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Tests and Measurement

Valentine Svensson, Sarah A Teichmann, Oliver Stegle
Technological advances have made it possible to measure spatially resolved gene expression at high throughput. However, methods to analyze these data are not established. Here we describe SpatialDE, a statistical test to identify genes with spatial patterns of expression variation from multiplexed imaging or spatial RNA-sequencing data. SpatialDE also implements 'automatic expression histology', a spatial gene-clustering approach that enables expression-based tissue histology.
March 19, 2018: Nature Methods
Vid Leko, Smitha Sripathy, Robin L Adrianse, Taylor Loe, Angela Park, Uyen Lao, Eric J Foss, Marisa S Bartolomei, Antonio Bedalov
Forward genetic screens using reporter genes inserted into the heterochromatin have been extensively used to investigate mechanisms of epigenetic control in model organisms. Technologies including short hairpin RNAs (shRNAs) and clustered regularly interspaced short palindromic repeats (CRISPR) have enabled such screens in diploid mammalian cells. Here we describe a large-scale shRNA screen for regulators of X-chromosome inactivation (XCI), using a murine cell line with firefly luciferase and hygromycin resistance genes knocked in at the C-terminus of the methyl CpG binding protein 2 (MeCP2) gene on the inactive X-chromosome (Xi)...
March 2, 2018: Journal of Visualized Experiments: JoVE
Xing Chen, Detlef Wolf, Juliane Siebourg-Polster, Christian Czech, Ulrike Bonati, Dirk Fischer, Omar Khwaja, Martin Strahm
Progressive and irreversible muscle atrophy characterizes Spinal Muscular Atrophy (SMA) and other similar muscle disorder diseases. Objective assessment of muscle functions is an essential and important, although challenging, prerequisite for successful clinical trials. Current clinical rating scales restrain the movement abnormalities to certain predefined coarse-grained individual items. The Kinect 3-D sensor has emerged as a low-cost and portable motion sensing technology used to capture and track people's movement in many medical and research fields...
February 12, 2018: Journal of Visualized Experiments: JoVE
José R Agudo, Jiwon Han, Jinyoung Park, Sinyoung Kwon, Soebiakto Loekman, Giovanni Luzi, Christoph Linderberger, Antonio Delgado, Andreas Wierschem
Two different experimental methods for determining the threshold of particle motion as a function of geometrical properties of the bed from laminar to turbulent flow conditions are presented. For that purpose, the incipient motion of a single bead is studied on regular substrates that consist of a monolayer of fixed spheres of uniform size that are regularly arranged in triangular and quadratic symmetries. The threshold is characterized by the critical Shields number. The criterion for the onset of motion is defined as the displacement from the original equilibrium position to the neighboring one...
February 22, 2018: Journal of Visualized Experiments: JoVE
Jacey L Janz Vernoski, Jack R Bjorkland, Talia J Kramer, Steven T Oczak, Alexandra L Borstad
Proprioception may be the least well measured of all contributors to the neural control of movement. New precise, reliable measures of proprioception are needed for clinical diagnosis of impairment, and to measure outcomes of proprioceptive training. The purpose of this simple, non-invasive method is to temporarily knockdown upper limb proprioception in healthy adults, to an extent that would be useful in the development and testing of upper limb proprioception measures. Knockdown models have two main advantages over studying humans with impaired proprioception: participant availability and the ability to control the extent of impairment across participants...
March 3, 2018: Journal of Visualized Experiments: JoVE
Tiffany Guess, Hoyin Lai, Serenah E Smith, Linda Sircy, Kirsten Cunningham, David E Nelson, Erin E McClelland
The polysaccharide capsule of Cryptococcus neoformans is the primary virulence factor and one of the most commonly studied aspects of this pathogenic yeast. Capsule size can vary widely between strains, has the ability to grow rapidly when introduced to stressful or low nutrient conditions, and has been positively correlated with strain virulence. For these reasons, the size of the capsule is of great interest to C. neoformans researchers. The growth of the C. neoformans capsule is induced during phenotypic testing to help understand the effects of different treatments on the yeast or size differences between strains...
February 27, 2018: Journal of Visualized Experiments: JoVE
Andrey Zavadsky, Lev Shemer
This manuscript describes an experimental procedure that allows obtaining diverse quantitative information on temporal and spatial evolution of water waves excited by time-dependent and steady wind forcing. Capacitance-type wave gauge and Laser Slope Gauge (LSG) are used to measure instantaneous water surface elevation and two components of the instantaneous surface slope at a number of locations along the test section of a wind-wave facility. The computer-controlled blower provides airflow over the water in the tank whose rate can vary in time...
