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https://www.readbyqxmd.com/read/28108446/chaincleaner-improves-genome-alignment-specificity-and-sensitivity
#1
Hernando G Suarez, Bjoern E Langer, Pradnya Ladde, Michael Hiller
MOTIVATION: Accurate alignments between entire genomes are crucial for comparative genomics. However, computing sensitive and accurate genome alignments is a challenging problem, complicated by genomic rearrangements. RESULTS: Here we present a fast approach, called chainCleaner, that improves the specificity in genome alignments by accurately detecting and removing local alignments that obscure the evolutionary history of genomic rearrangements. Systematic tests on alignments between the human and other vertebrate genomes show that chainCleaner (i) improves the alignment of numerous orthologous genes, (ii) exposes alignments between exons of orthologous genes that were masked before by alignments to pseudogenes, and (iii) recovers hundreds of kilobases in local alignments that otherwise would fall below a minimum score threshold...
January 19, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28108055/a-healthy-woman-with-sudden-memory-loss
#2
Ryota Inokuchi, Hiromu Maehara, Yoko Yamaguchi, Kei Kira, Kent Doi, Naoto Morimura
No abstract text is available yet for this article.
January 17, 2017: Journal of Emergency Medicine
https://www.readbyqxmd.com/read/28107422/comparison-of-hapmap-and-1000-genomes-reference-panels-in-a-large-scale-genome-wide-association-study
#3
Paul S de Vries, Maria Sabater-Lleal, Daniel I Chasman, Stella Trompet, Tarunveer S Ahluwalia, Alexander Teumer, Marcus E Kleber, Ming-Huei Chen, Jie Jin Wang, John R Attia, Riccardo E Marioni, Maristella Steri, Lu-Chen Weng, Rene Pool, Vera Grossmann, Jennifer A Brody, Cristina Venturini, Toshiko Tanaka, Lynda M Rose, Christopher Oldmeadow, Johanna Mazur, Saonli Basu, Mattias Frånberg, Qiong Yang, Symen Ligthart, Jouke J Hottenga, Ann Rumley, Antonella Mulas, Anton J M de Craen, Anne Grotevendt, Kent D Taylor, Graciela E Delgado, Annette Kifley, Lorna M Lopez, Tina L Berentzen, Massimo Mangino, Stefania Bandinelli, Alanna C Morrison, Anders Hamsten, Geoffrey Tofler, Moniek P M de Maat, Harmen H M Draisma, Gordon D Lowe, Magdalena Zoledziewska, Naveed Sattar, Karl J Lackner, Uwe Völker, Barbara McKnight, Jie Huang, Elizabeth G Holliday, Mark A McEvoy, John M Starr, Pirro G Hysi, Dena G Hernandez, Weihua Guan, Fernando Rivadeneira, Wendy L McArdle, P Eline Slagboom, Tanja Zeller, Bruce M Psaty, André G Uitterlinden, Eco J C de Geus, David J Stott, Harald Binder, Albert Hofman, Oscar H Franco, Jerome I Rotter, Luigi Ferrucci, Tim D Spector, Ian J Deary, Winfried März, Andreas Greinacher, Philipp S Wild, Francesco Cucca, Dorret I Boomsma, Hugh Watkins, Weihong Tang, Paul M Ridker, Jan W Jukema, Rodney J Scott, Paul Mitchell, Torben Hansen, Christopher J O'Donnell, Nicholas L Smith, David P Strachan, Abbas Dehghan
An increasing number of genome-wide association (GWA) studies are now using the higher resolution 1000 Genomes Project reference panel (1000G) for imputation, with the expectation that 1000G imputation will lead to the discovery of additional associated loci when compared to HapMap imputation. In order to assess the improvement of 1000G over HapMap imputation in identifying associated loci, we compared the results of GWA studies of circulating fibrinogen based on the two reference panels. Using both HapMap and 1000G imputation we performed a meta-analysis of 22 studies comprising the same 91,953 individuals...
2017: PloS One
https://www.readbyqxmd.com/read/28104589/anchored-phylogenomics-improves-the-resolution-of-evolutionary-relationships-in-the-rapid-radiation-of-protea-l
#4
Nora Mitchell, Paul O Lewis, Emily Moriarty Lemmon, Alan R Lemmon, Kent E Holsinger
PREMISE OF THE STUDY: Estimating phylogenetic relationships in relatively recent evolutionary radiations is challenging, especially if short branches associated with recent divergence result in multiple gene tree histories. We combine anchored enrichment next-generation sequencing with species tree analyses to produce a robust estimate of phylogenetic relationships in the genus Protea (Proteaceae), an iconic radiation in South Africa. METHODS: We sampled multiple individuals within 59 out of 112 species of Protea and 6 outgroup species for a total of 163 individuals, and obtained sequences for 498 low-copy, orthologous nuclear loci using anchored phylogenomics...
