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The Pope

Tiphaine Vidal, Pauline Lusley, Marc Leconte, Claude de Vallavieille-Pope, Laurent Huber, Sébastien Saint-Jean
Cultivar mixtures can be used to improve the sustainability of disease management within farming systems by growing cultivars that differ in their disease resistance level in the same field. The impact of canopy aerial architecture on rain-splash dispersal could amplify disease reduction within mixtures. We designed a controlled conditions experiment to study single splash-dispersal events and their consequences for disease. We quantified this impact through the spore interception capacities of the component cultivars of a mixture...
2017: PloS One
Michael M Tice, Kimbra Quezergue, Michael C Pope
As part of its biosignature detection package, the Mars 2020 rover will carry PIXL, the Planetary Instrument for X-ray Lithochemistry, a spatially resolved X-ray fluorescence (μXRF) spectrometer. Understanding the types of biosignatures detectable by μXRF and the rock types μXRF is most effective at analyzing is therefore an important goal in preparation for in situ Mars 2020 science and sample selection. We tested mesoscale chemical mapping for biosignature interpretation in microbialites. In particular, we used μXRF to identify spatial distributions and associations between various elements ("fluorescence microfacies") to infer the physical, biological, and chemical processes that produced the observed compositional distributions...
November 2017: Astrobiology
Welkin H Pope, Deborah Jacobs-Sera
Current sequencing technologies allow for the rapid and inexpensive sequencing of complete bacteriophage genomes, using small quantities of nucleic acid as starting material. Determination of the location and function of the gene features within the genome sequence, or annotation, is a necessary next step prior to submission to a public database, publication in a scientific journal, or advanced comparative genomic and proteomic studies. Gene prediction can be largely accomplished through the use of several freely available programs...
2018: Methods in Molecular Biology
Daniel A Russell
Next-generation DNA sequencing (NGS) technologies have made generating genomic sequence for organisms of interest affordable and commonplace. However, NGS platforms and analysis software are generally tuned to be used on large and complex genomes or metagenomic samples. Determining the complete genome sequence of a single bacteriophage requires a somewhat different perspective, workflow, and sensitivity to the nature of phages. Because phage genomes consist of mostly coding regions (see Pope/Jacobs-Sera chapter), a very high standard should be adopted when completing these genomes so that the subsequent steps of annotation and analysis are not sabotaged by sequencing errors...
2018: Methods in Molecular Biology
Julie McDonald, Nadia Swami, Ashley Pope, Sarah Hales, Rinat Nissim, Gary Rodin, Breffni Hannon, Camilla Zimmermann
BACKGROUND: Early involvement of palliative care improves patient quality of life; however, quantitative studies have not yet demonstrated a similar effect for caregivers, for whom the construct of quality of life is less well developed. AIM: To conceptualise quality of life of caregivers from their own perspective and to explore differences in themes between those who did or did not receive an early palliative care intervention. DESIGN: Qualitative grounded theory study...
November 1, 2017: Palliative Medicine
Antonio R Castilla, Nathaniel S Pope, Megan O'Connell, María F Rodriguez, Laurel Treviño, Alonso Santos, Shalene Jha
Animal pollination mediates both reproduction and gene flow for the majority of plant species across the globe. However, past functional studies have focused largely on seed production; although useful, this focus on seed set does not provide information regarding species-specific contributions to pollen-mediated gene flow. Here we quantify pollen dispersal for individual pollinator species across more than 690 ha of tropical forest. Specifically, we examine visitation, seed production, and pollen-dispersal ability for the entire pollinator community of a common tropical tree using a series of individual-based pollinator-exclusion experiments followed by molecular-based fractional paternity analyses...
