bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic convergence and network analysis approach to identify candidate genes in Alzheimer's disease
Authors: Talwar Puneet , Silla Yumnam , Grover Sandeep , Gupta Meenal , Agarwal Rachna , Kushwaha Suman , Kukreti Ritushree 
Published: March 2014

Abstract

Background
Alzheimer’s disease (AD) is one of the leading genetically complex and heterogeneous disorder that is influenced by both genetic and environmental factors. The underlying risk factors remain largely unclear for this heterogeneous disorder. In recent years, high throughput methodologies, such as genome-wide linkage analysis (GWL), genome-wide association (GWA) studies, and genome-wide expression profiling (GWE), have led to the identification of several candidate genes associated with AD. However, due to lack of consistency within their findings, an integrative approach is warranted. Here, we have designed a rank based gene prioritization approach involving convergent analysis of multi-dimensional data and protein-protein interaction (PPI) network modelling.

Results
Our approach employs integration of three different AD datasets- GWL,GWA and GWE to identify overlapping candidate genes ranked using a novel cumulative rank score (SR) based method followed by prioritization using clusters derived from PPI network. SR for each gene is calculated by addition of rank assigned to individual gene based on either p value or score in three datasets. This analysis yielded 108 plausible AD genes. Network modelling by creating PPI using proteins encoded by these genes and their direct interactors resulted in a layered network of 640 proteins. Clustering of these proteins further helped us in identifying 6 significant clusters with 7 proteins (EGFR, ACTB, CDC2, IRAK1, APOE, ABCA1 and AMPH) forming the central hub nodes. Functional annotation of 108 genes revealed their role in several biological activities such as neurogenesis, regulation of MAP kinase activity, response to calcium ion, endocytosis paralleling the AD specific attributes. Finally, 3 potential biochemical biomarkers were found from the overlap of 108 AD proteins with proteins from CSF and plasma proteome. EGFR and ACTB were found to be the two most significant AD risk genes.

Conclusions
With the assumption that common genetic signals obtained from different methodological platforms might serve as robust AD risk markers than candidates identified using single dimension approach, here we demonstrated an integrated genomic convergence approach for disease candidate gene prioritization from heterogeneous data sources linked to AD.
Comparative transcriptomics of Atlantic Salmo salar, chum Oncorhynchus keta and pink salmon O. gorbuscha during infections with salmon lice Lepeophtheirus salmonis
Authors: Sutherland Ben JG , Koczka Kim W , Yasuike Motoshige , Jantzen Stuart G , Yazawa Ryosuke , Koop Ben F , Jones Simon RM 
Published: March 2014

Abstract

Background
Salmon species vary in susceptibility to infections with the salmon louse (Lepeophtheirus salmonis). Comparing mechanisms underlying responses in susceptible and resistant species is important for estimating impacts of infections on wild salmon, selective breeding of farmed salmon, and expanding our knowledge of fish immune responses to ectoparasites. Herein we report three L. salmonis experimental infection trials of co-habited Atlantic Salmo salar, chum Oncorhynchus keta and pink salmon O. gorbuscha, profiling hematocrit, blood cortisol concentrations, and transcriptomic responses of the anterior kidney and skin to the infection.

Results
In all trials, infection densities (lice per host weight (g)) were consistently highest on chum salmon, followed by Atlantic salmon, and lowest in pink salmon. At 43 days post-exposure, all lice had developed to motile stages, and infection density was uniformly low among species. Hematocrit was reduced in infected Atlantic and chum salmon, and cortisol was elevated in infected chum salmon. Systemic transcriptomic responses were profiled in all species and large differences in response functions were identified between Atlantic and Pacific (chum and pink) salmon. Pink and chum salmon up-regulated acute phase response genes, including complement and coagulation components, and down-regulated antiviral immune genes. The pink salmon response involved the largest and most diverse iron sequestration and homeostasis mechanisms. Pattern recognition receptors were up-regulated in all species but the active components were often species-specific. C-type lectin domain family 4 member M and acidic mammalian chitinase were specifically up-regulated in the resistant pink salmon.

