bluuebunny/crossref_metadata_2025_split huggingface dataset:
Non-targeted transcription factors motifs are a systemic component of ChIP-seq datasets
Authors: Worsley Hunt Rebecca , Wasserman Wyeth W 
Published: July 2014

Abstract
Background
The global effort to annotate the non-coding portion of the human genome relies heavily on chromatin immunoprecipitation data generated with high-throughput DNA sequencing (ChIP-seq). ChIP-seq is generally successful in detailing the segments of the genome bound by the immunoprecipitated transcription factor (TF), however almost all datasets contain genomic regions devoid of the canonical motif for the TF. It remains to be determined if these regions are related to the immunoprecipitated TF or whether, despite the use of controls, there is a portion of peaks that can be attributed to other causes.

Results
Analyses across hundreds of ChIP-seq datasets generated for sequence-specific DNA binding TFs reveal a small set of TF binding profiles for which predicted TF binding site motifs are repeatedly observed to be significantly enriched. Grouping related binding profiles, the set includes: CTCF-like, ETS-like, JUN-like, and THAP11 profiles. These frequently enriched profiles are termed ‘zingers’ to highlight their unanticipated enrichment in datasets for which they were not the targeted TF, and their potential impact on the interpretation and analysis of TF ChIP-seq data. Peaks with zinger motifs and lacking the ChIPped TF’s motif are observed to compose up to 45% of a ChIP-seq dataset. There is substantial overlap of zinger motif containing regions between diverse TF datasets, suggesting a mechanism that is not TF-specific for the recovery of these regions.

Conclusions
Based on the zinger regions proximity to cohesin-bound segments, a loading station model is proposed. Further study of zingers will advance understanding of gene regulation.
Are serum-free and xeno-free culture conditions ideal for large scale clinical grade expansion of Wharton’s jelly derived mesenchymal stem cells? A comparative study
Authors: Swamynathan Priyanka , Venugopal Parvathy , Kannan Suresh , Thej Charan , Kolkundar Udaykumar , Bhagwat Swaroop , Ta Malancha , Majumdar Anish Sen , Balasubramanian Sudha 
Published: July 2014

Abstract
Introduction
Mesenchymal stromal/stem cells (MSCs) for clinical use have largely been isolated from the bone marrow, although isolation of these cells from many different adult and fetal tissues has been reported as well. One such source of MSCs is the Whartons Jelly (WJ) of the umbilical cord, as it provides an inexhaustible source of stem cells for potential therapeutic use. Isolation of MSCs from the umbilical cord also presents little, if any, ethical concerns, and the process of obtaining the cord tissue is relatively simple with appropriate consent from the donor. However, a great majority of studies rely on the use of bovine serum containing medium for isolation and expansion of these cells, and porcine derived trypsin for dissociating the cells during passages, which may pose potential risks for using these cells in clinical applications. It is therefore of high priority to develop a robust production process by optimizing culture variables to efficiently and consistently generate MSCs that retain desired regenerative and differentiation properties while minimizing risk of disease transmission.

Methods
We have established a complete xeno-free, serum-free culture condition for isolation, expansion and characterization of WJ-MSCs, to eliminate the use of animal components right from initiation of explant culture to clinical scale expansion and cryopreservation. Growth kinetics, in vitro differentiation capacities, immunosuppressive potential and immunophenotypic characterization of the cells expanded in serum-free media have been compared against those cultured under standard fetal bovine serum (FBS) containing medium. We have also compared the colony-forming frequency and genomic stability of the large scale expanded cells. Secretome analysis was performed to compare the angiogenic cytokines and functional angiogenic potency was proved by Matrigel assays.

Results
Results presented in this report identify one such serum-free, xeno-free medium for WJ expansion. Cells cultured in serum-free, xeno-free medium exhibit superior growth kinetics and functional angiogenesis, alongside other MSC characteristics.

