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https://www.readbyqxmd.com/read/28736864/brain-tumor-segmentation-using-holistically-nested-neural-networks-in-mri-images
#1
Ying Zhuge, Andra V Krauze, Holly Ning, Jason Y Cheng, Barbara C Arora, Kevin Camphausen, Robert W Miller
PURPOSE: Gliomas are rapidly progressive, neurologically devastating, largely fatal brain tumors. Magnetic Resonance Imaging (MRI) is a widely used technique employed in the diagnosis and management of gliomas in clinical practice. MRI is also the standard imaging modality used to delineate the brain tumor target as part of treatment planning for the administration of radiation therapy. Despite more than 20 years of research and development, computational brain tumor segmentation in MRI images remains a challenging task...
July 24, 2017: Medical Physics
https://www.readbyqxmd.com/read/28724409/hybrid-assembly-with-long-and-short-reads-improves-discovery-of-gene-family-expansions
#2
Jason R Miller, Peng Zhou, Joann Mudge, James Gurtowski, Hayan Lee, Thiruvarangan Ramaraj, Brian P Walenz, Junqi Liu, Robert M Stupar, Roxanne Denny, Li Song, Namrata Singh, Lyza G Maron, Susan R McCouch, W Richard McCombie, Michael C Schatz, Peter Tiffin, Nevin D Young, Kevin A T Silverstein
BACKGROUND: Long-read and short-read sequencing technologies offer competing advantages for eukaryotic genome sequencing projects. Combinations of both may be appropriate for surveys of within-species genomic variation. METHODS: We developed a hybrid assembly pipeline called "Alpaca" that can operate on 20X long-read coverage plus about 50X short-insert and 50X long-insert short-read coverage. To preclude collapse of tandem repeats, Alpaca relies on base-call-corrected long reads for contig formation...
July 19, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28721204/initial-genome-sequencing-of-the-sugarcane-cp-96-1252-complex-hybrid
#3
Jason R Miller, Kari A Dilley, Derek M Harkins, Manolito G Torralba, Kelvin J Moncera, Karen Beeri, Karrie Goglin, Timothy B Stockwell, Granger G Sutton, Reed S Shabman
The CP 96-1252 cultivar of sugarcane is a complex hybrid of commercial importance. DNA was extracted from lab-grown leaf tissue and sequenced. The raw Illumina DNA sequencing results provide 101 Gbp of genome sequence reads. The dataset is available from https://www.ncbi.nlm.nih.gov/bioproject/PRJNA345486/.
2017: F1000Research
https://www.readbyqxmd.com/read/28708763/day-to-day-experience-in-resolution-of-pain-after-surgery
#4
Timothy T Houle, Scott Miller, Jason E Lang, Jessica L Booth, Regina S Curry, Lynnette Harris, Carol A Aschenbrenner, James C Eisenach
We know little about the individual pain experience of patients recovering from surgery in the first weeks after hospital discharge. Here we examine individual differences in the day-to-day experience after two major surgeries: lower limb total major joint arthroplasty (TJA) and cesarean delivery (CD). Fifty-five TJA patients and 157 CD patients were recruited to complete questionnaires and record their daily pain experiences after surgery. After hospital discharge, patients recorded their pain intensity once daily for 60 days (CD) or twice daily for 2 weeks, once daily for two weeks, weekly for 8 weeks and monthly for 3 months (TJA)...
July 11, 2017: Pain
https://www.readbyqxmd.com/read/28707873/light-activation-of-calcein-inhibits-vesicle-release-of-catecholamines
#5
Brooke A Miller, Jason B Papke, Vytas P Bindokas, Amy B Harkins
Calcein, a fluorescent fluid phase marker, has been used to track and visualize cellular processes such as synaptic vesicle fusion. It is also the fluorophore for Live cells in the commonly used Live/Dead viability assay. In pilot studies designed to determine fusion pore open size and vesicle movement in secretory cells, imaging analysis revealed that calcein reduced the number of vesicles released from the cells when stimulated with nicotine. Using amperometry to detect individual vesicle release events, we show that when calcein is present in the media, the number of vesicles that fuse with the cellular membrane are reduced when cells are stimulated with either nicotine or high K+...
July 14, 2017: ACS Chemical Neuroscience
https://www.readbyqxmd.com/read/28696992/triathlon-medical-coverage-a-guide-for-medical-directors
#6
Chad A Asplund, Thomas K Miller, Lawrence Creswell, Andrew Getzin, Andrew Hunt, John Martinez, Jason Diehl, William D Hiller, Paul Berlin
Interest and participation in triathlon has grown rapidly over the past 20 yr and with this growth, there has been an increase in the number of new events. To maximize the safety of participation, triathlons require medical directors to plan and oversee medical care associated with event participation. Provision of proper medical care requires knowledge of staffing requirements, common triathlon medical conditions, impact of course design, communication skill, and a familiarity of administrative requirements...
