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https://www.readbyqxmd.com/read/28812996/reliable-detection-of-herpes-simplex-virus-sequence-variation-by-high-throughput-resequencing
#1
Alison M Morse, Kaitlyn R Calabro, Justin M Fear, David C Bloom, Lauren M McIntyre
High-throughput sequencing (HTS) has resulted in data for a number of herpes simplex virus (HSV) laboratory strains and clinical isolates. The knowledge of these sequences has been critical for investigating viral pathogenicity. However, the assembly of complete herpesviral genomes, including HSV, is complicated due to the existence of large repeat regions and arrays of smaller reiterated sequences that are commonly found in these genomes. In addition, the inherent genetic variation in populations of isolates for viruses and other microorganisms presents an additional challenge to many existing HTS sequence assembly pipelines...
August 16, 2017: Viruses
https://www.readbyqxmd.com/read/28811656/phageterm-a-tool-for-fast-and-accurate-determination-of-phage-termini-and-packaging-mechanism-using-next-generation-sequencing-data
#2
Julian R Garneau, Florence Depardieu, Louis-Charles Fortier, David Bikard, Marc Monot
The worrying rise of antibiotic resistance in pathogenic bacteria is leading to a renewed interest in bacteriophages as a treatment option. Novel sequencing technologies enable description of an increasing number of phage genomes, a critical piece of information to understand their life cycle, phage-host interactions, and evolution. In this work, we demonstrate how it is possible to recover more information from sequencing data than just the phage genome. We developed a theoretical and statistical framework to determine DNA termini and phage packaging mechanisms using NGS data...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28789704/immuno-diagnosis-of-mycobacterium-tuberculosis-in-sputum-and-reduction-of-timelines-for-its-positive-cultures-to-within-3%C3%A2-h-by-pathogen-specific-thymidylate-kinase-expression-assays
#3
Misaki Wayengera, Ivan Mwebaza, Johnson Welishe, Alice Bayiyana, David P Kateete, Eddie Wampande, Samuel Kirimunda, Edgar Kigozi, Fred Katabazi, Carol Musubika, Samuel Kyobe, Peace Babirye, Benon Asiimwe, Moses L Joloba
BACKGROUND: Laboratory diagnosis of Tuberculosis (TB) is traditionally based on microscopy and or culture. Microscopy is however, only sensitive to a specified degree of bacillary load not present in HIV co-infected persons. Traditional cultures of Mycobacterium tuberculosis (M. tb), on the other hand, take weeks to read-thereby delaying the critical decision whether or not, to treat. Although nucleic acids amplification tests (NAATS) applied directly on sputum or cultures can increase the sensitivity for TB diagnosis among those with HIV co-infection as well as reduce time-lines for positive culture detection, they do not replace the need for smear microscopy and culture...
August 8, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28789579/reading-on-the-right-when-there-s-nothing-left-probabilistic-tractography-reveals-hemispheric-asymmetry-in-pure-alexia
#4
Michele Veldsman, Tobias Loetscher, Amanda Wood, Amy Brodtmann
We present a patient with reading inexpertise and right hemianopia following left posterior cerebral artery (PCA) stroke. We examine the extent of disruption to reading performance and the extent of white matter tract damage relative to a patient with more limited PCA infarction and isolated right hemianopia. We show white matter disconnection of the temporal occipital fusiform cortex in our pure alexia patient. Connectivity-based laterality indices revealed right hemisphere laterality in the alexia patient; this was not associated with improved reading function...
August 9, 2017: Neurocase
https://www.readbyqxmd.com/read/28781912/nursing-review-section-of-surgical-neurology-international-part-1-lumbar-disc-disease
#5
Nancy E Epstein, Renee D Hollingsworth
BACKGROUND: Patients with lumbar disc disease may present with low back pain, pain that radiates down into the lower extremity (radiculopathy), and leg pain that increases with ambulation (neurogenic claudication). Patients may first undergo diagnostic studies [(magnetic resonance imaging (MRI) and computed tomographic (CT) examinations] to determine whether there is any significant nerve root or thecal sac compression. METHODS: Increasingly, patients with low back pain with/without radiculopathy are being screened by nurses rather than by neurologists or neurosurgeons/orthopedists...
