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https://www.readbyqxmd.com/read/29788279/well-annotated-micrornaomes-do-not-evidence-pervasive-mirna-loss
#1
James E Tarver, Richard S Taylor, Mark N Puttick, Graeme T Lloyd, Walker Pett, Bastian Fromm, Bettina E Schirrmeister, Davide Pisani, Kevin J Peterson, Philip C J Donoghue
microRNAs are conserved non-coding regulatory factors implicated in diverse physiological and developmental processes in multicellular organisms, as causal macroevolutionary agents and for phylogeny inference. However, the conservation and phylogenetic utility of microRNAs has been questioned on evidence of pervasive loss. Here we show that apparent widespread losses are, largely, an artefact of poorly sampled and annotated microRNAomes. Using a curated dataset of animal microRNAomes, we reject the view that miRNA families are never lost, but they are rarely lost (92% are never lost)...
May 18, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29784376/spectral-reconstruction-for-shifted-excitation-raman-difference-spectroscopy-serds
#2
Shuxia Guo, Olga Chernavskaia, Jürgen Popp, Thomas Bocklitz
Fluorescence emission is one of the major obstacles to apply Raman spectroscopy in biological investigations. It is usually several orders more intense than Raman scattering and hampers further analysis. In cases where the fluorescence emission is too intense to be efficiently removed via routine mathematical baseline correction algorithms, an alternative approach is needed. One alternative approach is shifted-excitation Raman difference spectroscopy (SERDS), where two Raman spectra are recorded with two slightly different excitation wavelengths...
August 15, 2018: Talanta
https://www.readbyqxmd.com/read/29780669/an-examination-of-the-impact-of-olson-s-extinction-on-tetrapods-from-texas
#3
Neil Brocklehurst
It has been suggested that a transition between a pelycosaurian-grade synapsid dominated fauna of the Cisuralian (early Permian) and the therapsid dominated fauna of the Guadalupian (middle Permian) was accompanied by, and possibly driven by, a mass extinction dubbed Olson's Extinction. However, this interpretation of the record has recently been criticised as being a result of inappropriate time-binning strategies: calculating species richness within international stages or substages combines extinctions occurring throughout the late Kungurian stage into a single event...
2018: PeerJ
https://www.readbyqxmd.com/read/29779238/the-role-of-transbronchial-cryobiopsy-in-lung-transplantation
#4
M Angeles Montero, Javier de Gracia, Mario Culebras, Jacqueline Mugnier, Antonio Álvarez, Cristina Berastegui, Cristian Ortiz-Villalón
INTRODUCTION: Lung transplant monitoring is usually assessed by forceps transbronchial biopsies. These types of biopsies show limited reliability and high degree of variability due to insufficient material and compression artefact, which lead to misinterpretation and eventually mistreatment of the transplanted patients. The following study was undertaken to assess the diagnostic yield, histological quality and safety of cryobiopsy in comparison with conventional forceps biopsy for sampling lung tissue in transplant recipients...
May 19, 2018: Histopathology
https://www.readbyqxmd.com/read/29778801/injury-and-stress-responses-of-adult-neural-crest-derived-cells
#5
REVIEW
Vadims Parfejevs, Ana T Antunes, Lukas Sommer
Multipotent neural crest cells can self-renew and give rise to a plethora of neural and non-neural cell types in the vertebrate embryo. Intriguingly, cells reminiscent of such neural crest stem cells (NCSCs) have also been isolated from various postnatal and adult neural crest (NC)-derived structures. However, it has been debated whether NCSC-like cells in the adult correspond to 'in vitro artefacts' emerging upon isolation or fulfil a physiological role in vivo. Here, we discuss recent findings indicating that in different adult NC derivatives, injury or stress responses induce a NCSC-like state, presumably by reprogramming of differentiated cells such as Schwann cells...
