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https://www.readbyqxmd.com/read/28334800/optimization-of-a-novel-biophysical-model-using-large-scale-in-vivo-antisense-hybridization-data-displays-improved-prediction-capabilities-of-structurally-accessible-rna-regions
#1
Jorge Vazquez-Anderson, Mia K Mihailovic, Kevin C Baldridge, Kristofer G Reyes, Katie Haning, Seung Hee Cho, Paul Amador, Warren B Powell, Lydia M Contreras
Current approaches to design efficient antisense RNAs (asRNAs) rely primarily on a thermodynamic understanding of RNA-RNA interactions. However, these approaches depend on structure predictions and have limited accuracy, arguably due to overlooking important cellular environment factors. In this work, we develop a biophysical model to describe asRNA-RNA hybridization that incorporates in vivo factors using large-scale experimental hybridization data for three model RNAs: a group I intron, CsrB and a tRNA. A unique element of our model is the estimation of the availability of the target region to interact with a given asRNA using a differential entropic consideration of suboptimal structures...
February 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334030/measuring-mortality-due-to-hiv-associated-tuberculosis-among-adults-in-south-africa-comparing-verbal-autopsy-minimally-invasive-autopsy-and-research-data
#2
Aaron S Karat, Mpho Tlali, Katherine L Fielding, Salome Charalambous, Violet N Chihota, Gavin J Churchyard, Yasmeen Hanifa, Suzanne Johnson, Kerrigan McCarthy, Neil A Martinson, Tanvier Omar, Kathleen Kahn, Daniel Chandramohan, Alison D Grant
BACKGROUND: The World Health Organization (WHO) aims to reduce tuberculosis (TB) deaths by 95% by 2035; tracking progress requires accurate measurement of TB mortality. International Classification of Diseases (ICD) codes do not differentiate between HIV-associated TB and HIV more generally. Verbal autopsy (VA) is used to estimate cause of death (CoD) patterns but has mostly been validated against a suboptimal gold standard for HIV and TB. This study, conducted among HIV-positive adults, aimed to estimate the accuracy of VA in ascertaining TB and HIV CoD when compared to a reference standard derived from a variety of clinical sources including, in some, minimally-invasive autopsy (MIA)...
2017: PloS One
https://www.readbyqxmd.com/read/28334006/assessing-various-infrared-ir-microscopic-imaging-techniques-for-post-mortem-interval-evaluation-of-human-skeletal-remains
#3
Claudia Woess, Seraphin Hubert Unterberger, Clemens Roider, Monika Ritsch-Marte, Nadin Pemberger, Jan Cemper-Kiesslich, Petra Hatzer-Grubwieser, Walther Parson, Johannes Dominikus Pallua
Due to the influence of many environmental processes, a precise determination of the post-mortem interval (PMI) of skeletal remains is known to be very complicated. Although methods for the investigation of the PMI exist, there still remains much room for improvement. In this study the applicability of infrared (IR) microscopic imaging techniques such as reflection-, ATR- and Raman- microscopic imaging for the estimation of the PMI of human skeletal remains was tested. PMI specific features were identified and visualized by overlaying IR imaging data with morphological tissue structures obtained using light microscopy to differentiate between forensic and archaeological bone samples...
2017: PloS One
https://www.readbyqxmd.com/read/28333010/quantitative-assessment-of-breast-cosmetic-outcome-after-whole-breast-irradiation
#4
Jay P Reddy, Xiudong Lei, Sheng-Cheng Huang, Krista M Nicklaus, Michelle C Fingeret, Simona F Shaitelman, Kelly K Hunt, Thomas A Buchholz, Fatima Merchant, Mia K Markey, Benjamin D Smith
PURPOSE: To measure, by quantitative analysis of digital photographs, breast cosmetic outcome within the setting of a randomized trial of conventionally fractionated (CF) and hypofractionated (HF) whole-breast irradiation (WBI), to identify how quantitative cosmesis metrics were associated with patient- and physician-reported cosmesis and whether they differed by treatment arm. METHODS AND MATERIALS: From 2011 to 2014, 287 women aged ≥40 with ductal carcinoma in situ or early invasive breast cancer were randomized to HF-WBI (42...