July 2017: Current Sports Medicine Reports
https://www.readbyqxmd.com/read/28683970/oxidative-stress-and-cardiovascular-risk-obesity-diabetes-smoking-and-pollution-part-3-of-a-3-part-series
#7
REVIEW
Bernd Niemann, Susanne Rohrbach, Mark R Miller, David E Newby, Valentin Fuster, Jason C Kovacic
Oxidative stress occurs whenever the release of reactive oxygen species (ROS) exceeds endogenous antioxidant capacity. In this paper, we review the specific role of several cardiovascular risk factors in promoting oxidative stress: diabetes, obesity, smoking, and excessive pollution. Specifically, the risk of developing heart failure is higher in patients with diabetes or obesity, even with optimal medical treatment, and the increased release of ROS from cardiac mitochondria and other sources likely contributes to the development of cardiac dysfunction in this setting...
July 11, 2017: Journal of the American College of Cardiology
https://www.readbyqxmd.com/read/28668251/bicycle-trains-cycling-and-physical-activity-a-pilot-cluster-rct
#8
Jason A Mendoza, Wren Haaland, Maya Jacobs, Mark Abbey-Lambertz, Josh Miller, Deb Salls, Winifred Todd, Rachel Madding, Katherine Ellis, Jacqueline Kerr
INTRODUCTION: Increasing children's cycling to school and physical activity are national health goals. The objective was to conduct an RCT of a bicycle train program to assess impact on students' school travel mode and moderate-to-vigorous physical activity (MVPA). STUDY DESIGN: Pilot cluster RCT with randomization at the school level and N=54 participants. SETTING/PARTICIPANTS: Fourth-fifth graders from four public schools serving low-income families in Seattle, WA in 2014 with analyses in 2015-2016...
June 23, 2017: American Journal of Preventive Medicine
https://www.readbyqxmd.com/read/28665414/etx2514-is-a-broad-spectrum-%C3%AE-lactamase-inhibitor-for-the-treatment-of-drug-resistant-gram-negative-bacteria-including-acinetobacter-baumannii
#9
Thomas F Durand-Réville, Satenig Guler, Janelle Comita-Prevoir, Brendan Chen, Neil Bifulco, Hoan Huynh, Sushmita Lahiri, Adam B Shapiro, Sarah M McLeod, Nicole M Carter, Samir H Moussa, Camilo Velez-Vega, Nelson B Olivier, Robert McLaughlin, Ning Gao, Jason Thresher, Tiffany Palmer, Beth Andrews, Robert A Giacobbe, Joseph V Newman, David E Ehmann, Boudewijn de Jonge, John O'Donnell, John P Mueller, Rubén A Tommasi, Alita A Miller
Multidrug-resistant (MDR) bacterial infections are a serious threat to public health. Among the most alarming resistance trends is the rapid rise in the number and diversity of β-lactamases, enzymes that inactivate β-lactams, a class of antibiotics that has been a therapeutic mainstay for decades. Although several new β-lactamase inhibitors have been approved or are in clinical trials, their spectra of activity do not address MDR pathogens such as Acinetobacter baumannii. This report describes the rational design and characterization of expanded-spectrum serine β-lactamase inhibitors that potently inhibit clinically relevant class A, C and D β-lactamases and penicillin-binding proteins, resulting in intrinsic antibacterial activity against Enterobacteriaceae and restoration of β-lactam activity in a broad range of MDR Gram-negative pathogens...
June 30, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28648824/sheath-cell-invasion-and-trans-differentiation-repair-mechanical-damage-caused-by-loss-of-caveolae-in-the-zebrafish-notochord
#10
Jamie Garcia, Jennifer Bagwell, Brian Njaine, James Norman, Daniel S Levic, Susan Wopat, Sara E Miller, Xiaojing Liu, Jason W Locasale, Didier Y R Stainier, Michel Bagnat
The notochord, a conserved axial structure required for embryonic axis elongation and spine development, consists of giant vacuolated cells surrounded by an epithelial sheath [1-3]. During morphogenesis, vacuolated cells maintain their structural integrity despite being under constant mechanical stress [4]. We hypothesized that the high density of caveolae present in vacuolated cells [5, 6] could buffer mechanical tension. Caveolae are 50- to 80-nm membrane invaginations lined by cage-like polygonal structures [7, 8] formed by caveolin 1 (Cav1) or Cav3 and one of the cavin proteins [6, 9-11]...
