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Charles Cole, Ashley Byrne, Anna E Beaudin, E Camilla Forsberg, Christopher Vollmers
RNA-sequencing (RNA-seq) is a powerful technique to investigate and quantify entire transcriptomes. Recent advances in the field have made it possible to explore the transcriptomes of single cells. However, most widely used RNA-seq protocols fail to provide crucial information regarding transcription start sites. Here we present a protocol, Tn5Prime, that takes advantage of the Tn5 transposase-based Smart-seq2 protocol to create RNA-seq libraries that capture the 5' end of transcripts. The Tn5Prime method dramatically streamlines the 5' capture process and is both cost effective and reliable...
March 14, 2018: Nucleic Acids Research
Konstadinos Plestis, Oleg Orlov, Vishal N Shah, Joshua Wong, Matthew Thomas, Alon Aharon, Cinthia Orlov, Georgia Panagopoulos, Scott Goldman
OBJECTIVES: Minimally invasive aortic valve replacement (MIAVR) can be technically demanding and may lead to prolonged operative time. We evaluated the intraoperative and postoperative patient outcomes following implementation of 2 facilitating technologies (FT) in MIAVR: the Cor-Knot titanium fastener and Custodiol-histidine-tryptophan-ketoglutarate solution. METHODS: A total of 299 patients underwent MIAVR from 2008 to 2016; 172 (57.5%) patients were included in the FT group and 127 (42...
March 14, 2018: Interactive Cardiovascular and Thoracic Surgery
Mingfei Zeng, Huachuan Cao
Short chain fatty acids (SCFA) and ketone bodies recently emerged as important physiological relevant metabolites because of their association with microbiota, immunology, obesity and other metabolic states. They were commonly analyzed by GC-MS with long run time and laborious sample preparation. In this study we developed a novel LC-MS/MS method using fast derivatization coupled with liquid-liquid extraction to detect SCFA and ketone bodies in plasma and feces. Several different derivatization reagents were evaluated to compare the efficiency, the sensitivity and chromatographic separation of structural isomers...
March 8, 2018: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
Ariana Sherdil, Stéphan Chabardès, Isabelle Guillemain, Sandrine Michallat, Shivadatta Prabhu, Karine Pernet-Gallay, Olivier David, Brigitte Piallat
PURPOSE: Our objective was to propose a new on demand non-human primate model of mesial temporal lobe seizures suitable for pre-clinical innovative therapeutic research. METHODS: Five macaques were stereotaxically implanted unilaterally with a deep recording electrode in the hippocampus. For each experiment, penicillin was injected into the hippocampus and animals were monitored during five consecutive hours. A total of 12-27 experiments with a mean cumulative dose of 162644 ± 70190 UI of penicillin have been performed per animal Injections were repeated at least once a week over a period of 98-276 days...
March 9, 2018: Epilepsy Research
Brenda Deliz, Kathya Ramos, Cynthia M Pérez
OBJECTIVE: To evaluate the sociodemographic characteristics and clinical and functional profile of amyotrophic lateral sclerosis (ALS) patients evaluated at Puerto Rico's Muscular Dystrophy Association-supported (MDA) clinics. METHODS: A retrospective review of 76 medical records of ALS patients evaluated at any of four MDA-sponsored clinics in Puerto Rico. RESULTS: The mean age of diagnosis was 57.4 ± 11.1 yrs. Most of the patients (52.3%) were women...
March 2018: Puerto Rico Health Sciences Journal
Shanon Seger, Manuel Stritt, Enrico Vezzali, Oliver Nayler, Patrick Hess, Peter M A Groenen, Anna K Stalder
Intratracheal administration of bleomycin induces fibrosis in the lung, which is mainly assessed by histopathological grading that is subjective. Current literature highlights the need of reproducible and quantitative pulmonary fibrosis analysis. If some quantitative studies looked at fibrosis parameters separately, none of them quantitatively assessed both aspects: lung tissue remodeling and collagenization. To ensure reliable quantification, support vector machine learning was used on digitalized images to design a fully automated method that analyzes two important aspects of lung fibrosis: (i) areas having substantial tissue remodeling with appearance of dense fibrotic masses and (ii) collagen deposition...
2018: PloS One
Davina Gale, Andrew R J Lawson, Karen Howarth, Mikidache Madi, Bradley Durham, Sarah Smalley, John Calaway, Shannon Blais, Greg Jones, James Clark, Peter Dimitrov, Michelle Pugh, Samuel Woodhouse, Michael Epstein, Ana Fernandez-Gonzalez, Alexandra S Whale, Jim F Huggett, Carole A Foy, Gerwyn M Jones, Hadas Raveh-Amit, Karin Schmitt, Alison Devonshire, Emma Green, Tim Forshew, Vincent Plagnol, Nitzan Rosenfeld
INTRODUCTION: Detection and monitoring of circulating tumor DNA (ctDNA) is rapidly becoming a diagnostic, prognostic and predictive tool in cancer patient care. A growing number of gene targets have been identified as diagnostic or actionable, requiring the development of reliable technology that provides analysis of multiple genes in parallel. We have developed the InVision™ liquid biopsy platform which utilizes enhanced TAm-Seq™ (eTAm-Seq™) technology, an amplicon-based next generation sequencing method for the identification of clinically-relevant somatic alterations at low frequency in ctDNA across a panel of 35 cancer-related genes...