Conclusions
We report here that WJ-MSCs cultured and expanded in Mesencult XF, SF Medium retain all necessary characteristics attributed to MSC for potential therapeutic use.
Heme-Binding Properties of HupD Functioning as a Substrate-Binding Protein in a Heme-Uptake ABC-Transporter System in Listeria monocytogenes
Authors: Okamoto Yasunori , Sawai Hitomi , Ogura Mariko , Uchida Takeshi , Ishimori Koichiro , Hayashi Takashi , Aono Shigetoshi 
Published: July 2014

Abstract
The HupDCG protein complex is a putative ABC-transporter for heme in the pathogenic Gram-positive bacterium Listeria monocytogenes, where HupD functions as a heme-binding protein. UV–vis absorption, EPR, and resonance Raman spectroscopy have revealed that HupD binds a heme with two histidine residues as the axial ligands. His105 and His259 are identified as the axial ligands by site-directed mutagenesis. HupD is the first example of a heme-binding protein having a bis-histidine coordination environment among the heme-binding proteins working in bacterial heme acquisition systems. While mutation of His259 to Ala resulted in a loss in the heme-binding ability of HupD, the H105A variant of HupD retained its heme-binding ability with lower heme-binding affinity compared with the wild type. These results suggest that His259 is an essential ligand for heme acquisition by HupD and that His105 might be responsible for regulation of the heme-binding affinity of HupD during the heme-transport process.
Role Refinement in Access Control: Model and Analysis
Authors: Xia Hao , Dawande Milind , Mookerjee Vijay 
Published: July 2014

Access control mechanisms in software systems administer user privileges by granting users permission to perform certain operations while denying unauthorized access to others. Such mechanisms are essential to ensure that important business functions in an organization are conducted securely and smoothly. Currently, the dominant access control approach in most major software systems is role-based access control. In this approach, permissions are first assigned to roles, and users acquire permissions by becoming members of certain roles. However, given the dynamic nature of organizations, a fixed set of roles usually cannot meet the demands that users (existing or new) have to conduct business. The typical response to this problem is to myopically create new roles to meet immediate demand that cannot be satisfied by an existing set of roles. This ad hoc creation of roles invariably leads to a proliferation in the number of roles with the accompanying administrative overhead. Based on discussions with practitioners, we propose a role refinement scheme that reconstructs a system of roles to reduce the cost of role management. We first show that the role-refinement problem is strongly NP-hard and then provide two polynomial-time approximation algorithms (a greedy algorithm and a randomized rounding algorithm) and establish their performance guarantees. Finally, numerical experiments—based on a real data set from a firm's enterprise resource planning system—are conducted to demonstrate the applicability and performance of our refinement scheme.
The resurrection of the spectacle
Authors: Schallenberg André 
Published: July 2014

Abstract
One major topic of the European performance/avant-garde scene of the last century was 'reality', mostly accompanied by the contentious catchword 'post-dramatic' and work with lay people or 'experts'. However, productions that seemed political or revolutionary often revealed themselves to be nothing more than part of a marketing strategy by theatres aimed at unlocking new spaces of spectatorship. However, alongside these attempts, an alternative practice has emerged amongst young artists, who once again emphasise the artistic, subjective and ritual character of theatre, in order to bring it back to its origins. Using the example of three current productions, this article aims to show the means these artists work with and why this theatre is in its own way significantly more political than many alleged 'reality' productions.
From affective reading to the theory of affect: Reading / Feeling, Tanja Baudoin, Frédérique Bergholtz and Vivien Ziherl (eds.) (2013), Amsterdam: If I Can't Dance, I Don't Want To Be Part of Your Revolution
Authors: Založnik Jasmina 
Published: July 2014

Abstract
The reader Reading / Feeling is the result of a two-year art-theory research programme organised by the Dutch organization If I Can't Dance. Its innovation is not reflected in the selection of texts, but in the methodological approach of opening up a different (affective, paranoid) mode of reading. The compilation offers to a reader various entry points that are not to be taken in only rationally, but also experientially, to be precise, through an affective response.
Biopolitics, Deleuzianism and the destiny of aesthetics
Authors: Apostolou-Hölscher Stefan 
Published: July 2014

Abstract
In the second half of the eighteenth century, the emergence of a concept of 'life itself' as living not only has an impact on the economical and political fields but deeply touches on traditional understandings of the work of art as well. The birth of aesthetics within philosophy is just a consequence of, not the reason for, new practices and procedures in the field of art. Until now, the strict rules of Poetics had governed and distributed mimesis, keeping the different arts separate whilst subsuming their subjects under the idea of an organic unity. With the aesthetic and biopolitical turn in the second half of the eighteenth century, every measure is lost.
Sticky tales for affect: Episodes of situated thought
Authors: Caspão Paula 
Published: July 2014