July 10, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28645855/training-surgical-residents-with-a-haptic-robotic-central-venous-catheterization-simulator
#11
David F Pepley, Adam B Gordon, Mary A Yovanoff, Katelin A Mirkin, Scarlett R Miller, David C Han, Jason Z Moore
OJECTIVE: Ultrasound guided central venous catheterization (CVC) is a common surgical procedure with complication rates ranging from 5 to 21 percent. Training is typically performed using manikins that do not simulate anatomical variations such as obesity and abnormal vessel positioning. The goal of this study was to develop and validate the effectiveness of a new virtual reality and force haptic based simulation platform for CVC of the right internal jugular vein. DESIGN: A CVC simulation platform was developed using a haptic robotic arm, 3D position tracker, and computer visualization...
June 20, 2017: Journal of Surgical Education
https://www.readbyqxmd.com/read/28630710/hdac-inhibitor-conjugated-polymeric-prodrug-micelles-for-doxorubicin-delivery
#12
Suchithra A Senevirathne, Katherine E Washington, Jason B Miller, Michael C Biewer, David Oupicky, Daniel J Siegwart, Mihaela C Stefan
Amphiphilic diblock copolymers bearing histone deacetylase inhibitors (HDACi) (4-phenyl butyric acid and valproic acid) were synthesized by the ring-opening polymerization of γ-4-phenylbutyrate-ε-caprolactone (PBACL), γ-valproate-ε-caprolactone (VPACL), and ε-caprolactone (CL) from a poly(ethylene glycol) macroinitiator (PEG). These amphiphilic diblock copolymers self-assembled into stable pro-drug micelles and demonstrated excellent biocompatibility. High loading of doxorubicin (DOX) up to 5.1 wt% was achieved...
March 21, 2017: Journal of Materials Chemistry. B, Materials for Biology and Medicine
https://www.readbyqxmd.com/read/28630212/a-pilot-study-of-stereotactic-body-radiation-therapy-combined-with-cytoreductive-nephrectomy-for-metastatic-renal-cell-carcinoma
#13
Anurag K Singh, Timothy B Winslow, Mohammad Habiby Kermany, Vincent Goritz, Lilia Heit, Austin Miller, Nicholas C Hoffend, Leighton C Stein, Lalith Kumaraswamy, Graham W Warren, Wiam Bshara, Kunle Odunsi, Junko Matsuzaki, Scott I Abrams, Thomas Schwaab, Jason B Muhitch
<p>While stereotactic body radiation therapy (SBRT) can reduce tumor volumes in metastatic renal cell carcinoma (mRCC) patients, little is known regarding the immunomodulatory effects of high-dose radiation in the tumor microenvironment. The main objectives of this pilot study were to assess the safety and feasibility of nephrectomy following SBRT treatment of mRCC patients and analyze the immunological impact of high-dose radiation.</p> <br /><br />Experimental Design: Human RCC cell lines were irradiated and evaluated for immunomodulation...
June 19, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28624396/hybrid-magnetic-resonance-imaging-and-positron-emission-tomography-with-fluorodeoxyglucose-to-diagnose-active-cardiac-sarcoidosis
#14
Marc R Dweck, Ronan Abgral, Maria Giovanna Trivieri, Philip M Robson, Nicolas Karakatsanis, Venkatesh Mani, Anna Palmisano, Marc A Miller, Anuradha Lala, Helena L Chang, Javier Sanz, Johanna Contreras, Jagat Narula, Valentin Fuster, Maria Padilla, Zahi A Fayad, Jason C Kovacic
OBJECTIVES: The purpose of this study was to explore the diagnostic usefulness of hybrid cardiac magnetic resonance (CMR) and positron emission tomography (PET) using 18F-fluorodeoxyglucose (FDG) for active cardiac sarcoidosis. BACKGROUND: Active cardiac sarcoidosis (aCS) is underdiagnosed and has a high mortality. METHODS: Patients with clinical suspicion of aCS underwent hybrid CMR/PET with late gadolinium enhancement (LGE) and FDG to assess the pattern of injury and disease activity, respectively...
June 9, 2017: JACC. Cardiovascular Imaging
https://www.readbyqxmd.com/read/28620111/dietary-fats-and-cardiovascular-disease-a-presidential-advisory-from-the-american-heart-association
#15
REVIEW
Frank M Sacks, Alice H Lichtenstein, Jason H Y Wu, Lawrence J Appel, Mark A Creager, Penny M Kris-Etherton, Michael Miller, Eric B Rimm, Lawrence L Rudel, Jennifer G Robinson, Neil J Stone, Linda V Van Horn
Cardiovascular disease (CVD) is the leading global cause of death, accounting for 17.3 million deaths per year. Preventive treatment that reduces CVD by even a small percentage can substantially reduce, nationally and globally, the number of people who develop CVD and the costs of caring for them. This American Heart Association presidential advisory on dietary fats and CVD reviews and discusses the scientific evidence, including the most recent studies, on the effects of dietary saturated fat intake and its replacement by other types of fats and carbohydrates on CVD...
