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Chen-Shan Chin, Paul Peluso, Fritz J Sedlazeck, Maria Nattestad, Gregory T Concepcion, Alicia Clum, Christopher Dunn, Ronan O'Malley, Rosa Figueroa-Balderas, Abraham Morales-Cruz, Grant R Cramer, Massimo Delledonne, Chongyuan Luo, Joseph R Ecker, Dario Cantu, David R Rank, Michael C Schatz
While genome assembly projects have been successful in many haploid and inbred species, the assembly of noninbred or rearranged heterozygous genomes remains a major challenge. To address this challenge, we introduce the open-source FALCON and FALCON-Unzip algorithms ( to assemble long-read sequencing data into highly accurate, contiguous, and correctly phased diploid genomes. We generate new reference sequences for heterozygous samples including an F1 hybrid of Arabidopsis thaliana, the widely cultivated Vitis vinifera cv...
October 17, 2016: Nature Methods
Stephen W Marshall, Kevin M Guskiewicz, Viswanathan Shankar, Michael McCrea, Robert C Cantu
BACKGROUND: The epidemiology of sports-related concussion is not well-described in the literature. This paper presents a descriptive epidemiology of concussion in seven high school and collegiate sports. METHODS: We used the data from Concussion Prevention Initiative (CPI), which enrolled 8905 athletes at 210 high schools and 26 colleges in a prospective cohort study of 7 sports (football, men's and women's soccer, men's and women's lacrosse, and men's and women's ice hockey) between 1999 and 2001...
December 2015: Injury Epidemiology
Joseph Arthur, Sriram Yennu, Kresnier Perez Zapata, Hilda Cantu, Jimin Wu, Diane Liu, Eduardo Bruera
BACKGROUND: Data on the use of question prompt sheets (QPS) in palliative care is limited. Our team previously developed a single page QPS using a Delphi process. The main objective of this study was to determine the perception of helpfulness of a QPS in patient-physician communication among advanced cancer outpatients. METHODS: 100/104(96%) eligible patients and 68/68(100%) caregivers received the QPS during their first palliative care clinic. 12 palliative medicine specialists also participated in the study...
October 12, 2016: Journal of Pain and Symptom Management
Maxine de la Cruz, Akhila Reddy, Vishidha Balankari, Margeaux Epner, Susan Frisbee-Hume, Jimin Wu, Diane Liu, Sriram Yennurajalingam, Hilda Cantu, Janet Williams, Eduardo Bruera
BACKGROUND: Improper use, storage, and disposal of prescribed opioids can lead to diversion or accidental poisoning. Our previous study showed a large proportion of cancer patients have unsafe opioid practices. Our objective was to determine whether an improvement occurred in the patterns of use, storage, and disposal of opioids among cancer outpatients after the implementation of a patient educational program. PATIENTS AND METHODS: Our palliative care (PC) clinic provides every patient with educational material (EM) on safe opioid use, storage, and disposal every time they receive an opioid prescription...
October 14, 2016: Oncologist
Ana Georgina Cobián Güemes, Merry Youle, Vito Adrian Cantú, Ben Felts, James Nulton, Forest Rohwer
Viruses are the most abundant and the most diverse life form. In this meta-analysis we estimate that there are 4.80×10(31) phages on Earth. Further, 97% of viruses are in soil and sediment-two underinvestigated biomes that combined account for only ∼2.5% of publicly available viral metagenomes. The majority of the most abundant viral sequences from all biomes are novel. Our analysis drawing on all publicly available viral metagenomes observed a mere 257,698 viral genotypes on Earth-an unrealistically low number-which attests to the current paucity of viral metagenomic data...
September 29, 2016: Annual Review of Virology
Michael W Collins, Anthony P Kontos, David O Okonkwo, Jon Almquist, Julian Bailes, Mark Barisa, Jeffrey Bazarian, O Josh Bloom, David Brody, Robert Cantu, Javier Cardenas, Jay Clugston, Randall Cohen, Ruben Echemendia, R J Elbin, Richard Ellenbogen, Janna Fonseca, Gerard Gioia, Kevin Guskiewicz, Robert Heyer, Gillian Hotz, Grant L Iverson, Barry Jordan, Geoffrey Manley, Joseph Maroon, Thomas McAllister, Michael McCrea, Anne Mucha, Elizabeth Pieroth, Kenneth Podell, Matthew Pombo, Teena Shetty, Allen Sills, Gary Solomon, Danny G Thomas, Tamara C Valovich McLeod, Tony Yates, Ross Zafonte
BACKGROUND: Conventional management for concussion involves prescribed rest and progressive return to activity. Recent evidence challenges this notion and suggests that active approaches may be effective for some patients. Previous concussion consensus statements provide limited guidance regarding active treatment. OBJECTIVE: To describe the current landscape of treatment for concussion and to provide summary agreements related to treatment to assist clinicians in the treatment of concussion...
