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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
Miten Jain, Hugh E Olsen, Daniel J Turner, David Stoddart, Kira V Bulazel, Benedict Paten, David Haussler, Huntington F Willard, Mark Akeson, Karen H Miga
The human genome reference sequence remains incomplete owing to the challenge of assembling long tracts of near-identical tandem repeats in centromeres. We implemented a nanopore sequencing strategy to generate high-quality reads that span hundreds of kilobases of highly repetitive DNA in a human Y chromosome centromere. Combining these data with short-read variant validation, we assembled and characterized the centromeric region of a human Y chromosome.
March 19, 2018: Nature Biotechnology
Joseph B DeShields, Rachel A Bomberger, James W Woodhall, David L Wheeler, Natalia Moroz, Dennis A Johnson, Kiwamu Tanaka
On-site diagnosis of plant diseases can be a useful tool for growers for timely decisions enabling the earlier implementation of disease management strategies that reduce the impact of the disease. Presently in many diagnostic laboratories, the polymerase chain reaction (PCR), particularly real-time PCR, is considered the most sensitive and accurate method for plant pathogen detection. However, laboratory-based PCRs typically require expensive laboratory equipment and skilled personnel. In this study, soil-borne pathogens of potato are used to demonstrate the potential for on-site molecular detection...
February 23, 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
Jonathan T Ting, Brian R Lee, Peter Chong, Gilberto Soler-Llavina, Charles Cobbs, Christof Koch, Hongkui Zeng, Ed Lein
This protocol is a practical guide to the N-methyl-D-glucamine (NMDG) protective recovery method of brain slice preparation. Numerous recent studies have validated the utility of this method for enhancing neuronal preservation and overall brain slice viability. The implementation of this technique by early adopters has facilitated detailed investigations into brain function using diverse experimental applications and spanning a wide range of animal ages, brain regions, and cell types. Steps are outlined for carrying out the protective recovery brain slice technique using an optimized NMDG artificial cerebrospinal fluid (aCSF) media formulation and enhanced procedure to reliably obtain healthy brain slices for patch clamp electrophysiology...
February 26, 2018: Journal of Visualized Experiments: JoVE
Masahiko Mukaino, Kei Ohtsuka, Hiroki Tanikawa, Fumihiro Matsuda, Junya Yamada, Norihide Itoh, Eiichi Saitoh
Three-dimensional gait analysis (3DGA) is shown to be a useful clinical tool for the evaluation of gait abnormality due to movement disorders. However, the use of 3DGA in actual clinics remains uncommon. Possible reasons could include the time-consuming measurement process and difficulties in understanding measurement results, which are often presented using a large number of graphs. Here we present a clinician-friendly 3DGA method developed to facilitate the clinical use of 3DGA. This method consists of simplified preparation and measurement processes that can be performed in a short time period in clinical settings and intuitive results presentation to facilitate clinicians' understanding of results...
March 4, 2018: Journal of Visualized Experiments: JoVE
Sandra Claes, Thomas D'huys, Anneleen Van Hout, Dominique Schols, Tom Van Loy
G protein-coupled receptors (GPCRs) are of great importance to the pharmaceutical industry as they are involved in many human diseases and include well-validated targets for therapeutic intervention. Discovery of lead compounds, including small synthetic molecules, that specifically inhibit the receptor's function, is an important initial step in drug development and relies on sensitive, specific, and robust cell-based assays. Here, we describe a kinetic cellular assay with a fluorescent readout primarily designed to identify receptor-specific antagonists that inhibit the intracellular Ca2+ release evoked upon the activation of the CXC chemokine receptor 4 (CXCR4) by its endogenous ligand, the CXC chemokine ligand 12 (CXCL12)...
February 20, 2018: Journal of Visualized Experiments: JoVE
Gizem Ertürk, Rolf Lood
The ability to detect and quantitate biomolecules in complex solutions has always been highly sought-after within natural science; being used for the detection of biomarkers, contaminants, and other molecules of interest. A commonly used technique for this purpose is the Enzyme-linked Immunosorbent Assay (ELISA), where often one antibody is directed towards a specific target molecule, and a second labeled antibody is used for the detection of the primary antibody, allowing for the absolute quantification of the biomolecule under study...
February 16, 2018: Journal of Visualized Experiments: JoVE
Ariel Finkielsztein, Lorraine Mascarenhas, Veronika Butin-Israeli, Ronen Sumagin
Polymorphonuclear neutrophil-derived microparticles (PMN)-MPs) are lipid bilayer, spherical microvesicles with sizes ranging from 50-1,000 nm in diameter. MPs are a newly evolving, important part of cell-to-cell communication and signaling machinery. Because of their size and the nature of their release, until recently MP existence was overlooked. However, with improved technology and analytical methods their function in health and disease is now emerging. The protocols presented here are aimed at isolating and characterizing PMN-MPs by flow cytometry and immunoblotting...
