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Clarity for mapping

Alon Greenbaum, Ken Y Chan, Tatyana Dobreva, David Brown, Deepak H Balani, Rogely Boyce, Henry M Kronenberg, Helen J McBride, Viviana Gradinaru
Bone tissue harbors unique and essential physiological processes, such as hematopoiesis, bone growth, and bone remodeling. To enable visualization of these processes at the cellular level in an intact environment, we developed "Bone CLARITY," a bone tissue clearing method. We used Bone CLARITY and a custom-built light-sheet fluorescence microscope to detect the endogenous fluorescence of Sox9-tdTomato(+) osteoprogenitor cells in the tibia, femur, and vertebral column of adult transgenic mice. To obtain a complete distribution map of these osteoprogenitor cells, we developed a computational pipeline that semiautomatically detects individual Sox9-tdTomato(+) cells in their native three-dimensional environment...
April 26, 2017: Science Translational Medicine
Hannah M O'Rourke, Souraya Sidani
Social connectedness is critical to older adults' well-being, but is defined inconsistently and its determinants and outcomes have not been comprehensively described. The current scoping review mapped the definitions, determinants, and outcomes of social connectedness for older adults. By identifying the conceptual features described in most articles, social connectedness was defined as: the opposite of loneliness, a subjective evaluation of the extent to which one has meaningful, close, and constructive relationships with others (i...
April 11, 2017: Journal of Gerontological Nursing
Yi Feng, Peng Cui, Xiaowei Lu, Brian Hsueh, Fredrik Möller Billig, Livia Zarnescu Yanez, Raju Tomer, Derek Boerboom, Peter Carmeliet, Karl Deisseroth, Aaron J W Hsueh
Optimal distribution of heterogeneous organelles and cell types within an organ is essential for physiological processes. Unique for the ovary, hormonally regulated folliculogenesis, ovulation, luteal formation/regression and associated vasculature changes lead to tissue remodeling during each reproductive cycle. Using the CLARITY approach and marker immunostaining, we identified individual follicles and corpora lutea in intact ovaries. Monitoring lifetime changes in follicle populations showed age-dependent decreases in total follicles and percentages of advanced follicles...
March 23, 2017: Scientific Reports
Deborah Murdoch-Eaton, Lucy Bowen
PURPOSE: The "educational alliance" concept articulates a collaborative framework to facilitate effective feedback through transparency of opportunities aligned with learner stage and intended educational outcomes. Using this framework, we evaluated feedback across a 5 year undergraduate medical program to support embedding a successful learner - teacher "educational alliance". METHOD: A comprehensive mapping exercise used an iterative action research process of source documentary analysis, consultations with key curriculum stakeholders and qualitative analysis...
March 10, 2017: Medical Teacher
M Najafi, A El Kaffas, B Han, D Cooper, S Hancock, D Hristov
PURPOSE: Clarity Autoscan ultrasound monitoring system allows acquisition of raw radiofrequency (RF) ultrasound data prior and during radiotherapy. This enables the computation of 3D Quantitative Ultrasound (QUS) tissue parametric maps from. We aim to evaluate whether QUS parameters undergo changes with radiotherapy and thus potentially be used as early predictors and/or markers of treatment response in prostate cancer patients. METHODS: In-vivo evaluation was performed under IRB protocol to allow data collection in prostate patients treated with VMAT whereby prostate was imaged through the acoustic window of the perineum...
June 2016: Medical Physics
Jiwon Woo, Mirae Lee, Jeong Min Seo, Hyo Suk Park, Yong Eun Cho
Recently, a bio-electrochemical technique known as CLARITY was reported for three-dimensional phenotype mapping within transparent tissues, allowing clearer whole-body and organ visualization with CB-perfusion (CUBIC) and leading to the development of whole-body clearing and transparency of intact tissues with the PACT (passive clarity technique) and PARS (perfusion-assisted agent release in situ) methodologies. We evaluated the structure-function relationships in circuits of the whole central nervous system (CNS) and various internal organs using improved methods with optimized passive clarity...
December 2, 2016: Experimental & Molecular Medicine
Jin Chen, Zheng-Wen Shen, Wei-Wen Xi, Yu Zhang
Four-dimensional computer tomography (4D-CT) has a great value in lung cancer radiotherapy for its capability in providing lung information with respiratory motion. We employed a global graph cuts super-resolution (SR) reconstruction method to reconstruct high-resolution lung 4D-CT images. First, the high-resolution images reconstruction energy function was built based on a Maximum a posteriori Markov Random Field (MAP-MRF) formulation. The energy function was then transformed to a graph formulation, which was solved using graph cut algorithm...
