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https://www.readbyqxmd.com/read/28093407/protein-multiple-sequence-alignment-benchmarking-through-secondary-structure-prediction
#1
Quan Le, Fabian Sievers, Desmond G Higgins
MOTIVATION: Multiple sequence alignment (MSA) is commonly used to analyse sets of homologous protein or DNA sequences. This has lead to the development of many methods and packages forMSAover the past 30 years. Being able to compare different methods has been problematic and has relied on gold standard benchmark datasets of 'true' alignments or on MSA simulations. A number of protein benchmark datasets have been produced which rely on a combination of manual alignment and/or automated superposition of protein structures...
January 16, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28077348/user-centered-design-of-serious-games-for-older-adults-following-3-years-of-experience-with-exergames-for-seniors-a-study-design
#2
Ellen Brox, Stathis Th Konstantinidis, Gunn Evertsen
BACKGROUND: Seniors need sufficient balance and strength to manage in daily life, and sufficient physical activity is required to achieve and maintain these abilities. This can be a challenge, but fun and motivational exergames can be of help. However, most commercial games are not suited for this age group for several reasons. Many usability studies and user-centered design (UCD) protocols have been developed and applied, but to the best of our knowledge none of them are focusing on seniors' use of games for physical activity...
January 11, 2017: JMIR Serious Games
https://www.readbyqxmd.com/read/28028481/brain-transcriptomes-of-harbor-seals-demonstrate-gene-expression-patterns-of-animals-undergoing-a-metabolic-disease-and-a-viral-infection
#3
Stephanie M Rosales, Rebecca L Vega Thurber
Diseases of marine mammals can be difficult to diagnose because of their life history and protected status. Stranded marine mammals have been a particularly useful resource to discover and comprehend the diseases that plague these top predators. Additionally, advancements in high-throughput sequencing (HTS) has contributed to the discovery of novel pathogens in marine mammals. In this study, we use a combination of HTS and stranded harbor seals (Phoca vitulina) to better understand a known and unknown brain disease...
2016: PeerJ
https://www.readbyqxmd.com/read/28008366/pervasive-assistive-technology-for-people-with-dementia-a-ucd-case
#4
Julia Rosemary Thorpe, Kristoffer V H Rønn-Andersen, Paulina Bień, Ali Gürcan Özkil, Birgitte Hysse Forchhammer, Anja M Maier
Smart mobile and wearable technology offers exciting opportunities to support people with dementia (PwD). Its ubiquity and popularity could even benefit user adoption - a great challenge for assistive technology (AT) for PwD that calls for user-centred design (UCD) methods. This study describes a user-centred approach to developing and testing AT based on off-the-shelf pervasive technologies. A prototype is created by combining a smartphone, smartwatch and various applications to offer six support features...
December 2016: Healthcare Technology Letters
https://www.readbyqxmd.com/read/27997202/peptigram-a-web-based-application-for-peptidomics-data-visualization
#5
Jean Manguy, Peter Jehl, Eugène T Dillon, Norman E Davey, Denis C Shields, Thérèse A Holton
Tandem mass spectrometry (MS/MS) techniques, developed for protein identification, are increasingly being applied in the field of peptidomics. Using this approach, the set of protein fragments observed in a sample of interest can be determined to gain insights into important biological processes such as signaling and other bioactivities. As the peptidomics era progresses, there is a need for robust and convenient methods to inspect and analyze MS/MS derived data. Here, we present Peptigram, a novel tool dedicated to the visualization and comparison of peptides detected by MS/MS...
December 20, 2016: Journal of Proteome Research
https://www.readbyqxmd.com/read/27979940/draft-genome-sequence-of-enterococcus-faecalis-strain-ucd-pd3
#6
Dana R De Vries, Alexandra L Martin, Holly H Ganz, Jonathan A Eisen, David A Coil
Here, we present the draft genome sequence of Enterococcus faecalis strain UCD-PD3. The assembly contains 2,861,314 bp in 73 contigs. This strain was isolated from a feral domestic cat (Felis catus) anal sac secretion sample, as part of a project on isolating and characterizing the microbes present in feline anal sacs.