March 2, 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
Akile Sarıoğlu Büke, Özlem Sürel Karabilgin Öztürkçü, Yusuf Yılmaz, İskender Sayek
BACKGROUND: Professionalism education is one of the major elements of surgical residency education. AIMS: To evaluate the studies on core professionalism education programs in surgical professionalism education. STUDY DESIGN: Systematic review. METHODS: This systematic literature review was performed to analyze core professionalism programs for surgical residency education published in English with at least three of the following features: program developmental model/instructional design method, aims and competencies, methods of teaching, methods of assessment, and program evaluation model or method...
March 15, 2018: Balkan Medical Journal
Trudy Mooren, Yoke Rabaia, Suzan Mitwalli, Relinde Reiffers, Rosemarijn Koenen, Marguerithe de Man
BACKGROUND: Families with a child who has a disability have extra difficulties, particularly when services are hard to reach or less available. In a collaborative project, the Institute of Community and Public Health, the Palestinian community-based rehabilitation programme, and international non-governmental organisations cooperated to share and develop expertise and knowledge on increasing families' resilience through establishing family groups. This contribution focuses on the use of the Multi-Family Approach (MFA) in a Palestinian context...
February 21, 2018: Lancet
Sanaa Al Najjar, Tamer Al Shaer
BACKGROUND: To meet the emerging needs of the increasing numbers of patients with non-communicable diseases and to provide optimum care with optimum contact time and minimum waiting time, as stated in UNRWA guidelines, the mobile phone text messaging system was implemented in UNRWA centres to remind patients of upcoming appointments and to thereby improve the quality of care for vulnerable patients and regulate the work load in the clinics for non-communicable diseases. The aim of this study was to assess the causes for lack of adherence to the appointment system at UNRWA centres...
February 21, 2018: Lancet
Said Alyacoubi, Yousef Abuowda, Loai Albarqouni, Bettina Böttcher, Khamis Elessi
BACKGROUND: Disease severity scores such as CURB-65 are often used to guide the management of patients with community-acquired pneumonia. Early and adequate empirical antibiotic treatment reduces mortality. The aim of this study was to examine the severity assessment and management of patients presenting with community-acquired pneumonia at the European Gaza Hospital in the Gaza Strip and to compare this to the best available evidence. METHODS: Medical records of all patients admitted to the European Gaza Hospital with a diagnosis of community-acquired pneumonia between Dec 1, 2015, and March 31, 2016, were reviewed retrospectively...
February 21, 2018: Lancet
Mohammed B Sarhan, Rula Ghandour, Niveen M E Abu Rmeileh
BACKGROUND: The burden of type 2 diabetes is increasing rapidly in the occupied Palestinian territory. Different counselling interventions have been applied worldwide to reduce HbA1c concentrations in patients with type 2 diabetes. Achieving good glycaemic control is important for prevention of complications of type 2 diabetes. The aim of this modelling study was to assess the effectiveness of different counselling interventions in improving glycaemic control in patients with type 2 diabetes...
February 21, 2018: Lancet
Mohammed N Alkhatib, Tamer Abd-Alghafoor, AlaaEldeen Elmassry, Loai Albarqouni, Bettina Böttcher, Maha Alfaqawi
BACKGROUND: Stroke is a leading cause of morbidity and mortality worldwide. The aim of this study was to assess the standard of care for patients with acute ischaemic stroke at the internal medicine department of Nasser Hospital, Gaza Strip. METHODS: For this retrospective clinical audit, we selected a random sample of 100 medical records for patients with stroke who were admitted to Nasser Hospital between January and August, 2016. Clinical practice was compared with the recommendations in the 2013 American Heart Association and American Stroke Association guidelines...
February 21, 2018: Lancet
Koren Hanson, Kevin P Haggerty, Charles B Fleming, Martie L Skinner, Mary Casey-Goldstein, W Alex Mason, Ronald W Thompson, Cleve Redmond
OBJECTIVE: As legalization of nonmedical retail marijuana increases, states are implementing public health campaigns designed to prevent increases in youth marijuana use. This study investigated which types of marijuana-related messages were rated most highly by parents and their teens and whether these preferences differed by age and marijuana use. METHOD: Nine marijuana-focused messages were developed as potential radio, newspaper, or television announcements...
March 2018: Journal of Studies on Alcohol and Drugs
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
Erica M Eaton, Molly Magill, Christy Capone, Margaret A Cramer, Nadine R Mastroleo, Racheal Reavy, Brian Borsari
OBJECTIVE: Colleges continue to experience a high number of referred students because of campus alcohol violations. Subsequently, there has been a trend to use peer-implemented minimal interventions (PMIs), often using motivational interviewing (MI). However, little is known about how PMIs facilitate behavior change. This study aims to examine the mechanisms of behavior change within PMIs and their influence on alcohol reduction among mandated students. METHOD: Participants (N = 146; mean age = 18...
March 2018: Journal of Studies on Alcohol and Drugs
John W Finney
OBJECTIVE: In recent years, a shift has occurred from identifying variables that mediate the effects of psychosocial interventions for problematic alcohol use to trying to identify effective mechanisms of behavior change (MOBCs) that lead to better drinking-related and other outcomes. Although implementing interventions targeting specific MOBCs has considerable conceptual and intuitive appeal, it is important that strong empirical evidence be available that supports such implementation...
March 2018: Journal of Studies on Alcohol and Drugs
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