June 15, 2017: Circulation
https://www.readbyqxmd.com/read/28618540/six-vertex-model-and-schramm-loewner-evolution
#16
Richard Kenyon, Jason Miller, Scott Sheffield, David B Wilson
Square ice is a statistical mechanics model for two-dimensional ice, widely believed to have a conformally invariant scaling limit. We associate a Peano (space-filling) curve to a square ice configuration, and more generally to a so-called six-vertex model configuration, and argue that its scaling limit is a space-filling version of the random fractal curve SLE_{κ}, Schramm-Loewner evolution with parameter κ, where 4<κ≤12+8sqrt[2]. For square ice, κ=12. At the "free-fermion point" of the six-vertex model, κ=8+4sqrt[3]...
May 2017: Physical Review. E
https://www.readbyqxmd.com/read/28610627/multiple-biomarkers-predict-disease-severity-progression-and-mortality-in-copd
#17
Rachel L Zemans, Sean Jacobson, Jason Keene, Katerina Kechris, Bruce E Miller, Ruth Tal-Singer, Russell P Bowler
BACKGROUND: Chronic obstructive pulmonary disease (COPD) is a heterogeneous disease characterized by multiple subtypes and variable disease progression. Blood biomarkers have been variably associated with subtype, severity, and disease progression. Just as combined clinical variables are more highly predictive of outcomes than individual clinical variables, we hypothesized that multiple biomarkers may be more informative than individual biomarkers to predict subtypes, disease severity, disease progression, and mortality...
June 13, 2017: Respiratory Research
https://www.readbyqxmd.com/read/28608431/response-to-the-letter-to-the-editor
#18
Jason P Stopyra, Chadwick D Miller, Simon A Mahler
We appreciate the insights and concerns raised in the above letter to the editor. The authors have thoughtfully highlighted some important distinctions between the original derivation of NOTR and our validation study.(1,2) Specifically, the original NOTR derivation included cardiac death, acute myocardial infarction (MI), unstable angina (UA), and "urgent and emergent" revascularization in a composite safety endpoint (and did not include "elective" coronary revascularizations). Our study included death, MI, and any coronary revascularization events, but did not include UA...
June 13, 2017: Academic Emergency Medicine: Official Journal of the Society for Academic Emergency Medicine
https://www.readbyqxmd.com/read/28587290/interpreting-microbial-biosynthesis-in-the-genomic-age-biological-and-practical-considerations
#19
REVIEW
Ian J Miller, Marc G Chevrette, Jason C Kwan
Genome mining has become an increasingly powerful, scalable, and economically accessible tool for the study of natural product biosynthesis and drug discovery. However, there remain important biological and practical problems that can complicate or obscure biosynthetic analysis in genomic and metagenomic sequencing projects. Here, we focus on limitations of available technology as well as computational and experimental strategies to overcome them. We review the unique challenges and approaches in the study of symbiotic and uncultured systems, as well as those associated with biosynthetic gene cluster (BGC) assembly and product prediction...
June 6, 2017: Marine Drugs
https://www.readbyqxmd.com/read/28577881/gene-enriched-draft-genome-of-the-cattle-tick-rhipicephalus-microplus-assembly-by-the-hybrid-pacific-biosciences-illumina-approach-enabled-analysis-of-the-highly-repetitive-genome
#20
Roberto A Barrero, Felix D Guerrero, Michael Black, John McCooke, Brett Chapman, Faye Schilkey, Adalberto A Pérez de León, Robert J Miller, Sara Bruns, Jason Dobry, Galina Mikhaylenko, Keith Stormo, Callum Bell, Quanzhou Tao, Robert Bogden, Paula M Moolhuijzen, Adam Hunter, Matthew I Bellgard
The genome of the cattle tick Rhipicephalus microplus, an ectoparasite with global distribution, is estimated to be 7.1Gbp in length and consists of approximately 70% repetitive DNA. We report the draft assembly of a tick genome that utilized a hybrid sequencing and assembly approach to capture the repetitive fractions of the genome. Our hybrid approach produced an assembly consisting of 2.0Gbp represented in 195,170 scaffolds with a N50 of 60,284bp. The Rmi v2.0 assembly is 51.46% repetitive with a large fraction of unclassified repeats, short interspersed elements, long interspersed elements and long terminal repeats...
June 1, 2017: International Journal for Parasitology
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