December 15, 2016: Genome Announcements
https://www.readbyqxmd.com/read/27956536/factors-associated-with-delays-in-chemotherapy-initiation-among-patients-with-breast-cancer-at-a-comprehensive-cancer-center
#7
Katya Losk, Ines Vaz-Luis, Kristen Camuso, Rafael Batista, Max Lloyd, Mustafa Tukenmez, Mehra Golshan, Nancy U Lin, Craig A Bunnell
BACKGROUND: National guidelines endorse time-dependent quality metrics for breast cancer care. We examined factors associated with delays in chemotherapy initiation at an NCI-Designated Comprehensive Cancer Center. PATIENTS AND METHODS: We identified 523 patients who received postoperative adjuvant chemotherapy between January 2011 and December 2013 at our center. We defined 28 days from last definitive surgery (LDS) to chemotherapy as the target time frame, and an unacceptable delay in chemotherapy initiation (UCD) as greater than 42 days from LDS...
December 2016: Journal of the National Comprehensive Cancer Network: JNCCN
https://www.readbyqxmd.com/read/27908535/mortality-profile-of-patients-with-rheumatoid-arthritis-in-france-and-its-change-in-10-years
#8
Jérôme Avouac, Fazia Amrouche, Christophe Meune, Grégoire Rey, André Kahan, Yannick Allanore
OBJECTIVE: To study the mortality profile of patients with rheumatoid arthritis (RA) in France. METHODS: Data were collected between 2000 and 2011 from the French Epidemiological Center for the Medical Causes of Death database; all death certificates from adults that either mentioned RA as an underlying cause of death (UCD) or as an associated cause of death (ACD) were evaluated using multiple-cause-of-death analysis. The different causes of death and their frequency were reported, together with the ratio of observed/expected number of death (O/E ratio) to measure the strength of association between RA listed as an ACD and the corresponding UCD...
October 29, 2016: Seminars in Arthritis and Rheumatism
https://www.readbyqxmd.com/read/27834067/novel-pathogenic-variant-c-580c-t-in-the-cps1-gene-in-a-newborn-with-carbamoyl-phosphate-synthetase-1-deficiency-identified-by-whole-exome-sequencing
#9
Rihwa Choi, Hyung Doo Park, Mina Yang, Chang Seok Ki, Soo Youn Lee, Jong Won Kim, Junghan Song, Yun Sil Chang, Won Soon Park
Diagnosis of the urea cycle disorder (USD) carbamoyl-phosphate synthetase 1 (CPS1) deficiency (CPS1D) based on only the measurements of biochemical intermediary metabolites is not sufficient to properly exclude other UCDs with similar symptoms. We report the first Korean CPS1D patient using whole exome sequencing (WES). A four-day-old female neonate presented with respiratory failure due to severe metabolic encephalopathy with hyperammonemia (1,690 μmol/L; reference range, 11.2-48.2 μmol/L). Plasma amino acid analysis revealed markedly elevated levels of alanine (2,923 μmol/L; reference range, 131-710 μmol/L) and glutamine (5,777 μmol/L; reference range, 376-709 μmol/L), whereas that of citrulline was decreased (2 μmol/L; reference range, 10-45 μmol/L)...
January 2017: Annals of Laboratory Medicine
https://www.readbyqxmd.com/read/27824287/interview-with-david-j-brayden
#10
David J Brayden
David Brayden speaks to Hannah Makin, Commissioning Editor: David Brayden is a Full Professor (Advanced Drug Delivery) at the School of Veterinary Medicine, University College Dublin (UCD) and also a Fellow of the UCD Conway Institute. Following a PhD in Pharmacology at the University of Cambridge, UK (1989), and a postdoctoral research fellowship at Stanford University, CA, USA, he set up Elan Biotechnology Research's in vitro pharmacology laboratory in Dublin (1991). At Elan, he became a senior scientist and project manager of several of Elan's joint-venture drug delivery research collaborations with US biotech companies...
