bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrating gene and protein expression data with genome-scale metabolic networks to infer functional pathways
Authors: Pey Jon , Valgepea Kaspar , Rubio Angel , Beasley John E , Planes Francisco J 
Published: December 2013

Abstract

Background
The study of cellular metabolism in the context of high-throughput -omics data has allowed us to decipher novel mechanisms of importance in biotechnology and health. To continue with this progress, it is essential to efficiently integrate experimental data into metabolic modeling.

Results
We present here an in-silico framework to infer relevant metabolic pathways for a particular phenotype under study based on its gene/protein expression data. This framework is based on the Carbon Flux Path (CFP) approach, a mixed-integer linear program that expands classical path finding techniques by considering additional biophysical constraints. In particular, the objective function of the CFP approach is amended to account for gene/protein expression data and influence obtained paths. This approach is termed integrative Carbon Flux Path (iCFP). We show that gene/protein expression data also influences the stoichiometric balancing of CFPs, which provides a more accurate picture of active metabolic pathways. This is illustrated in both a theoretical and real scenario. Finally, we apply this approach to find novel pathways relevant in the regulation of acetate overflow metabolism in Escherichia coli. As a result, several targets which could be relevant for better understanding of the phenomenon leading to impaired acetate overflow are proposed.

Conclusions
A novel mathematical framework that determines functional pathways based on gene/protein expression data is presented and validated. We show that our approach is able to provide new insights into complex biological scenarios such as acetate overflow in Escherichia coli.
Restoration of LRIG1 suppresses bladder cancer cell growth by directly targeting EGFR activity
Authors: Chang Lei , Shi Runlin , Yang Tao , Li Fan , Li Guohao , Guo Yonglian , Lang Bin , Yang Weimin , Zhuang Qianyuan , Xu Hua 
Published: December 2013

Abstract

Background
Recently, leucine-rich repeats and immunoglobulin-like domains 1 (LRIG1), a negative regulator of EGFR, was discovered is a novel agent for suppressing bladder cancer. The aim of this study was to investigate the impact of LRIG1 on the biological features of aggressive bladder cancer cells and the possible mechanisms of enhanced apoptosis induced by upregulation of LRIG1.

Methods
In this study, we examined the mRNA and protein expression of LRIG1 and EGFR in bladder cancers and normal bladder. Meanwhile, we overexpressed LRIG1 with adenovirus vector in T24/5637 bladder cancer cell lines, and we used real time-PCR, western blot, and co-immunoprecipitation analysis in order to examine the effects of LRIG1 gene on EGFR. Furthermore, we evaluate the impact of LRIG1 gene on the function of human bladder cancer cells and EGFR signaling.

Results
The expression of LRIG1 was decreased, while the expression of EGFR was increased in the majority of bladder cancer, and the ratio of EGFR/LRIG1 was increased in tumors versus normal tissue. We found that upregulation of LRIG1 induced cell apoptosis and cell growth inhibition, and further reversed invasion in bladder cancer cell lines in vitro by inhibiting phosphorylation of downstream MAPK and AKT signaling pathway.

Conclusion
Taken together, our findings provide us with an insight into LRIG1 function, and we conclude that LRIG1 evolved in bladder cancer as a rare feedback negative attenuator of EGFR, thus could offer a novel therapeutic target to treat patients with bladder cancer.
Modification of heparanase gene expression in response to conditioning and LPS treatment: strong correlation to rs4693608 SNP
Authors: Ostrovsky Olga , Shimoni Avichai , Baryakh Polina , Morgulis Yan , Mayorov Margarita , Beider Katia , Shteingauz Anna , Ilan Neta , Vlodavsky Israel , Nagler Arnon 
Published: December 2013