2017: Surgical Neurology International
https://www.readbyqxmd.com/read/28780361/untreated-urban-waste-contaminates-indian-river-sediments-with-resistance-genes-to-last-resort-antibiotics
#6
Nachiket P Marathe, Chandan Pal, Swapnil S Gaikwad, Viktor Jonsson, Erik Kristiansson, D G Joakim Larsson
Efficient sewage treatment is critical for limiting environmental transmission of antibiotic-resistant bacteria. In many low and middle income countries, however, large proportions of sewage are still released untreated into receiving water bodies. In-depth knowledge of how such discharges of untreated urban waste influences the environmental resistome is largely lacking. Here, we highlight the impact of uncontrolled discharge of partially treated and/or untreated wastewater on the structure of bacterial communities and resistome of sediments collected from Mutha river flowing through Pune city in India...
July 25, 2017: Water Research
https://www.readbyqxmd.com/read/28768875/relevance-of-assembly-activating-protein-for-adeno-associated-virus-vector-production-and-capsid-protein-stability-in-mammalian-and-insect-cells
#7
Stefanie Große, Magalie Penaud-Budloo, Anne-Kathrin Herrmann, Kathleen Börner, Julia Fakhiri, Vibor Laketa, Chiara Krämer, Ellen Wiedtke, Manuel Gunkel, Lucie Ménard, Eduard Ayuso, Dirk Grimm
The discovery that Adeno-associated virus 2 (AAV2) encodes an eighth protein, called assembly-activating protein (AAP), transformed our understanding of wild-type AAV biology. Concurrently, it raised questions about the role of AAP during production of recombinant vectors based on natural or molecularly engineered AAV capsids. Here, we show that AAP is indeed essential for generation of functional recombinant AAV2 vectors in both, mammalian and insect cell-based vector production systems. Surprisingly, we observed that AAV2 capsid proteins VP1-3 are unstable in the absence of AAP2, likely due to rapid proteasomal degradation...
August 2, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28768866/reverse-engineering-field-isolates-of-myxoma-virus-demonstrates-that-some-gene-disruptions-or-loss-of-function-do-not-explain-virulence-changes-observed-in-the-field
#8
June Liu, Isabella M Cattadori, Derek G Sim, John-Sebastian Eden, Edward C Holmes, Andrew F Read, Peter J Kerr
The coevolution of myxoma virus (MYXV) and wild European rabbits in Australia and Europe is a paradigm for the evolution of a pathogen in a new host species. Genomic analyses have identified the mutations that have characterized this evolutionary process, but defining causal mutations in the pathways from virulence to attenuation and back to virulence has not been possible. Using reverse genetics we examined the role of six selected mutations found in Australian field isolates of MYXV that fall in known or potential virulence genes...
August 2, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28767924/elderly-with-knee-osteoarthritis-should-perform-nutritional-assessment-integrative-literature-review
#9
Isabelle Ferreira da Silva Souza, Rosa Sá de Oliveira Neta, Juliana Maria Gazzola, Marcelo Cardoso de Souza
To review scientific literature to assess nutritional status of elderly patients with osteoarthritis in the last 16 years. This is an integrative literature review that included articles published in national and international journals indexed in PubMed, SciELO and BIREME. We selected 14 articles, and English language was predominant. The year of publication of articles ranged from 2006 to 2016, and most of papers were cross-sectional studies. To gather papers and for posterior evaluate, we used a validated data collection instrument and the included studies were critical analyzed by reading, gathering and analysis of articles...
April 2017: Einstein
https://www.readbyqxmd.com/read/28767009/a-no-man-s-land-of-sex-reading-stephen-gordon-and-her-critics
#10
Katherine A Costello
One of the most read novels of lesbian, transgender, and queer criticism, Radclyffe Hall's novel The Well of Loneliness (1928) has given rise to numerous and contradictory interpretations of the protagonist Stephen Gordon's complex relationship to her body. Some have argued that she is a historically specific example of female masculinity, others that she is a lesbian who wishes she were more feminine, and others still that she is a prototypical transsexual character. Focusing on the exemplary essays by Jack Halberstam, Teresa de Lauretis, and Jay Prosser, I argue that the coexistence of mutually exclusive interpretations of Stephen Gordon's relationship to her femaleness suggests that the novel is, in fact, a demand to readers to unmoor identity from sex and to recognize what I call "sexual indeterminacy...