Conclusions
Experimental exposures consistently indicated increased susceptibility in chum and Atlantic salmon, and resistance in pink salmon, with differences in infection density occurring within the first three days of infection. Transcriptomic analysis suggested candidate resistance functions including local inflammation with cytokines, specific innate pattern recognition receptors, and iron homeostasis. Suppressed antiviral immunity in both susceptible and resistant species indicates the importance of future work investigating co-infections of viral pathogens and lice.
Epidermal growth factor receptor gene polymorphisms are associated with prognostic features of breast cancer
Authors: Leite Marcelo Sobral , Giacomin Letícia Carlos , Piranda Diogo Nascimento , Festa-Vasconcellos Juliana Simões , Indio-do-Brasil Vanessa , Koifman Sérgio , de Moura-Neto Rodrigo Soares , de Carvalho Marcelo Alex , Vianna-Jorge Rosane 
Published: March 2014

AbstractBackgroundThe epidermal growth factor receptor (EGFR) is differently expressed in breast cancer, and its presence may favor cancer progression. We hypothesized that twoEGFRfunctional polymorphisms, a (CA)n repeat in intron 1, and a single nucleotide polymorphism,R497K, may affectEGFRexpression and breast cancer clinical profile.MethodsThe study population consisted of 508 Brazilian women with unilateral breast cancer, and no distant metastases. Patients were genotyped for the(CA)nandR497Kpolymorphisms, and the associations between(CA)npolymorphism and EGFR transcript levels (n = 129), or between either polymorphism and histopathological features (n = 505) were evaluated. The REMARK criteria of tumor marker evaluation were followed.Results(CA)n lengths ranged from 14 to 24 repeats, comprehending 11 alleles and 37 genotypes. The most frequent allele was(CA)16(0.43; 95% CI = 0.40–0.46), which was set as the cut-off length to define theShortallele. Variant(CA)ngenotypes had no significant effect in tumoralEGFRmRNA levels, but patients with two(CA)n Longalleles showed lower chances of being negative for progesterone receptor (ORadjusted = 0.42; 95% CI = 0.19–0.91). The evaluation ofR497Kpolymorphism indicated a frequency of 0.21 (95% CI = 0.19 – 0.24) for the variant (Lys) allele. Patients with variantR497Kgenotypes presented lower proportion of worse lymph node status (pN2 or pN3) when compared to the reference genotypeArg/Arg(ORadjusted = 0.32; 95% CI = 0.17–0.59), which resulted in lower tumor staging (ORadjusted = 0.34; 95% CI = 0.19-0.63), and lower estimated recurrence risk (OR = 0.50; 95% CI = 0.30-0.81). The combined presence of bothEGFRpolymorphisms (Lysallele of R497K andLong/Long (CA)n) resulted in lower TNM status (ORadjusted = 0.22; 95% CI = 0.07-0.75) and lower ERR (OR = 0.25; 95% CI = 0.09-0.71). When tumors were stratified according to biological classification, the favorable effects of variantEGFRpolymorphisms were preserved for luminal A tumors, but not for other subtypes.ConclusionsThe data suggest that the presence of the variant forms ofEGFRpolymorphisms may lead to better prognosis in breast cancer, especially in patients with luminal A tumors.
Functional proteomic analysis reveals the involvement of KIAA1199 in breast cancer growth, motility and invasiveness
Authors: Jami Mohammad-Saeid , Hou Jinxuan , Liu Miao , Varney Michelle L , Hassan Hesham , Dong Jixin , Geng Liying , Wang Jing , Yu Fang , Huang Xin , Peng Hong , Fu Kai , Li Yan , Singh Rakesh K , Ding Shi-Jian 
Published: March 2014