April 1, 2017: International Journal of Radiation Oncology, Biology, Physics
https://www.readbyqxmd.com/read/28330427/comparison-of-airway-response-in-na%C3%A3-ve-and-ovalbumin-sensitized-mice-during-short-term-inhalation-exposure-to-chlorine
#5
Mia Johansson, Åsa Gustafsson, Gunnar Johanson, Mattias Öberg
OBJECTIVE: It has been suggested that asthmatics are more susceptible than healthy individuals to airborne irritating chemicals in general. However, there is limited human data available to support this hypothesis due to ethical and practical difficulties. We explored a murine model of ovalbumin (OVA)-induced airway inflammation to study susceptibility during acute exposure to chemicals with chlorine as a model substance. METHODS: Naïve and OVA sensitized female BALB/c mice were exposed to chlorine at four different concentrations (0, 5, 30 and 80 ppm) for 15 minutes with online recording of the respiratory function by plethysmography...
February 2017: Inhalation Toxicology
https://www.readbyqxmd.com/read/28329761/somatic-mutations-reveal-asymmetric-cellular-dynamics-in-the-early-human-embryo
#6
Young Seok Ju, Inigo Martincorena, Moritz Gerstung, Mia Petljak, Ludmil B Alexandrov, Raheleh Rahbari, David C Wedge, Helen R Davies, Manasa Ramakrishna, Anthony Fullam, Sancha Martin, Christopher Alder, Nikita Patel, Steve Gamble, Sarah O'Meara, Dilip D Giri, Torril Sauer, Sarah E Pinder, Colin A Purdie, Åke Borg, Henk Stunnenberg, Marc van de Vijver, Benita K T Tan, Carlos Caldas, Andrew Tutt, Naoto T Ueno, Laura J van 't Veer, John W M Martens, Christos Sotiriou, Stian Knappskog, Paul N Span, Sunil R Lakhani, Jórunn Erla Eyfjörd, Anne-Lise Børresen-Dale, Andrea Richardson, Alastair M Thompson, Alain Viari, Matthew E Hurles, Serena Nik-Zainal, Peter J Campbell, Michael R Stratton
Somatic cells acquire mutations throughout the course of an individual's life. Mutations occurring early in embryogenesis are often present in a substantial proportion of, but not all, cells in postnatal humans and thus have particular characteristics and effects. Depending on their location in the genome and the proportion of cells they are present in, these mosaic mutations can cause a wide range of genetic disease syndromes and predispose carriers to cancer. They have a high chance of being transmitted to offspring as de novo germline mutations and, in principle, can provide insights into early human embryonic cell lineages and their contributions to adult tissues...
March 22, 2017: Nature
https://www.readbyqxmd.com/read/28326182/birt-hogg-dub%C3%A3-syndrome-a-case-report-and-a-review-of-the-literature
#7
REVIEW
Dea Kejlberg Jensen, Anders Villumsen, Anne-Bine Skytte, Mia Gebauer Madsen, Mette Sommerlund, Elisabeth Bendstrup
Background: Birt-Hogg-Dubé syndrome (BHDS) is a rare autosomal dominant inherited syndrome caused by mutations in the folliculin coding gene (FLCN). The clinical manifestations of the syndrome involve the skin, lungs, and kidneys. Because of the rarity of the syndrome, guidelines for diagnosis and management of the patients with BHDS are lacking. Objective: To present a case story and a review of the literature on BHDS in order to give an update on genetics, clinical manifestations, diagnosis, treatment, prognosis and follow-up strategies...
