1 alteration has been reported; however, no additional molecular abnormalities have been found so far. We identified an acquired CBL mutation and 11q-acquired uniparental disomy (11q-aUPD) in a patient with chronic myelomonocytic leukemia (CMML) secondary to FPD with RUNX1 mutation but not in the same patient during refractory cytopenia. This finding suggests that alterations of the CBL gene and RUNX1 gene may cooperate in the pathogenesis of CMML in patients with FPD/AML. The presence of CBL mutations and 11q-aUPD was an important “second hit” that could be an indicator of leukemic transformation of MDS or AML in patients with FPD/AML.
Classification of microarrays; synergistic effects between normalization, gene selection and machine learning
Authors: Önskog Jenny , Freyhult Eva , Landfors Mattias , Rydén Patrik , Hvidsten Torgeir R 
Published: December 2011

Abstract

Background
Machine learning is a powerful approach for describing and predicting classes in microarray data. Although several comparative studies have investigated the relative performance of various machine learning methods, these often do not account for the fact that performance (e.g. error rate) is a result of a series of analysis steps of which the most important are data normalization, gene selection and machine learning.

Results
In this study, we used seven previously published cancer-related microarray data sets to compare the effects on classification performance of five normalization methods, three gene selection methods with 21 different numbers of selected genes and eight machine learning methods. Performance in term of error rate was rigorously estimated by repeatedly employing a double cross validation approach. Since performance varies greatly between data sets, we devised an analysis method that first compares methods within individual data sets and then visualizes the comparisons across data sets. We discovered both well performing individual methods and synergies between different methods.

Conclusion
Support Vector Machines with a radial basis kernel, linear kernel or polynomial kernel of degree 2 all performed consistently well across data sets. We show that there is a synergistic relationship between these methods and gene selection based on the T-test and the selection of a relatively high number of genes. Also, we find that these methods benefit significantly from using normalized data, although it is hard to draw general conclusions about the relative performance of different normalization procedures.
Timing the origin of human malarias: the lemur puzzle
Authors: Pacheco M Andreína , Battistuzzi Fabia U , Junge Randall E , Cornejo Omar E , Williams Cathy V , Landau Irene , Rabetafika Lydia , Snounou Georges , Jones-Engel Lisa , Escalante Ananias A 
Published: December 2011

Abstract

Background
Timing the origin of human malarias has been a focus of great interest. Previous studies on the mitochondrial genome concluded that Plasmodium in primates, including those parasitic to humans, radiated relatively recently during a process where host switches were common. Those investigations, however, assumed constant rate of evolution and tightly bound (fixed) calibration points based on host fossils or host distribution. We investigate the effect of such assumptions using different molecular dating methods. We include parasites from Lemuroidea since their distribution provides an external validation to time estimates allowing us to disregard scenarios that cannot explain their introduction in Madagascar.

Results
We reject the assumption that the Plasmodium mitochondrial genome, as a unit or each gene separately, evolves at a constant rate. Our analyses show that Lemuroidea parasites are a monophyletic group that shares a common ancestor with all Catarrhini malarias except those related to P. falciparum. However, we found no evidence that this group of parasites branched with their hosts early in the evolution of primates. We applied relaxed clock methods and different calibrations points to explore the origin of primate malarias including those found in African apes. We showed that previous studies likely underestimated the origin of malarial parasites in primates.