October 12, 2016: Neurosurgery
Edith Rojas-Anaya, Antonio Cantú-Covarrubias, José Francisco Morales Álvarez, Elizabeth Loza-Rubio
Papillomas occur more frequently in cattle than other domestic animals. The causal agent of bovine papillomatosis is a virus that belongs to the family Papillomaviridae. In Tamaulipas, Mexico, the virus is considered a serious problem and has impeded the export of cattle to the United States, resulting in serious economic losses. Owing to the lack of information regarding the subtypes of papillomaviruses that infect cattle in Mexico, the aim of this study was to determine the subtypes in Tamaulipas. Fifty-two warts were analyzed with the use of polymerase chain reaction (PCR) involving primers that amplify the E7 gene of bovine papillomavirus (BPV)...
October 2016: Canadian Journal of Veterinary Research, Revue Canadienne de Recherche Vétérinaire
A A Abbas, J M Diamond, C Chehoud, B Chang, J J Kotzin, J C Young, I Imai, A R Haas, E Cantu, D J Lederer, K Meyer, R K Milewski, K M Olthoff, A Shaked, J D Christie, F D Bushman, R G Collman
Primary graft dysfunction (PGD) is a principal cause of early morbidity and mortality after lung transplantation, but its pathogenic mechanisms are not fully clarified. Thus far, studies using standard clinical assays have not linked microbial factors to PGD. We previously used comprehensive metagenomic methods to characterize viruses in lung allografts >1 month post-transplant and found that levels of Anellovirus, mainly Torque teno viruses (TTV), were significantly higher than in non-transplant healthy controls...
October 12, 2016: American Journal of Transplantation
Fabian Cantu Reinhard, Mala Sainna, Pranav Upadhayay, Alex Balan, Devesh Kumar, Simonetta Fornarini, Maria Elisa Crestoni, Samuel de Visser
Cytochrome P450 enzymes are heme containing mono-oxygenases that mainly react through oxygen atom transfer. Specific features of substrate and oxidant that determine the reaction rate constant for oxygen atom transfer are still poorly understood and, therefore, we did a systematic gas-phase study on reactions by iron(IV)-oxo porphyrin cation radical structures with arenes. We present here the first results obtained by using Fourier transform-ion cyclotron resonance mass spectrometry and provide rate constants and product distributions for the assayed reactions...
October 11, 2016: Chemistry: a European Journal
María Teresa Sánchez-Ávila, Karla Lorena Chávez Caraza, Adrián Marcelo González Gil, Jaime Javier Cantú Pompa, Edgar Moreno Medrano, Luis Alonso Morales-Garza
BACKGROUND: Hydrogen breath tests (HBT) are used to confirm the diagnosis of carbohydrate intolerance or small intestinal bacterial overgrowth (SIBO). OBJECTIVE: Determine the existence of a correlation between the presence and intensity of symptoms experimented by the patient after the ingestion of a carbohydrate load and the test result. MATERIALS AND METHODS: This is an observational, retrospective and analytic study, in which all patients' files from year 2008 to 2014 containing a report of a HBT performed at Hospital San José TEC de Monterrey were revised...
July 2016: Revista de Gastroenterología del Perú: órgano Oficial de la Sociedad de Gastroenterología del Perú
Debbe Thompson, Dora Cantu, Madhur Rajendran, Mayur Rajendran, Tanay Bhargava, Yuting Zhang, Cheng Chen, Yan Liu, Zhigang Deng
INTRODUCTION: Exergames require body movement to play and may be an effective method for enhancing teen physical activity (PA). However, results have been mixed. Innovative methods are needed to develop Exergames that increase and maintain PA. Self-representational avatars, or avatars created from a digital image of an individual, may increase PA (e.g., intensity, duration) during Exergame play. This article addresses this novel idea by describing the development of an Exergame played with a self-representational avatar...
September 28, 2016: Games for Health
D L Dickstein, M Y Pullman, C Fernandez, J A Short, L Kostakoglu, K Knesaurek, L Soleimani, B D Jordan, W A Gordon, K Dams-O'Connor, B N Delman, E Wong, C Y Tang, S T DeKosky, J R Stone, R C Cantu, M Sano, P R Hof, S Gandy
Chronic traumatic encephalopathy (CTE) is a neurodegenerative disorder most commonly associated with repetitive traumatic brain injury (TBI) and characterized by the presence of neurofibrillary tangles of tau protein, known as a tauopathy. Currently, the diagnosis of CTE can only be definitively established postmortem. However, a new positron emission tomography (PET) ligand, [(18)F]T807/AV1451, may provide the antemortem detection of tau aggregates, and thus various tauopathies, including CTE. Our goal was to examine [(18)F]T807/AV1451 retention in athletes with neuropsychiatric symptoms associated with a history of multiple concussions...
2016: Translational Psychiatry
Jörg Wissel, Julian P Harriss, Olivier Simon, Kati Sternberg, Nicolas Roche, Carlos Cantú-Brito, Svetlana E Khatkova, Patrik Säterö
No abstract text is available yet for this article.