2017: European Clinical Respiratory Journal
https://www.readbyqxmd.com/read/28325361/warthin-like-papillary-renal-cell-carcinoma-clinicopathologic-morphologic-immunohistochemical-and-molecular-genetic-analysis-of-11-cases
#8
Faruk Skenderi, Monika Ulamec, Tomas Vanecek, Petr Martinek, Reza Alaghehbandan, Maria Pane Foix, Iva Babankova, Delia Perez Montiel, Isabel Alvarado-Cabrero, Marian Svajdler, Pavol Dubinský, Dana Cempirkova, Michal Pavlovsky, Semir Vranic, Ondrej Daum, Ondrej Ondic, Kristyna Pivovarcikova, Kvetoslava Michalova, Milan Hora, Pavla Rotterova, Adela Stehlikova, Martin Dusek, Michal Michal, Ondrej Hes
Oncocytic papillary renal cell carcinoma (PRCC) is a distinct subtype of PRCC, listed as a possible new variant of PRCC in the 2016 WHO classification. It is composed of papillae aligned by large single-layered eosinophilic cells showing linearly arranged oncocytoma-like nuclei. We analyzed clinicopathologic, morphologic, immunohistochemical and molecular-genetic characteristics of 11 oncocytic PRCCs with prominent tumor lymphocytic infiltrate, morphologically resembling Warthin's tumor. The patients were predominantly males (8/11, 73%), with an average age of 59years (range 14-76), and a mean tumor size of 7cm (range 1-22cm)...
April 2017: Annals of Diagnostic Pathology
https://www.readbyqxmd.com/read/28324093/association-between-radiation-therapy-surgery-or-observation-for-localized-prostate-cancer-and-patient-reported-outcomes-after-3-years
#9
Daniel A Barocas, JoAnn Alvarez, Matthew J Resnick, Tatsuki Koyama, Karen E Hoffman, Mark D Tyson, Ralph Conwill, Dan McCollum, Matthew R Cooperberg, Michael Goodman, Sheldon Greenfield, Ann S Hamilton, Mia Hashibe, Sherrie H Kaplan, Lisa E Paddock, Antoinette M Stroup, Xiao-Cheng Wu, David F Penson
Importance: Understanding the adverse effects of contemporary approaches to localized prostate cancer treatment could inform shared decision making. Objective: To compare functional outcomes and adverse effects associated with radical prostatectomy, external beam radiation therapy (EBRT), and active surveillance. Design, Setting, and Participants: Prospective, population-based, cohort study involving 2550 men (≤80 years) diagnosed in 2011-2012 with clinical stage cT1-2, localized prostate cancer, with prostate-specific antigen levels less than 50 ng/mL, and enrolled within 6 months of diagnosis...
March 21, 2017: JAMA: the Journal of the American Medical Association
https://www.readbyqxmd.com/read/28323968/impaired-glycine-mia-in-type-2-diabetes-and-potential-mechanisms-contributing-to-glucose-homeostasis
#10
Richard Yan-Do, Patrick E MacDonald
The onset and/or progression of type 2 diabetes (T2D) can be prevented if intervention is early enough. As such, much effort has been placed on the search for indicators predictive of pre-diabetes and disease onset or progression. An increasing body of evidence suggests that changes in plasma glycine may be one such biomarker. Circulating glycine levels are consistently low in patients with T2D. Levels of this non-essential amino acid correlate negatively with obesity and insulin resistance. Plasma glycine correlates positively with glucose disposal, and rises with interventions such as exercise and bariatric surgery that improve glucose homeostasis...
March 15, 2017: Endocrinology
https://www.readbyqxmd.com/read/28322282/maternal-immune-activation-dysregulation-of-the-fetal-brain-transcriptome-and-relevance-to-the-pathophysiology-of-autism-spectrum-disorder
#11
M V Lombardo, H M Moon, J Su, T D Palmer, E Courchesne, T Pramparo
Maternal immune activation (MIA) via infection during pregnancy is known to increase risk for autism spectrum disorder (ASD). However, it is unclear how MIA disrupts fetal brain gene expression in ways that may explain this increased risk. Here we examine how MIA dysregulates rat fetal brain gene expression (at a time point analogous to the end of the first trimester of human gestation) in ways relevant to ASD-associated pathophysiology. MIA downregulates expression of ASD-associated genes, with the largest enrichments in genes known to harbor rare highly penetrant mutations...
