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https://www.readbyqxmd.com/read/29346504/baum-improving-genome-assembly-by-adaptive-unique-mapping-and-local-overlap-layout-consensus-approach
#1
Anqi Wang, Zhanyu Wang, Zheng Li, Lei M Li
Motivation: It is highly desirable to assemble genomes of high continuity and consistency at low cost. The current bottleneck of draft genome continuity using the Second Generation Sequencing (SGS) reads is primarily caused by uncertainty among repetitive sequences. Even though the Single-Molecule Real-Time sequencing technology is very promising to overcome the uncertainty issue, its relatively high cost and error rate add burden on budget or computation. Many long-read assemblers take the overlap-layout-consensus (OLC) paradigm, which is less sensitive to sequencing errors, heterozygosity and variability of coverage...
January 15, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29327964/endoscopic-removal-of-gastrointestinal-foreign-bodies-in-two-african-grey-parrots-psittacus-erithacus-and-a-hyacinth-macaw-anodorhynchus-hyacinthinus
#2
Robert J Cotton, Stephen J Divers
Two African grey parrots ( Psittacus erithacus) and one hyacinth macaw ( Anodorhynchus hyacinthinus) were examined because of varying clinical signs ranging from general lethargy to seizure-like episodes and regurgitation. Radiography and fluoroscopy in the 3 birds demonstrated variable degrees of gastric abnormalities, suggesting the presence of foreign material or stricture-like defects. Upper gastrointestinal rigid endoscopy by ingluviotomy revealed foreign bodies that were removed endoscopically. Minor postoperative complications were pulmonary congestion or mild aspiration and cardiac arrhythmia, both of which resolved, and no serious deleterious effects were associated with endoscopy in the short or long term...
December 2017: Journal of Avian Medicine and Surgery
https://www.readbyqxmd.com/read/29327953/multicentric-cryptococcosis-in-a-congo-african-grey-parrot-psittacus-erithacus-erithacus
#3
Raina S K Schunk, Nicholas E Sitinas, Katherine E Quesenberry, Jessica L Grodio
An approximately 10-year-old, female Congo African grey parrot ( Psittacus erithacus erithacus) developed progressive, unilateral exophthalmos and buphthalmos. Survey radiographs revealed a large, coelomic, soft tissue mass, which was confirmed on computed tomography scan. Aspirates of both the contents of the buphthalmic globe and coelomic mass were consistent with Cryptococcus species. Initial results were later confirmed with serum antigen latex agglutination and polymerase chain reaction testing, and the organism was then identified as Cryptococcus neoformans with DNA sequencing...
December 2017: Journal of Avian Medicine and Surgery
https://www.readbyqxmd.com/read/29316266/inference-by-exclusion-in-the-red-tailed-black-cockatoo-calyptorhynchus-banksii
#4
Lorraine Subias, Andrea S Griffin, David Guez
Inference by exclusion is the ability to select a given option by excluding the others. When designed appropriately, tests of this ability can reveal choices that cannot be explained by associative processes. Over the past decade, exclusion reasoning has been explored in several non-human taxonomic groups including birds, mainly in Corvids and Parrots. To increase our understanding of the taxonomic distribution of exclusion reasoning and therefore its evolution, we investigated exclusion performances in Red-tailed Black cockatoos (Calyptorhynchus banksii), an Australian relative of the Goffin cockatoo (Cacatua goffinia), using a food-finding task...
January 9, 2018: Integrative Zoology
https://www.readbyqxmd.com/read/29297838/repair-of-a-femoral-fracture-in-a-congo-african-grey-parrot-psittacus-erithacus-erithacus-with-a-paracortical-clamp-cerclage-technique
#5
Pavel Slunsky, Lesley Halter, Svenja Florczak, Alexander Haake, Leo Brunnberg, Kerstin Müller
A 1-yr-old female Congo African grey parrot ( Psittacus erithacus erithacus) was admitted with a lameness of the right pelvic limb. On the radiographs a closed, caudolaterally displaced, comminuted, diaphyseal fracture of the femur was diagnosed. Surgery under general anesthesia was performed in order to repair the fracture with a paracortical-clamp-cerclage technique. This straightforward and effective technique has been developed as a low-cost treatment for simple and comminuted diaphyseal fractures in dogs and cats...
December 2017: Journal of Zoo and Wildlife Medicine: Official Publication of the American Association of Zoo Veterinarians
https://www.readbyqxmd.com/read/29287155/comparison-of-three-computed-tomographic-angiography-protocols-to-assess-diameters-of-major-arteries-in-african-grey-parrots-psittacus-erithacus
#6
Pin Huan Yu, Yen Lin Lee, Chia Li Chen, Chau-Hwa Chi
OBJECTIVE To evaluate 3 contrast medium infusion (CMI) protocols for CT angiography (CTA) and measurement of major artery diameters in African grey parrots (Psittacus erithacus). ANIMALS 9 African grey parrots with no detectable cardiovascular disease. PROCEDURES Each bird was anesthetized and underwent placement of an IV catheter in the left basilic vein and 16-slice CTA scanning (started at peak aortic enhancement) with each of 3 CMI protocols at ≥ 1-month intervals. Protocol 1 involved catheter flushing with saline (0...
