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https://www.readbyqxmd.com/read/28341652/exploring-evolutionary-relationships-across-the-genome-using-topology-weighting
#1
Simon H Martin, Steven M Van Belleghem
We introduce the concept of topology weighting, a method for quantifying relationships between taxa that are not necessarily monophyletic, and visualising how these relationships change across the genome. A given set of taxa can be related in a limited number of ways, but if each taxon is represented by multiple sequences, the number of possible topologies becomes very large. Topology weighting reduces this complexity by quantifying the contribution of each 'taxon topology' to the full tree. We describe our method for topology weighting by iterative sampling of sub-trees (Twisst), and test it on both simulated and real genomic data...
March 24, 2017: Genetics
https://www.readbyqxmd.com/read/28339637/provider-perspectives-on-the-implementation-of-psychosocial-risk-screening-in-pediatric-cancer
#2
Anne E Kazak, Lamia P Barakat, Martha A Askins, Maureen McCafferty, Alyssa Lattomus, Nicole Ruppe, Janet Deatrick
Objective:  Psychosocial risk screening is an important initial step in delivering evidence-based care. This qualitative descriptive study identified how multidisciplinary pediatric oncology health-care providers perceive psychosocial risk screening to identify factors in uptake and implementation. Methods:  A script guided digitally recorded (transcribed) interviews regarding psychosocial screening and challenges to facilitators of screening. Participants were 15 multidisciplinary staff (physicians, nurses, social workers, psychologists, physician assistant) at nine sites, three using the Psychosocial Assessment Tool© for research and six for clinical care...
February 16, 2017: Journal of Pediatric Psychology
https://www.readbyqxmd.com/read/28339108/very-high-energy-electron-vhee-beams-in-radiation-therapy-treatment-plan-comparison-between-vhee-vmat-and-ppbs
#3
Emil Schüler, Kjell Eriksson, Elin Hynning, Steven L Hancock, Susan M Hiniker, Magdalena Bazalova-Carter, Tony Wong, Quynh-Thu Le, Billy W Loo, Peter G Maxim
PURPOSE: The aim of this study was to evaluate the performance of very high energy electron beams (VHEE) beams in comparison to clinically derived treatment plans generated with volumetric modulated arc therapy (VMAT) and proton pencil beam scanning (PPBS) technology. We developed a custom optimization script that could be applied automatically across modalities to eliminate operator bias during IMRT optimization. METHODS: Four clinical cases were selected (prostate cancer, lung cancer, pediatric brain tumor, and head and neck cancer (HNC))...
March 24, 2017: Medical Physics
https://www.readbyqxmd.com/read/28337927/suicide-in-the-mountain-west-region-of-the-united-states
#4
Carolyn M Pepper
BACKGROUND: The Mountain West region of the United States consistently reports the highest rates of suicide in the country. This pattern could reflect a regional culture-of-suicide script in support of suicide that implicitly influences individual's behavior. AIMS: The primary aim of this study was to investigate whether suicide rates are elevated in the Mountain West across a wide range of demographic groups, thereby supporting a regional cultural script. METHOD: Suicide rates in the Mountain West between 1999 and 2014 were compared to the rest of the country across a wide range of demographic categories and levels of population density using the Center for Disease Control Multiple Causes of Death dataset published on the WONDER online database...
March 24, 2017: Crisis
https://www.readbyqxmd.com/read/28337688/when-the-script-doesn-t-fit-%C3%A2-an-exercise-in-clinical-reasoning
#5
Daniel J Wheeler, Thomas Cascino, Bradley A Sharpe, Denise M Connor
No abstract text is available yet for this article.
