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https://www.readbyqxmd.com/read/29447188/comparing-deep-learning-and-concept-extraction-based-methods-for-patient-phenotyping-from-clinical-narratives
#1
Sebastian Gehrmann, Franck Dernoncourt, Yeran Li, Eric T Carlson, Joy T Wu, Jonathan Welt, John Foote, Edward T Moseley, David W Grant, Patrick D Tyler, Leo A Celi
In secondary analysis of electronic health records, a crucial task consists in correctly identifying the patient cohort under investigation. In many cases, the most valuable and relevant information for an accurate classification of medical conditions exist only in clinical narratives. Therefore, it is necessary to use natural language processing (NLP) techniques to extract and evaluate these narratives. The most commonly used approach to this problem relies on extracting a number of clinician-defined medical concepts from text and using machine learning techniques to identify whether a particular patient has a certain condition...
2018: PloS One
https://www.readbyqxmd.com/read/29445342/the-a-2b-adenosine-receptor-modulates-the-epithelial-mesenchymal-transition-through-the-balance-of-camp-pka-and-mapk-erk-pathway-activation-in-human-epithelial-lung-cells
#2
Chiara Giacomelli, Simona Daniele, Chiara Romei, Laura Tavanti, Tommaso Neri, Ilaria Piano, Alessandro Celi, Claudia Martini, Maria L Trincavelli
The epithelial-mesenchymal transition (EMT) is a complex process in which cell phenotype switches from the epithelial to mesenchymal one. The deregulations of this process have been related with the occurrence of different diseases such as lung cancer and fibrosis. In the last decade, several efforts have been devoted in understanding the mechanisms that trigger and sustain this transition process. Adenosine is a purinergic signaling molecule that has been involved in the onset and progression of chronic lung diseases and cancer through the A 2B adenosine receptor subtype activation, too...
2018: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/29443377/identification-of-%C3%AE-fetoprotein-specific-t-cell-receptors-for-hepatocellular-carcinoma-immunotherapy
#3
Wei Zhu, Yibing Peng, Lan Wang, Yuan Hong, Xiaotao Jiang, Qi Li, Heping Liu, Lei Huang, Juan Wu, Esteban Celis, Todd Merchen, Edward Kruse, Yukai He
Hepatocellular carcinoma (HCC) is the major form of liver cancer for which there is no effective therapy. Genetic modification with T cell receptors (TCR) specific for HCC-associated antigens, such as α-fetoprotein (AFP), can potentially redirect human T cells to specifically recognize and kill HCC tumor cells to achieve antitumor effects. In this study, by using lentivector and peptide immunization, we identified a population of CD8-T cells in HLA-A2 transgenic AAD mice that recognized AFP 158 epitope on human HCC cells...
February 14, 2018: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://www.readbyqxmd.com/read/29442291/health-related-information-seeking-behaviors-and-preferences-among-mexican-patients-with-cancer
#4
Enrique Soto-Perez-de-Celis, Viridana Perez-Montessoro, Patricia Rojo-Castillo, Yanin Chavarri-Guerra
Understanding the preferred sources of health-related information among patients with cancer is essential for designing successful cancer education and prevention strategies. However, little is known about health-related information-seeking practices among patients living in low- and middle-income countries. We studied the preferred sources of health-related information among Mexican patients with cancer and explored which factors influence these choices. The health-related information-seeking practices among patients with cancer treated at a public hospital in Mexico City were evaluated using questions from the Spanish Version of the Health Information National Trends Survey...
February 13, 2018: Journal of Cancer Education: the Official Journal of the American Association for Cancer Education
https://www.readbyqxmd.com/read/29437922/-staphylococcus-aureus-hemx-modulates-glutamyl-trna-reductase-abundance-to-regulate-heme-biosynthesis
#5
Jacob E Choby, Caroline M Grunenwald, Arianna I Celis, Svetlana Y Gerdes, Jennifer L DuBois, Eric P Skaar
Staphylococcus aureus is responsible for a significant amount of devastating disease. Its ability to colonize the host and cause infection is supported by a variety of proteins that are dependent on the cofactor heme. Heme is a porphyrin used broadly across kingdoms and is synthesized de novo from common cellular precursors and iron. While heme is critical to bacterial physiology, it is also toxic in high concentrations, requiring that organisms encode regulatory processes to control heme homeostasis. In this work, we describe a posttranscriptional regulatory strategy in S...