January 19, 2017: American Journal of Botany
https://www.readbyqxmd.com/read/28099383/a-case-of-a-gunshot-wound-to-the-fetus-in-utero
#5
Mitchell R Ladd, Kathryn Shaw, Sara Munoz-Blanco, Maureen Gilmore, Sandra DiBrito, Solange N Eloundou, Kent Stevens, Isam W Nasr, Dylan Stewart, Robert E Falcone
No abstract text is available yet for this article.
January 17, 2017: Journal of Trauma and Acute Care Surgery
https://www.readbyqxmd.com/read/28099204/narrowing-in-on-the-anti-%C3%AE-cell-specific-t-cells-looking-where-the-action-is
#6
Sally C Kent, Jenny Aurielle B Babon
PURPOSE OF THE REVIEW: By necessity, the vast majority of information we have on autoreactive T cells in human type 1 diabetes (T1D) has come from the study of peripheral blood of donors with T1D. It is not clear how representative the peripheral autoreactive T-cell repertoire is of the autoreactive T cells infiltrating the islets in T1D. We will summarize and discuss what is known of the immunohistopathology of insulitis, the T-cell receptor repertoire expressed by islet-infiltrating T cells, and the autoreactivity and function of islet-infiltrating T cells in T1D...
January 17, 2017: Current Opinion in Endocrinology, Diabetes, and Obesity
https://www.readbyqxmd.com/read/28098354/concealed-accessory-pathways-with-a-single-ventricular-and-two-discrete-atrial-insertion-sites
#7
Ryan T Kipp, Raed Abu Sham'a, Ito Hiroyuki, Frederick T Han, Marwan Refaat, Jonathan C Hsu, Michael E Field, Douglas E Kopp, Gregory M Marcus, Melvin M Scheinman, Kurt S Hoffmayer
BACKGROUND: Atrioventricular reciprocating tachycardia utilizing a concealed accessory pathway is common. It is well appreciated that some patients may have multiple accessory pathways with separate atrial and ventricular insertion sites. METHODS: We present three cases of AVRT utilizing concealed pathways with evidence that each utilizing a single ventricular insertion and two discrete atrial insertion sites. RESULTS: In case one, two discrete atrial insertion sites were mapped in two separate procedures, and only during the second ablation was the Kent potential identified...
January 18, 2017: Pacing and Clinical Electrophysiology: PACE
https://www.readbyqxmd.com/read/28097045/homeopathy-a-safe-much-less-expensive-non-invasive-viable-alternative-for-the-treatment-of-patients-suffering-from-loss-of-lumbar-lordosis
#8
Saiful Haque, Debarsi Das, Saugato Bhattacharya, Tathagato Sarkar, Anisur Rahman Khuda-Bukhsh
OBJECTIVES: Loss of lumbar lordosis causing pain and curvature of the vertebral skeleton to one side is a relatively uncommon disease. To our knowledge, successful treatment of loss of lumbar lordosis with any potentized homeopathic drug diluted above Avogadro's limit (that is, above a potency of 12C) has not been documented so far. In this communication, we intend to document a relatively rare case of loss of lumbar lordosis with osteophytic lippings, disc desiccation, and protrusion, causing a narrowing of secondary spinal canal and a bilateral neural foramina, leading to vertebral column curvature with acute pain in an adolescent boy...
December 2016: Journal of Pharmacopuncture
https://www.readbyqxmd.com/read/28096505/the-neuropilin-2-isoform-nrp2b-uniquely-supports-tgf%C3%AE-mediated-progression-in-lung-cancer
#9
Robert M Gemmill, Patrick Nasarre, Joyce Nair-Menon, Federico Cappuzzo, Lorenza Landi, Armida D'Incecco, Hidetaka Uramoto, Takeshi Yoshida, Eric B Haura, Kent Armeson, Harry A Drabkin
Neuropilins (NRP1 and NRP2) are co-receptors for heparin-binding growth factors and class 3 semaphorins. Different isoforms of NRP1 and NRP2 are produced by alternative splicing. We found that in non-small cell lung cancer (NSCLC) cell lines, transforming growth factor-β (TGFβ) signaling preferentially increased the abundance of NRP2b. NRP2b and NRP2a differ only in their carboxyl-terminal regions. Although the presence of NRP2b inhibited cultured cell proliferation and primary tumor growth, NRP2b enhanced cellular migration, invasion into Matrigel, and tumorsphere formation in cultured cells in response to TGFβ signaling and promoted metastasis in xenograft mouse models...