March 21, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28321160/mir-1181-inhibits-invasion-and-proliferation-via-stat3-in-pancreatic-cancer
#12
Jie Wang, Xing-Jun Guo, You-Ming Ding, Jian-Xin Jiang
AIM: To examine the role of microRNA 1181 (miR-1181) in invasion and proliferation in pancreatic cancer. METHODS: We analyzed the expression of miR-1181 in several pancreatic cancer cell lines and generated stable MIA-PaCa-2 and PANC-1 cell lines with up-regulated miR-1181 expression using an adenovirus delivery system. We then investigated miR-1181's effect on invasion and proliferation of pancreatic cancer cells by transwell assay, wound healing assay, cell counting kit-8 assay and colony-forming assay, and explored any underlying mechanisms by western bolt...
March 7, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/28320891/the-normal-ranges-of-cardiovascular-parameters-measured-using-the-ultrasonic-cardiac-output-monitor
#13
Giles N Cattermole, P Y Mia Leung, Grace Y L Ho, Peach W S Lau, Cangel P Y Chan, Stewart S W Chan, Brendan E Smith, Colin A Graham, Timothy H Rainer
The ultrasonic cardiac output monitor (USCOM) is a noninvasive transcutaneous continuous wave Doppler method for assessing hemodynamics. There are no published reference ranges for normal values in adults (aged 18-60 years) for this device. This study aimed to (1) measure cardiovascular indices using USCOM in healthy adults aged 18-60 years; (2) combine these data with those for healthy children (aged 0-12), adolescents (aged 12-18), and the elderly (aged over 60) from our previously published studies in order to present normal ranges for all ages, and (3) establish normal ranges of USCOM-derived variables according to both weight and age...
March 2017: Physiological Reports
https://www.readbyqxmd.com/read/28320059/effects-of-treadmill-exercise-on-advanced-osteoarthritis-pain-in-rats
#14
Joshua Allen, Ian Imbert, Joshua Havelin, Terry Henderson, Glenn Stevenson, Lucy Liaw, Tamara King
OBJECTIVE: Exercise is commonly recommended for patients with osteoarthritis (OA) pain. However, whether exercise is beneficial in ameliorating persistent NSAID-resistant ongoing pain associated with advanced OA is unknown. METHODS: Rats treated with intra-articular monosodium iodoacetate (MIA) or saline underwent treadmill exercise or remained sedentary starting 10 days post-injection. Tactile sensory thresholds and weight bearing were assessed followed by radiographs at weekly intervals...
March 20, 2017: Arthritis & Rheumatology
https://www.readbyqxmd.com/read/28319181/correction-past1-modulates-drosophila-eye-development
#15
Orly Dorot, Hermann Steller, Daniel Segal, Mia Horowitz
[This corrects the article DOI: 10.1371/journal.pone.0169639.].
2017: PloS One
https://www.readbyqxmd.com/read/28316773/vitamin-d-treatment-during-pregnancy-prevents-autism-related-phenotypes-in-a-mouse-model-of-maternal-immune-activation
#16
Stephanie Vuillermot, Wei Luan, Urs Meyer, Darryl Eyles
BACKGROUND: Prenatal exposure to infection is a recognized environmental risk factor for neuropsychiatric disorders of developmental origins such as autism or schizophrenia. Experimental work in animals indicates that this link is mediated by maternal immune activation (MIA) involving interactions between cytokine-associated inflammatory events, oxidative stress, and other pathophysiological processes such as hypoferremia and zinc deficiency. Maternal administration of the viral mimic polyriboinosinic-polyribocytidylic acid (poly(I:C)) in mice produces several behavioral phenotypes in adult offspring of relevance to autism spectrum disorder (ASD) and other neurodevelopmental disorders...