February 6, 2018: MBio
https://www.readbyqxmd.com/read/29436306/what-every-oncologist-should-know-about-geriatric-assessment-for-older-patients-with-cancer-young-international-society-of-geriatric-oncology-position-paper
#6
Kah Poh Loh, Enrique Soto-Perez-de-Celis, Tina Hsu, Nienke A de Glas, Nicolò Matteo Luca Battisti, Capucine Baldini, Manuel Rodrigues, Stuart M Lichtman, Hans Wildiers
Aging is a heterogeneous process. Most newly diagnosed cancers occur in older adults, and it is important to understand a patient's underlying health status when making treatment decisions. A geriatric assessment provides a detailed evaluation of medical, psychosocial, and functional problems in older patients with cancer. Specifically, it can identify areas of vulnerability, predict survival and toxicity, assist in clinical treatment decisions, and guide interventions in routine oncology practice; however, the uptake is hampered by limitations in both time and resources, as well as by a lack of expert interpretation...
February 2018: Journal of Oncology Practice
https://www.readbyqxmd.com/read/29435944/cancer-and-aging-in-ibero-america
#7
REVIEW
E Soto-Perez-de-Celis, R Cordoba, R Gironés, T Karnakis, I Paredero, Y Chavarri-Guerra, A P Navarrete-Reyes, J A Avila-Funes
Population aging represents a worldwide challenge. In Ibero-America (Spain, Portugal, and the American countries in which the Spanish or Portuguese language are spoken), the number of older adults is growing, leading to an increase in aging-related diseases such as cancer. Older adults already account for half of all cancer cases in Ibero-America, and this proportion will continue to increase. Furthermore, Ibero-American healthcare systems are not adequately prepared to provide care for older adults with cancer, mainly due to a lack of resources and generalized paucity of geriatric training for healthcare providers...
February 12, 2018: Clinical & Translational Oncology
https://www.readbyqxmd.com/read/29431605/multifactorial-chromosomal-variants-regulate-polymyxin-resistance-in-extensively-drug-resistant-klebsiella-pneumoniae
#8
Miranda E Pitt, Alysha G Elliott, Minh Duc Cao, Devika Ganesamoorthy, Ilias Karaiskos, Helen Giamarellou, Cely S Abboud, Mark A T Blaskovich, Matthew A Cooper, Lachlan J M Coin
Extensively drug-resistant Klebsiella pneumoniae (XDR-KP) infections cause high mortality and are disseminating globally. Identifying the genetic basis underpinning resistance allows for rapid diagnosis and treatment. XDR isolates sourced from Greece and Brazil, including 19 polymyxin-resistant and five polymyxin-susceptible strains, were subjected to whole genome sequencing. Seventeen of the 19 polymyxin-resistant isolates harboured variations upstream or within mgrB. The most common mutation identified was an insertion at nucleotide position 75 in mgrB via an ISKpn26-like element in the ST258 lineage and ISKpn13 in one ST11 isolate...
February 12, 2018: Microbial Genomics
https://www.readbyqxmd.com/read/29426464/a-new-multiplex-pcr-assay-to-distinguish-among-three-cryptic-galba-species-intermediate-hosts-of-fasciola-hepatica
#9
Pilar Alda, Manon Lounnas, Antonio Alejandro Vázquez, Rolando Ayaqui, Manuel Calvopiña, Maritza Celi-Erazo, Robert T Dillon, Philippe Jarne, Eric S Loker, Flavia Caroll Muñiz Pareja, Jenny Muzzio-Aroca, Alberto Orlando Nárvaez, Oscar Noya, Luiggi Martini Robles, Richar Rodríguez-Hidalgo, Nelson Uribe, Patrice David, Jean-Pierre Pointier, Sylvie Hurtrez-Boussès
A molecular tool described here allows in one step for specific discrimination among three cryptic freshwater snail species (genus Galba) involved in fasciolosis transmission, a worldwide infectious disease of humans and livestock. The multiplex PCR approach taken targets for each species a distinctive, known microsatellite locus which is amplified using specific primers designed to generate an amplicon of a distinctive size that can be readily separated from the amplicons of the other two species on an agarose gel...
