Proteomic patterns of cultured breast cancer cells and epithelial mammary cells.

Breast cancer is one of the leading causes of death from cancer among women in western countries. The different types of breast cancer are grouped into invasive and noninvasive forms. Among the invasive types, ductal infiltrating carcinoma (DIC) is the most common and aggressive form. Using an in vitro model consisting of a DIC-derived cell line (8701-BC) and a nontumoral mammary epithelial cell line (HB2), we used the proteomics approach to search for homology and differences in protein expression patterns between tumoral and nontumoral phenotypes. Within an analysis window comprising 1,750 discernible spots we have currently catalogued 140 protein spots of potential interest. Fifty-eight of them were identified by gel matching with reference maps, immunodetection, or N-terminal microsequencing and classified into four functional groups. Twelve proteins were found differentially expressed in two cell lines: four were uniquely present in the neoplastic cell proteome and eight in epithelial cells. In addition, 53 proteins displayed different relative expression levels between the two cell lines, that is, 44 were more elevated in cancer cells and 9 in HB2 cells. Among proteins with greater relative abundance in cancer cells we identified glycolytic enzymes (or their isoforms), which may indicate that the known metabolic dysregulation in cancer can reflect oncogenic-related defects of glycolytic gene expression

NetMe 2.0: a web-based platform for extracting and modeling knowledge from biomedical literature as a labeled graph

Motivation: The rapid increase of bio-medical literature makes it harder and harder for scientists to keep pace with the discoveries on which they build their studies. Therefore, computational tools have become more widespread, among which network analysis plays a crucial role in several life-science contexts. Nevertheless, building correct and complete networks about some user-defined biomedical topics on top of the available literature is still challenging. Results: We introduce NetMe 2.0, a web-based platform that automatically extracts relevant biomedical entities and their relations from a set of input texts—i.e. in the form of full-text or abstract of PubMed Central’s papers, free texts, or PDFs uploaded by users—and models them as a BioMedical Knowledge Graph (BKG). NetMe 2.0 also implements an innovative Retrieval Augmented Generation module (Graph-RAG) that works on top of the relationships modeled by the BKG and allows the distilling of well-formed sentences that explain their content. The experimental results show that NetMe 2.0 can infer comprehensive and reliable biological networks with significant Precision–Recall metrics when compared to state-of-the-art approaches

NETME: on-the-fly knowledge network construction from biomedical literature

Background: The rapidly increasing biological literature is a key resource to automatically extract and gain knowledge concerning biological elements and their relations. Knowledge Networks are helpful tools in the context of biological knowledge discovery and modeling. Results: We introduce a novel system called NETME, which, starting from a set of full-texts obtained from PubMed, through an easy-to-use web interface, interactively extracts biological elements from ontological databases and then synthesizes a network inferring relations among such elements. The results clearly show that our tool is capable of inferring comprehensive and reliable biological networks

The racist bodily imaginary: the image of the body-in-pieces in (post)apartheid culture

This paper outlines a reoccurring motif within the racist imaginary of (post)apartheid culture: the black body-in-pieces. This disturbing visual idiom is approached from three conceptual perspectives. By linking ideas prevalent in Frantz Fanon’s description of colonial racism with psychoanalytic concepts such as Lacan’s notion of the corps morcelé, the paper offers, firstly, an account of the black body-in-pieces as fantasmatic preoccupation of the (post)apartheid imaginary. The role of such images is approached, secondly, through the lens of affect theory which eschews a representational ‘reading’ of such images in favour of attention to their asignifying intensities and the role they play in effectively constituting such bodies. Lastly, Judith Butler’s discussion of war photography and the conditions of grievability introduces an ethical dimension to the discussion and helps draw attention to the unsavory relations of enjoyment occasioned by such images

RNAdetector: a free user-friendly stand-alone and cloud-based system for RNA-Seq data analysis

Background: RNA-Seq is a well-established technology extensively used for transcriptome profiling, allowing the analysis of coding and non-coding RNA molecules. However, this technology produces a vast amount of data requiring sophisticated computational approaches for their analysis than other traditional technologies such as Real-Time PCR or microarrays, strongly discouraging non-expert users. For this reason, dozens of pipelines have been deployed for the analysis of RNA-Seq data. Although interesting, these present several limitations and their usage require a technical background, which may be uncommon in small research laboratories. Therefore, the application of these technologies in such contexts is still limited and causes a clear bottleneck in knowledge advancement. Results: Motivated by these considerations, we have developed RNAdetector, a new free cross-platform and user-friendly RNA-Seq data analysis software that can be used locally or in cloud environments through an easy-to-use Graphical User Interface allowing the analysis of coding and non-coding RNAs from RNA-Seq datasets of any sequenced biological species. Conclusions: RNAdetector is a new software that fills an essential gap between the needs of biomedical and research labs to process RNA-Seq data and their common lack of technical background in performing such analysis, which usually relies on outsourcing such steps to third party bioinformatics facilities or using expensive commercial software