May 17, 2018: Developmental Biology
https://www.readbyqxmd.com/read/29775214/pressurized-hot-water-extraction-of-bioactive-compounds-from-artichoke-by-products
#6
Imma Pagano, Anna Lisa Piccinelli, Rita Celano, Luca Campone, Patrizia Gazzerro, Mariateresa Russo, Luca Rastrelli
Artichoke by-products are a suitable source of health-promoting ingredients for the production of dietary supplements and food additives. A pressurized hot water extraction (PHWE) was developed to recover caffeoylquinic acids (CQAs) and flavone glycosides (FLs) from agro-industrial artichoke by-products. The main factors influencing PHWE efficiency and CQA isomerization (temperature, numbers of cycles, modifier and extraction time) were carefully studied and optimized by response surface design. The proposed PHWE procedure provides an exhaustive extraction of CQAs and FLs (recoveries: 93-105 and 90-105%) from artichoke external bracts and leaves of different cultivars (p > 0...
May 18, 2018: Electrophoresis
https://www.readbyqxmd.com/read/29773229/oldowan-technological-behaviour-at-hwk-ee-olduvai-gorge-tanzania
#7
Ignacio de la Torre, Rafael Mora
HWK EE (Olduvai Gorge, Tanzania) is a late Oldowan site dated to ∼1.7 Ma that contains a large fossil and lithic assemblage. This paper reports on the technology of the recently excavated stone tool collection, over 18,000 pieces. Our results indicate that reduction sequences were generally short, flaking productivity was low, and knapping methods were largely simple and expedient, lacking the technical skills observed in other Oldowan assemblages. Conspicuous differences are observed in the chaînes opératoires of the three main raw materials used at HWK EE: the quartzite reduction sequence can be reconstructed in full at the site, most of the lava detached pieces are missing, and there is a preferential use of chert for retouched tools...
May 14, 2018: Journal of Human Evolution
https://www.readbyqxmd.com/read/29772060/nucleocytoplasmic-shuttling-the-ins-and-outs-of-quantitative-imaging
#8
Chris Molenaar, Kate L Weeks
Nucleocytoplasmic protein shuttling is integral to the transmission of signals between the nucleus and the cytoplasm. The nuclear/cytoplasmic distribution of proteins of interest can be determined via fluorescence microscopy, following labelling of the target protein with fluorophore-conjugated antibodies (immunofluorescence) or by tagging the target protein with an autofluorescent protein, such as green fluorescent protein (GFP). The latter enables live cell imaging, a powerful approach that precludes many of the artefacts associated with indirect immunofluorescence in fixed cells...
May 17, 2018: Clinical and Experimental Pharmacology & Physiology
https://www.readbyqxmd.com/read/29768471/performance-based-approach-for-movement-artifact-removal-from-electroencephalographic-data-recorded-during-locomotion
#9
Evyatar Arad, Ronny P Bartsch, Jan W Kantelhardt, Meir Plotnik
The appreciation for the need to record electroencephalographic (EEG) signals from humans while walking has been steadily growing in recent years, particularly in relation to understanding gait disturbances. Movement artefacts (MA) in EEG signals originate from mechanical forces applied to the scalp electrodes, inducing small electrode movements relative to the scalp which, in turn, cause the recorded voltage to change irrespectively of cortical activity. These mechanical forces, and thus MA, may have various sources (e...
2018: PloS One
https://www.readbyqxmd.com/read/29768454/fireproxies-a-computational-model-providing-insight-into-heat-affected-archaeological-lithic-assemblages
#10
Andrew C Sorensen, Fulco Scherjon
Evidence for fire use becomes increasingly sparse the further back in time one looks. This is especially true for Palaeolithic assemblages. Primary evidence of fire use in the form of hearth features tends to give way to clusters or sparse scatters of more durable heated stone fragments. In the absence of intact fireplaces, these thermally altered lithic remains have been used as a proxy for discerning relative degrees of fire use between archaeological layers and deposits. While previous experimental studies have demonstrated the physical effects of heat on stony artefacts, the mechanisms influencing the proportion of fire proxy evidence within archaeological layers remain understudied...