February 15, 2018: Veterinary Parasitology
https://www.readbyqxmd.com/read/29419803/antibacterial-activities-of-azole-complexes-combined-with-silver-nanoparticles
#10
Nestor J Bello-Vieda, Homero F Pastrana, Manuel F Garavito, Alba G Ávila, Adriana M Celis, Alvaro Muñoz-Castro, Silvia Restrepo, John J Hurtado
Growing antimicrobial resistance is considered a potential threat for human health security by health organizations, such as the WHO, CDC and FDA, pointing to MRSA as an example. New antibacterial drugs and complex derivatives are needed to combat the development of bacterial resistance. Six new copper and cobalt complexes of azole derivatives were synthesized and isolated as air-stable solids and characterized by melting point analyses, elemental analyses, thermogravimetric analyses (TGA), and infrared and ultraviolet/visible spectroscopy...
February 8, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29417042/sample-size-for-cluster-sampling
#11
Bárbara Olenka Sánchez-Palomino, Andrea Celi-Villacorta, Laura Cecilia Gómez-Arrambide, German F Alvarado
No abstract text is available yet for this article.
July 2017: Journal of Family Medicine and Primary Care
https://www.readbyqxmd.com/read/29414780/decarboxylation-involving-a-ferryl-propionate-and-a-tyrosyl-group-in-a-radical-relay-yields-heme-em-b-em
#12
Bennett R Streit, Arianna I Celis, Garrett C Moraski, Krista Shisler, Eric M Shepard, Kenton R Rodgers, Gudrun S Lukat-Rodgers, Jennifer L DuBois
The H2O2-dependent oxidative decarboxylation of coproheme III is the final step in the biosynthesis of heme<em> b</em> in many microbes. However, the coproheme decarboxylase reaction mechanism is unclear. The structure of the decarboxylase in complex with coproheme III suggested that the substrate iron, reactive propionates, and an active-site tyrosine convey a net 2e-/2H+ from each propionate to an activated form of H2O2 Time-resolved EPR spectroscopy revealed that Tyr-145 forms a radical species within 30 sec of the reaction of the enzyme-coproheme complex with H2O2 This radical disappeared over the next 270 sec, consistent with a catalytic intermediate...
February 2, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29414470/improved-tribocorrosion-performance-of-bio-functionalized-tio2-nanotubes-under-two-cycle-sliding-actions-in-artificial-saliva
#13
Sofia A Alves, André L Rossi, Ana R Ribeiro, Fatih Toptan, Ana M Pinto, Tolou Shokuhfar, Jean-Pierre Celis, Luís A Rocha
After insertion into bone, dental implants may be subjected to tribocorrosive conditions resulting in the release of metallic ions and solid wear debris, which can induce to peri-implant inflammatory reactions accompanied by bone loss, and ultimately implant loosening. Despite the promising ability of TiO2 nanotubes (NTs) to improve osseointegration and avoid infection-related failures, the understanding of their degradation under the simultaneous action of wear and corrosion (tribocorrosion) is still very limited...
February 1, 2018: Journal of the Mechanical Behavior of Biomedical Materials
https://www.readbyqxmd.com/read/29406727/distinguishing-active-site-characteristics-of-chlorite-dismutases-with-their-cyanide-complexes
#14
Zachary Geeraerts, Arianna I Celis, Jeffrey A Mayfield, Megan Lorenz, Kenton R Rodgers, Jennifer L DuBois, Gudrun S Lukat-Rodgers
O2-evolving chlorite dismutases (Clds) efficiently convert chlorite (ClO2-) to O2 and Cl-. Dechloromonas aromatica Cld (DaCld) is a highly active chlorite-decomposing homopentameric enzyme, typical of Clds found in perchlorate and chlorate respiring bacteria. The Gram-negative, human pathogen Klebsiella pneumoniae contains a homodimeric Cld (KpCld) that also decomposes ClO2-, albeit with a 10-fold lower activity and a lower turnover number compared to DaCld. The interactions between the distal pocket and heme ligand of the DaCld and KpCld active sites have been probed via kinetic, thermodynamic and spectroscopic behaviors of their cyanide complexes for insight into active site characteristics that are deterministic for chlorite decomposition...