February 13, 2018: Journal of Visualized Experiments: JoVE
Marija D Ivanovic, Jovana Petrovic, Andrej Savic, Goran Gligoric, Marjan Miletic, Miodrag Vukcevic, Bosko Bojovic, Ljupco Hadzievski, Tom D P Allsop, David J Webb
The ventilators involved in non-invasive mechanical ventilation commonly provide ventilator support via a facemask. The interface of the mask with a patient promotes air leaks that cause errors in the feedback information provided by a pneumatic sensor and hence patient-ventilator asynchrony with multiple negative consequences. Our objective is to test the possibility of using chest-wall motion measured by an optical fibre-grating sensor as a more accurate non-invasive ventilator triggering mechanism.
 Approach: The basic premise of our approach is that the measurement accuracy can be improved by using a triggering signal that precedes pneumatic triggering in the neuro-ventilatory coupling sequence...
March 19, 2018: Physiological Measurement
Yousef Jaradat, Morten Birkeland Nielsen, Petter Kristensen, Rita Bast-Pettersen
BACKGROUND: Shift work is associated with sleep disturbances, mental health problems, and job dissatisfaction. Disparities between male and female nurses in the effect of shift work on mental distress and job satisfaction have been scarcely studied. We aimed to examine differences between female and male nurses in the associations between shift work and job satisfaction and mental health. METHODS: In this cross-sectional study, male and female nurses were recruited to rate their job satisfaction on the Generic Job Satisfaction Scale and to complete the General Health Questionnaire (GHQ-30)...
February 21, 2018: Lancet
Rola Abu Dalfa, Khaled I Abu El Aish, Mohamed El Raai, Nermeen El Gazaly, Ahmed Shatat
BACKGROUND: Diarrhoea causes 15% of under-5 mortality in developing countries. Zinc (Zn) stores in the body are known to be depleted during acute diarrhoea. The aim of this study was to evaluate the efficacy of Zn given with standard treatment to children with acute or moderate diarrhoea. METHODS: In this quasi-unmasked, parallel-group study, we enrolled children with diarrhoea at El-Dorra Paediatric Hospital, Gaza Strip, occupied Palestinian territory. Inclusion criteria were children with more than three unformed stools in the preceding 24 h, duration of diarrhoea up to 72 h, and ability to accept oral fluids or feeds...
February 21, 2018: Lancet
Raed Tafish, Khaled I Abu El Aish, Walid Madi
BACKGROUND: General anaesthesia and spinal anaesthesia are commonly used for caesarean sections. The aim of this study was to compare the outcomes from caesarean sections with these two types of anaesthesia. METHODS: In this quasi-controlled trial, we enrolled women undergoing caesarean sections at Al-Helal Al-Emirati Hospital, Rafah, Gaza Strip. Women were assigned either to general anaesthesia (20% intravenous propofol for anaesthesia induction followed by atracurium for muscle relaxation, and nitrous oxide and oxygen for anaesthesia maintenance) or to spinal anaesthesia (0·5% hyperbaric solution bupivacaine with 20 μg fentanyl intrathecally)...
February 21, 2018: Lancet
Aeysha Chaudhry, Shakoor Hajat, Najwa Rizkallah, Ala'a Abu-Rub
BACKGROUND: Vitamin A and vitamin D are essential for a child's growth and development. However, research on micronutrients in the occupied Palestinian territory is scarce. The aim of this study was to ascertain the prevalence and risk factors of vitamin A and vitamin D deficiencies in children living in the occupied Palestinian territory. METHODS: The Palestinian Micronutrient Survey in 2013 measured concentrations of vitamin A in 1054 children (569 children in the West Bank and 485 children in the Gaza Strip) and vitamin D in 150 children (75 children in the West Bank and 75 children in the Gaza Strip)...
February 21, 2018: Lancet
Giulia Canali, Victoria Tittle, Akihiro Seita
BACKGROUND: The United Nations Relief and Works Agency for Palestine Refugees in the Near East (UNRWA) estimated that in 2016, 11% of Palestine refugees older than 40 years living in Jordan were diagnosed with diabetes and that the disease is controlled in only 45% of Palestine refugees with diabetes. As medication adherence is one of the most important modifiable self-care behaviours to achieve adequate metabolic control, the aims of this study were to measure medication adherence and to review the factors associated with different levels of medication adherence in patients with diabetes...
February 21, 2018: Lancet
Yi Chen, Zhenzhu Tang, Shuai Tang, Zhiyong Shen, Qiuying Zhu, Rongjian Li, Wenbo Huang, Yuman Huang, Fuxiong Liang, Lu Wang, Huanhuan Chen, Yuhua Ruan, Yiming Shao, Sian Hsiang-Te Tsuei, Guanghua Lan
OBJECTIVE: Since 2003, the Chinese central government has implemented several harm reduction and preventive measures to control HIV. We aim to describe epidemiological trends of HIV, hepatitis C virus (HCV), and syphilis in Guangxi drug users after the policy implementation. METHOD: A total of 12,161-15,870 drug users in Guangxi, China, were recruited annually from 2009 to 2015 through community outreach or snowball sampling. The participants' demographics, behavior, and infection status were used to characterize rates of protective behaviors and disease prevalence (HIV, syphilis, and HCV)...