AbstractHeparanase is an endo-β-glucuronidase that specifically cleaves the saccharide chains of HSPGs, important structural and functional components of the ECM. Cleavage of HS leads to loss of the structural integrity of the ECM and release of HS-bound cytokines, chemokines, and bioactive angiogenic- and growth-promoting factors. Our previous study revealed a highly significant correlation of HPSE gene SNPs rs4693608 and rs4364254 and their combination with the risk of developing GVHD. We now demonstrate that HPSE is up-regulated in response to pretransplantation conditioning, followed by a gradual decrease thereafter. Expression of heparanase correlated with the rs4693608 HPSE SNP before and after conditioning. Moreover, a positive correlation was found between recipient and donor rs4693608 SNP discrepancy and the time of neutrophil and platelet recovery. Similarly, the discrepancy in rs4693608 HPSE SNP between recipients and donors was found to be a more significant factor for the risk of aGVHD than patient genotype. The rs4693608 SNP also affected HPSE gene expression in LPS-treated MNCs from PB and CB. Possessors of the AA genotype exhibited up-regulation of heparanase with a high ratio in the LPS-treated MNCs, whereas individuals with genotype GG showed down-regulation or no effect on HPSE gene expression. HPSE up-regulation was mediated by TLR4. The study emphasizes the importance of rs4693608 SNP for HPSE gene expression in activated MNCs, indicating a role in allogeneic stem cell transplantation, including postconditioning, engraftment, and GVHD.
Staging hyperrealism: Tracing the influence of the televisual in Thomas Ostermeier’s Woyzeck
Authors: Conway Elisha 
Published: December 2013

Abstract
Building upon Umberto Eco and Jean Baudrillard’s theories of hyperrealism, this article explores hyperrealist theatre through the example of Thomas Ostermeier’s 2004 production of Georg Büchner’s Woyzeck. The article demonstrates that the production’s hyperrealism can be divided into two types: aesthetic hyperrealism and cultural hyperrealism. Aesthetic hyperrealism is the instance of an object appearing as ‘the real thing’, in effect hiding its nature as a sign. The production’s aesthetic hyperrealism is seen in the semiosis of the scenography (i.e. scenography built upon the direct sign). The aesthetic hyperrealism of Ostermeier’s Woyzeck, a feature of the production’s iconicity, is derived from the influence of the televisual iconic sign. Cultural hyperrealism is the cultural desire for things that are more (as in extra or better) than real. Cultural hyperrealism is framed, in Ostermeier’s production, by the social relationships of the fictional world (i.e. sensationalized social interactions that are ‘more’ than real). In Ostermeier’s Woyzeck, cultural hyperrealism is indebted to the influence of TV soap operas.
At MoMA show, some forget you should not touch the art
Authors: Listengarten Julia 
Published: December 2013

Abstract
This article draws on the ‘TypeBound’ art exhibition (Spring 2009, University of Central Florida) to examine a series of issues that emerge out of renegotiating the meaning of museum space as a performative and creative environment. The article discusses the ways in which ‘TypeBound’ engages in interdisciplinary artistic explorations to approach books as sculpture, writing and typesetting as a visual encounter for both artists and viewers and reading as a performative act. What are the tensions in integrating literal, visual and performative possibilities of ‘book’ art to dialogue with the museum visitor/viewer/spectator/reader? And what are the complications that are triggered by the reimagining of the cultural significance of written word when literary text is viewed as an interplay between literature and visual art in a performative museum space?
Theodoros Terzopoulos’s production of Heiner Müller’s Mauser: Metaphoric political theatre through space, body and dialogue
Authors: Kim Jae Kyoung 
Published: December 2013

Abstract
This article examines the metaphoric characteristics of Theodoros Terzopoulos’s production of Heiner Müller’s Mauser by analysing its metaphors of space, body and dialogue. It analyses how Greek director Terzopoulos transformed German political theatre rooted in Brechtian aesthetics into Greek political theatre rooted in Greek tragedy. In this adaptation, the director’s utilization of space and sets played an essential role in staging his artistic vision; the utilization of space not only closely restrained the actors’ performance but also defined the historical relations among Greek people in the theatre including the actors, narrators, audience members and their ancestors who were symbolically represented through portraits. To trace the process of this adaptation, this article, first, refers to Terzopoulos’s apprenticeship in the Berliner Ensemble and his relationship with Müller and analyses how these two artists influenced each other through their common interest in Greek tragedy. Next, it analyses how Terzopoulos adapted Müller’s Mauser based on an episode in Greek history, the Greek Civil War, and then recreated it visually through experimental sets and metaphoric movements as an extension of his major Greek tragedy productions. Signifying a microcosm of Greek society, the space and sets revealed veiled meanings one by one as the actors deconstructed the sets and the audience defined their position in the space by observing the change of sets. Terzopoulos’s production ultimately gives us an example of the way directors stage political theatre for spectators in their own time and place.
Multimedia theatre before the digital age
Authors: Salihbegovic Fahrudin 
Published: December 2013