February 6, 2018: Biochemistry
https://www.readbyqxmd.com/read/29390091/identification-and-characterization-at-the-single-cell-level-of-cytokine-producing-circulating-cells-in-children-with-dengue
#15
Federico Perdomo-Celis, Felipe Romero, Doris M Salgado, Rocío Vega, Jairo Rodríguez, Juana Angel, Manuel A Franco, Harry B Greenberg, Carlos F Narváez
In this study we identified, at the single-cell level, naturally induced cytokine-producing circulating cells (CPCC) in children with dengue virus (DENV) infection ranging clinically from mild to severe disease. Tumor necrosis factor (TNF)-α- and Interleukin (IL)-6-CPCC were detected in children with primary or secondary acute DENV infection and the pattern of these cytokines was similar to that seen in the supernatant of cultured PBMC and partially comparable to that found in the plasma. Monocytes, B cells (BC), and myeloid dendritic cells (mDC) were the primary CPCC detected, and the frequency of mDC was significantly higher in severe disease...
January 30, 2018: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/29367125/graph-cuts-and-neural-networks-for-segmentation-and-porosity-quantification-in-synchrotron-radiation-x-ray-%C3%AE-ct-of-an-igneous-rock-sample
#16
Anderson Alvarenga de Moura Meneses, Dayara Bastos Palheta, Christiano Jorge Gomes Pinheiro, Regina Cely Rodrigues Barroso
X-ray Synchrotron Radiation Micro-Computed Tomography (SR-µCT) allows a better visualization in three dimensions with a higher spatial resolution, contributing for the discovery of aspects that could not be observable through conventional radiography. The automatic segmentation of SR-µCT scans is highly valuable due to its innumerous applications in geological sciences, especially for morphology, typology, and characterization of rocks. For a great number of µCT scan slices, a manual process of segmentation would be impractical, either for the time expended and for the accuracy of results...
December 21, 2017: Applied Radiation and Isotopes
https://www.readbyqxmd.com/read/29366920/ca2-levels-in-daphnia-hemolymph-may-explain-occurrences-of-daphniid-species-along-recent-ca-gradients-in-canadian-soft-water-lakes
#17
Andrea C Durant, Martha P Celis-Salgado, Shayan Ezatollahpour, Norman D Yan, Shelley Arnott, Andrew Donini
Calcium levels are declining in eastern North American and western European lakes. This widespread issue is affecting the composition of crustacean zooplankton communities, as the presence and abundance of several calcium-rich daphniid species are declining, while two other daphniids, D. catawba and D. ambigua, that apparently tolerate low calcium environments, are prospering. The physiological basis for low calcium tolerance of these daphniids is unknown. In this study the presence of one Ca-rich (D. pulicaria) and one Ca-poor (D...
January 20, 2018: Comparative Biochemistry and Physiology. Part A, Molecular & Integrative Physiology
https://www.readbyqxmd.com/read/29354822/ab-initio-calculations-of-heavy-actinide-hexahalide-compounds-do-these-heavy-actinides-behave-like-their-isoelectronic-lanthanide-analogues
#18
Cristian Celis-Barros, Dayán Páez-Hernández, María J Beltrán-Leiva, Ramiro Arratia-Perez
Research on heavy actinides has experienced an increased interest in the last few years due to new synthetic techniques and recent technological advances that have allowed for obtaining important information even from very small samples. This area presents challenges not only from the experimental point of view but also from the theoretical perspective. This work deals with a multiconfigurational CASSCF and NEVPT2 benchmark study based on a two-step methodology that considers first correlation effects and then the spin-orbit coupling applied to berkelium (Bk), californium (Cf), einsteinium (Es) and fermium (Fm) hexahalides...
January 22, 2018: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29347809/transient-subdiffusion-from-an-ising-environment
#19
G Muñoz-Gil, C Charalambous, M A García-March, M F Garcia-Parajo, C Manzo, M Lewenstein, A Celi
We introduce a model in which a particle performs a continuous-time random walk (CTRW) coupled to an environment with Ising dynamics. The particle shows locally varying diffusivity determined by the geometrical properties of the underlying Ising environment, that is, the diffusivity depends on the size of the connected area of spins pointing in the same direction. The model shows anomalous diffusion when the Ising environment is at critical temperature. We show that any finite scale introduced by a temperature different from the critical one, or a finite size of the environment, cause subdiffusion only during a transient time...
November 2017: Physical Review. E
https://www.readbyqxmd.com/read/29337803/from-big-data-to-artificial-intelligence-harnessing-data-routinely-collected-in-the-process-of-care
#20
Barret Rush, David J Stone, Leo Anthony Celi
No abstract text is available yet for this article.
February 2018: Critical Care Medicine
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