March 2018: Journal of Studies on Alcohol and Drugs
Jesus Idigoras, Francisco Javier Aparicio, Lidia Contreras-Bernal, Susana Ramos-Terrón, María Alcaire, Juan R Sanchez-Valencia, Ana Borras, Angel Barranco, Juan Antonio Anta
A compromise between high power conversion efficiency and long-term stability of hybrid organic-inorganic metal halide perovskite solar cells is necessary for their outdoor photovoltaic application and commercialization. Herein, a method to improve the stability of perovskite solar cells under water and moisture exposure consisting in the encapsulation of the cell with an ultrathin plasma polymer is reported. The deposition of the polymer is carried out at room temperature by the remote plasma vacuum deposition of adamantane powder...
March 19, 2018: ACS Applied Materials & Interfaces
Michael S McLachlan, Emma Undeman, Fangyuan Zhao, Matthew MacLeod
Predicting human exposure to an environmental contaminant based on its emissions is one of the great challenges of environmental chemistry. It has been done successfully on a local or regional scale for some persistent organic pollutants. Here we assess whether it can be done at a global scale, using PCB 153 as a test chemical. The global multimedia fate model BETR Global and the human exposure model ACC-HUMAN were employed to predict the concentration of PCB 153 in human milk for 56 countries around the world from a global historical emissions scenario...
March 19, 2018: Environmental Science. Processes & Impacts
Hiroyasu Kurokawa, Koji Shiratsuchi, Shunichi Suda, Yuko Nagura, Soshi Suzuki, Nobuyuki Moritake, Kabun Yamauchi, Masashi Miyazaki
In this study, we investigated the effect of light irradiation and primer/adhesive application on the polymerization reaction and elastic modulus (E) of self-adhesive resin cement (SAC) through ultrasonic velocity (V) measurements. The V values of longitudinal and shear waves were determined based on the transit time through the specimens and specimen thicknesses, and were used to calculate the E values. Analysis of variance and Tukey tests revealed that V increased rapidly, reaching a plateau at 2,700-2,900 m/s, when the SACs were light-irradiated...
March 17, 2018: Dental Materials Journal
Chiaki Yabuki, Akitomo Rikuta, Ryosuke Murayama, Syunsuke Akiba, Soshi Suzuki, Toshiki Takamizawa, Hiroyasu Kurokawa, Masashi Miyazaki
The purpose of this study was to investigate the effect of acid erosion on the bonding performance of universal adhesives. Freshly extracted bovine teeth were cut into enamel slabs and assigned to either the Er or the control group. Specimens in the Er group were immersed in citric acid solution (pH 2.1) twice a day and stored in artificial saliva, while control specimens were simply stored in artificial saliva. Differences in the mean values between the control and Er groups were greater than expected, despite accounting for the effect of differences in the adhesive systems (p=0...
March 17, 2018: Dental Materials Journal
Sakornrat Khongkhunthian, Thanapat Sastraruji, Srikanjana Klayraung, Siriporn Okonogi
The aim of this study was to determine the efficacy of two local anesthetic rice nanogels (RNG) on pain reduction from needle insertion in oral cavity. Nanogel base was prepared using modified rice as gelling agent. The average particle size of RNG determined by photon correlation spectrophotometer was 485 ± 70 nm. Lidocaine hydrochloride (LH) and prilocaine hydrochloride (PH) were incorporated into RNG to obtain anesthetic RNG containing 5% and 20% LH or PH. Clinical efficacy test of each gel was performed in oral cavity of 100 healthy volunteers (25-60 years old)...
2018: Drug Discoveries & Therapeutics
Emine Çamtosun, Zeynep Şıklar, Merih Berberoğlu
OBJECTIVES: Continuation of GH treatment in adolescents with severe childhood onset Idiopathic Growth Hormone Deficiency (IGHD) during the transition period, irrespective of achievement of final height is still debatable.We aimed to investigate the metabolic profile, BMD and body composition of the patients with isolated childhood onset GHD in whom GH treatments were terminated after they reached their final height, prospectively six months after the cessation of therapy. METHODS: Twelve patients, 6 of which with peak GH <5 ng/mL (Permanent GHD, Group 1), and 6 of which with peak GH >5 ng/mL (Transient GHD, Group 2) after insulin stimulation test were evaluated for anthropometric and laboratory parameters including fasting blood glucose (FBG), fasting insulin (FI), lipid profile, BMD, body composition measurements, and 24 hours ambulatory blood pressure monitoring before (baseline) and at six months after discontinuation of GH...
March 19, 2018: Journal of Clinical Research in Pediatric Endocrinology
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