Terminology for Medical Journalism: Terminological Resources, Neology, and the COVID-19 Syndemic

This article aims to investigate the terminological needs of journalists reporting medical news in the context of the current COVID-19 syndemic. It presents the work context – medical journalism – and the professional group selected – dubbed ‘occasional medical journalists’, a subset of medical journalists – and analyses their terminological needs. It further offers a critical description of a selection of terminological and terminographic resources currently available to the professional category at hand, highlighting room for improvement. Lastly, it briefly explores the interdependence between the professional group, the syndemic, and neology, and provides a sample ad hoc terminological entry conceived to facilitate the correct use of Coronavirus-related terminology in the press

Reconfiguring the Dead Body: Shapes of the After-life in Gunther Von Hagens and Seamus Heaney

This article focuses on the revisitation of the dead body as exemplified, theoretically, by Gunther von Hagens’ Body Worlds and, experientially and textually, by the bodies that emerged out of North-Western European bogs celebrated in Seamus Heaney’s bog poems sequence (1969, 1972, 1975). Von Hagens’ work, demiurge-like in nature, defamiliarizes the dead body by turning it into a self-confessed art object that defies the life-death dichotomy and begs for a third option. Bog bodies, on the other hand, are the fruit of peculiar microbiological conditions whereby the dead body is mummified and made available for retrieval, observation, study and, ultimately, exhibition – a visual-verbal art object. The article first lays out its theoretical framework by providing working definitions of both Gilles Deleuze’s devenir and remediation. It then questions the ontological status of the dead body as revisited by von Hagens, self-appointed demiurge, and the Bog, Northern-European laboratory. It further focuses on the layers of remediation that the defamiliarized dead body undergoes: from Body Worlds’ self-proclaimed status as pedagogic art to Heaney’s verses lingering on the giveness and materiality of bog bodies, the dead body is shown as defying the life-death dichotomy, constructing its unprecedented after-life

Science-related Populism and Social Actors in Martin Geddes’ Early Representations of COVID-19. A Case Study

This article focuses on five blogs written by British conspiracy theorist Martin Geddes, available on his personal website. The blogs were written from March to December 2020 and represent an early testimony of COVID-19 scepticism. The article aims to analyse Geddes’ conspirational counter-narrative of the coronavirus syndemic by focusing on four elements: the generic characteristics of the corpus, Geddes’ construal of ethos, his texts’ connection to the theoretical framework of science-related populism and, lastly, the representation of select social actors in the corpus and how such representation sustains Geddes’ conspirational arguments. These elements provide insight into the idiom of conspiracy theorists and their construction of counter-information and counter- knowledge

RNA-Sequence analysis of primary alveolar macrophages after in vitro infection with porcine reproductive and respiratory syndrome virus strains of differing virulence

Porcine reproductive and respiratory syndrome virus (PRRSV) mainly infects porcine alveolar macrophages (PAMs), resulting in porcine reproductive and respiratory syndrome (PRRS) in pigs. Most of the transcriptomic studies on PAMs infected with PRRSV conducted thus far have made use of microarray technology. Here, we investigated the transcriptome of PAMs in vitro at 12 h post-infection with two European PRRSV strains characterized by low (Lelystad, LV) and high (Lena) virulence through RNA-Seq. The expression levels of genes, isoforms, alternative transcription start sites (TSS) and differential promoter usage revealed a complex pattern of transcriptional and post-transcriptional gene regulation upon infection with the two strains. Gene ontology analysis confirmed that infection of PAMs with both the Lena and LV strains affected signaling pathways directly linked to the innate immune response, including interferon regulatory factors (IRF), RIG1-like receptors, TLRs and PKR pathways. The results confirmed that interferon signaling is crucial for transcriptional regulation during PAM infection. IFN-beta 1 and IFN-alpha omega, but not IFN-alpha, were up-regulated following infection with either the LV or Lena strain. The down-regulation of canonical pathways, such as the interplay between the innate and adaptive immune responses, cell death and TLR3/TLR7 signaling, was observed for both strains, but Lena triggered a stronger down-regulation than LV. This analysis contributes to a better understanding of the interactions between PRRSV and PAMs and outlines the differences in the responses of PAMs to strains with different levels of virulence, which may lead to the development of new PRRSV control strategies