August 20, 2016: Nan Fang Yi Ke da Xue Xue Bao, Journal of Southern Medical University
Emily S Jentes, R Ryan Lash, Michael A Johansson, Tyler M Sharp, Ronnie Henry, Oliver J Brady, Mark J Sotir, Simon I Hay, Harold S Margolis, Gary W Brunette
BACKGROUND: International travel can expose travellers to pathogens not commonly found in their countries of residence, like dengue virus. Travellers and the clinicians who advise and treat them have unique needs for understanding the geographic extent of risk for dengue. Specifically, they should assess the need for prevention measures before travel and ensure appropriate treatment of illness post-travel. Previous dengue-risk maps published in the Centers for Disease Control and Prevention's Yellow Book lacked specificity, as there was a binary (risk, no risk) classification...
June 2016: Journal of Travel Medicine
A Murray, L Daines, D Archibald, R Hawkes, L Grant, N Mutrie
INTRODUCTION: Golf is a sport played in 206 countries worldwide by over 50 million people. It is possible that participation in golf, which is a form of physical activity, may be associated with effects on longevity, the cardiovascular, metabolic and musculoskeletal systems, as well as on mental health and well-being. We outline our scoping review protocol to examine the relationships and effects of golf on physical and mental health. METHODS AND ANALYSIS: Best practice methodological frameworks suggested by Arksey and O'Malley, Levac et al and the Joanna Briggs Institute will serve as our guide, providing clarity and rigour...
June 2016: British Journal of Sports Medicine
Theresa A Harrison, Zhiguo He, Kristin Boggs, Gilles Thuret, Hong-Xiang Liu, Dennis M Defoe
PURPOSE: The corneal endothelium is widely believed to consist of geometrically regular cells interconnected by junctional complexes. However, while en face visualization of the endothelial apical surface reveals characteristic polygonal borders, the overall form of the component cells has rarely been observed. METHODS: To visualize the shape of individual endothelial cells within the native monolayer, two independent Cre/LoxP-based cell labeling approaches were used...
2016: Molecular Vision
M Depypere, V Saegeman, K Lagrou
Different reports of Pneumocystis jirovecii pneumonia (PcP) outbreaks on oncology and transplant units suggest the possibility of a person-to-person transmission. Based on these reports, we searched retrospectively for possible PcP clusters in UZ Leuven in 2013. A movement and transmission map was established for all patients (n = 21) with a positive PcP PCR on BAL fluid. BAL fluid samples from all patients with a positive PCR on the mitochondrial large subunit mRNA of P. jirovecii and possible cross exposure were typed with multilocus sequence typing (MLST)...
June 2016: European Journal of Clinical Microbiology & Infectious Diseases
Brigit Obrist, Marcel Tanner, Trudy Harpham
Urbanisation remains a challenge in the new millennium and will continue to have important implications for human health. This leads to lively debates in the field of international health, but with minimal engagement of anthropology. To stimulate active involvement, our paper highlights main issues addressed in this special issue and maps directions for future research. Our collection of papers addresses hot topics in urban health research, ranging from everyday health practice to mental health, chronic and degenerative illness, old age and social safety networks, and examines them from a complementary, anthropological perspective...
December 1, 2003: Anthropology & Medicine
Zhe He, Michael Halper, Yehoshua Perl, Gai Elhanan
As SNOMED usage becomes more ingrained within applications, its range of concept descriptors, and particularly its synonym adequacy, becomes more important. A simulated clinical scenario involving various term-based concept searches is used to assess whether SNOMED's concept descriptors provide sufficient differentiation to enable possible concept selection between similar terms. Four random samples from different SNOMED concept populations are utilized. Of particular interest are concepts mapped duplicately into UMLS concepts due to shared term patterns...
October 2012: MIX-HS'12: Proceedings of the 2nd International Workshop on Managing Interoperability and Complexity in Health Systems October 29, 2012, Maui, Hawaii, USA / Sponsored By ACM SIGIR & ACM SIGWEB ; Program Chairs: Cui Tao, Mayo Clinic, Di..
Eunsoo Lee, Jungyoon Choi, Youhwa Jo, Joo Yeon Kim, Yu Jin Jang, Hye Myeong Lee, So Yeun Kim, Ho-Jae Lee, Keunchang Cho, Neoncheol Jung, Eun Mi Hur, Sung Jin Jeong, Cheil Moon, Youngshik Choe, Im Joo Rhyu, Hyun Kim, Woong Sun
Understanding the structural organization of organs and organisms at the cellular level is a fundamental challenge in biology. This task has been approached by reconstructing three-dimensional structure from images taken from serially sectioned tissues, which is not only labor-intensive and time-consuming but also error-prone. Recent advances in tissue clearing techniques allow visualization of cellular structures and neural networks inside of unsectioned whole tissues or the entire body. However, currently available protocols require long process times...
