Genome-wide profiling of uncapped mRNA

Gene transcripts are under extensive posttranscriptional regulation, including the regulation of their stability. A major route for mRNA degradation produces uncapped mRNAs, which can be generated by decapping enzymes, endonucleases, and small RNAs. Profiling uncapped mRNA molecules is important for the understanding of the transcriptome, whose composition is determined by a balance between mRNA synthesis and degradation. In this chapter, we describe a method to profile these uncapped mRNAs at the genome scale

Refractive index in holographic superconductors

With the probe limit, we investigate the behavior of the electric permittivity and effective magnetic permeability and related optical properties in the s-wave holographic superconductors. In particular, our result shows that unlike the strong coupled systems which admit a gravity dual of charged black holes in the bulk, the electric permittivity and effective magnetic permeability are unable to conspire to bring about the negative Depine-Lakhtakia index at low frequencies, which implies that the negative phase velocity does not appear in the holographic superconductors under such a situation.Comment: JHEP style, 1+15 pages, 11 figures, version to appear in JHE

Impact of the Mk VI SkinSuit on skin microbiota of terrestrial volunteers and an International Space Station-bound astronaut

Microgravity induces physiological deconditioning due to the absence of gravity loading, resulting in bone mineral density loss, atrophy of lower limb skeletal and postural muscles, and lengthening of the spine. SkinSuit is a lightweight compression suit designed to provide head-to-foot (axial) loading to counteract spinal elongation during spaceflight. As synthetic garments may impact negatively on the skin microbiome, we used 16S ribosomal RNA (rRNA) gene amplicon procedures to define bacterial skin communities at sebaceous and moist body sites of five healthy male volunteers undergoing SkinSuit evaluation. Each volunteer displayed a diverse, distinct bacterial population at each skin site. Short (8 h) periods of dry hyper-buoyancy flotation wearing either gym kit or SkinSuit elicited changes in the composition of the skin microbiota at the genus level but had little or no impact on community structure at the phylum level or the richness and diversity of the bacterial population. We also determined the composition of the skin microbiota of an astronaut during pre-flight training, during an 8-day visit to the International Space Station involving two 6–7 h periods of SkinSuit wear, and for 1 month after return. Changes in composition of bacterial skin communities at five body sites were strongly linked to changes in geographical location. A distinct ISS bacterial microbiota signature was found which reversed to a pre-flight profile on return. No changes in microbiome complexity or diversity were noted, with little evidence for colonisation by potentially pathogenic bacteria; we conclude that short periods of SkinSuit wear induce changes to the composition of the skin microbiota but these are unlikely to compromise the healthy skin microbiome

Holographic Superconductors from Einstein-Maxwell-Dilaton Gravity

We construct holographic superconductors from Einstein-Maxwell-dilaton gravity in 3+1 dimensions with two adjustable couplings $\alpha$ and the charge $q$ carried by the scalar field. For the values of $\alpha$ and $q$ we consider, there is always a critical temperature at which a second order phase transition occurs between a hairy black hole and the AdS RN black hole in the canonical ensemble, which can be identified with the superconducting phase transition of the dual field theory. We calculate the electric conductivity of the dual superconductor and find that for the values of $\alpha$ and $q$ where $\alpha/q$ is small the dual superconductor has similar properties to the minimal model, while for the values of $\alpha$ and $q$ where $\alpha/q$ is large enough, the electric conductivity of the dual superconductor exhibits novel properties at low frequencies where it shows a "Drude Peak" in the real part of the conductivity.Comment: 25 pages, 13 figures; v2, typos corrected; v3, refs added, to appear in JHE

Developing countries and neglected diseases: challenges and perspectives

It is now commonly admitted that the so-called (most) neglected tropical diseases have been given little attention. According to World Health Organization, neglected diseases are hidden diseases as they affect almost exclusively extremely poor populations living in remote areas beyond the reach of health service. The European Parliament recognised that, to our shame, Neglected Diseases have not received the attention they deserve from EU actions. In the Millennium Development Goals they were given very little attention and mentioned just as other disease. Investing in drugs for these diseases is thought to be not marketable or profitable. However, despite their low mortality, neglected diseases are causing severe and permanent disabilities and deformities affecting approximately 1 billion people in the world, yielding more than 20 millions of Disability Adjusted Life Years (56.6 million according to Lancet's revised estimates) and important socio-economic losses. Urgent pragmatic and efficient measures are needed both at international and national levels

Are chimpanzees really so poor at understanding imperative pointing? Some new data and an alternative view of canine and ape social cognition