November 10, 2017: Proceedings of the National Academy of Sciences of the United States of America
Duncan Cole, Emma Rengasamy, Shafqat Batchelor, Charles Pope, Stephen Riley, Anne Marie Cunningham
BACKGROUND: Medical curricula are increasingly using small group learning and less didactic lecture-based teaching. This creates new challenges and opportunities in how students are best supported with information technology. We explored how university-supported and external social media could support collaborative small group working on our new undergraduate medical curriculum. METHODS: We made available a curation platform ( and a wiki within our virtual learning environment as part of year 1 Case-Based Learning, and did not discourage the use of other tools such as Facebook...
November 10, 2017: BMC Medical Education
Sujay Nagaraj, Cheryl Barnabe, Orit Schieir, Janet Pope, Susan J Bartlett, Gilles Boire, Edward Keystone, Diane Tin, Boulos Haraoui, J Carter Thorne, Vivian P Bykerk, Carol Hitchon
OBJECTIVE: Health inequities exist in chronic diseases for Aboriginal people. This study compared early rheumatoid arthritis (ERA) presentation, treatment and outcomes between Aboriginal and Caucasian patients in a large Canadian cohort study. METHODS: Longitudinal data from the Canadian early ArThritis CoHort (CATCH), a prospective multicenter ERA study, were analyzed for participants who self-identified as Aboriginal or Caucasian ethnicity. Disease characteristics at presentation, prognostic factors, frequency of remission and disease-modifying therapy strategies were contrasted between population groups...
November 10, 2017: Arthritis Care & Research
Majid Jafari, Faramarz Mehrnejad, Farahnoosh Doustdar
Pardaxin, with a bend-helix-bend-helix structure, is a membrane-active antimicrobial peptide that its membrane activity depends on the lipid bilayer composition. Herein, all-atom molecular dynamics (MD) simulations were performed to provide further molecular insight into the interactions, structural dynamics, orientation behavior, and cationic residues snorkeling of pardaxin in the DMPC, DPPC, POPC, POPG, POPG/POPE (3:1), and POPG/POPE (1:3) lipid bilayers. The results showed that the C-terminal helix of the peptide was maintained in all six types of the model-bilayers and pardaxin was tilted into the DMPC, DPPC, and POPG/POPE mixed bilayers more than the POPC and POPG bilayers...
2017: PloS One
Hui-Min Chung, Tom D'Elia, Joseph F Ross, Samuel M Alvarado, Molly-Catherine Brantley, Lydia P Bricker, Courtney R Butler, Carson Crist, Julia M Dane, Brett W Farran, Sierra Hobbs, Michelle Lapak, Conner Lovell, Nicholas Ludergnani, Allison McMullen, Sohail A Mirza, Noah Thrift, Donald P Vaughan, Grace Worley, Amara Ejikemeuwa, May Zaw, Claude F Albritton, Sarah C Bertrand, Shanzay S Chaudhry, Vzair A Cheema, Camilla Do, Michael L Do, Huyen M Duong, Dalia H El-Desoky, Kelsey M Green, Rhea N Lee, Lauren A Thornton, James M Vu, Mah Noor Zahra, Steven G Cresawn, Ty H Stoner, Rebecca A Garlena, Deborah Jacobs-Sera, Welkin H Pope, Daniel A Russell, Graham F Hatfull
We report here the complete genome sequences of four subcluster L3 mycobacteriophages newly isolated from soil samples, using Mycobacterium smegmatis mc(2)155 as the host. Comparative genomic analyses with four previously described subcluster L3 phages reveal strong nucleotide similarity and gene conservation, with several large insertions/deletions near their right genome ends.
November 9, 2017: Genome Announcements
Sanghamitra Saha, Wenbo Yan, Jacqueline M Washington, William B Davis, W Brad Barbazuk, Rosa Medellin, Aissa Mendez, Jacqueline R Ramos, Rachna Sadana, Miranda Edmonds, Guanqiao Feng, Maria Ilyas, Joshua Kaiser, Stephen J Monroe, Thinh V Pham, Steven G Cresawn, Rebecca A Garlena, Ty H Stoner, Daniel A Russell, Welkin H Pope, Deborah Jacobs-Sera, Graham F Hatfull
We report here the genome sequences of three newly isolated phages that infect Mycobacterium smegmatis mc(2)155. Phages Findley, Hurricane, and TBond007 were discovered in geographically distinct locations and are related to cluster K mycobacteriophages, with Findley being similar to subcluster K2 phages and Hurricane and TBond007 being similar to subcluster K3 phages.