2018: PloS One
Francesca Malvano, Luigi Maritato, Giovanni Carapella, Pasquale Orgiani, Roberto Pilloton, Marisa Di Matteo, Donatella Albanese
Due to their interesting ferroelectric, conductive and dielectric properties, in recent years, perovskite-structured materials have begun to attract increasing interest in the biosensing field. In this study, a strontium titanate perovskite layer (SrTiO₃) has been synthesized on a platinum electrode and exploited for the development of an impedimetric label-free immunosensor for Escherichia coli O157:H7 detection. The electrochemical characterization of the perovskite-modified electrode during the construction of the immunosensor, as well as after the interaction with different E...
March 16, 2018: Biosensors
Bartłomiej Czech, Lampros Lamprou, Samuel McCandlish, James Sully
The Berry connection describes transformations induced by adiabatically varying Hamiltonians. We study how zero modes of the modular Hamiltonian are affected by varying the region that supplies the modular Hamiltonian. In the vacuum of a 2D conformal field theory, global conformal symmetry singles out a unique modular Berry connection, which we compute directly and in the dual three-dimensional anti-de Sitter (AdS_{3}) picture. In certain cases, Wilson loops of the modular Berry connection compute lengths of curves in AdS_{3}, reproducing the differential entropy formula...
March 2, 2018: Physical Review Letters
Yushu Jin, Yusuke Makida, Tatsuya Uchida, Ryoichi Kuwano
A chemoselective hydrogenation of isoquinoline carbocycles was achieved by using the catalyst prepared from Ru(methallyl)2(cod) and trans-chelate chiral ligand PhTRAP. The unique chemoselectivity achieved in this hydrogenation could be ascribed to the trans-chelation of the chiral ligand. The procedure for preparing the catalyst strongly affects the reproducibility of the carbocycle hydrogenation. Various 5-, 6-, 7-, and 8-substituted isoquinolines were selectively hydrogenated at their carbocycles to afford 5,6,7,8-tetrahydroisoquinolines as major products in high yields with moderate or good enantioselectivities...
March 16, 2018: Journal of Organic Chemistry
Syeda Sabrina, Mykola Tasinkevych, Suzanne Ahmed, Allan M Brooks, Monica Olvera de la Cruz, Thomas E Mallouk, Kyle J M Bishop
The propulsion of micro- and nanoparticles using ultrasound is an attractive strategy for the remote manipulation of colloidal matter using biocompatible energy inputs. However, the physical mechanisms underlying acoustic propulsion are poorly understood, and our ability to transduce acoustic energy into different types of particle motions remains limited. Here, we show that the three-dimensional shape of a colloidal particle can be rationally engineered to direct desired particle motions powered by ultrasound...
March 16, 2018: ACS Nano
Zhen Li, Shouzhen Jiang, Yanyan Huo, Tingyin Ning, Aihua Liu, Chao Zhang, Yuan He, Minghong Wang, Chonghui Li, Baoyuan Man
We report a three-dimensional (3D) SERS substrate with different numbers of silver nanoparticle (Ag NP) layers using multilayer graphene oxide (GO) as a spacer. The SERS performance of the 3D nanostructure was investigated and it was found that the SERS effect increased as the number of Ag NP layers increased, and showed almost no change for more than four layers. We found that the SERS performance of the 3D nanostructures can be mainly attributed to the topmost hot spots which are closely related to the Ag NP layers in the 3D nanostructure...
March 16, 2018: Nanoscale
Laura E Erban, Stephen B Balogh, Daniel E Campbell, Henry A Walker
Urban water systems consist of natural and engineered flows of water interacting in complex ways. System complexity can be understood via mass conservative models that account for the interrelationships among all major flows and storages. We have developed a generic urban water system model in the R package CityWaterBalance . CityWaterBalance provides a reproducible workflow for studying urban water systems by facilitating automated retrievals of open data and post-processing with open source R functions. It allows the user to 1) rapidly assemble a quantitative, comprehensive assessment of flows thorough an urban area, and 2) easily change the spatial and temporal boundaries of analysis...
February 1, 2018: Open Water
Sonia Kapur, Anna Zajicek
How are the images of abused South Asian marriage migrants shaped by domestic violence advocates? We explore the social constructions of battered Asian Indian marriage migrants in the victim advocates' narratives. First, we find the narratives both reproduce and challenge the dominant stereotypes, utilizing some individualistic typifications while constructing these images with an understanding of the broader context of battered South Asian women's experiences. Second, depending on the issue (e.g., economic dependence or religion), the advocates paint either a multidimensional or a one-dimensional picture of their clients...
