Archiving “sensitive” social media data: ‘In Her Shoes’, a case study

Social media play an increasingly significant role in activist and social movements around the globe. Archiving social media is a relatively new phenomenon and an area which needs greater clarity, understanding and uniformity. When it comes to archiving and cataloguing sensitive social media collections, such as personal abortion stories, the process is even more ambiguous. The campaign to repeal the Eighth Amendment (a constitutional ban on abortion) in Ireland saw many such stories shared through online media, particularly in the lead-up to the 2018 referendum. Using the ‘In Her Shoes: Women of the Eighth’ Facebook dataset as a case study, this article will explore the ethical issues of archiving sensitive data from Facebook. It will describe challenges to archiving social media data, incorporating issues such as copyright and user consent to archiving. Many stories in the collection covered sensitive issues such as intimate partner violence, suicide because of unplanned pregnancy and attempts to bring on miscarriage by harmful and dangerous means. We outline some of the actions we undertook to address these challenges, including: developing a Stakeholder Advisory Forum, publishing an Ethical Protocol, developing a self-care protocol for researchers, and establishing a Notice and Action Policy. We suggest these actions will contribute to a best-practice framework for archiving sensitive social media data

20 years on: The legacy of Daksha Emson for perinatal psychiatry

The tragedy of Daksha’s death illustrates both the importance of perinatal mental health and the stigma associated with doctors seeking help. With this letter, we express our hope that the lasting legacy of her and others’ tragic stories lies in the continuing improvement and worldwide expansion of perinatal psychiatric services and training so that those in greatest need receive the best care possible wherever — and whoever — they are

Species-wide Whole Genome Sequencing Reveals Historical Global Spread And Recent Local Persistence In Shigella Flexneri

Shigella flexneri is the most common cause of bacterial dysentery in low-income countries. Despite this, S. flexneri remains largely unexplored from a genomic standpoint and is still described using a vocabulary based on serotyping reactions developed over half-a-century ago. Here we combine whole genome sequencing with geographical and temporal data to examine the natural history of the species. Our analysis subdivides S. flexneri into seven phylogenetic groups (PGs); each containing two-or-more serotypes and characterised by distinct virulence gene complement and geographic range. Within the S. flexneri PGs we identify geographically restricted sub-lineages that appear to have persistently colonised regions for many decades to over 100 years. Although we found abundant evidence of antimicrobial resistance (AMR) determinant acquisition, our dataset shows no evidence of subsequent intercontinental spread of antimicrobial resistant strains. The pattern of colonisation and AMR gene acquisition suggest that S. flexneri has a distinct life-cycle involving local persistence. DOI: 10.7554/eLife.07335.0014Wellcome Trust [098051]Wellcome Trust/NISCHR ISSF project at Cardiff UniversityMRC [MR/L015080/1]Cardiff University - Cardiff University Research Infrastructure Fund)Institut PasteurInstitut de Veille SanitaireFrench Government 'Investissement d'Avenir' program (Integrative Biology of Emerging Infectious Diseases Laboratory of Excellence) [ANR-10-LABX-62-IBEID

An assessment of population structure in eight breeds of cattle using a whole genome SNP panel

<p>Abstract</p> <p>Background</p> <p>Analyses of population structure and breed diversity have provided insight into the origin and evolution of cattle. Previously, these studies have used a low density of microsatellite markers, however, with the large number of single nucleotide polymorphism markers that are now available, it is possible to perform genome wide population genetic analyses in cattle. In this study, we used a high-density panel of SNP markers to examine population structure and diversity among eight cattle breeds sampled from <it>Bos indicus </it>and <it>Bos taurus</it>.</p> <p>Results</p> <p>Two thousand six hundred and forty one single nucleotide polymorphisms (SNPs) spanning all of the bovine autosomal genome were genotyped in Angus, Brahman, Charolais, Dutch Black and White Dairy, Holstein, Japanese Black, Limousin and Nelore cattle. Population structure was examined using the linkage model in the program STRUCTURE and Fst estimates were used to construct a neighbor-joining tree to represent the phylogenetic relationship among these breeds.</p> <p>Conclusion</p> <p>The whole-genome SNP panel identified several levels of population substructure in the set of examined cattle breeds. The greatest level of genetic differentiation was detected between the <it>Bos taurus </it>and <it>Bos indicus </it>breeds. When the <it>Bos indicus </it>breeds were excluded from the analysis, genetic differences among beef versus dairy and European versus Asian breeds were detected among the <it>Bos taurus </it>breeds. Exploration of the number of SNP loci required to differentiate between breeds showed that for 100 SNP loci, individuals could only be correctly clustered into breeds 50% of the time, thus a large number of SNP markers are required to replace the 30 microsatellite markers that are currently commonly used in genetic diversity studies.</p

Angiotensin-(1-7) and angiotensin-(1-9): function in cardiac and vascular remodeling

The renin angiotensin system (RAS) is integral to cardiovascular physiology, however, dysregulation of this system largely contributes to the pathophysiology of cardiovascular disease (CVD). It is well established that angiotensin II (Ang II), the main effector of the RAS, engages the angiotensin type 1 receptor and promotes cell growth, proliferation, migration and oxidative stress, all processes which contribute to remodeling of the heart and vasculature, ultimately leading to the development and progression of various CVDs including heart failure and atherosclerosis. The counter-regulatory axis of the RAS, which is centered on the actions of angiotensin converting enzyme 2 (ACE2) and the resultant production of angiotensin-(1-7) (Ang-(1-7) from Ang II, antagonizes the actions of Ang II via the receptor Mas, thereby providing a protective role in CVD. More recently, another ACE2 metabolite, Ang-(1-9), has been reported to be a biologically active peptide within the counter-regulatory axis of the RAS. This review will discuss the role of the counter-regulatory RAS peptides, Ang-(1-7) and Ang-(1-9) in the cardiovascular system, with a focus on their effects in remodeling of the heart and vasculature