March 23, 2017: Journal of General Internal Medicine
https://www.readbyqxmd.com/read/28334266/phenopolis-an-open-platform-for-harmonization-and-analysis-of-genetic-and-phenotypic-data
#6
Nikolas Pontikos, Jing Yu, Ismail Moghul, Lucy Withington, Fiona Blanco-Kelly, Tom Vulliamy, Tsz Lun Wong, Cian Murphy, Valentina Cipriani, Alessia Fiorentino, Gavin Arno, Daniel Greene, Julius Ob Jacobsen, Tristan Clark, David S Gregory, Andrea Nemeth, Stephanie Halford, Chris F Inglehearn, Susan Downes, Graeme C Black, Andrew R Webster, Alison J Hardcastle, Vincent Plagnol
Summary: Phenopolis is an open-source web server providing an intuitive interface to genetic and phenotypic databases. It integrates analysis tools such as variant filtering and gene prioritisation based on phenotype. The Phenopolis platform will accelerate clinical diagnosis, gene discovery and encourage wider adoption of the Human Phenotype Ontology in the study of rare genetic diseases. Availability and Implementation: A demo of the website is available at https://phenopolis...
March 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334219/a-network-model-predicts-the-intensity-of-residue-protein-thermal-coupling
#7
Luciano Censoni, Heloisa Dos Santos Muniz, Leandro Martínez
Motivation: The flow of vibrational energy in proteins has been shown not to obey expectations for isotropic media. The existence of preferential pathways for energy transport, with probable connections to allostery mechanisms, has been repeatedly demonstrated. Here, we investigate whether, by representing a set of protein structures as networks of interacting amino acid residues, we are able to model heat diffusion and predict residue-protein vibrational couplings, as measured by the Anisotropic Thermal Diffusion (ATD) computational protocol of modified molecular dynamics simulations...
March 7, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28331548/discovering-feature-relevancy-and-dependency-by-kernel-guided-probabilistic-model-building-evolution
#8
Nestor Rodriguez, Sergio Rojas-Galeano
BACKGROUND: Discovering relevant features (biomarkers) that discriminate etiologies of a disease is useful to provide biomedical researchers with candidate targets for further laboratory experimentation while saving costs; dependencies among biomarkers may suggest additional valuable information, for example, to characterize complex epistatic relationships from genetic data. The use of classifiers to guide the search for biomarkers (the so-called wrapper approach) has been widely studied...
2017: BioData Mining
https://www.readbyqxmd.com/read/28329635/compliance-with-indoor-tanning-laws-for-minors-among-salons-and-business-in-the-united-states
#9
Courtney Choy, Brenda Cartmel, Rachel Clare, Leah M Ferrucci
Indoor tanning is an established risk factor for skin cancer, yet indoor tanning is quite common among adolescents. Laws exists in some states to limit access to indoor tanning by minors, but there is limited research on industry compliance with these laws.We conducted a telephone survey with a random sample of businesses (n=412) offering indoor tanning in the 14 states with indoor tanning bans for minors as of May 2015. Female research assistants posing as minors conducted telephone interviews with employees using a standardized script...
September 15, 2016: Dermatology Online Journal
https://www.readbyqxmd.com/read/28327037/meeting-patients-unmet-needs
#10
(no author information available yet)
Macmillan consultant nurse (breast) Victoria Harmer qualified with distinction in 1995 and has devoted her career to caring for patients with cancer. She specialised in breast cancer 17 years ago, after taking up a clinical nurse specialist post at London's St Mary's Hospital. She has been in her current role at Imperial College Healthcare NHS Trust since October 2016, and is also a published author and script adviser for television programmes featuring breast cancer storylines.
March 22, 2017: Nursing Standard
https://www.readbyqxmd.com/read/28323250/the-atomic-simulation-environment-a-python-library-for-working-with-atoms
#11
Ask Larsen, Jens Mortensen, Jakob Blomqvist, Ivano Castelli, Rune Christensen, Marcin Dulak, Jesper Friis, Michael Groves, Bjork Hammer, Cory Hargus, Eric Hermes, Paul Jennings, Peter Jensen, James Kermode, John Kitchin, Esben Kolsbjerg, Joseph Kubal, Kristen Kaasbjerg, Steen Lysgaard, Jon Maronsson, Tristan Maxson, Thomas Olsen, Lars Pastewka, Andrew Peterson, Carsten Rostgaard, Jakob Schiøtz, Ole Schütt, Mikkel Strange, Kristian Thygesen, Tejs Vegge, Lasse Vilhelmsen, Michael Walter, Zhenhua Zeng, Karsten Wedel Jacobsen
The Atomic Simulation Environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simula- tions. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library make it possible to perform very complex simulation tasks. For example, a sequence of calculations may be performed with the use of a simple "for-loop" construction. Calculations of energy, forces, stresses and other quantities are performed through interfaces to many external electronic structure codes or force fields using a uniform interface...