March 1, 2018: Violence Against Women
Ruili Shi, Pengju Wang, Lingli Tang, Xiaoming Huang, Yonggang Chen, Yan Su, Jijun Zhao
Using a genetic algorithm incorporated in density functional theory, we explore the ground state structures of fluoride anion-water clusters F-(H2O)n with n = 1-10. The F-(H2O)n clusters prefer structures in which the F- anion remains at the surface of the structure and coordinates with four water molecules, as the F-(H2O)n clusters have strong F--H2O interactions as well as strong hydrogen bonds between H2O molecules. The strong interaction between the F- anion and adjacent H2O molecule leads to a longer O-H distance in the adjacent molecule than in an individual water molecule...
March 16, 2018: Journal of Physical Chemistry. A
Lisa Menegazzo, Valentina Scattolini, Roberta Cappellari, Benedetta Maria Bonora, Mattia Albiero, Mario Bortolozzi, Filippo Romanato, Giulio Ceolotto, Saula Vigili de Kreutzeberg, Angelo Avogaro, Gian Paolo Fadini
AIMS: Diabetes is associated with an excess release of neutrophil extracellular traps (NETs) and an enhanced NETosis, a neutrophil cell death programme instrumental to anti-microbial defences, but also involved in tissue damage. We herein investigated whether the antidiabetic drug metformin protects against NETosis. METHODS: We measured NET components in the plasma of patients with pre-diabetes who were randomized to receive metformin or placebo for 2 months. To control for the effect on glucose, we also measured NET components in the plasma of patients with type 2 diabetes before and after treatment with insulin or dapagliflozin...
March 15, 2018: Acta Diabetologica
C Fielder Camm, Alexander Emery, Elizabeth Rose-Innes, Sergei Pavlitchouk, Nikant Sabharwal, Andrew D Kelion
BACKGROUND: Using myocardial perfusion scintigraphy (MPS), an increase in left ventricular (LV) volumes or a decrease in ejection fraction (EF) from rest to stress may be clinically important. The variation in these measures between the low-dose stress acquisition and high-dose rest acquisition in a one-day stress-rest protocol has not been established. We assessed the reproducibility of gated volumetric indices between stress and rest and the normal variation in ungated TID ratio for a one-day stress-rest99m Tc-tetrofosmin protocol...
March 15, 2018: Journal of Nuclear Cardiology: Official Publication of the American Society of Nuclear Cardiology
M Irani, N Zaninovic, C Canon, C O'Neill, V Gunnala, Q Zhan, G Palermo, D Reichman, Z Rosenwaks
STUDY QUESTION: Is there a benefit to assessing ploidy in delayed embryos reaching the morula stage on Day 6 of development? SUMMARY ANSWER: Day-6 morulae should be considered for biopsy in women <40 years old undergoing preimplantation genetic testing for aneuploidy (PGT-A) because they are associated with acceptable, albeit reduced, euploidy and implantation rates (IRs). WHAT IS KNOWN ALREADY: Embryo development and morphology have been shown to correlate with aneuploidy and pregnancy rates...
March 13, 2018: Human Reproduction
Vincent Clesi, Mohamed Ali Bouhifd, Nathalie Bolfan-Casanova, Geeth Manthilake, Federica Schiavi, Caroline Raepsaet, Hélène Bureau, Hicham Khodja, Denis Andrault
Hydrogen has been thought to be an important light element in Earth's core due to possible siderophile behavior during core-mantle segregation. We reproduced planetary differentiation conditions using hydrogen contents of 450 to 1500 parts per million (ppm) in the silicate phase, pressures of 5 to 20 GPa, oxygen fugacity varying within IW-3.7 and IW-0.2 (0.2 to 3.7 log units lower than iron-wüstite buffer), and Fe alloys typical of planetary cores. We report hydrogen metal-silicate partition coefficients of ~2 × 10-1 , up to two orders of magnitude lower than reported previously, and indicative of lithophile behavior...
March 2018: Science Advances
Philipp Marx, Wojciech Kowalczyk, Aydin Demircioglu, Gary Neil Brault, Hermann Wendt, Sharaf-Eldin Shehada, Konstantinos Tsagakis, Mohamed El Gabry, Heinz Jakob, Daniel Wendt
The aim of the present in vitro study was the evaluation of the fluid dynamical performance of the Carpentier-Edwards PERIMOUNT Magna Ease depending on the prosthetic size (21, 23, and 25 mm) and the cardiac output (3.6-6.4 L/min). A self-constructed flow channel in combination with particle image velocimetry (PIV) enabled precise results with high reproducibility, focus on maximal and local peek velocities, strain, and velocity gradients. These flow parameters allow insights into the generation of forces that act on blood cells and the aortic wall...
2018: BioMed Research International
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