Genome-wide identification of coding and non-coding conserved sequence tags in human and mouse genomes

<p>Abstract</p> <p>Background</p> <p>The accurate detection of genes and the identification of functional regions is still an open issue in the annotation of genomic sequences. This problem affects new genomes but also those of very well studied organisms such as human and mouse where, despite the great efforts, the inventory of genes and regulatory regions is far from complete. Comparative genomics is an effective approach to address this problem. Unfortunately it is limited by the computational requirements needed to perform genome-wide comparisons and by the problem of discriminating between conserved coding and non-coding sequences. This discrimination is often based (thus dependent) on the availability of annotated proteins.</p> <p>Results</p> <p>In this paper we present the results of a comprehensive comparison of human and mouse genomes performed with a new high throughput grid-based system which allows the rapid detection of conserved sequences and accurate assessment of their coding potential. By detecting clusters of coding conserved sequences the system is also suitable to accurately identify potential gene loci.</p> <p>Following this analysis we created a collection of human-mouse conserved sequence tags and carefully compared our results to reliable annotations in order to benchmark the reliability of our classifications. Strikingly we were able to detect several potential gene loci supported by EST sequences but not corresponding to as yet annotated genes.</p> <p>Conclusion</p> <p>Here we present a new system which allows comprehensive comparison of genomes to detect conserved coding and non-coding sequences and the identification of potential gene loci. Our system does not require the availability of any annotated sequence thus is suitable for the analysis of new or poorly annotated genomes.</p

ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterization

Alternative splicing (AS) is now emerging as a major mechanism contributing to the expansion of the transcriptome and proteome complexity of multicellular organisms. The fact that a single gene locus may give rise to multiple mRNAs and protein isoforms, showing both major and subtle structural variations, is an exceptionally versatile tool in the optimization of the coding capacity of the eukaryotic genome. The huge and continuously increasing number of genome and transcript sequences provides an essential information source for the computational detection of genes AS pattern. However, much of this information is not optimally or comprehensively used in gene annotation by current genome annotation pipelines. We present here a web resource implementing the ASPIC algorithm which we developed previously for the investigation of AS of user submitted genes, based on comparative analysis of available transcript and genome data from a variety of species. The ASPIC web resource provides graphical and tabular views of the splicing patterns of all full-length mRNA isoforms compatible with the detected splice sites of genes under investigation as well as relevant structural and functional annotation. The ASPIC web resource—available at —is dynamically interconnected with the Ensembl and Unigene databases and also implements an upload facility

Identification of tumor-associated cassette exons in human cancer through EST-based computational prediction and experimental validation

Background: Many evidences report that alternative splicing, the mechanism which produces mRNAs and proteins with different structures and functions from the same gene, is altered in cancer cells. Thus, the identification and characterization of cancer-specific splice variants may give large impulse to the discovery of novel diagnostic and prognostic tumour biomarkers, as well as of new targets for more selective and effective therapies. Results: We present here a genome-wide analysis of the alternative splicing pattern of human genes through a computational analysis of normal and cancer-specific ESTs from seventeen anatomical groups, using data available in AspicDB, a database resource for the analysis of alternative splicing in human. By using a statistical methodology, normal and cancer-specific genes, splice sites and cassette exons were predicted in silico. The condition association of some of the novel normal/tumoral cassette exons was experimentally verified by RT-qPCR assays in the same anatomical system where they were predicted. Remarkably, the presence in vivo of the predicted alternative transcripts, specific for the nervous system, was confirmed in patients affected by glioblastoma. Conclusion: This study presents a novel computational methodology for the identification of tumor-associated transcript variants to be used as cancer molecular biomarkers, provides its experimental validation, and reports specific biomarkers for glioblastoma

Factors influencing choice of chemotherapy in metastatic colorectal cancer (mCRC)

Management of metastatic colorectal cancer requires a multimodal approach and must be performed by an experienced, multidisciplinary expert team. The optimal choice of the individual treatment modality, according to disease localization and extent, tumor biology, and patient clinical characteristics, will be one that can maintain quality of life and long-term survival, and even cure selected patients. This review is an overview of the different therapeutic approaches available in metastatic colorectal cancer, for the purpose of defining personalized therapeutic algorithms according to tumor biology and patient clinical features