November 9, 2017: Genome Announcements
Rodney A King, Tina M Slowan-Pomeroy, Jodi E Thomas, Tithe Ahmed, Katie L Alexander, James M Biddle, Makenzie K Daniels, Jenna R Rowlett, Taylor E Senay, Claire A Rinehart, Amanda K Staples, Naomi S Rowland, Bobby L Gaffney, Christine B Emmons, Maya D Hauk, Rebecca L Nguyen, Leonard Naegele, Summer S Strickland, Laura A Briggs, Alexander N Rush, Sanghamitra Saha, Rachna Sadana, Steven G Cresawn, Daniel A Russell, Rebecca A Garlena, Welkin H Pope, Deborah Jacobs-Sera, Graham F Hatfull
Bacteriophages AlleyCat, Edugator, and Guillsminger were isolated on Mycobacterium smegmatis mc(2)155 from enriched soil samples. All are members of mycobacteriophage subcluster K5, with genomes of 62,112 to 63,344 bp. Each genome contains 92 to 99 predicted protein-coding genes and one tRNA. Guillsminger is the first mycobacteriophage to carry an IS1380 family transposon.
November 9, 2017: Genome Announcements
Julia Y Lee-Soety, Shantanu Bhatt, Tamarah L Adair, J Alfred Bonilla, Karen K Klyczek, Melinda Harrison, Rebecca A Garlena, Charles A Bowman, Daniel A Russell, Welkin H Pope, Deborah Jacobs-Sera, Steven G Cresawn, Graham F Hatfull
Twelve siphoviral phages isolated using Arthrobacter sp. strain ATCC 21022 were sequenced. The phages all have relatively small genomes, ranging from 15,319 to 15,556 bp. All 12 phages are closely related to previously described cluster AN Arthrobacter phages.
November 9, 2017: Genome Announcements
Nicholas P Edgington, Stephanie M Voshell, Vassie C Ware, Francis F Akoto, Alexa A Alhout, Gurvina J Atwal, John B Balyozian, Zachary A Cadieux, Brianna M Chop, Steven G Cresawn, Netta Cudkevich, Dylan Z Faltine-Gonzalez, Rebecca A Garlena, Blair J Gilmer, Lee H Graham, Matthew S Grapel, Maaz M Haleem, Deborah Jacobs-Sera, Margaret A Kenna, Maryam A Khan, Taylor N Klein, Jamie B Korenberg, Brooke P Lichak, Catherine M Mageeney, Lauren N McKinley, Kourtney R Mendello, Cameron M Myers, Alexander T Nguyen, Bryan A Pasqualucci, Welkin H Pope, Lauren M Pyfer, Wascar A Ramirez, Julia R Reisner, Daniel A Russell, Paulene A Sapao, Virginia C Saux, Inderjeet Singh, Ty H Stoner, Rachel H Swope, Matthew J Thoonkuzhy, Madeleine L Walters, Lauren A Vargas, Croldy A Veliz, Kevin D Zhang, Caitlin M Zuilkoski, Graham F Hatfull
Mycobacteriophages Chancellor, Mitti, and Wintermute infect Mycobacterium smegmatis mc(2)155 and are closely related to phages Cheetobro and Fionnbharth in subcluster K4. Genome sizes range from 57,697 bp to 58,046 bp. Phages are predicted to be temperate and to infect the pathogen Mycobacterium tuberculosis.