Abstract
The article takes the form of a travelogue, embodying a method of geographically and affectively situated research and writing. It is an episode of documentation of a long-term journey of 'inadequate' study focusing on affect and theory, affect and writing, affect and place (affect and displacement). Convoking the notion of 'permeable ways of being' (Brennan, 2004), the text generates a half-theoretical, half-fictional discursive movement that doesn't go straight, reporting and reflecting on a recent collective artistic residency meant to study forms of life; on the very process of writing as cross-temporal and cross-geographical; on daily economies of affect that glide into affect morals.
Getting Affective
Authors: Kraigher Amelia 
Published: July 2014

Abstract
This issue focuses on the issues of affectivity and emotionality in contemporary theatre and on their (performative) theorisations. It draws from theorisations and/or case studies to develop diverse discussions about the mentioned aspects of the performing arts that also result from the modes of production themselves; in addition, it raises issues regarding emotions in the theatre, both in the past and today, and reflects on the manner in which theatre art is determined and driven by passions. It also addresses the phenomenon of the actor's fear of passion (convulsions, stress and the resulting burnout of artists…), the question of the (absence of) courage of theatre creators and theoreticians, which also includes a reflection on the history of stage fright, different trainings of actors' emotions, their objectives and methods; it reflects on passions from the aspect of theatre excess, the passion for prohibition and the question of conventions, on the authenticity of emotions in (contemporary) theatre and performance - doing all this in order to unfold the notion of passion as an issue of the political.
Authentic emotion and body-subject: Are these tears for real?
Authors: Kolenc Bara 
Published: July 2014

Abstract
The article discusses the phenomenon of aversion to exaggerated emotionality, characteristic of contemporary art. At the backdrop of historical subjectivity from the beginning of the twentieth century to the present day, defined by the dissolution of the authenticity of the Self and the emergence of a deconstructed, mediated subject, the author addresses the causes and conditions of this phenomenon. She tackles the questions of representation and the unrepresentable, which she traces through the aesthetic of realism and its demand for authentic emotions, modernism and its denial of indication and postmodern artistic practices, which are paradoxically defined not only by a general skepticism toward the authentic, but also toward the absolute inauthenticity of the raw mediation of signs and stand-in structures.
Affect and the performing arts: Biopolitics, transformation and potentiality
Authors: Bajda Anja 
Published: July 2014

Abstract
In this article the author explores affect within the representational framework, which is questioned as the paradigm of the theatrical convention. In relation to affective labour, physical presence and the real, being the core of theatrical illusion, it explores the emancipatory potential of performing arts conceived through the presence of affect. Actual virtuality becomes the key term with which to signify possibility, constituted within the creative act, as operative in the symbolic (field). The implications of the presence of affect within the performance are examined through its analytical introduction into the Slovenian theatrical performance Mandićmachine.
Address at the presentation of the Evergreen Crocodile Award
Authors: Repnik Vlado G. , Kardum Simon , Štromajer Igor 
Published: July 2014

Abstract
Address at the presentation of the Evergreen Crocodile Award for Lifetime Achievement to Dragan Živadinov - Slovenian theatre director and cosmonaut candidate, conceptual initiator of style formations retrogardism and telecosmism, founder of the Scipion Nasice Sisters Theatre, the Red Pilot Cosmokinetic Theatre and the Noordung Cosmokinetic Cabinet; author of the 50 year theatre projectile 1995-2045 - Noordung, Biomechanics Noordung, postgravitational theatrical abstracts and one of the three initiators of the Cultural Centre of European Space Technologies (KSEVT) in Vitanje - at the Borštnik Theatre Festival in Maribor on 19 October 2013.
The desire to be affected
Authors: Rozas Ixiar 
Published: July 2014

Abstract
In this article, the author connects affects with Lygia Clark's resonant body, with a story about Suely Rolnik and with the performing art piece Fissure no. 3: txoriak by Basque artist Idoia Zabaleta. In these three vignettes, the three authors and creators activate affects in a double movement: centripetal and centrifugal. To affect somebody, we first affect ourselves. And by doing so we change and alter others, according to Brian Massumi's theory of affects as something transindividual that goes beyond us. In this twofold movement, we can also make the familiar strange and the strange familiar, a condition that Kaja Silverman believes to be essential in creative work that considers itself political in today's context.
Beyond pathos: Interview with Annika Tudeer
Authors: Koch Christian 
Published: July 2014

