Virtual libraries of tissue and clinical samples: potential role of a 3-D microscope.

Our international innovative teaching group from different European Universities (De Montfort University, DMU, UK; and the Spanish University of Alcalá, University Miguel Hernández and University of San Pablo CEU), in conjunction with practicing biomedical scientists in the National Health Service (UK) and biomedical researchers, are developing two complete e-learning packages for teaching and learning medical parasitology, named DMU e-Parasitology (accessible at: http://parasitology.dmu.ac.uk), and biology and chemistry, named DMU e-Biology (accessible at: http://parasitology.dmu.ac.uk/ebiology/index.htm), respectively. Both packages will include a virtual microscope with a complete library of digitised tissue images, clinical slides and cell culture slides/mini-videos for enhancing the teaching and learning of a myriad of techniques applicable to health science undergraduate and postgraduate students. Thus, these packages include detecting human parasites, by becoming familiar with their infective structures and/or organs (e.g. eggs, cysts) and/or explore pathogenic tissues stained with traditional (e.g. haematoxylin & eosin) or more modern (e.g. immunohistochemistry) techniques. The Virtual Microscope (VM) module in the DMU e-Parasitology package is almost completed (accessible at: http://parasitology.dmu.ac.uk/learn/microscope.htm) and contains a section for the three major groups of human-pathogenic parasites (Peña-Fernández et al., 2018) [1]. Digitised slides are provided with the functionality of a microscope by using the gadget Zoomify®, and we consider that they can enhance learning, as previous studies reported in the literature have reported similar sensitivity and specificity rates for identification of parasites for both digitised and real slides. The DMU e-Biology’s VM, currently in development, will provide healthy and pathological tissue samples from a range of mammalian tissues and organs. This communication will provide a description of both virtual libraries and the process of developing them. In conjunction, we will use a three-dimensional (3D) super-resolution microscopy, 3D Cell Explorer (Nanolive, Lausanne, Switzerland), to incorporate potential 3D microscopic photographs/short videos of cells to provide students with information about the spatial arrangement and morphologies of cells that are essential for life

Non-perturbative renormalisation and running of BSM four-quark operators in Nf=2 QCD

We perform a non-perturbative study of the scale-dependent renormalisation factors of a complete set of dimension-six four-fermion operators without power subtractions. The renormalisation-group (RG) running is determined in the continuum limit for a specific Schrödinger Functional (SF) renormalisation scheme in the framework of lattice QCD with two dynamical flavours (Nf= 2). The theory is regularised on a lattice with a plaquette Wilson action and O(a)-improved Wilson fermions. For one of these operators, the computation had been performed in Dimopoulos et al. (JHEP 0805, 065 (2008). arXiv:0712.2429); the present work completes the study for the rest of the operator basis, on the same simulations (configuration ensembles). The related weak matrix elements arise in several operator product expansions; in Δ F= 2 transitions they contain the QCD long-distance effects, including contributions from beyond-Standard Model (BSM) processes. Some of these operators mix under renormalisation and their RG-running is governed by anomalous dimension matrices. In Papinutto et al. (Eur Phys J C 77(6), 376 (2017). arXiv:1612.06461) the RG formalism for the operator basis has been worked out in full generality and the anomalous dimension matrix has been calculated in NLO perturbation theory. Here the discussion is extended to the matrix step-scaling functions, which are used in finite-size recursive techniques. We rely on these matrix-SSFs to obtain non-perturbative estimates of the operator anomalous dimensions for scales ranging from O(Λ QCD) to O(MW)

Manejo florestal comunitário madeireiro na região Transamazônica.

bitstream/item/38633/1/ManejFlorestalcomunitario.pdfCartilha

Analysis of the potential of sustainable forest-based bioenergy for climate change mitigation

Current climate mitigation policies are likely to become a strong driver of increased demand for renewable energy sources and particularly for bioenergy. Therefore, it is becoming more and more important to assess the potential amount of biomass that will be available for future energy production and the costs, in terms of greenhouse gas (GHG) emissions, connected to extraction of these potentials. The estimate of emissions produced by different bioenergy sources is important for evaluating the advantages of biomass-based energy compared to fossil fuel use. This allows promotion of energy sources that are the most advantageous for climate mitigation

PileLineGUI: a desktop environment for handling genome position files in next-generation sequencing studies

Next-generation sequencing (NGS) technologies are making sequence data available on an unprecedented scale. In this context, new catalogs of Single Nucleotide Polymorphism and mutations generated by resequencing studies are usually stored in genome position files (e.g. Variant Call Format, SAMTools pileup, BED, GFF) comprising of large lists of genomic positions, which are difficult to handle by researchers. Here, we present PileLineGUI, a novel desktop application primarily designed for manipulating, browsing and analysing genome position files (GPF), with specific support to somatic mutation finding studies. The developed tool also integrates a new genome browser module specially designed for inspecting GPFs. PileLineGUI is free, multiplatform and designed to be intuitively used by biomedical researchers. PileLineGUI is available at: http://sing.ei.uvigo.es/pileline/pilelinegui.html

Inhomogeneous ferrimagnetic-like behavior in Gd2/3Ca1/3MnO3 single crystals

We present a study of the magnetic properties of Gd2/3Ca1/3MnO3 single crystals at low temperatures. We show that this material behave as an inhomogeneous ferrimagnet. In addition to small saturation magnetization at 5 K, we have found history dependent effects in the magnetization and the presence of exchange bias. These features are compatible with microscopic phase separation in the clean Gd2/3Ca1/3MnO3 system studied.Comment: 7 pages, 6 figures, submitted Journal of Magnetism and Magnetic Material