September 2016: PM & R: the Journal of Injury, Function, and Rehabilitation
Jose R De La Torre, Christian Bautista-Piña, J Alfonso Ortega-S, Antonio Cantu-Covarruvias, Maria Genoveva Alvarez-Ojeda, Dora Romero-Salas, Scott E Henke, Clayton D Hilton, David G Hewitt, Randy W De Young, Tyler A Campbell, Fred C Bryant
Serum samples from 18 axis deer ( Axis axis ) and 19 fallow deer ( Dama dama ) were analyzed with an enzyme-linked immunosorbent assay for Neospora caninum antibodies. Two axis (11%) and two fallow deer (11%) were positive for N. caninum antibodies.
September 26, 2016: Journal of Wildlife Diseases
Amador Pérez-Tomás, Monica Lira-Cantú, Gustau Catalan
This paper presents the first antiferroelectric solar cell. Here this study shows that antiferroelectric thin films photovoltaic current can be switched on when biased into the polar phase to generate above-bandgap photovoltages in excess of 100 V and photovoltaic fields of several megavolts per centimeter, the largest ever measured for any material.
September 15, 2016: Advanced Materials
Andrea Mafficini, Eliana Amato, Ivana Cataldo, Borislav C Rusev, Luca Bertoncello, Vincenzo Corbo, Michele Simbolo, Claudio Luchini, Matteo Fassan, Cinzia Cantù, Roberto Salvia, Giovanni Marchegiani, Giampaolo Tortora, Rita T Lawlor, Claudio Bassi, Aldo Scarpa
OBJECTIVE: To identify molecular prognostic factors and potentially actionable mutations in ampulla of Vater cancer (AVC). BACKGROUND: The largely variable outcomes of AVCs make clinical decisions difficult regarding the need of postsurgical therapy, which is based on morphological and immunohistochemical classification that do not adequately consider the varying degrees of heterogeneity present in many AVCs. No approved targeted therapies for AVC exist, but some show promising results requiring better molecular characterization to identify potential responders...
September 8, 2016: Annals of Surgery
Laura Ortega-Cervantes, Adriana Aguilar-Lemarroy, Aurora Elizabeth Rojas-García, Briscia Socorro Barrón-Vivanco, Verónica Vallejo-Ruiz, David Cantú-De León, Yael Yvette Bernal Hernández, Armando Jáuregui-Martínez, Irma Martha Medina-Díaz
OBJECTIVE: In Mexico cervical cancer (CC) is the most common cause of death from neoplasia in women. Study aimed to analyze the current distribution of Human papillomavirus (HPV) types in women from Nayarit, Mexico, with Squamous intraepithelial lesions (SIL) and Cervical cancer (CC). METHODOLOGY: Between January 2011 and July 2013, cervical samples were collected from female residents of the Mexican state of Nayarit and were analyzed by means of a LINEAR ARRAY® HPV genotyping test...
July 2016: International Journal of Health Sciences
A Alvarado-Lassman, J M Méndez-Contreras, A Martínez-Sibaja, E S Rosas-Mendoza, N A Vallejo-Cantú
The high liquid content in fruit and vegetable wastes makes it convenient to mechanically separate these wastes into mostly liquid and solid fractions by means of pretreatment. Then, the liquid fraction can be treated using a high rate anaerobic biofilm reactor to produce biogas, simultaneously reducing the amount of solids that must be landfilled. In this work, the specific composition of municipal solid waste in a public market was determined; then, the sorted organic fraction of Municipal Solid Waste (MSW) was treated mechanically to separate and characterize the mostly liquid and solid fractions...
September 9, 2016: Environmental Technology
Mélanie Massonnet, Abraham Morales-Cruz, Rosa Figueroa-Balderas, Daniel P Lawrence, Kendra Baumgartner, Dario Cantu
The ascomycete Neofusicoccum parvum, one of the causal agents of Botryosphaeria dieback, is a destructive wood-infecting fungus and a serious threat to grape production worldwide. The capability of colonizing woody tissue combined with the secretion of phytotoxic compounds is thought to underlie its pathogenicity and virulence. Here, we describe the repertoire of virulence factors and their transcriptional dynamics as the fungus feeds on different substrates and colonizes the woody stem. We assembled and annotated a highly contiguous genome using single molecule real-time DNA sequencing...
September 8, 2016: Molecular Plant Pathology
Joseph S Harrison, Evan M Cornett, Dennis Goldfarb, Paul A DaRosa, Zimeng M Li, Feng Yan, Bradley M Dickson, Angela H Guo, Daniel V Cantu, Lilia Kaustov, Peter J Brown, Cheryl H Arrowsmith, Dorothy A Erie, Michael B Major, Rachel E Klevit, Krzysztof Krajewski, Brian Kuhlman, Brian D Strahl, Scott B Rothbart
The epigenetic inheritance of DNA methylation requires UHRF1, a histone- and DNA-binding RING E3 ubiquitin ligase that recruits DNMT1 to sites of newly replicated DNA through ubiquitylation of histone H3. UHRF1 binds DNA with selectivity towards hemi-methylated CpGs (HeDNA); however, the contribution of HeDNA sensing to UHRF1 function remains elusive. Here, we reveal that the interaction of UHRF1 with HeDNA is required for DNA methylation but is dispensable for chromatin interaction, which is governed by reciprocal positive cooperativity between the UHRF1 histone- and DNA-binding domains...
2016: ELife
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