November 8, 2016: Therapeutic Delivery
https://www.readbyqxmd.com/read/27822689/factors-affecting-the-variability-in-the-observed-levels-of-urinary-cadmium-among-children-and-nonsmoker-adolescents
#11
Ram B Jain
Data from the National Health and Nutrition Examination Survey for 1999-2012 were used to evaluate factors that affect observed levels of urine cadmium (UCd) among children aged 6-11 years and nonsmoker adolescents aged 12-19 years. Adjusted UCd levels were found to be statistically significantly higher for female nonsmoker adolescents than male nonsmoker adolescents (p < 0.01). Non-Hispanic white (NHW) participants had statistically significantly lower adjusted levels of UCd (<0.01) than non-Hispanic black (NHB) participants for both children (p < 0...
November 7, 2016: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/27795241/draft-genome-sequence-of-curtobacterium-sp-strain-ucd-kpl2560-phylum-actinobacteria
#12
Brian A Klein, Katherine P Lemon, Lina L Faller, Guillaume Jospin, Jonathan A Eisen, David A Coil
Here, we present the draft genome sequence of the actinobacterium Curtobacterium sp. strain UCD-KPL2560, which was isolated from the running surface of an indoor track field house in Medford, MA, USA (42.409716°N, -71.115169°W). The genome assembly contains 3,480,487 bp in 156 contigs.
October 6, 2016: Genome Announcements
https://www.readbyqxmd.com/read/27738036/draft-genome-sequence-of-gordonia-sp-strain-ucd-tk1-phylum-actinobacteria
#13
Tynisha M Koenigsaecker, Jonathan A Eisen, David A Coil
Here, we present the draft genome of Gordonia sp. strain UCD-TK1. The assembly contains 5,470,576 bp in 98 contigs. This strain was isolated from a disinfected ambulatory surgery center.
October 13, 2016: Genome Announcements
https://www.readbyqxmd.com/read/27738035/draft-genome-sequence-of-tenacibaculum-soleae-ucd-kl19
#14
Karley M Lujan, Jonathan A Eisen, David A Coil
Here, we present the draft genome sequence of Tenacibaculum soleae strain UCD-KL19. The assembly contains 3,012,701 bp in 46 contigs. This strain was isolated from a seagrass leaf (Zostera marina) collected from Bodega Bay, CA, as a part of an undergraduate student research project on isolating bacteria from seagrass.
October 13, 2016: Genome Announcements
https://www.readbyqxmd.com/read/27725292/development-of-a-cognitive-framework-of-patient-record-summary-review-in-the-formative-phase-of-user-centered-design
#15
Jan Horsky, Harley Z Ramelson
Excellent usability characteristics allow electronic health record (EHR) systems to more effectively support clinicians providing care and contribute to better quality and safety. The Office of the National Coordinator for Health IT (ONC) therefore requires all vendors to follow a User-Centered Design (UCD) process to increase the usability of their products in order to meet certification criteria for the Safety-Enhanced Design part of the Meaningful Use (stage 2) EHR incentive program. This report describes the initial stage of a UCD process in which foundational design concepts were formulated...
December 2016: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/27707662/dietary-predictors-of-urinary-cadmium-among-pregnant-women-and-children
#16
Meghan Moynihan, Karen E Peterson, Alejandra Cantoral, Peter X K Song, Andrew Jones, Maritsa Solano-González, John D Meeker, Niladri Basu, Martha Maria Téllez-Rojo
BACKGROUND: Cadmium is a toxic metal with modifiable exposure sources including diet. In pregnant women and children, unique dietary habits may contribute to DCd, and the relationship of diet to overall cadmium exposure can depend on specific factors during these transitional time periods. OBJECTIVES: This study aimed to identify and quantify food sources of DCd, describe the distribution of UCd, and determine the relationship of DCd and intake of specific foods with UCd, stratified by maternal smoking history, among pregnant women and children in a well-characterized Mexico City birth cohort...