AbstractBackgroundKIAA1199is a recently identified novel gene that is up-regulated in human cancer with poor survival. Our proteomic study on signaling polarity in chemotactic cells revealed KIAA1199 as a novel protein target that may be involved in cellular chemotaxis and motility. In the present study, we examined the functional significance of KIAA1199 expression in breast cancer growth, motility and invasiveness.MethodsWe validated the previous microarray observation by tissue microarray immunohistochemistry using a TMA slide containing 12 breast tumor tissue cores and 12 corresponding normal tissues. We performed the shRNA-mediated knockdown of KIAA1199 in MDA-MB-231 and HS578T cells to study the role of this protein in cell proliferation, migration and apoptosisin vitro. We studied the effects of KIAA1199 knockdownin vivoin two groups of mice (n = 5). We carried out the SILAC LC-MS/MS based proteomic studies on the involvement of KIAA1199 in breast cancer.ResultsKIAA1199 mRNA and protein was significantly overexpressed in breast tumor specimens and cell lines as compared with non-neoplastic breast tissues from large-scale microarray and studies of breast cancer cell lines and tumors. To gain deeper insights into the novel role of KIAA1199 in breast cancer, we modulated KIAA1199 expression using shRNA-mediated knockdown in two breast cancer cell lines (MDA-MB-231 and HS578T), expressing higher levels of KIAA1199. The KIAA1199 knockdown cells showed reduced motility and cell proliferationin vitro. Moreover, when the knockdown cells were injected into the mammary fat pads of female athymic nude mice, there was a significant decrease in tumor incidence and growth. In addition, quantitative proteomic analysis revealed that knockdown of KIAA1199 in breast cancer (MDA-MB-231) cells affected a broad range of cellular functions including apoptosis, metabolism and cell motility.ConclusionsOur findings indicate that KIAA1199 may play an important role in breast tumor growth and invasiveness, and that it may represent a novel target for biomarker development and a novel therapeutic target for breast cancer.
Study of zeolite influence on analytical characteristics of urea biosensor based on ion-selective field-effect transistors
Authors: Shelyakina Margaryta K , Soldatkin Oleksandr O , Arkhypova Valentyna M , Kasap Berna O , Akata Burcu , Dzyadevych Sergei V 
Published: March 2014

Abstract
A possibility of the creation of potentiometric biosensor by adsorption of enzyme urease on zeolite was investigated. Several variants of zeolites (nano beta, calcinated nano beta, silicalite, and nano L) were chosen for experiments. The surface of pH-sensitive field-effect transistors was modified with particles of zeolites, and then the enzyme was adsorbed. As a control, we used the method of enzyme immobilization in glutaraldehyde vapour (without zeolites). It was shown that all used zeolites can serve as adsorbents (with different effectiveness). The biosensors obtained by urease adsorption on zeolites were characterized by good analytical parameters (signal reproducibility, linear range, detection limit and the minimal drift factor of a baseline). In this work, it was shown that modification of the surface of pH-sensitive field-effect transistors with zeolites can improve some characteristics of biosensors.
Separated boundary value problems for second-order impulsive q-integro-difference equations
Authors: Thaiprayoon Chatthai , Tariboon Jessada , Ntouyas Sotiris K 
Published: March 2014

Abstract
This article studies the existence and uniqueness of solutions for a boundary value problem of nonlinear second-order impulsive

q
k

-integro-difference equations with separated boundary conditions. Several new results are obtained by applying a variety of fixed point theorems. Some examples are presented to illustrate the results.

MSC:26A33, 39A13, 34A37.
Tolerance of pentose utilising yeast to hydrogen peroxide-induced oxidative stress
Authors: Spencer Jennifer , Phister Trevor G , Smart Katherine A , Greetham Darren 
Published: March 2014

Abstract

Background
Bioethanol fermentations follow traditional beverage fermentations where the yeast is exposed to adverse conditions such as oxidative stress. Lignocellulosic bioethanol fermentations involve the conversion of pentose and hexose sugars into ethanol. Environmental stress conditions such as osmotic stress and ethanol stress may affect the fermentation performance; however, oxidative stress as a consequence of metabolic output can also occur. However, the effect of oxidative stress on yeast with pentose utilising capabilities has yet to be investigated.

Results
Assaying for the effect of hydrogen peroxide-induced oxidative stress on Candida, Pichia and Scheffersomyces spp. has demonstrated that these yeast tolerate hydrogen peroxide-induced oxidative stress in a manner consistent with that demonstrated by Saccharomyces cerevisiae. Pichia guillermondii appears to be more tolerant to hydrogen peroxide-induced oxidative stress when compared to Candida shehatae, Candida succiphila or Scheffersomyces stipitis.