January 17, 2017: Science Signaling
https://www.readbyqxmd.com/read/28096247/order-matters-the-order-of-somatic-mutations-influences-cancer-evolution
#10
David G Kent, Anthony R Green
Cancers evolve as a consequence of multiple somatic lesions, with competition between subclones and sequential subclonal evolution. Some driver mutations arise either early or late in the evolution of different individual tumors, suggesting that the final malignant properties of a subclone reflect the sum of mutations acquired rather than the order in which they arose. However, very little is known about the cellular consequences of altering the order in which mutations are acquired. Recent studies of human myeloproliferative neoplasms show that the order in which individual mutations are acquired has a dramatic impact on the cell biological and molecular properties of tumor-initiating cells...
January 17, 2017: Cold Spring Harbor Perspectives in Medicine
https://www.readbyqxmd.com/read/28094880/milk-ejection-patterns-remain-consistent-during-the-first-and-second-lactations
#11
Hazel Gardner, Jacqueline C Kent, Danielle K Prime, Ching-Tat Lai, Peter E Hartmann, Donna T Geddes
OBJECTIVE: Milk ejection is a critical physiological process for successful lactation in humans and without it little milk can be removed. Individual milk ejection patterns have been shown to remain consistent between breasts at different lactation stages and using different vacuum patterns with an electric breast pump. Little is known about the milk ejection characteristics during the second lactation period in the same mother. The objective of this study was to examine milk ejection characteristics in the same woman over two lactations...
January 17, 2017: American Journal of Human Biology: the Official Journal of the Human Biology Council
https://www.readbyqxmd.com/read/28092055/differentiating-emotional-processing-and-attention-in-psychopathy-with-functional-neuroimaging
#12
Nathaniel E Anderson, Vaughn R Steele, J Michael Maurer, Vikram Rao, Michael R Koenigs, Jean Decety, David S Kosson, Vince D Calhoun, Kent A Kiehl
Individuals with psychopathy are often characterized by emotional processing deficits, and recent research has examined the specific contexts and cognitive mechanisms that underlie these abnormalities. Some evidence suggests that abnormal features of attention are fundamental to emotional deficits in persons with psychopathy, but few studies have demonstrated the neural underpinnings responsible for such effects. Here, we use functional neuroimaging to examine attention-emotion interactions among incarcerated individuals (n = 120) evaluated for psychopathic traits using the Hare Psychopathy Checklist-Revised (PCL-R)...
January 16, 2017: Cognitive, Affective & Behavioral Neuroscience
https://www.readbyqxmd.com/read/28089359/transient-and-long-time-kinetic-responses-of-the-cadaveric-leg-during-internal-and-external-foot-rotation
#13
Alexander R Mait, Adwait Mane, Jason L Forman, John Paul Donlon, Bingbing Nie, Richard W Kent
The purpose of this study was to determine the long-time and transient characteristics of the moment generated by external (ER) and internal (IR) rotation of the calcaneus with respect to the tibia. Two human cadaver legs were disarticulated at the knee joint while maintaining the connective tissue between the tibia and fibula. An axial rotation of 21° was applied to the proximal tibia to generate either ER or IR while the fibula was unconstrained and the calcaneus was permitted to translate in the transverse plane...
January 7, 2017: Journal of Biomechanics
https://www.readbyqxmd.com/read/28088206/comparing-accelerometer-pedometer-and-a-questionnaire-for-measuring-physical-activity-in-bronchiectasis-a-validity-and-feasibility-study
#14
B O'Neill, S M McDonough, J J Wilson, I Bradbury, K Hayes, A Kirk, L Kent, D Cosgrove, J M Bradley, M A Tully
BACKGROUND: There are challenges for researchers and clinicians to select the most appropriate physical activity tool, and a balance between precision and feasibility is needed. Currently it is unclear which physical activity tool should be used to assess physical activity in Bronchiectasis. The aim of this research is to compare assessment methods (pedometer and IPAQ) to our criterion method (ActiGraph) for the measurement of physical activity dimensions in Bronchiectasis (BE), and to assess their feasibility and acceptability...