Climate fluctuations during the Holocene in NW Iberia: high and low latitude linkages

International audienceHigh resolution benthic foraminiferal oxygen and carbon stable isotopes (?18O, ?13C) from core EUGC-3B are used here to infer rapid climatic changes for the last 8500 yr in the Ría de Muros (NW Iberian Margin). Benthic foraminiferal ?18O and ?13C potentially register migrations in the position of the hydrographic front formed between two different intermediate water masses: Eastern North Atlantic Central Water of subpolar origin (ENACWsp), and subtropical origin (ENACWsp). The isotopic records have been compared with two well established North Atlantic marine Holocene paleoceanographic records from low (Sea Surface Temperatures anomalies off Cape Blanc, NW Africa) and high latitudes (Hematite Stained Grains percentage, subpolar North Atlantic). This comparison clearly demonstrates that there is a strong link between high- and low-latitude climatic perturbations at centennial-millennial time scales during the Holocene. Spectral analyses also points at a pole-to-equator propagation of the so-called 1500 yr cycles. Our results demonstrate that during the Holocene, the NW Iberian Margin has undergone a series of cold episodes which are likely triggered at high latitudes in the North Atlantic and are rapidly propagated towards lower latitudes. Conceivably, the propagation of these rapid climatic changes involves a shift of atmospheric and oceanic circulatory systems and so a migration of the hydrographical fronts and water masses all along the North Atlantic area

WhichGenes: a web-based tool for gathering, building, storing and exporting gene sets with application in gene set enrichment analysis

WhichGenes is a web-based interactive gene set building tool offering a very simple interface to extract always-updated gene lists from multiple databases and unstructured biological data sources. While the user can specify new gene sets of interest by following a simple four-step wizard, the tool is able to run several queries in parallel. Every time a new set is generated, it is automatically added to the private gene-set cart and the user is notified by an e-mail containing a direct link to the new set stored in the server. WhichGenes provides functionalities to edit, delete and rename existing sets as well as the capability of generating new ones by combining previous existing sets (intersection, union and difference operators). The user can export his sets configuring the output format and selecting among multiple gene identifiers. In addition to the user-friendly environment, WhichGenes allows programmers to access its functionalities in a programmatic way through a Representational State Transfer web service. WhichGenes front-end is freely available at http://www.whichgenes.org/, WhichGenes API is accessible at http://www.whichgenes.org/api/

Chimpanzee Rights: The Philosophers' Brief

In December 2013, the Nonhuman Rights Project (NhRP) filed a petition for a common law writ of habeas corpus in the New York State Supreme Court on behalf of Tommy, a chimpanzee living alone in a cage in a shed in rural New York (Barlow, 2017). Under animal welfare laws, Tommy’s owners, the Laverys, were doing nothing illegal by keeping him in those conditions. Nonetheless, the NhRP argued that given the cognitive, social, and emotional capacities of chimpanzees, Tommy’s confinement constituted a profound wrong that demanded remedy by the courts. Soon thereafter, the NhRP filed habeas corpus petitions on behalf of Kiko, another chimpanzee housed alone in Niagara Falls, and Hercules and Leo, two chimpanzees held in research facilities at Stony Brook University. Thus began the legal struggle to move these chimpanzees from captivity to a sanctuary, an effort that has led the NhRP to argue in multiple courts before multiple judges. The central point of contention has been whether Tommy, Kiko, Hercules, and Leo have legal rights. To date, no judge has been willing to issue a writ of habeas corpus on their behalf. Such a ruling would mean that these chimpanzees have rights that confinement might violate. Instead, the judges have argued that chimpanzees cannot be bearers of legal rights because they are not, and cannot be persons. In this book we argue that chimpanzees are persons because they are autonomous

When the most potent combination of antibiotics selects for the greatest bacterial load: the Smile-Frown transition

Final published PDF version of article deposited in accordance with SHERPA RoMEO guidelinesConventional wisdom holds that the best way to treat infection with antibiotics is to ‘hit early and hit hard’. A favoured strategy is to deploy two antibiotics that produce a stronger effect in combination than if either drug were used alone. But are such synergistic combinations necessarily optimal? We combine mathematical modelling, evolution experiments, whole genome sequencing and genetic manipulation of a resistance mechanism to demonstrate that deploying synergistic antibiotics can, in practice, be the worst strategy if bacterial clearance is not achieved after the first treatment phase. As treatment proceeds, it is only to be expected that the strength of antibiotic synergy will diminish as the frequency of drug-resistant bacteria increases. Indeed, antibiotic efficacy decays exponentially in our five-day evolution experiments. However, as the theory of competitive release predicts, drug-resistant bacteria replicate fastest when their drug-susceptible competitors are eliminated by overly-aggressive treatment. Here, synergy exerts such strong selection for resistance that an antagonism consistently emerges by day 1 and the initially most aggressive treatment produces the greatest bacterial load, a fortiori greater than if just one drug were given. Whole genome sequencing reveals that such rapid evolution is the result of the amplification of a genomic region containing four drug-resistance mechanisms, including the acrAB efflux operon. When this operon is deleted in genetically manipulated mutants and the evolution experiment repeated, antagonism fails to emerge in five days and antibiotic synergy is maintained for longer. We therefore conclude that unless super-inhibitory doses are achieved and maintained until the pathogen is successfully cleared, synergistic antibiotics can have the opposite effect to that intended by helping to increase pathogen load where, and when, the drugs are found at sub-inhibitory concentrations