Abstract
In this interview with Annika Tudeer, we pursue the question of possibility and the place of emotionality in contemporary theatre. At the forefront of the interview is the process-oriented practice of the Finnish theatre company OBLIVIA, which oriented itself very heavily around conceptual approaches of the 1970s through the 1990s but which in recent times has increasingly opened itself up by incorporating chance as a constructive principle for using affects and emotions as a medium of communication with the audience. In its more recent works, the company has allocated more room to that which one might call the pathos of acting. This serves a new performative aesthetics that endeavours to overcome the analytical approach to the theatre dispositive.
Remakes a la española. El proceso de adaptación de series extranjeras en España
Authors: Puebla Martínez Belén , Carrillo Pascual Elena , Copado Sánchez-Rico Paola 
Published: July 2014

Las adaptaciones o remakes responden al éxito de determinados productos a nivel mundial, lo que incita a pensar en el creciente desarrollo de una cultura audiovisualcada vez más global. De esta forma, con el siguiente trabajo pretendemos analizar cuáles son las diferencias y las similitudes entre una serie de ficción extranjera y su adaptación en la televisión española, poniendo especial interés en averiguar cuáles son los elementos que sufren una mayor adaptación, así como de qué forma se modifican los guiones para conseguir un producto adecuado para el público español. Para ello, haremos un recorrido por las series de ficción adaptadas en España (en las cinco cadenas generalistas) en el periodo comprendido desde el año 2000 hasta 2013 a través de un análisis cualitativo en el que estudiaremos variables relacionadas con el contenido de los productos audiovisuales (características formales, personajes,cabecera, tramas, estética y diálogos) que nos permitan su comparación.
David Cronenberg. “La Mosca” o el regreso a lo humano no-humano
Authors: Andrade Gaytán Noel J. 
Published: July 2014

Desde el terreno del cine podemos analizar tanto a la sociedad como a sus integrantes. Apoyados en los ojos de los diferentes realizadores, podemos percibir una cuestión fundamental: ¿qué tan distinta es la realidad del otro lado de la pantalla?, ¿el espectador, realmente, está seguro de su condición ontológica de existencia? Cuestiones que resuenan y resoplan en el trabajo fílmico de un director en específico: David Cronenberg. En su filmografía y, en particular en La Mosca (The Fly, 1986), nos abre la posibilidad de hacer reflexiones de largo aliento. Si cuestionamos filosóficamente la noción del “yo” moderno, también debe cuestionarse su recubrimiento: su carne. Hemos intentado analizar el mundo a tal grado, que más que describirlo para adquirir un conocimiento cuasi perfectible, lo hemos puesto en la plancha de disección a la manera de carne frígida y mortecina. En un sentido superficial se piensa que la Nueva Carne postula el triunfo humano ante la muerte, como atisbaba ya Mary Shelley en su trágico Frankenstein; pero no, antes bien, pretende la fusión no sólo con todo objeto en el espacio sino con todo momento en el tiempo. Es un regreso al cronotopo mítico: a su axis mundi.
Ciudades educadoras y ciudades creativas, las nuevas fórmulas de la pedagogía social en el siglo XXI
Authors: Ramos Fernández Fernando , López Atrio Laura 
Published: July 2014