Conclusions
The use of fossils from the host as absolute calibration and the assumption of a strict clock likely underestimate time when performing molecular dating analyses on malarial parasites. Indeed, by exploring different calibration points, we found that the time for the radiation of primate parasites may have taken place in the Eocene, a time consistent with the radiation of African anthropoids. The radiation of the four human parasite lineages was part of such events. The time frame estimated in this investigation, together with our phylogenetic analyses, made plausible a scenario where gorillas and humans acquired malaria from a Pan lineage.
Recombination hotspots and host susceptibility modulate the adaptive value of recombination during maize streak virus evolution
Authors: Monjane Adérito L , van der Walt Eric , Varsani Arvind , Rybicki Edward P , Martin Darren P 
Published: December 2011

Abstract

Background

Maize streak virus -strain A (MSV-A; Genus Mastrevirus, Family Geminiviridae), the maize-adapted strain of MSV that causes maize streak disease throughout sub-Saharan Africa, probably arose between 100 and 200 years ago via homologous recombination between two MSV strains adapted to wild grasses. MSV recombination experiments and analyses of natural MSV recombination patterns have revealed that this recombination event entailed the exchange of the movement protein - coat protein gene cassette, bounded by the two genomic regions most prone to recombination in mastrevirus genomes; the first surrounding the virion-strand origin of replication, and the second around the interface between the coat protein gene and the short intergenic region. Therefore, aside from the likely adaptive advantages presented by a modular exchange of this cassette, these specific breakpoints may have been largely predetermined by the underlying mechanisms of mastrevirus recombination. To investigate this hypothesis, we constructed artificial, low-fitness, reciprocal chimaeric MSV genomes using alternating genomic segments from two MSV strains; a grass-adapted MSV-B, and a maize-adapted MSV-A. Between them, each pair of reciprocal chimaeric genomes represented all of the genetic material required to reconstruct - via recombination - the highly maize-adapted MSV-A genotype, MSV-MatA. We then co-infected a selection of differentially MSV-resistant maize genotypes with pairs of reciprocal chimaeras to determine the efficiency with which recombination would give rise to high-fitness progeny genomes resembling MSV-MatA.

Results
Recombinants resembling MSV-MatA invariably arose in all of our experiments. However, the accuracy and efficiency with which the MSV-MatA genotype was recovered across all replicates of each experiment depended on the MSV susceptibility of the maize genotypes used and the precise positions - in relation to known recombination hotspots - of the breakpoints required to re-create MSV-MatA. Although the MSV-sensitive maize genotype gave rise to the greatest variety of recombinants, the measured fitness of each of these recombinants correlated with their similarity to MSV-MatA.

Conclusions
The mechanistic predispositions of different MSV genomic regions to recombination can strongly influence the accessibility of high-fitness MSV recombinants. The frequency with which the fittest recombinant MSV genomes arise also correlates directly with the escalating selection pressures imposed by increasingly MSV-resistant maize hosts.
High resolution melting analysis for the detection of EMS induced mutations in wheat Sbella genes
Authors: Botticella Ermelinda , Sestili Francesco , Hernandez-Lopez Antonio , Phillips Andrew , Lafiandra Domenico 
Published: December 2011

Abstract

Background
Manipulation of the amylose-amylopectin ratio in cereal starch has been identified as a major target for the production of starches with novel functional properties. In wheat, silencing of starch branching enzyme genes by a transgenic approach reportedly caused an increase of amylose content up to 70% of total starch, exhibiting novel and interesting nutritional characteristics.
In this work, the functionality of starch branching enzyme IIa (SBEIIa) has been targeted in bread wheat by TILLING. An EMS-mutagenised wheat population has been screened using High Resolution Melting of PCR products to identify functional SNPs in the three homoeologous genes encoding the target enzyme in the hexaploid genome.

Results
This analysis resulted in the identification of 56, 14 and 53 new allelic variants respectively for SBEIIa-A, SBEIIa-B and SBEIIa-D. The effects of the mutations on protein structure and functionality were evaluated by a bioinformatic approach. Two putative null alleles containing non-sense or splice site mutations were identified for each of the three homoeologous SBEIIa genes; qRT-PCR analysis showed a significant decrease of their gene expression and resulted in increased amylose content. Pyramiding of different single null homoeologous allowed to isolate double null mutants showing an increase of amylose content up to 21% compared to the control.