Abstract
In this article I intend to provide a short overview of the historically rich interrelationship between theatre and multimedia, up to the present time where a set of similar practical and theoretical questions has reappeared following the influence of digital multimedia on contemporary performing practice. My aim is to trace the roots of multimedia theatre. I will argue that the most important and vital feature of theatre is its ability to absorb all other media, in other words, its totality and multimediality. I will explore the role of the projected moving image used in theatre projects from the invention of cinema to the film-theatre of Josef Svoboda. I will also provide a short historical overview of the development of the concept of ‘total theatre’ and in particular, analyse the role of the projected image in this context.
I will first address the concept of Gesamtkunstwerk – ‘total Artwork’ and Wagner’s understanding of theatre (opera) as total art. Subsequently, I will analyse what influence the invention of film had on the theatre, discussing various approaches to the application of the moving image to the theatre from the first part of the twentieth century, which seems to have been ‘reinvented’ in contemporary multimedia theatre. My examples are drawn from the work of the film pioneer Georges Méliès; the German theatre maker Erwin Piscator; Bauhaus artists Oskar Schlemmer, Walter Gropius, László Moholy-Nagy, and Frederic Kiesler; and the Czech film-theatre of Josef Svoboda.
History vs Hollingsworth: The scenographic subversion of Canadian history
Authors: Thistle Lindsay 
Published: December 2013

Abstract
Founded by Michael Hollingsworth and Deanne Taylor in the late 1970s, VideoCabaret is one of Canada’s most prolific theatre companies and has become known for its unconventional scenography. Hollingsworth later began a one-of-a-kind historical epic – a 21-part play series, which chronicles over 400 years of Canadian history – The History of the Village of the Small Huts. In 1985, Hollingsworth directed the first play of the cycle, New France and almost every year since, a part of the cycle has been produced throughout Toronto at Theatre Passe Muraille’s Backspace, The Theatre Centre, Factory Theatre, Cameron House, a sold out run at Stratford, and recently at the Young Centre for the Performing Arts. This article analyses VideoCabaret’s unique scenographic approach and the impact of the scenography on Canada’s historical narrative. The script is created with a unique scenographic design in mind. Costumes become exaggerated portraits of the figure they represent and immediate triggers of recognition. The show takes place in a black-box theatre with oversized, grotesque or two dimensional props. Actors come and go from the lights without being seen to appear or exit, much the same way these figures come and go in Canadian history. Such an approach contrasts the stark black box with the chaotic happenings of the play. By addressing the costumes, props, lighting and set, we can see how the subversive scenographic choices interact with the audiences’ traditional assumptions of what Canadian history is and how it is told. This article will also show how the scenography of VideoCabaret both constructs and challenges the narratives of Canadian history, and by extension, Canadian identity.
How to ‘Enlighten’ museum visitors: Curating Derby Museum’s Enlightenment Exhibition
Authors: Dunning Louise 
Published: December 2013