La Carta de Ciudades Educadoras sistematiza los vínculos entre ciudad y educación. La ciudad es el marco para establecer relaciones, construir identidades y adquirir conocimientos en el proceso educativo. El concepto de ciudades educadoras, surgido a finales de siglo XX, y sus instrumentos, los Proyectos Educativos de Ciudad (PEC), reclaman la participación del conjunto de los ciudadanos en los asuntos públicos y que gobierno local cree las condiciones que faciliten la contribución de los agentes sociales y educativos. Este artículo se refiere a la experiencia llevada a cabo en la ciudad industrial de Vigo (España) por la Concejalía de Educación (durante el mandato 2007-2011, bajo la responsabilidad de la concejala, profesora y psicopedagoga Laura López Atrio, y sus investigaciones posteriores sobre la materia), cuyo modelo puede servir de referente para el desarrollo de otras experiencias semejantes. Sus resultados constituyen un elemento trasladable a otros escenarios urbanos, especialmente en aquellos donde a la población nativa de origen se suman amplios colectivos de inmigrantes asentados, especialmente de Hispanoamérica, el Norte de África y Centro Europa. La Carta de Ciudades educadoras, aprobada el año 1990, revisada en noviembre 2004, en Génova en el marco del VIII Congreso de Ciudades Educadoras, expresa y recoge la filosofía en la que se asienta este movimiento educativo y social, al tiempo que fija los parámetros científicos, dentro de los que han de desarrollarse los vínculos entre ciudad y educación. Todos los recursos de la ciudad han de ser aprovechados para la formación de ciudadanos, cultos, libres y participativos.
Catecholamine-secreting carotid body paraganglioma: successful preoperative control of hypertension and clinical symptoms using high-dose long-acting octreotide
Authors: Elshafie Omayma , Al Badaai Yahya , Alwahaibi Khalifa , Qureshi Asim , Hussein Samir , Al Azzri Faisal , Almamari Ali , Woodhouse Nicholas 
Published: July 2014

SummaryA 48-year-old hypertensive and diabetic patient presented with a 10-year history of progressive right facial pain, tinnitus, hearing loss, sweating, and palpitations. Investigations revealed a 5.6 cm vascular tumor at the carotid bifurcation. Her blood pressure (BP) was 170/110, on lisinopril 20 mg od and amlodipine 10 mg od and 100 U of insulin daily. A catecholamine-secreting carotid body paraganglioma (CSCBP) was suspected; the diagnosis was confirmed biochemically by determining plasma norepinephrine (NE) level, 89 000 pmol/l, and chromogranin A (CgA) level, 279 μg/l. Meta-iodobenzylguanidine and octreotide scanning confirmed a single tumor in the neck. A week after giving the patient a trial of octreotide 100 μg 8 h, the NE level dropped progressively from 50 000 to 25 000 pmol/l and CgA from 279 to 25 μg/l. Treatment was therefore continued with labetalol 200 mg twice daily (bid) and long-acting octreotide-LA initially using 40 mg/month and later increasing to 80 mg/month. On this dose and with a reduced labetalol intake of 100 mg bid, BP was maintained at 130/70 and her symptoms resolved completely. CgA levels returned to normal in the first week and these were maintained throughout the 3 month treatment period. During tumor resection, there were minimal BP fluctuations during the 10 h procedure. We conclude that short-term high-dose octreotide-LA might prove valuable in the preoperative management of catecholamine-secreting tumors. To the best of our knowledge, this is the first report on the successful use of octreotide in a CSCBP.Learning pointsThe value of octreotide scanning in the localization of extra-adrenal pheochromocytoma.Control of catecholamine secretion using high-dose octreotide.This is a report of a rare cause of secondary diabetes and hypertension.
Immersive Virtual Reality for Training and Decision Making: Preliminary Results of Experiments Performed With a Plant Simulator
Authors: Colombo S.. , Nazir S.. , Manca D.. 
Published: July 2014

Summary
The use of immersive virtual reality (IVR) for training is an idea that has existed for a long time; the real, unclarified doubt about its use is whether it does really increase performance with respect to traditional methods such as classroom and on-the-job training. The most critical point of traditional training methods is the difficulty to train operators about a system's deviations from nominal conditions. But even the more-advanced simulation-supported training approach, commercially represented by the operator-training simulator (OTS), is not immune to flaws because it is affected both by the subjectivity of the assessment (making useless the operators’ benchmarking) and by the impossibility of training simultaneously the field operator (FOP) with the control-room operator (CROP) (i.e., team training). The plant simulator (PS) enables overcoming the inherent limitations of the training methods. But the efficacy of using immersive virtual environments (IVEs) was, and to some extent still is, to be proved. This paper goes in that direction by explaining the preliminary results of an experiment campaign performed in a PS, which demonstrates the clear benefit of using IVR for training (field) operators. The paper even highlights that, if a PS is used, the benefits are not just limited to the training but can also be extended to operations management.