2018: PloS One
https://www.readbyqxmd.com/read/29767635/detecting-atrial-fibrillation-from-short-single-lead-ecgs-using-statistical-and-morphological-features
#11
Mohamed Athif, Pamodh Chanuka Yasawardene, Chathuri Daluwatte
Point of care ECG devices can improve the early detection of atrial fibrillation (AF). Efficiency of such devices depend on the capability of automatic AF detection against normal sinus rhythm and other arrhythmias from a short single lead ECG record in the presence of noise and artefacts. The objective of this study was to develop an algorithm that classifies a short single lead ECG record into "Normal", "AF", "Other" and "Noisy" classes, and identify challenges in developing such algorithms and potential mitigation steps...
May 16, 2018: Physiological Measurement
https://www.readbyqxmd.com/read/29765641/combined-morphological-and-phylogenomic-re-examination-of-malawimonads-a-critical-taxon-for-inferring-the-evolutionary-history-of-eukaryotes
#12
Aaron A Heiss, Martin Kolisko, Fleming Ekelund, Matthew W Brown, Andrew J Roger, Alastair G B Simpson
Modern syntheses of eukaryote diversity assign almost all taxa to one of three groups: Amorphea, Diaphoretickes and Excavata (comprising Discoba and Metamonada). The most glaring exception is Malawimonadidae, a group of small heterotrophic flagellates that resemble Excavata by morphology, but branch with Amorphea in most phylogenomic analyses. However, just one malawimonad, Malawimonas jakobiformis , has been studied with both morphological and molecular-phylogenetic approaches, raising the spectre of interpretation errors and phylogenetic artefacts from low taxon sampling...
April 2018: Royal Society Open Science
https://www.readbyqxmd.com/read/29765604/deciphering-mineralogical-changes-and-carbonation-development-during-hydration-and-ageing-of-a-consolidated-ternary-blended-cement-paste
#13
Francis Claret, Sylvain Grangeon, Annick Loschetter, Christophe Tournassat, Wout De Nolf, Nicholas Harker, Faiza Boulahya, Stéphane Gaboreau, Yannick Linard, Xavier Bourbon, Alejandro Fernandez-Martinez, Jonathan Wright
To understand the main properties of cement, a ubiquitous material, a sound description of its chemistry and mineralogy, including its reactivity in aggressive environments and its mechanical properties, is vital. In particular, the porosity distribution and associated sample carbonation, both of which affect cement's properties and durability, should be quantified accurately, and their kinetics and mechanisms of formation known both in detail and in situ . However, traditional methods of cement mineralogy analysis ( e...
March 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/29764458/cone-beam-computed-tomography-in-implant-dentistry-recommendations-for-clinical-use
#14
Reinhilde Jacobs, Benjamin Salmon, Marina Codari, Bassam Hassan, Michael M Bornstein
BACKGROUND: In implant dentistry, three-dimensional (3D) imaging can be realised by dental cone beam computed tomography (CBCT), offering volumetric data on jaw bones and teeth with relatively low radiation doses and costs. The latter may explain why the market has been steadily growing since the first dental CBCT system appeared two decades ago. More than 85 different CBCT devices are currently available and this exponential growth has created a gap between scientific evidence and existing CBCT machines...
May 15, 2018: BMC Oral Health
https://www.readbyqxmd.com/read/29762768/emergence-of-mature-cortical-activity-in-wakefulness-and-sleep-in-healthy-pre-term-and-full-term-infants
#15
Kimberley Whitehead, Pureza Laudiano-Dray, Judith Meek, Lorenzo Fabrizi
Study Objectives: Cortical activity patterns develop rapidly over the equivalent of the last trimester of gestation, in parallel with the establishment of sleep architecture. However, the emergence of mature cortical activity in wakefulness compared to sleep states in healthy pre-term infants is poorly understood. Methods: To investigate whether cortical activity has a different developmental profile in each sleep-wake state, we recorded 11-channels EEG, EOG and respiratory movement for one hour from 115 infants 34-43 weeks corrected age, with 0...