Conclusion
TILLING has successfully been used to generate novel alleles for SBEIIa genes known to control amylose content in wheat. Single and double null SBEIIa genotypes have been found to show a significant increase in amylose content.
Role of aldosterone on lung structural remodelling and right ventricular function in congestive heart failure
Authors: Chabot Andreanne , Jiang Bao Hua , Shi Yanfen , Tardif Jean-Claude , Dupuis Jocelyn 
Published: December 2011

Abstract

Background
The mechanisms of benefit of mineralocorticoid receptors antagonists in congestive heart failure (CHF) are still debated. We hypothesized that aldosterone contributes to pulmonary remodelling and right ventricular (RV) dysfunction associated with CHF by stimulation of lung myofibroblasts (MYFs) proliferation.

Methods
Rats with moderate to large myocardial infarcts (MI) and CHF were studied. Two weeks after MI, spironolactone 100 mg/kg/day (n = 21) or no treatment (n = 24) were given for 3 weeks and compared to sham (n = 8).

Results
Infarct size was similar by ultrasound and pathologic measures in both MI groups.
The MI-untreated group developed important lung remodelling with nearly doubling of dry lung weight (p < 0.01), reduced left ventricular (LV) fractional shortening (16 ± 2% vs. 53 ± 1%; mean ± SEM, p < 0.0001), pulmonary hypertension (RV systolic pressure: 40 ± 3 mmHg vs. 27 ± 1 mmHg, p < 0.01) and RV hypertrophy (RV/(LV + septum): 38 ± 3% vs. 24 ± 1%, p < 0.05). Spironolactone had no effect on these parameters and did not improve LV or RV performance (tricuspid annular plane systolic excursion and RV myocardial performance index) measured by echocardiography. CHF induced a restrictive respiratory syndrome with histological lung fibrosis: this was also unaffected by spironolactone. Finally, isolated lung MYFs did not proliferate after exposure to aldosterone.

Conclusion
Aldosterone does not significantly contribute to pulmonary remodelling and RV dysfunction associated with CHF. Other mechanisms are responsible for the beneficial effects of spironolactone in CHF.
Chromosomal aberrations and aneuploidy in oral potentially malignant lesions: distinctive features for tongue
Authors: Castagnola Patrizio , Malacarne Davide , Scaruffi Paola , Maffei Massimo , Donadini Alessandra , Di Nallo Emanuela , Coco Simona , Tonini Gian Paolo , Pentenero Monica , Gandolfo Sergio , Giaretti Walter 
Published: December 2011

AbstractBackgroundThe mucosae of the oral cavity are different at the histological level but appear all equally exposed to common genotoxic agents. As a result of this exposure, changes in the mucosal epithelia may develop giving rise to Oral Potentially Malignant Lesions (OPMLs), which with time may in turn progress to Oral Squamous Cell Carcinomas (OSCCs). Therefore, much effort should be devoted to identify features able to predict the likeliness of progression associated with an OPML. Such features may be helpful in assisting the clinician to establish both appropriate therapies and follow-up schedules. Here, we report a pilot study that compared the occurrence of DNA aneuploidy and chromosomal copy number aberrations (CNAs) in the OPMLs from different oral anatomical subsites.MethodsSamples from histologically diagnosed OPMLs were processed for high resolution DNA flow cytometry (hr DNA-FCM) in order to determine the relative DNA content expressed by the DNA index (DI). Additionally, array-Comparative Genomic Hybridization (a-CGH) analysis was performed on DNA obtained from diploid nuclei suspensions directly. When aneuploid nuclei were detected, these were physically separated from diploid nuclei on the base of their DI values by means of a DNA-FCM-Sorter in order to improve the a-CGH analysis.ResultsTongue OPMLs were more frequently associated with DNA aneuploidy and CNAs than OPMLs arising from all the other mucosal subsites.ConclusionsWe suggest that the follow-up and the management of the patients with tongue OPMLs should receive a distinctive special attention. Clearly, this hypothesis should be validated in a prospective clinical study.