March 21, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/28322404/device-and-programming-abstractions-for-spatiotemporal-control-of-active-micro-particle-swarms
#12
Amy T Lam, Karina G Samuel-Gama, Jonathan Griffin, Matthew Loeun, Lukas C Gerber, Zahid Hossain, Nate J Cira, Seung Ah Lee, Ingmar H Riedel-Kruse
We present a hardware setup and a set of executable commands for spatiotemporal programming and interactive control of a swarm of self-propelled microscopic agents inside a microfluidic chip. In particular, local and global spatiotemporal light stimuli are used to direct the motion of ensembles of Euglena gracilis, a unicellular phototactic organism. We develop three levels of programming abstractions (stimulus space, swarm space, and system space) to create a scripting language for directing swarms. We then implement a multi-level proof-of-concept biotic game using these commands to demonstrate their utility...
March 21, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28321364/effect-of-method-of-deduplication-on-estimation-of-differential-gene-expression-using-rna-seq
#13
Anna V Klepikova, Artem S Kasianov, Mikhail S Chesnokov, Natalia L Lazarevich, Aleksey A Penin, Maria Logacheva
BACKGROUND: RNA-seq is a useful tool for analysis of gene expression. However, its robustness is greatly affected by a number of artifacts. One of them is the presence of duplicated reads. RESULTS: To infer the influence of different methods of removal of duplicated reads on estimation of gene expression in cancer genomics, we analyzed paired samples of hepatocellular carcinoma (HCC) and non-tumor liver tissue. Four protocols of data analysis were applied to each sample: processing without deduplication, deduplication using a method implemented in SAMtools, and deduplication based on one or two molecular indices (MI)...
2017: PeerJ
https://www.readbyqxmd.com/read/28321144/summaries-of-safety-labeling-changes-approved-by-the-fda-boxed-warnings-highlights-october-december-2016
#14
Brenda J Rose
The FDA's MedWatch program safety labeling changes for boxed warnings are compiled quarterly for drugs and therapeutic biologics where important changes have been made to the safety information. Search of Drug Safety Labeling Changes (SLC) database was conducted on December 31, 2016 for date range "10/1/2016-12/31/2016", labeling section "Boxed Warning". These and other label changes are searchable in the Drug Safety Labeling Changes (SLC) database, where data are available to the public in downloadable and searchable formats...
February 2017: Hospital Pharmacy
https://www.readbyqxmd.com/read/28319684/what-do-we-do-with-what-we-learn-statistical-learning-of-orthographic-regularities-impacts-written-word-processing
#15
Fabienne Chetail
Individuals rapidly become sensitive to recurrent patterns present in the environment and this occurs in many situations. However, evidence of a role for statistical learning of orthographic regularities in reading is mixed, and its role has peripheral status in current theories of visual word recognition. Additionally, exactly which regularities readers learn to be sensitive to is still unclear. To address these two issues, three experiments were conducted with artificial scripts. In Experiments 1a and 1b, participants were exposed to a flow of artificial words (five characters) for a few minutes, with either two or four bigrams occurring very frequently...