Abstract
How many times have we, the museum visitor, stood in front of a display case full of objects and let our eyes glance over them, not really taking in any of them individually? Not understanding why they were grouped as they are, or bothering to read the labels that the curator has painstakingly written and positioned? This is the challenge of temporary (and permanent) exhibitions displays today in our fast moving, social media savvy world. Museum objects have to work hard to be noticed and appreciated. Taking an object out of its ‘natural environment’ is always artificial, even if the museum goes to great lengths to replicate the environment that it would have been used in (e.g. with ‘room sets’). This is particularly the case with functional (and often decorative) objects, like cups and saucers, hosiery, jewellery, barometers, balls of twine or an egg timer. Once they are placed in a case, their use alters. They are elevated far beyond their original function. They become an ‘object’ to be admired, looked at with interest, or with indifference. They have the power to fascinate and inspire. But to do that, they must first be displayed in a way that shows them off advantageously and with interpretation that explains their importance and use without boring or confusing the reader. Add to this an often complex message that the museum wishes to convey to the visitors, and curators really have their work cut out. This was the challenge that I faced when I curated the Enlightenment exhibition at Derby Museums (22 June–25 August 2013). This exhibition was the result of five years of collecting by ourselves, Buxton Museum and Art Gallery and Strutt’s North Mill, Belper. Funded by the Heritage Lottery Fund Collecting Cultures programme, we collected over 100 eighteenth-century objects to enrich our collections, to develop a better understanding of the Enlightenment period in Derbyshire and to help put the Derwent Valley Mills World Heritages Site into context. So although I and the collections team were in raptures over a plate showing a peculiar looking polar bear and were discussing how this one item could be linked to trade, exploitation, fashion, taste, travel and a fascination with natural history, my challenge was how to display this object so the museum’s visitors were excited by it too.
Designing a new documentary landscape: A renegotiation of documentary voice through animated collage
Authors: Bevan Greg , Bosward Marc 
Published: December 2013

Abstract
Documentaries represent issues and aspects of the socio-historical world. They do so through a selection and combination of audio and visual components. Inevitably, this practice makes intrinsic claims about documentary’s ability to represent the world both accurately and reliably. Facts, information, balance and reliability are the bedrock of documentary vocabulary. Comparatively few practitioners have genuinely interrogated the veracity of their craft; authenticity, evidence and objectivity remain central to the language of their practice. As the result of a mediated process, a documentary film is, at best, a crafted version of reality and its conventions are designed and developed to convince audiences of the authenticity of their particular representation of the world. Documentary’s traditional journalistic and pseudo-scientific status has hampered its development as a discursive art form capable of exploring a much broader sphere of human experience. Using a selection of still images, this article aims to contextualize, reflect on and illuminate the short, animated documentary Fforest (2009) by G. Bevan and M. Bosward. Drawing on the practice and principles of collage, the film seeks to expand the language of documentary production by deliberately undermining traditional approaches to knowledge, authority and fact. It explores potential new terrain for documentary by generating a non-realist, visual aesthetic that is not bound to traditional discourses of ‘sobriety’, whilst reaffirming the documentary as a composition which must be designed and assembled, in which authorial voice must be constructed rather than simply stated, and in which meaning is not necessarily explicit.
Reviews
Authors: Sporton Gregory , Sporton Gregory , Sporton Gregory , Bean Simonian , Donovan Nicola , Kuksa Iryna 
Published: December 2013

Abstract
Apollo, 24 Preludes and Aeternum (2013) The Royal Ballet, March
The Oracle (2013), Meryl Tankard (dir.), London: Queen Elizabeth Hall, May
The Perfect American, Phelem McDermott (dir.), Philip Glass (2013) English National Opera, June
LOLPERA, Angela Lopez (dir.), Ellen Warkentine and Andrew Pedroza (2012) Los Angeles: Hollywood Fringe Festival, 24 June
LACE:HERE:NOW, Nottingham, September 2012–February 2013
‘I Have Seen the Future: Norman Bel Geddes Designs America’ (2012–2013) Harry Ransom Center, The University of Texas at Austin, 11 September–6 January
‘Visions of The Future’ (2012) the tenth biennial Fleur Cowles Flair Symposium, Harry Ransom Center, The University of Texas at Austin, 1–3 November
Multiple Hürthle cell adenomas in a patient with thyroid hormone resistance
Authors: Xifra Gemma , Mauri Silvia , Gironès Jordi , Rodríguez Hermosa José Ignacio , Oriola Josep , Ricart Wifredo , Fernández-Real José Manuel 
Published: December 2013