January 14, 2017: Respiratory Research
https://www.readbyqxmd.com/read/28088123/antibody-dependent-cellular-cytotoxicity-and-influenza-virus
#15
REVIEW
Hillary A Vanderven, Sinthujan Jegaskanda, Adam K Wheatley, Stephen J Kent
Antibodies are a key defence against influenza infection and disease, but neutralizing antibodies are often strain-specific and of limited utility against divergent or pandemic viruses. There is now considerable evidence that influenza-specific antibodies with Fc-mediated effector functions, such as antibody-dependent cellular cytotoxicity (ADCC), can assist in the clearance of influenza infection in vitro and in animal models. Further, ADCC-mediating antibodies that recognize a broad array of influenza strains are common in humans, likely as a result of being regularly exposed to influenza infections...
January 11, 2017: Current Opinion in Virology
https://www.readbyqxmd.com/read/28080076/adverse-childhood-experiences-and-risk-for-suicidal-behavior-in-male-iraq-and-afghanistan-veterans-seeking-ptsd-treatment
#16
Timothy D Carroll, Joseph M Currier, Wesley H McCormick, Kent D Drescher
OBJECTIVE: Adverse childhood experiences (ACEs) are associated with increased risk for suicide and appear to occur in disproportionately high rates among men who served in the U.S. military. However, research has yet to examine a comprehensive range of ACEs among Iraq/Afghanistan veterans with combat-related posttraumatic stress disorder (PTSD) or whether these premilitary stressors may contribute to suicidal behavior in this highly vulnerable population. METHOD: A sample of 217 men entering a residential program for combat-related PTSD completed measures for ACEs, combat exposure, and lifetime suicidal ideation and attempts...
January 12, 2017: Psychological Trauma: Theory, Research, Practice and Policy
https://www.readbyqxmd.com/read/28075558/immunological-principles-guiding-the-rational-design-of-particles-for-vaccine-delivery
#17
Katelyn T Gause, Adam K Wheatley, Jiwei Cui, Yan Yan, Stephen J Kent, Frank Caruso
Despite the immense public health successes of immunization over the past century, effective vaccines are still lacking for globally important pathogens such as human immunodeficiency virus, malaria, and tuberculosis. Exciting recent advances in immunology and biotechnology over the past few decades have facilitated a shift from empirical to rational vaccine design, opening possibilities for improved vaccines. Some of the most important advancements include (i) the purification of subunit antigens with high safety profiles, (ii) the identification of innate pattern recognition receptors (PRRs) and cognate agonists responsible for inducing immune responses, and (iii) developments in nano- and microparticle fabrication and characterization techniques...
January 11, 2017: ACS Nano
https://www.readbyqxmd.com/read/28075076/new-codes-new-payment-opportunities-for-2017
#18
Kent J Moore, Barbara Hayes
No abstract text is available yet for this article.
January 2017: Family Practice Management
https://www.readbyqxmd.com/read/28073977/the-effects-of-a-modified-hot-water-treatment-on-anastrepha-ludens-diptera-tephritidae-infested-mango
#19
Emilio Hernández, Marysol Aceituno-Medina, Jorge Toledo, Bigail Bravo, José Caro-Corrales, Pablo Montoya, Robert Mangan
The Mexican fruit fly, Anastrepha ludens (Loew), is a quarantine pest in mango (Mangifera indica L.) that can be controlled by using a hot water treatment (HWT). This treatment is normally followed by a 30-min hydrocooling (HYC) process that reduces the negative effects that the treatment has on fruit quality. However, if hot water-treated fruits are immediately immersed in water at 21 °C, the survival rate of third-instar A. ludens may be increased. The current approved treatment protocol states that if HYC is used, then treated fruit should undergo an additional 10-min HWT or on platform for 30 min before HYC...
January 10, 2017: Journal of Economic Entomology
https://www.readbyqxmd.com/read/28073938/sonic-hedgehog-guides-axons-via-zipcode-binding-protein-1-mediated-local-translation
#20
Lea Lepelletier, Sébastien D Langlois, Christopher B Kent, Kristy Welshhans, Steves Morin, Gary J Bassell, Patricia T Yam, Frédéric Charron
: Sonic hedgehog (Shh) attracts spinal cord commissural axons toward the floorplate. How Shh elicits changes in the growth cone cytoskeleton that drive growth cone turning is unknown. We find that the turning of rat commissural axons up a Shh gradient requires protein synthesis. In particular, Shh stimulation increases β-actin protein at the growth cone, even when the cell bodies have been removed. Thus Shh induces the local translation of β-actin at the growth cone. We hypothesised that this requires zipcode binding protein 1 (ZBP1), an mRNA binding protein that transports β-actin mRNA and releases it for local translation upon phosphorylation...
January 10, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
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