August 2, 2017: Journal of Lesbian Studies
https://www.readbyqxmd.com/read/28762979/in-house-time-resolved-photocrystallography-on-the-millisecond-timescale-using-a-gated-x-ray-hybrid-pixel-area-detector
#11
Nicolas Casaretto, Dominik Schaniel, Paul Alle, Emmanuel Wenger, Pascal Parois, Bertrand Fournier, El Eulmi Bendeif, Cyril Palin, Sébastien Pillet
With the remarkable progress of accelerator-based X-ray sources in terms of intensity and brightness, the investigation of structural dynamics from time-resolved X-ray diffraction methods is becoming widespread in chemistry, biochemistry and materials science applications. Diffraction patterns can now be measured down to the femtosecond time-scale using X-ray free electron lasers or table-top laser plasma X-ray sources. On the other hand, the recent developments in photon counting X-ray area detectors offer new opportunities for time-resolved crystallography...
August 1, 2017: Acta Crystallographica Section B, Structural Science, Crystal Engineering and Materials
https://www.readbyqxmd.com/read/28762415/biocompatible-3d-printed-polymers-via-fused-deposition-modelling-direct-c2c12-cellular-phenotype-in-vitro
#12
Rowan P Rimington, Andrew J Capel, Steven D R Christie, Mark P Lewis
The capability to 3D print bespoke biologically receptive parts within short time periods has driven the growing prevalence of additive manufacture (AM) technology within biological settings, however limited research concerning cellular interaction with 3D printed polymers has been undertaken. In this work, we used skeletal muscle C2C12 cell line in order to ascertain critical evidence of cellular behaviour in response to multiple bio-receptive candidate polymers; polylactic acid (PLA), acrylonitrile butadiene styrene (ABS), polyethylene terephthalate (PET) and polycarbonate (PC) 3D printed via fused deposition modelling (FDM)...
August 1, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28760108/retrospective-evaluation-of-glycemic-control-with-basal-bolus-or-neutral-protamine-hagedorn-insulin-regimens-in-patients-receiving-continuous-enteral-nutrition-therapy-in-medicine-wards
#13
Dema Hijaze, Auryan Szalat
Reasonable glycemic control is difficult to achieve in patients with diabetes mellitus (DM) receiving continuous enteral nutrition therapy (CENT). There are no solid evidence-based medicine guidelines regarding this issue in these patients. The purpose of this study was to determine if the use of a basal-bolus insulin regimen is more effective than neutral protamine Hagedorn (NPH) insulin alone in controlling blood glucose in non-critically ill patients with DM receiving CENT. We performed a retrospective, records-based review comparing basal-bolus with NPH insulin regimen in these patients, hospitalized in the internal medicine wards in our hospital...
August 2017: Nutrition in Clinical Practice
https://www.readbyqxmd.com/read/28759277/the-experience-of-decision-making-in-the-care-of-children-with-palliative-care-needs-the-experiences-of-jordanian-mothers
#14
Maha Atout, Pippa Hemingway, Jane Seymour
The purpose of this study was to explore the experience of decision making in the care of children with palliative care needs in Jordan, from the perspective of their mothers. This study employed a collective qualitative case study approach. Data were collected in 3 pediatric wards in a Jordanian hospital. The study used 2 data collection methods: participant observation (197 observational hours) and 56 semi-structured interviews with 24 mothers, 12 physicians and 20 nurses. The findings show how Jordanian mothers seek to transfer the role of decision making to physicians, as they perceive themselves to be unable to make decisions about critical issues related to the treatment of their children...
July 31, 2017: Compr Child Adolesc Nurs
https://www.readbyqxmd.com/read/28759167/titsmall-but-mighty-functional-peptides-encoded-by-small-orfs-in-plants
#15
REVIEW
Polly Yingshan Hsu, Philip N Benfey
Peptides encoded by small open reading frames (sORFs, usually < 100 codons) play critical regulatory roles in plant development and environmental responses. Despite their importance, only a small number of these peptides have been identified and characterized. Genomic studies have revealed that many plant genomes contain thousands of possible sORFs, which could potentially encode small peptides. The challenge is to distinguish translated sORFs from non-translated ones. Here we highlight advances in methodologies for identifying these hidden sORFs in plant genomes, including ribosome profiling and proteomics...