Summary
Background: Thyroid hormone resistance (RTH) is a rare cause of thyroid dysfunction. High TSH levels, as described in RTH syndrome, are known to be associated with an increased risk of developing thyroid nodules with subsequent growth and malignancy.
Patient findings: In 2006, a 29-year-old Caucasian man presented with a palpable mass in the neck. Increased free thyroxine and triiodothyronine levels were found in the context of unsuppressed TSH levels, despite no signs or symptoms of hyperthyroidism. Ultrasonography revealed a multinodular and enlarged goitre, and fine-needle aspiration cytology revealed suspicious features of malignancy. After excluding pituitary tumour and levothyroxine (l-T4) treatment, the patient was diagnosed with generalized RTH. Screening for all the known mutations in thyroid hormone receptor-β (TR
β (THRB)) was negative. Thyroidectomy disclosed five Hürthle adenomas and three hyperplasic nodules. Euthyroidism was achieved after surgery with 6.1 μg/kg per day of l-T4.
Conclusion: RTH may be a risk factor that predisposes to the development of multiple Hürthle cell adenomas. To our knowledge, this is the first case of multiple Hürthle cell adenomas in a patient with RTH.

Learning points

High TSH levels, as described in RTH syndrome, are known to be associated with an increased risk of developing thyroid nodules, with subsequent growth and malignancy.

The exact role of TR
β mutants in thyroid carcinogenesis is still undefined.

We report the first case of multiple Hürthle cell adenomas associated with RTH.
Identifying Signatures of Selection in Genetic Time Series
Authors: Feder Alison F , Kryazhimskiy Sergey , Plotkin Joshua B 
Published: December 2013

Abstract
Both genetic drift and natural selection cause the frequencies of alleles in a population to vary over time. Discriminating between these two evolutionary forces, based on a time series of samples from a population, remains an outstanding problem with increasing relevance to modern data sets. Even in the idealized situation when the sampled locus is independent of all other loci, this problem is difficult to solve, especially when the size of the population from which the samples are drawn is unknown. A standard χ2-based likelihood-ratio test was previously proposed to address this problem. Here we show that the χ2-test of selection substantially underestimates the probability of type I error, leading to more false positives than indicated by its P-value, especially at stringent P-values. We introduce two methods to correct this bias. The empirical likelihood-ratio test (ELRT) rejects neutrality when the likelihood-ratio statistic falls in the tail of the empirical distribution obtained under the most likely neutral population size. The frequency increment test (FIT) rejects neutrality if the distribution of normalized allele-frequency increments exhibits a mean that deviates significantly from zero. We characterize the statistical power of these two tests for selection, and we apply them to three experimental data sets. We demonstrate that both ELRT and FIT have power to detect selection in practical parameter regimes, such as those encountered in microbial evolution experiments. Our analysis applies to a single diallelic locus, assumed independent of all other loci, which is most relevant to full-genome selection scans in sexual organisms, and also to evolution experiments in asexual organisms as long as clonal interference is weak. Different techniques will be required to detect selection in time series of cosegregating linked loci.
Evidence for Paternal Age-Related Alterations in Meiotic Chromosome Dynamics in the Mouse
Authors: Vrooman Lisa A , Nagaoka So I , Hassold Terry J , Hunt Patricia A 
Published: December 2013

AbstractIncreasing age in a woman is a well-documented risk factor for meiotic errors, but the effect of paternal age is less clear. Although it is generally agreed that spermatogenesis declines with age, the mechanisms that account for this remain unclear. Because meiosis involves a complex and tightly regulated series of processes that include DNA replication, DNA repair, and cell cycle regulation, we postulated that the effects of age might be evident as an increase in the frequency of meiotic errors. Accordingly, we analyzed spermatogenesis in male mice of different ages, examining meiotic chromosome dynamics in spermatocytes at prophase, at metaphase I, and at metaphase II. Our analyses demonstrate that recombination levels are reduced in the first wave of spermatogenesis in juvenile mice but increase in older males. We also observed age-dependent increases in XY chromosome pairing failure at pachytene and in the frequency of prematurely separated autosomal homologs at metaphase I. However, we found no evidence of an age-related increase in aneuploidy at metaphase II, indicating that cells harboring meiotic errors are eliminated by cycle checkpoint mechanisms, regardless of paternal age. Taken together, our data suggest that advancing paternal age affects pairing, synapsis, and recombination between homologous chromosomes—and likely results in reduced sperm counts due to germ cell loss—but is not an important contributor to aneuploidy.