Conclusions
Sensitivity to hydrogen peroxide-induced oxidative stress increased in the presence of minimal media; however, addition of amino acids and nucleobases was observed to increase tolerance. In particular adenine increased tolerance and methionine reduced tolerance to hydrogen peroxide-induced oxidative stress.
Blending mass self-communication with advertising in Facebook and LinkedIn: Challenges for social media and user empowerment
Authors: Heyman Rob , Pierson Jo 
Published: March 2014

Abstract
The commodification process on Facebook and LinkedIn limits the potential of mass self-communication on these SNS. This is especially noticeable with regard to personal identifiable information (PII) used in advertising. This article is an analysis of Facebook and LinkedIn through desk research and website analysis of their advertising products. We illustrate how the commodification of personal identifiable information influences user empowerment, defined as mass self-communication. We have found that users are not able to control production, selection and distribution of PII, when this information is used in advertising. The commodification of PII is now portraying and distributing user-generated content and PII differently. Economically interesting content is shown more prominently, but commercial messages are also invading UGC to become economically valuable.
Predicting, securing and shaping the future: Mechanisms of governance in online social environments
Authors: Humphreys Sal 
Published: March 2014

Abstract
In online environments, the issues of governance, privacy and security are in a state of emergence, with consensus on institutional frameworks and practices not yet settled. The dynamic relations between governments, corporations and citizens are being renegotiated through the algorithmic formations of data mining and through contract law in the form of End User Licence Agreements. To analyse how the current practices and discourses associated with the socio-technical assemblages of online social worlds work within the broader political economy this article considers discourses associated with risk and security (Dean 2010), practices and discourses associated with algorithms (Gillespie forthcoming 2014) and the new shape of ‘predictive surveillance’ in the form of panspectralism (Palmås 2011). The emerging patterns of governance through contractual law and algorithms are enabling the discursive construction of a differently balanced set of relations between citizens, governments and corporations. The overlapping interests of these stakeholders are considered, and the strong alliances between corporations and the security arms of governments are identified.
Technology design and power: Freedom and control in communication networks
Authors: Shepherd Tamara , Landry Normand 
Published: March 2014

Abstract
The design of technologies with particular sets of affordances for user action reflects and embeds particular sociopolitical values in the technological artefacts themselves. In relation to networked communication technologies like the Internet, design values of openness and decentralization accord with the hegemonic value of freedom as an inherently positive social and political concept. Yet freedom is also an elastic concept that contains the possibility for the freedom of powerful interests to exert controls – technological, state and legal – over the very networks designed to facilitate freedom. This article reviews how such controls are made manifest, with a particular focus on the role of technology design, in the areas of surveillance, censorship and intellectual property. It then concludes by addressing how such controls might be resisted using the affordances of open and decentralized networks. The interplay between freedom and control in communication networks is crucial for the construction of contemporary modes of citizenship, publics and participation.
The geopolitical vs. the network political: Internet designers and governance
Authors: Braman Sandra 
Published: March 2014

Abstract
With the recognition that communication networks in general and the Internet in particular are not only infrastructural but socio-technical in nature comes the responsibility to think such networks through from the perspective of how they influence – and/or are – forms of power and governance. The notion of citizenship is one that appears relative to both social and technical systems, and thus at their conjuncture, because it is the concept through which the rights and responsibilities of individuals relative to governance are refracted. It was in fact the case that citizenship was a concern for those responsible for technical design of the Internet as that history both unfolded through and is recorded in the technical document series known as the Internet Requests for Comments, or RFCs. This paper analyzes the two types of citizenship of concern from the perspective of Internet design – geopolitical (oriented around the state) and network political (oriented around the network) – and interactions between the two as they were discussed within and affected the Internet design process. These network-inspired ideas about citizenship in turn contribute to the ongoing discussion about the evolution of new forms of citizenship in today’s environment, including in particular those that are global and/or technological in nature.
Current perspectives and future challenges in feminism and media studies
Authors: Dorer Johanna , Hipfl Brigitte 
Published: March 2014

Abstract
This contribution gives an overview of the historical analysis, current assessment and future prospects of feminism. The challenges of future feminist media studies are presented in the context of the appeal by Nancy Fraser, who assumes that the fundamental claims of second-wave feminism are still of central relevance. These observations are based on the contributions that were compiled by Lisa McLaughlin and Cynthia Carter on the occasion of the tenth anniversary of the international journal ‘Feminist Media Studies’.
Reviews
Authors: Corredoira Loreto , Lobinger Katharina , Balestrini Mara 
Published: March 2014