Confronting the digital:Doing ethnography in modern organizational settings

Digital technologies pervade modern life. As a result, organizational ethnographers must contend with informants interacting in face-to-face and digitally mediated encounters (e.g., through email, Facebook Messenger, and Skype). This overlap of informants’ digital and physical interactions challenges ethnographers’ ability to demonstrate authenticity and multivocality in their accounts of contemporary organizing. Drawing on recent theorizing about the nature of digital artifacts and two cases of ethnographic fieldwork, we argue that digital artifacts afford ethnographers different modes of being co-present with research participants: digital as archive and digital as process. We offer guidelines to researchers on how to deploy these modes of co-presence in order to improve authenticity and multivocality in ethnographic studies of modern organizations. We also explore the implications for methodological concerns such as ethics, analytical choice, and reflexivity

Close encounters of a critical kind: a diffractive musing in/between new material feminism and object-oriented ontology

For a number of years, new material feminists have been developing new theoretical tools, new modes of conceptual analysis and new ethical frameworks. Object-oriented ontology, part of the speculative realism ‘movement’, has been engaged in something similar. Yet these endeavours have often taken place in ‘parallel universes’, despite sharing – or at least colliding around – a range of somewhat similar ontological and epistemological commitments. Composed as a diffractive musing encounter in which insights are read ‘through one another’ (Barad, 2007: 25) in order to ‘attend to … details and specificities of relations of difference and how they matter’ (Barad, 2007:71), the article brings Barad’s Meeting the Universe Halfway, already a ‘foundational’ text for new material feminism, into an encounter with a speculative realist text of the same ‘foundational’ status, Harman’s The Quadruple Object. The article develops a notion of diffractive musing as embodied, sensory struggle which instantiates intellectual generosity as a mode of critique. Following this, it puts diffractive musing to work theoretically via an encounter between object-oriented ontology and new material feminism. Keywords : new material feminism, speculative realism, diffraction, musing, critiqu

Computing the everyday: social media as data platforms

We conceive social media platforms as sociotechnical entities that variously shape user platform involvement and participation. Such shaping develops along three fundamental data operations that we subsume under the terms of encoding, aggregation, and computation. Encoding entails the engineering of user platform participation along narrow and standardized activity types (e.g., tagging, liking, sharing, following). This heavily scripted platform participation serves as the basis for the procurement of discrete and calculable data tokens that are possible to aggregate and, subsequently, compute in a variety of ways. We expose these operations by investigating a social media platform for shopping. We contribute to the current debate on social media and digital platforms by describing social media as posttransactional spaces that are predominantly concerned with charting and profiling the online predispositions, habits, and opinions of their user base. Such an orientation sets social media platforms apart from other forms of mediating online interaction. In social media, we claim, platform participation is driven toward an endless online conversation that delivers the data footprint through which a computed sociality is made the source of value creation and monetization

Bridging topological and functional information in protein interaction networks by short loops profiling

Protein-protein interaction networks (PPINs) have been employed to identify potential novel interconnections between proteins as well as crucial cellular functions. In this study we identify fundamental principles of PPIN topologies by analysing network motifs of short loops, which are small cyclic interactions of between 3 and 6 proteins. We compared 30 PPINs with corresponding randomised null models and examined the occurrence of common biological functions in loops extracted from a cross-validated high-confidence dataset of 622 human protein complexes. We demonstrate that loops are an intrinsic feature of PPINs and that specific cell functions are predominantly performed by loops of different lengths. Topologically, we find that loops are strongly related to the accuracy of PPINs and define a core of interactions with high resilience. The identification of this core and the analysis of loop composition are promising tools to assess PPIN quality and to uncover possible biases from experimental detection methods. More than 96% of loops share at least one biological function, with enrichment of cellular functions related to mRNA metabolic processing and the cell cycle. Our analyses suggest that these motifs can be used in the design of targeted experiments for functional phenotype detection.This research was supported by the Biotechnology and Biological Sciences Research Council (BB/H018409/1 to AP, ACCC and FF, and BB/J016284/1 to NSBT) and by the Leukaemia & Lymphoma Research (to NSBT and FF). SSC is funded by a Leukaemia & Lymphoma Research Gordon Piller PhD Studentship