2017: Molecular Autism
https://www.readbyqxmd.com/read/28315366/amygdala-functional-connectivity-is-associated-with-locus-of-control-in-the-context-of-cognitive-aging
#17
Ping Ren, Mia Anthony, Benjamin P Chapman, Kathi Heffner, Feng Lin
Locus of control (LOC) measures the extent to which individuals perceive control over their lives. Those with a more "internal" LOC feel self-sufficient and able to determine important aspects of their own future, while those with a more "external" LOC feel that their lives are governed by events beyond their control. Reduced internal LOC and increased external LOC have been found in cognitive disorders, but the neural substrates of these control perceptions are yet unknown. In the present study, we explored the relationship between amygdala functional connectivity and LOC in 18 amnestic mild cognitive impairment (MCI) and age-, sex-, and education-matched, 22 cognitively healthy controls (HC)...
March 14, 2017: Neuropsychologia
https://www.readbyqxmd.com/read/28306719/chromosome-19q13-disruption-alters-expressions-of-cyp2a7-mia-and-mia-rab4b-lncrna-and-contributes-to-fap-like-phenotype-in-apc-mutation-negative-familial-colorectal-cancer-patients
#18
Lai Fun Thean, Yu Hui Wong, Michelle Lo, Carol Loi, Min Hoe Chew, Choong Leong Tang, Peh Yean Cheah
Familial adenomatous polyposis (FAP) is an autosomal-dominantly inherited form of colorectal cancer (CRC) caused by mutation in the adenomatous polyposis coli (APC) gene. Our ability to exhaustively screen for APC mutations identify microsatellite-stable and APC-mutation negative familial CRC patients, enabling us to search for novel genes. We performed genome-wide scan on two affected siblings of one family and 88 ethnicity- and gender-matched healthy controls to identify deletions shared by the siblings. Combined loss of heterozygosity, copy number and allelic-specific copy number analysis uncovered 5 shared deletions...
2017: PloS One
https://www.readbyqxmd.com/read/28300113/global-warming-and-recurrent-mass-bleaching-of-corals
#19
Terry P Hughes, James T Kerry, Mariana Álvarez-Noriega, Jorge G Álvarez-Romero, Kristen D Anderson, Andrew H Baird, Russell C Babcock, Maria Beger, David R Bellwood, Ray Berkelmans, Tom C Bridge, Ian R Butler, Maria Byrne, Neal E Cantin, Steeve Comeau, Sean R Connolly, Graeme S Cumming, Steven J Dalton, Guillermo Diaz-Pulido, C Mark Eakin, Will F Figueira, James P Gilmour, Hugo B Harrison, Scott F Heron, Andrew S Hoey, Jean-Paul A Hobbs, Mia O Hoogenboom, Emma V Kennedy, Chao-Yang Kuo, Janice M Lough, Ryan J Lowe, Gang Liu, Malcolm T McCulloch, Hamish A Malcolm, Michael J McWilliam, John M Pandolfi, Rachel J Pears, Morgan S Pratchett, Verena Schoepf, Tristan Simpson, William J Skirving, Brigitte Sommer, Gergely Torda, David R Wachenfeld, Bette L Willis, Shaun K Wilson
During 2015-2016, record temperatures triggered a pan-tropical episode of coral bleaching, the third global-scale event since mass bleaching was first documented in the 1980s. Here we examine how and why the severity of recurrent major bleaching events has varied at multiple scales, using aerial and underwater surveys of Australian reefs combined with satellite-derived sea surface temperatures. The distinctive geographic footprints of recurrent bleaching on the Great Barrier Reef in 1998, 2002 and 2016 were determined by the spatial pattern of sea temperatures in each year...
March 15, 2017: Nature
https://www.readbyqxmd.com/read/28299837/mathiomica-msviewer-a-dynamic-viewer-for-mass-spectrometry-files-for-mathematica
#20
Raeuf Roushangar, George I Mias
MathIOmica-MSViewer is an add-on graphical user interface utility for the Mathematica software system which facilitates the visualization and exploration of spectra from open format mass spectrometry files (mzXML and mzML standard community formats). The viewer was designed for simplicity and handling of large mass spectrometry data files. To facilitate searches, users may use search filters for the spectra based on mass to charge ratios and retention times, and visualize precursor spectra associated to a parent spectrum...
March 15, 2017: Journal of Mass Spectrometry: JMS
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