March 16, 2017: Cognition
https://www.readbyqxmd.com/read/28319463/solid-cancer-incidence-among-the-life-span-study-of-atomic-bomb-survivors-1958-2009
#16
Eric J Grant, Alina Brenner, Hiromi Sugiyama, Ritsu Sakata, Atsuko Sadakane, Mai Utada, Elizabeth K Cahoon, Caitlin M Milder, Midori Soda, Harry M Cullings, Dale L Preston, Kiyohiko Mabuchi, Kotaro Ozasa
This is the third analysis of solid cancer incidence among the Life Span Study (LSS) cohort of atomic bomb survivors in Hiroshima and Nagasaki, adding eleven years of follow-up data since the previously reported analysis. For this analysis, several changes and improvements were implemented, including updated dose estimates (DS02R1) and adjustment for smoking. Here, we focus on all solid cancers in aggregate. The eligible cohort included 105,444 subjects who were alive and had no known history of cancer at the start of follow-up...
March 20, 2017: Radiation Research
https://www.readbyqxmd.com/read/28318985/functional-disconnection-of-thalamic-and-cerebellar-dentate-nucleus-networks-in-progressive-supranuclear-palsy-and-corticobasal-syndrome
#17
Neeraj Upadhyay, Antonio Suppa, Maria Cristina Piattella, Costanza Giannì, Matteo Bologna, Flavio Di Stasio, Nikolaos Petsas, Francesca Tona, Giovanni Fabbrini, Alfredo Berardelli, Patrizia Pantano
AIM: To assess functional rearrangement following neurodegeneration in the thalamus and dentate nucleus in patients with progressive supranuclear palsy (PSP) and corticobasal syndrome (CBS). METHODS: We recruited 19 patients with PSP, 11 with CBS and 14 healthy subjects. All the subjects underwent resting-state (rs) fMRI using a 3T system. Whole brain functional connectivity of the thalamus and dentate nucleus were calculated by means of a seed-based approach with FEAT script in FSL toolbox...
March 15, 2017: Parkinsonism & related Disorders
https://www.readbyqxmd.com/read/28315728/can-ambulance-telephone-triage-using-nhs-pathways-accurately-identify-paediatric-cardiac-arrest
#18
Charles D Deakin, Simon England, Debbie Diffey, Ian Maconochie
BACKGROUND: Most out-of-hospital paediatric cardiac arrests (CA) are not identified until a call is made to the emergency medical services. Accurate identification increases overall survival by enabling immediate ambulance dispatch and delivery of bystander CPR. European ambulance services use a variety of didactic telephone scripts to interrogate the caller and rapidly identify paediatric CA. The performance of these scripts has not been reported. This study aims to evaluate the diagnostic accuracy of the NHS Pathways as a telephone triage tool to identify patients less than 16 years age in cardiac arrest...
March 15, 2017: Resuscitation
https://www.readbyqxmd.com/read/28315548/the-caregiving-quandary%C3%A2
#19
Deborah A Boyle
Long before I became a cancer caregiver, I worried about families. Providing care without a script, expanding their workload, solo decision making, incessant worrying, managing expectations, overseeing medications-that is the lay caregiver's all-consuming world. However, when cancer entered my residence, I started living what I had historically observed from a distance. The double-duty caregiving at work and home overwhelmed me. Years of experience did little to prepare me for the emotional tsunami and physical toll caregiving took on me...
April 1, 2017: Clinical Journal of Oncology Nursing
https://www.readbyqxmd.com/read/28303176/abundance-distributions-for-tree-species-in-great-britain-a%C3%A2-two-stage-approach-to-modeling-abundance-using-species-distribution-modeling-and-random-forest
#20
Louise Hill, Andy Hector, Gabriel Hemery, Simon Smart, Matteo Tanadini, Nick Brown
High-quality abundance data are expensive and time-consuming to collect and often highly limited in availability. Nonetheless, accurate, high-resolution abundance distributions are essential for many ecological applications ranging from species conservation to epidemiology. Producing models that can predict abundance well, with good resolution over large areas, has therefore been an important aim in ecology, but poses considerable challenges. We present a two-stage approach to modeling abundance, combining two established techniques...
February 2017: Ecology and Evolution
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