There is considerable interest in comparative research on different species’ abilities to respond to human communicative cues such as gaze and pointing. It has been reported that some canines perform significantly better than monkeys and apes on tasks requiring the comprehension of either declarative or imperative pointing and these differences have been attributed to domestication in dogs. Here we tested a sample of chimpanzees on a task requiring comprehension of an imperative request and show that, though there are considerable individual differences, the performance by the apes rival those reported in pet dogs. We suggest that small differences in methodology can have a pronounced influence on performance on these types of tasks. We further suggest that basic differences in subject sampling, subject recruitment and rearing experiences have resulted in a skewed representation of canine abilities compared to those of monkeys and apes

Compliance with pathology testing guidelines in Australian general practice: Protocol for a secondary analysis of electronic health record data

© 2018 Author(s). Introduction In Australia, general practitioners usually are the first point of contact for patients with non-urgent medical conditions. Appropriate and efficient utilisation of pathology tests by general practitioners forms a key part of diagnosis and monitoring. However overutilisationand underutilisation of pathology tests have been reported across several tests and conditions, despite evidence-based guidelines outlining best practice in pathology testing. There are a limited number of studies evaluating the impact of these guidelines on pathology testing in general practice. The aim of our quantitative observational study is to define how pathology tests are used in general practice and investigate how test ordering practices align with evidence-based pathology guidelines. Methods and analysis Access to non-identifiable patient data will be obtained through electronic health records from general practices across three primary health networks in Victoria, Australia. Numbers and characteristics of patients, general practices, encounters, pathology tests and problems managed over time will be described. Overall rates of encounters and tests, alongside more detailed investigation between subcategories (encounter year, patient's age, gender, and location and general practice size), will also be undertaken. To evaluate how general practitioner test ordering coincides with evidence-based guidelines, five key candidate indicators will be investigated: Full blood counts for patients on clozapine medication; international normalised ratio measurements for patients on warfarin medication; glycated haemoglobin testing for monitoring patients with diabetes; vitamin D testing; and thyroid function testing. Ethics and dissemination Ethics clearance to collect data from general practice facilities has been obtained by the data provider from the RACGP National Research and Evaluation Ethics Committee (NREEC 17-008). Approval for the research group to use these data has been obtained from Macquarie University (5201700872). This study is funded by the Australian Government Department of Health Quality Use of Pathology Program (Agreement ID: 4-2QFVW4M). Findings will be reported to the Department of Health and disseminated in peer-reviewed academic journals and presentations (national and international conferences, industry forums)

IL-4-secreting CD4+ T cells are crucial to the development of CD8+ T-cell responses against malaria liver stages.

CD4+ T cells are crucial to the development of CD8+ T cell responses against hepatocytes infected with malaria parasites. In the absence of CD4+ T cells, CD8+ T cells initiate a seemingly normal differentiation and proliferation during the first few days after immunization. However, this response fails to develop further and is reduced by more than 90%, compared to that observed in the presence of CD4+ T cells. We report here that interleukin-4 (IL-4) secreted by CD4+ T cells is essential to the full development of this CD8+ T cell response. This is the first demonstration that IL-4 is a mediator of CD4/CD8 cross-talk leading to the development of immunity against an infectious pathogen

Noncommutative Vortices and Instantons from Generalized Bose Operators

Generalized Bose operators correspond to reducible representations of the harmonic oscillator algebra. We demonstrate their relevance in the construction of topologically non-trivial solutions in noncommutative gauge theories, focusing our attention to flux tubes, vortices, and instantons. Our method provides a simple new relation between the topological charge and the number of times the basic irreducible representation occurs in the reducible representation underlying the generalized Bose operator. When used in conjunction with the noncommutative ADHM construction, we find that these new instantons are in general not unitarily equivalent to the ones currently known in literature.Comment: 25 page

Towards strange metallic holography

We initiate a holographic model building approach to `strange metallic' phenomenology. Our model couples a neutral Lifshitz-invariant quantum critical theory, dual to a bulk gravitational background, to a finite density of gapped probe charge carriers, dually described by D-branes. In the physical regime of temperature much lower than the charge density and gap, we exhibit anomalous scalings of the temperature and frequency dependent conductivity. Choosing the dynamical critical exponent $z$ appropriately we can match the non-Fermi liquid scalings, such as linear resistivity, observed in strange metal regimes. As part of our investigation we outline three distinct string theory realizations of Lifshitz geometries: from F theory, from polarised branes, and from a gravitating charged Fermi gas. We also identify general features of renormalisation group flow in Lifshitz theories, such as the appearance of relevant charge-charge interactions when $z \geq 2$. We outline a program to extend this model building approach to other anomalous observables of interest such as the Hall conductivity.Comment: 71 pages, 8 figure