July 31, 2017: Proteomics
https://www.readbyqxmd.com/read/28758306/fear-of-pain-questionnaire-9-brief-assessment-of-pain-related-fear-and-anxiety
#16
D W McNeil, S G Kennedy, C L Randall, S H Addicks, C D Wright, K G Hursey, R Vaglienti
BACKGROUND: Fear and anxiety are important considerations in both acute and chronic pain. Effectively and efficiently measuring fear and anxiety associated with pain in healthcare settings is critical for identifying vulnerable patients. The length and administration time of current measures of pain-related fear and anxiety inhibit their routine use, as screening tools and otherwise, suggesting the need for a shorter, more efficient instrument. METHODS: A 9-item shortened version of the Fear of Pain Questionnaire - III (FPQ-III), the Fear of Pain Questionnaire-9 (FPQ-9), was developed based upon statistical analyses of archival data from 275 outpatients with chronic pain and 275 undergraduates...
July 31, 2017: European Journal of Pain: EJP
https://www.readbyqxmd.com/read/28753664/validation-of-a-novel-mho-microarray-for-a-comprehensive-characterisation-of-the-mycoplasma-hominis-action-in-hela-cell-infection
#17
Birgit Henrich, Freya Kretzmer, René Deenen, Karl Köhrer
Mycoplasma hominis is the second smallest facultative pathogen of the human urogenital tract. With less than 600 protein-encoding genes, it represents an ideal model organism for the study of host-pathogen interactions. For a comprehensive characterisation of the M. hominis action in infection a customized Mho microarray, which was based on two genome sequences (PG21 and LBD-4), was designed to analyze the dynamics of the mycoplasma transcriptome during infection and validated for M. hominis strain FBG. RNA preparation was evaluated and adapted to ensure the highest recovery of mycoplasmal mRNAs from in vitro HeLa cell infection assays...
2017: PloS One
https://www.readbyqxmd.com/read/28748537/differences-in-brain-morphology-and-working-memory-capacity-across-childhood
#18
Joe Bathelt, Susan E Gathercole, Amy Johnson, Duncan E Astle
Working memory (WM) skills are closely associated with learning progress in key areas such as reading and mathematics across childhood. As yet, however, little is known about how the brain systems underpinning WM develop over this critical developmental period. The current study investigated whether and how structural brain correlates of components of the working memory system change over development. Verbal and visuospatial short-term and working memory were assessed in 153 children between 5.58 and 15.92 years, and latent components of the working memory system were derived...
July 26, 2017: Developmental Science
https://www.readbyqxmd.com/read/28747504/targeted-genome-sequencing-reveals-varicella-zoster-virus-open-reading-frame-12-deletion
#19
Randall J Cohrs, Katherine S Lee, Addilynn Beach, Bridget Sanford, Nicholas L Baird, Christina Como, Chiharu Graybill, Dallas Jones, Eden Tekeste, Mitchell Ballard, Xiaomi Chen, David Yalacki, Seth Frietze, Kenneth Jones, Tihana Lenac Rovis, Stipan Jonjić, Jürgen Haas, Don Gilden
The neurotropic herpesvirus varicella zoster virus (VZV) establishes a life-long latent infection in humans following primary infection. The low abundance of VZV nucleic acids in human neurons has hindered an understanding of the mechanisms that regulate viral gene transcription during latency. To overcome this critical barrier, we optimized a targeted capture protocol to enrich VZV DNA and cDNA prior to whole-genome/transcriptome sequence analysis. Since the VZV genome is remarkably stable, it was surprising to detect that VZV32, a VZV laboratory strain with no discernable growth defect in tissue culture, contained a 2158-bp deletion in open reading frame (ORF) 12...
July 26, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28742088/genome-wide-identification-of-hami-melon-mirnas-with-putative-roles-during-fruit-development
#20
Hong Zhang, Lan Yin, Huaisong Wang, Guangzhi Wang, Xinli Ma, Meihua Li, Haibo Wu, Qiushi Fu, Yi Zhang, Hongping Yi
MicroRNAs represent a family of small endogenous, non-coding RNAs that play critical regulatory roles in plant growth, development, and environmental stress responses. Hami melon is famous for its attractive flavor and excellent nutritional value, however, the mechanisms underlying the fruit development and ripening remains largely unknown. Here, we performed small RNA sequencing to investigate the roles of miRNAs during Hami melon fruit development. Two batches of flesh samples were collected at four fruit development stages...
2017: PloS One
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