January 11, 2016: Scientific Reports
Raju Tomer, Matthew Lovett-Barron, Isaac Kauvar, Aaron Andalman, Vanessa M Burns, Sethuraman Sankaran, Logan Grosenick, Michael Broxton, Samuel Yang, Karl Deisseroth
The goal of understanding living nervous systems has driven interest in high-speed and large field-of-view volumetric imaging at cellular resolution. Light sheet microscopy approaches have emerged for cellular-resolution functional brain imaging in small organisms such as larval zebrafish, but remain fundamentally limited in speed. Here, we have developed SPED light sheet microscopy, which combines large volumetric field-of-view via an extended depth of field with the optical sectioning of light sheet microscopy, thereby eliminating the need to physically scan detection objectives for volumetric imaging...
December 17, 2015: Cell
Mary L Grasmeder, Carl A Verschuur
OBJECTIVES: To assess the perceived pitch and naturalness of popular music by cochlear implant (CI) users. METHODS: Eleven experienced post-lingually deafened adult CI users rated the pitch, naturalness, and clarity of a popular song with 10 frequency allocation settings, including the default. The alternative settings all had logarithmic frequency spacing and frequency shifts of less than one octave compared with the default map. For maps which were perceived as having incorrect pitch, participants adjusted the pitch of the song in real time using a slider, in order to normalize it, and the amount of adjustment was recorded...
September 2015: Cochlear Implants International
Pia Liljamo, Ulla-Mari Kinnunen, Kaija Saranto
BACKGROUND: Various classification schemes have been used for clinical and administrative purposes, but their concepts have seldom been cross-mapped. Cross-mapping is a formal method that can be used for examining existing classifications' validity. AIM: The aim was to cross-map two nursing classifications - the Finnish Classification of Nursing Interventions (FiCNI, version 3.0), developed for structured nursing documentation, and the Oulu Patient Classification (OPCq), created for daily assessment of nursing intensity - and evaluate their mutual consistency...
September 2016: Scandinavian Journal of Caring Sciences
Jennifer B Treweek, Ken Y Chan, Nicholas C Flytzanis, Bin Yang, Benjamin E Deverman, Alon Greenbaum, Antti Lignell, Cheng Xiao, Long Cai, Mark S Ladinsky, Pamela J Bjorkman, Charless C Fowlkes, Viviana Gradinaru
To facilitate fine-scale phenotyping of whole specimens, we describe here a set of tissue fixation-embedding, detergent-clearing and staining protocols that can be used to transform excised organs and whole organisms into optically transparent samples within 1-2 weeks without compromising their cellular architecture or endogenous fluorescence. PACT (passive CLARITY technique) and PARS (perfusion-assisted agent release in situ) use tissue-hydrogel hybrids to stabilize tissue biomolecules during selective lipid extraction, resulting in enhanced clearing efficiency and sample integrity...
November 2015: Nature Protocols
Sofia Boqvist, Lise-Lotte Fernström, Beatrix W Alsanius, Roland Lindqvist
This study investigated the effect of premature browning (PMB) on the survival of Escherichia coli O157:H7 in beef hamburgers after cooking with respect to interior colour of the hamburger and recommendations to cook hamburgers to a core temperature of 71 °C. Assessment of doneness by visual inspection or measurement of internal temperature was compared in terms of survival and the increased relative risk of illness due to PMB was estimated. At the last consume-by-day, hamburgers made from minced meat packaged in 80/20 O2/CO2 (MAP hamburger) and from meat minced at retail packaged in atmospheric condition (control hamburger) were inoculated with a gfp-tagged strain of E...
December 23, 2015: International Journal of Food Microbiology
S Mangaraj, T K Goswami, D K Panda
High value fruits namely, apple (cv. Royal Delicious), guava (cv. Baruipur) and litchi (cv. Shahi) harvested at their commercial maturity were considered for MA packaging to enhance storage life. Polymeric films namely LDPE, BOPP, PVC, PVDC of different thickness were used for MA packaging study and various film characteristics such as gas transmission rates, water vapour transmission rate, clarity, strength and durability were evaluated. Mathematical model was developed based on Arrhenius type equation to predict gas transmission rate (GTR) and the developed model was found to be very good fit with the mean relative deviation modulus value quite less than 10 %...
September 2015: Journal of Food Science and Technology
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