November 9, 2017: Genome Announcements
Janet E Pope, Jason J Lee, Christopher P Denton
Systemic sclerosis (SSc) is a complex inflammatory connective tissue disease characterized by skin thickening, organ fibrosis and vasculopathy [1, 2]. The underlying disease mechanisms and pathophysiology are not fully understood. However, it appears to be, at least in part, driven by autoimmunity and inflammation associated with microvascular dysfunction ultimately resulting in excess extracellular matrix deposition in target organs [2-4]. Clinical heterogeneity coupled with our lack of understanding of the disease pathogenesis means that current treatment strategies are mostly organ based therapies using anti-rheumatic drugs that were originally approved for other indications [5]...
November 9, 2017: Arthritis & Rheumatology
Tim Hahn, Nils R Winter, Christine Anderl, Karolien Notebaert, Alina Marie Wuttke, Celina Chantal Clément, Sabine Windmann
Facial Width-to-Height Ratio (fWHR) has been linked with dominant and aggressive behavior in human males. We show here that on portrait photographs published online, chief executive officers (CEOs) of companies listed in the Dow Jones stock market index and the Deutscher Aktienindex have a higher-than-normal fWHR, which also correlates positively with their company's donations to charitable causes and environmental awareness. Furthermore, we show that leaders of the world's most influential non-governmental organizations and even the leaders of the Roman Catholic Church, the popes, have higher fWHR compared to controls on public portraits, suggesting that the relationship between displayed fWHR and leadership is not limited to profit-seeking organizations...
2017: PloS One
Robin Orr, J Jay Dawes, Rodney Pope, Joseph Terry
The physical fitness of police officers must be developed in new cadets and sustained in incumbent officers. The aims of this study were to profile and compare the anthropometric and fitness characteristics of police academy cadets and incumbent officers of varying ages from a single police force. Retrospective data for 84 police academy cadets (♂=66, mean age=27.96±5.73 yrs; ♀=18, mean age=30.50±5.76 yrs) and 80 incumbent police officers (♂=73, mean age=39.43±8.28 yrs; ♀=7, mean age=37.86±3.67 yrs) were compiled...
November 6, 2017: Journal of Strength and Conditioning Research
Daniel D Buchanan, Jenna R Stewart, Mark Clendenning, Christophe Rosty, Khalid Mahmood, Bernard J Pope, Mark A Jenkins, John L Hopper, Melissa C Southey, Finlay A Macrae, Ingrid M Winship, Aung Ko Win
BackgroundGerm-line mutations in the exonuclease domains of the POLE and POLD1 genes are associated with an increased, but yet unquantified, risk of colorectal cancer (CRC).MethodsWe identified families with POLE or POLD1 variants by searching PubMed for relevant studies prior to October 2016 and by genotyping 669 population-based CRC cases diagnosed in patients under 60 years of age, from the Australasian Colorectal Cancer Family Registry. We estimated the age-specific cumulative risks (penetrance) using a modified segregation analysis...
November 9, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
Marco Bigoni, Giovanni Zatti, Nicolò Zanchi, Filippo Maria Anghilieri, Michele A Riva
Marcello Malpighi (1628-1694), who is referred to as the father of microscopical anatomy, histology, physiology and embryology was an Italian biologist and physician, well known for his discoveries on microscopical anatomy of kidney, circulating and lymphatic systems. As well as being a brilliant anatomist, Malpighi was also a valued physician so far as to became the personal physician of Pope Innocent XII (1615-1700). On 23 August 1691, one month after his election, the Pope fell to the ground hitting his left hip...
November 8, 2017: International Orthopaedics
Timothy E Quill, Linda Ganzini, Robert D Truog, Thaddeus Mason Pope
Patients with advanced illnesses sometimes request that physicians help hasten their death. Increasingly in North America and Europe, legal options allow physicians to perform this role. Among death-hastening options, the spotlight has been on physician-assisted death. However, voluntarily stopping eating and drinking (VSED) is also a course that patients may choose. Although VSED theoretically does not require physician involvement, clinician participation is critical in terms of initial assessment and ongoing management...
November 6, 2017: JAMA Internal Medicine
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