January 1, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/27687283/mentoring-for-new-graduates
#17
Helen Graham
The School of Veterinary Medicine in Dublin (UCD) has introduced an alumni mentoring programme for new veterinary and veterinary nursing graduates. Helen Graham, clinical education support manager, explains how it works.
October 1, 2016: Veterinary Record
https://www.readbyqxmd.com/read/27663197/efficacy-and-safety-of-i-v-sodium-benzoate-in-urea-cycle-disorders-a-multicentre-retrospective-study
#18
Marie-Caroline Husson, Manuel Schiff, Alain Fouilhoux, Aline Cano, Dries Dobbelaere, Anais Brassier, Karine Mention, Jean-Baptiste Arnoux, François Feillet, Brigitte Chabrol, Nathalie Guffon, Caroline Elie, Pascale de Lonlay
BACKGROUND: The efficacy and safety of intra-venous (i.v.) sodium benzoate for treating acute episodes of hyperammonemia in urea cycle enzyme disorders (UCD) is well known. However, published data do not provide a clear picture of the benefits and risks of this drug. We report a retrospective multicentre study on the use of i.v. sodium benzoate in patients treated for UCD between 2000 and 2010 in the 6 French reference centres for metabolic diseases. RESULTS: Sixty-one patients with UCDs - 22 ornithine transcarbamylase (20 confirmed, 2 suspected), 18 arginino-succinate synthetase, 15 carbamoyl phosphate synthetase, 3 arginosuccinate lyase, 1 arginase deficiency, 1 N-acetylglutamate synthetase, 1 HHH syndrome - required i...
September 23, 2016: Orphanet Journal of Rare Diseases
https://www.readbyqxmd.com/read/27635000/draft-genome-sequences-of-shewanella-sp-strain-ucd-frsp16_17-and-nine-vibrio-strains-isolated-from-abalone-feces
#19
Ashley Vater, Vivian Agbonavbare, Dylan A Carlin, Griselda M Carruthers, Adam Chac, Ladan Doroud, Samuel J Farris, Melanya Gudzeva, Guillaume Jospin, John A Kintner, Jonathon P Knauss, Yi Lor, Randi Pechacek, Eden S Rohner, Sierra M V Simmons, Mayya Verescshagina, Christian S Wirawan, Leonel Zagal, David A Coil
We present here the draft genome sequences for nine strains of Vibrio (V. cyclitrophicus, V. splendidus, V. tasmaniensis, and three unidentified) and one Shewanella strain. Strains were isolated from red (Haliotis rufescens) and white (Haliotis sorenseni) abalone, with and without exposure to "Candidatus Xenohaliotis californiensis," the causative agent of abalone withering syndrome.
2016: Genome Announcements
https://www.readbyqxmd.com/read/27617468/resident-perspectives-on-a-dermatology-quality-improvement-curriculum-the-university-of-colorado-experience
#20
Sammie J Roberts, Laura S Huff, Jason P Lott, Robert P Dellavalle, Cory A Dunnick
The Centers for Medicare and Medicaid Services (CMS) have prioritized the objective of optimizing quality healthcare though quality improvement initiatives, yet research on dermatology-specific QI programs and their perceptions among dermatology residents remains limited. We explore residents' opinions of a dermatology-specific QI scholarly project curriculum implemented at University of Colorado Denver (UCD) in 2010 and also evaluate residents' attitudes regarding the value of this curriculum in aiding them to meet ACGME core competencies...
April 18, 2016: Dermatology Online Journal
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