May 14, 2018: Sleep
https://www.readbyqxmd.com/read/29761363/scientific-iconoclasm-and-active-imagination-synthetic-cells-as-techno-scientific-mandalas
#16
Hub Zwart
Metaphors allow us to come to terms with abstract and complex information, by comparing it to something which is structured, familiar and concrete. Although modern science is "iconoclastic", as Gaston Bachelard phrases it (i.e. bent on replacing living entities by symbolic data: e.g. biochemical and mathematical symbols and codes), scientists are at the same time prolific producers of metaphoric images themselves. Synthetic biology is an outstanding example of a technoscientific discourse replete with metaphors, including textual metaphors such as the "Morse code" of life, the "barcode" of life and the "book" of life...
May 14, 2018: Life Sciences, Society and Policy
https://www.readbyqxmd.com/read/29760996/enhancement-of-morphological-and-vascular-features-in-oct-images-using-a-modified-bayesian-residual-transform
#17
Bingyao Tan, Alexander Wong, Kostadinka Bizheva
A novel image processing algorithm based on a modified Bayesian residual transform (MBRT) was developed for the enhancement of morphological and vascular features in optical coherence tomography (OCT) and OCT angiography (OCTA) images. The MBRT algorithm decomposes the original OCT image into multiple residual images, where each image presents information at a unique scale. Scale selective residual adaptation is used subsequently to enhance morphological features of interest, such as blood vessels and tissue layers, and to suppress irrelevant image features such as noise and motion artefacts...
May 1, 2018: Biomedical Optics Express
https://www.readbyqxmd.com/read/29759067/small-rna-profiling-of-low-biomass-samples-identification-and-removal-of-contaminants
#18
Anna Heintz-Buschart, Dilmurat Yusuf, Anne Kaysen, Alton Etheridge, Joëlle V Fritz, Patrick May, Carine de Beaufort, Bimal B Upadhyaya, Anubrata Ghosal, David J Galas, Paul Wilmes
BACKGROUND: Sequencing-based analyses of low-biomass samples are known to be prone to misinterpretation due to the potential presence of contaminating molecules derived from laboratory reagents and environments. DNA contamination has been previously reported, yet contamination with RNA is usually considered to be very unlikely due to its inherent instability. Small RNAs (sRNAs) identified in tissues and bodily fluids, such as blood plasma, have implications for physiology and pathology, and therefore the potential to act as disease biomarkers...
May 14, 2018: BMC Biology
https://www.readbyqxmd.com/read/29757471/image-based-retrospective-4d-mri-in-external-beam-radiotherapy-a-comparative-study-with-a-digital-phantom
#19
Chiara Paganelli, John Kipritidis, Danny Lee, Guido Baroni, Paul Keall, Marco Riboldi
PURPOSE: Several image-based retrospective sorting methods of 4D Magnetic Resonance Imaging (4D MRI) have been proposed for respiratory motion reconstruction in external beam radiotherapy. However, the optimal strategy for providing accurate and artefact-free 4D MRI, ideally corresponding to an average breathing cycle, is not yet defined. This study presents a proactive comparison of three published image-based sorting methods, to define a groundwork for benchmarking in 4D MRI. METHODS: Three published 4D MRI methods were selected for image retrospective sorting; body area, mutual information and navigator slice...
May 14, 2018: Medical Physics
https://www.readbyqxmd.com/read/29757285/microfluidic-chips-for-in-situ-crystal-x-ray-diffraction-and-in-situ-dynamic-light-scattering-for-serial-crystallography
#20
Yannig Gicquel, Robin Schubert, Svetlana Kapis, Gleb Bourenkov, Thomas Schneider, Markus Perbandt, Christian Betzel, Henry N Chapman, Michael Heymann
This protocol describes fabricating microfluidic devices with low X-ray background optimized for goniometer based fixed target serial crystallography. The devices are patterned from epoxy glue using soft lithography and are suitable for in situ X-ray diffraction experiments at room temperature. The sample wells are lidded on both sides with polymeric polyimide foil windows that allow diffraction data collection with low X-ray background. This fabrication method is undemanding and inexpensive. After the sourcing of a SU-8 master wafer, all fabrication can be completed outside of a cleanroom in a typical research lab environment...
April 24, 2018: Journal of Visualized Experiments: JoVE
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