Abstract
International Internet Law, Joanna Kulesza (2012) Translated by Magdalena Arent and Wojciech Wołoszyk, Oxford, UK: Routledge, 196 pp., ISBN-13: 9780415674683 (hbk), £80.
The Mediatization of Culture and Society, Hjarvard, Stig (2013) London: Routledge, 173 pp., ISBN: 978-0415692366, Eur 75,
Beyond Smart Cities. How Cities Network, Learn and Innovate, Campbell Tim (2013) London: Routledge, 236 pp., ISBN: 978-1849714266, Eur 45.
‘Think of me fondly’: Voice, body, affect and performance in Prince/Lloyd Webber’s The Phantom of the Opera
Authors: McKee Alison L. 
Published: March 2014

Abstract
This article argues that Lloyd Webber’s megamusical The Phantom of the Opera, and specifically Michael Crawford’s original performance of the title role in London, New York and Los Angeles, combined sound, voice, gesture and technology in a unique physical expression of desire that reinscribed, exceeded and even redefined spectacle at the level of both the visual and the aural realms (paradoxical as that may seem). This argument runs counter to existing arguments about the separation of scopophilia and audiophilia in the theatre and also departs from some of the arguments about the narrative in different forms which is often discussed as privileging sound and hearing over image and sight.
Anything Goes on an ocean liner: Musical comedy as a carnivalistic heterotopia
Authors: Burrows George 
Published: March 2014

Abstract
This article argues that the ocean-liner setting of the 1934 Broadway musical Anything Goes provides a rich place from which to explore how such seemingly frivolous musical comedy can otherwise be viewed as socially discursive and critical. It explores the way Anything Goes represents a typical product of the Great Depression and suggests its function in re-envisioning identities in the face of the apparent failure of the ‘American Dream’. The nature of the carnivalistic comedy offered in the shipboard narrative of Anything Goes further suggests that it offers an important salve for Depression-era anxiety. From this Bakhtinian perspective, Anything Goes is figured as a subversive space for the performance of social deviance of one sort or another. Bakhtin’s vision of carnival spaces suggests that musical comedy has an important function in social renewal but it also might be too utopian to articulate to ‘real’ society. However, Michel Foucault’s notion of heterotopias allows for a reconnection of Bakhtin’s utopianism with the ‘real’ world and thus serves to show that Anything Goes and, indeed, musical comedy more generally might be as vital a location as passenger ships for functional socio-critical discourse.
Introduction to the Bruce Kirle Memorial emerging scholars Debut Panel 2013: Celebrating and challenging inconsistency, authenticity and difference
Authors: Everett William A. 
Published: March 2014

Abstract
In 2007, the distinguished scholar of musical theatre Bruce Kirle died unexpectedly. In tribute to his contribution to this field of scholarship, the Music-Theatre-Dance focus group of the Association for Theatre in Higher Education (ATHE) established a competition for new scholars researching in the field. This is now the fifth season in which three prize-winning entries to this competition have been presented both as conference papers (at the 2013 ATHE Conference in Orlando), and as written articles in Studies in Musical Theatre. William A. Everett, respondent to the papers at the ATHE Conference, introduces them in this short introduction.
Muddy waters: The complexities of casting a musical about race
Authors: Accetta Valerie 
Published: March 2014

Abstract
In 2005, two high-school seniors from Glenelg Country Day School in Maryland were denied permission to perform the song ‘Muddy Water’ from the musical Big River on the C-SPAN television programme, Close Up (Close Up Foundation 2005). The broadcasting licence was not granted by the Rodgers and Hammerstein Organization because Jay Frisby, who played Huckleberry Finn, is African American, and Nick Lehan, a caucasian, played slave Jim. This article explores the event from numerous angles, detailing the media firestorm that followed. The author discusses the complexities of casting a musical about race and questions the terminology often used to describe casting practices. Are terms such as ‘colour-blind’ and ‘non-traditional casting’ accurate? More importantly, what ideology do these terms support?