Whole genome linkage disequilibrium maps in cattle

<p>Abstract</p> <p>Background</p> <p>Bovine whole genome linkage disequilibrium maps were constructed for eight breeds of cattle. These data provide fundamental information concerning bovine genome organization which will allow the design of studies to associate genetic variation with economically important traits and also provides background information concerning the extent of long range linkage disequilibrium in cattle.</p> <p>Results</p> <p>Linkage disequilibrium was assessed using r²among all pairs of syntenic markers within eight breeds of cattle from the <it>Bos taurus </it>and <it>Bos indicus </it>subspecies. <it>Bos taurus </it>breeds included Angus, Charolais, Dutch Black and White Dairy, Holstein, Japanese Black and Limousin while <it>Bos indicus </it>breeds included Brahman and Nelore. Approximately 2670 markers spanning the entire bovine autosomal genome were used to estimate pairwise r²values. We found that the extent of linkage disequilibrium is no more than 0.5 Mb in these eight breeds of cattle.</p> <p>Conclusion</p> <p>Linkage disequilibrium in cattle has previously been reported to extend several tens of centimorgans. Our results, based on a much larger sample of marker loci and across eight breeds of cattle indicate that in cattle linkage disequilibrium persists over much more limited distances. Our findings suggest that 30,000–50,000 loci will be needed to conduct whole genome association studies in cattle.</p

Non-toxic Salvia sclareoides Brot. extracts as a source of functional food ingredients: Phenolic profile, antioxidant activity and prion binding properties

Estudo de produção agronómica de espécis da salvia com vista à avaliação dos seus constituintes para o potencial controlo da doença de AlzaimerSalvia sclareoides is an aromatic herb native to Portugal, of which phenolic content (Folin–Ciocalteau method), chemical profile (HPLC/DAD), antioxidant activity (DPPH, β-carotene/linoleic acid assays), acute toxicity (MTT method, adapted for non-adherent cells), genotoxicity (short-term chromosomal aberration assay) and prion binding properties were evaluated in the acetone, water, ethanol, methanol and n-butanol extracts. The latter presented the highest phenolic content and antioxidant activity (DPPH assay), and was the single one with the flavonoids (+)-catechin, kaempferol O-glucoside and quercetin. Vanillic acid was the major component of all extracts but gallic, gentisic, caffeic, syringic, coumaric and ferulic acids were also found in some extracts. Only the n-butanol extract had components binding to the cellular form of human prion protein detected by NMR which showed specificity for two regions of the folded domain and for the unstructured N-terminal region. Extracts were not cytotoxic nor genotoxic, reinforcing the potential of S. sclareoides for nutraceutical purposes.Este trabalho é financiado por Fundos FEDER através do Programa Operacional Fatores de Competitividade – COMPETE e por Fundos Nacionais através da FCT – Fundação para a Ciência e a Tecnologia no âmbito do projeto «Refª do Projecto

Species-wide whole genome sequencing reveals historical global spread and recent local persistence in Shigella flexneri.

Shigella flexneri is the most common cause of bacterial dysentery in low-income countries. Despite this, S. flexneri remains largely unexplored from a genomic standpoint and is still described using a vocabulary based on serotyping reactions developed over half-a-century ago. Here we combine whole genome sequencing with geographical and temporal data to examine the natural history of the species. Our analysis subdivides S. flexneri into seven phylogenetic groups (PGs); each containing two-or-more serotypes and characterised by distinct virulence gene complement and geographic range. Within the S. flexneri PGs we identify geographically restricted sub-lineages that appear to have persistently colonised regions for many decades to over 100 years. Although we found abundant evidence of antimicrobial resistance (AMR) determinant acquisition, our dataset shows no evidence of subsequent intercontinental spread of antimicrobial resistant strains. The pattern of colonisation and AMR gene acquisition suggest that S. flexneri has a distinct life-cycle involving local persistence

Development and validation of a comprehensive genomic diagnostic tool for myeloid malignancies.

The diagnosis of hematologic malignancies relies on multidisciplinary workflows involving morphology, flow cytometry, cytogenetic, and molecular genetic analyses. Advances in cancer genomics have identified numerous recurrent mutations with clear prognostic and/or therapeutic significance to different cancers. In myeloid malignancies, there is a clinical imperative to test for such mutations in mainstream diagnosis; however, progress toward this has been slow and piecemeal. Here we describe Karyogene, an integrated targeted resequencing/analytical platform that detects nucleotide substitutions, insertions/deletions, chromosomal translocations, copy number abnormalities, and zygosity changes in a single assay. We validate the approach against 62 acute myeloid leukemia, 50 myelodysplastic syndrome, and 40 blood DNA samples from individuals without evidence of clonal blood disorders. We demonstrate robust detection of sequence changes in 49 genes, including difficult-to-detect mutations such as FLT3 internal-tandem and mixed-lineage leukemia (MLL) partial-tandem duplications, and clinically significant chromosomal rearrangements including MLL translocations to known and unknown partners, identifying the novel fusion gene MLL-DIAPH2 in the process. Additionally, we identify most significant chromosomal gains and losses, and several copy neutral loss-of-heterozygosity mutations at a genome-wide level, including previously unreported changes such as homozygosity for DNMT3A R882 mutations. Karyogene represents a dependable genomic diagnosis platform for translational research and for the clinical management of myeloid malignancies, which can be readily adapted for use in other cancers