Effect of Integration of Linseed and Vitamin E in Charolaise × Podolica Bulls’ Diet on Fatty Acids Profile, Beef Color and Lipid Stability

Dietary supplementation with oilseeds improves the fatty acid profiles of meat, but results are often inconsistent. This study aimed to assess the effects of dietary linseed and vitamin E supplementation on fatty acid profile, cholesterol content and color stability of beef samples. Dorsal subcutaneous fat samples were subjected to lipid stability assessment. Eighteen young bulls (385 ± 15 kg BW, age 8–9 months) were allocated into three homogeneous groups, each receiving ad libitum wheat straw and concentrate only (CON = 5.5 kg/day), concentrate with linseed (LIN = 80 g/kg, i.e., 440 g/head/day), and concentrate with linseed plus vitamin E (L + E = 80 g/kg, i.e., 440 g/head/day + 2500 IU/head/day of Vitamin E). Group L+E showed significantly lower cholesterol content, lower n-6/n-3 ratio and a higher PUFA percentage compared to the CON group. Meat color was affected by feeding LIN with a decrease in a*, b*, and C* compared to the CON group. The experimental diets increased H◦ values compared to the CON group. A positive effect of vitamin E in protecting lipids of dorsal subcutaneous depots from oxidation was detected in group L+E compared to group LIN. The supplementation with extruded linseeds in the diet had positive effects on the nutritional profile of the meat. When vitamin E was included, linseed did not alter the color of meat, and the lipid stability of the subcutaneous fat improved

Pig immune response to general stimulus and to porcine reproductive and respiratory syndrome virus infection: a meta-analysis approach

BACKGROUND: The availability of gene expression data that corresponds to pig immune response challenges provides compelling material for the understanding of the host immune system. Meta-analysis offers the opportunity to confirm and expand our knowledge by combining and studying at one time a vast set of independent studies creating large datasets with increased statistical power. In this study, we performed two meta-analyses of porcine transcriptomic data: i) scrutinized the global immune response to different challenges, and ii) determined the specific response to Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) infection. To gain an in-depth knowledge of the pig response to PRRSV infection, we used an original approach comparing and eliminating the common genes from both meta-analyses in order to identify genes and pathways specifically involved in the PRRSV immune response. The software Pointillist was used to cope with the highly disparate data, circumventing the biases generated by the specific responses linked to single studies. Next, we used the Ingenuity Pathways Analysis (IPA) software to survey the canonical pathways, biological functions and transcription factors found to be significantly involved in the pig immune response. We used 779 chips corresponding to 29 datasets for the pig global immune response and 279 chips obtained from 6 datasets for the pig response to PRRSV infection, respectively. RESULTS: The pig global immune response analysis showed interconnected canonical pathways involved in the regulation of translation and mitochondrial energy metabolism. Biological functions revealed in this meta-analysis were centred around translation regulation, which included protein synthesis, RNA-post transcriptional gene expression and cellular growth and proliferation. Furthermore, the oxidative phosphorylation and mitochondria dysfunctions, associated with stress signalling, were highly regulated. Transcription factors such as MYCN, MYC and NFE2L2 were found in this analysis to be potentially involved in the regulation of the immune response. The host specific response to PRRSV infection engendered the activation of well-defined canonical pathways in response to pathogen challenge such as TREM1, toll-like receptor and hyper-cytokinemia/ hyper-chemokinemia signalling. Furthermore, this analysis brought forth the central role of the crosstalk between innate and adaptive immune response and the regulation of anti-inflammatory response. The most significant transcription factor potentially involved in this analysis was HMGB1, which is required for the innate recognition of viral nucleic acids. Other transcription factors like interferon regulatory factors IRF1, IRF3, IRF5 and IRF8 were also involved in the pig specific response to PRRSV infection. CONCLUSIONS: This work reveals key genes, canonical pathways and biological functions involved in the pig global immune response to diverse challenges, including PRRSV infection. The powerful statistical approach led us to consolidate previous findings as well as to gain new insights into the pig immune response either to common stimuli or specifically to PRRSV infection