January 2018: American Journal of Veterinary Research
https://www.readbyqxmd.com/read/29283587/vocal-conditioning-in-kea-parrots-nestor-notabilis
#7
Amelia Wein, Raoul Schwing, Martine Hausberger, Rogelio Rodriguez, Ludwig Huber
In laboratory studies of vocal behavior in animals, subjects are normally isolated in a sound-insulated chamber for recording, but such socially isolated conditions may reduce the chances that they will vocalize. Indeed, past studies using such methods have faced the challenge that subjects remained silent. Knowledge of conditions under which subjects are more likely to vocalize could thus improve experimental design. This study investigated (a) whether kea (Nestor notabilis) could be trained to increase vocal production using operant conditioning and (b) the conditions under which such training was feasible...
December 28, 2017: Journal of Comparative Psychology
https://www.readbyqxmd.com/read/29279399/developmental-origins-of-mosaic-evolution-in-the-avian-cranium
#8
Ryan N Felice, Anjali Goswami
Mosaic evolution, which results from multiple influences shaping morphological traits and can lead to the presence of a mixture of ancestral and derived characteristics, has been frequently invoked in describing evolutionary patterns in birds. Mosaicism implies the hierarchical organization of organismal traits into semiautonomous subsets, or modules, which reflect differential genetic and developmental origins. Here, we analyze mosaic evolution in the avian skull using high-dimensional 3D surface morphometric data across a broad phylogenetic sample encompassing nearly all extant families...
December 26, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29274528/studies-on-immunity-and-immunopathogenesis-of-parrot-bornaviral-disease-in-cockatiels
#9
Samer Sadeq Hameed, Jianhua Guo, Ian Tizard, H L Shivaprasad, Susan Payne
We have demonstrated that vaccination of cockatiels (Nymphicus hollandicus) with killed parrot bornavirus (PaBV) plus recombinant PaBV-4 nucleoprotein (N) in alum was protective against disease in birds challenged with a virulent bornavirus isolate (PaBV-2). Unvaccinated birds, as well as birds vaccinated after challenge, developed gross and histologic lesions typical of proventricular dilatation disease (PDD). There was no evidence that vaccination either before or after challenge made the infection more severe...
December 20, 2017: Virology
https://www.readbyqxmd.com/read/29260428/parrot-beak-nails-revisited-case-series-and-comprehensive-review
#10
Stella X Chen, Philip R Cohen
The term "parrot beak nail" describes a morphologic change of the nail plate characterized by excessive forward curvature. It may be associated with systemic disease or, most commonly, occurs as an idiopathic finding complicated by delayed nail plate trimming. The characteristics of parrot beak nails in ten men are described, and the features of this acquired nail deformity are reviewed. Of the ten patients, six presented with concurrent neuropathies that resulted in frequent foot injuries or falls. While the true incidence of parrot beak nails is unknown, this nail deformity occurred in 2...
December 19, 2017: Dermatology and Therapy
https://www.readbyqxmd.com/read/29247662/cryptosporidium-spp-in-caged-exotic-psittacines-from-brazil-evaluation-of-diagnostic-methods-and-molecular-characterization
#11
Elis Domingos Ferrari, Alex Akira Nakamura, Ana Rita Moraes Nardi, Bruna Nicoleti Santana, Vinicius da Silva Camargo, Walter Bertequini Nagata, Katia Denise Saraiva Bresciani, Marcelo Vasconcelos Meireles
The aim of this study was to evaluate the prevalence of and diagnostic methods for Cryptosporidium spp. in caged adult exotic parrots from Southern and Southeastern Brazil. Oocysts were purified from fecal samples from 463 psittacines by centrifugal-flotation in Sheather's sugar solution. Cryptosporidium spp. were detected by malachite green negative staining and nested PCR targeting the 18S rRNA gene. Cryptosporidium species were identified by sequencing nested PCR amplicons. Samples were also tested by duplex real-time PCR targeting the 18S rRNA gene of Cryptosporidium galli and Cryptosporidium avian genotype III...
December 13, 2017: Experimental Parasitology
https://www.readbyqxmd.com/read/29244144/species-composition-of-sand-flies-diptera-psychodidae-and-modeling-the-spatial-distribution-of-main-vectors-of-cutaneous-leishmaniasis-in-hormozgan-province-southern-iran
#12
Ahmad Ali Hanafi-Bojd, Mehdi Khoobdel, Moussa Soleimani-Ahmadi, Kourosh Azizi, Abbas Aghaei Afshar, Seyed Aghil Jaberhashemi, Sajjad Fekri, Reza Safari
Cutaneous Leishmaniasis (CL) is one of the main neglected vector-borne diseases in the Middle East, including Iran. This study aimed to map the spatial distribution and species composition of sand flies in Hormozgan Province and to predict the best ecological niches for main CL vectors in this area. A database that included all earlier studies on sand flies in Hormozgan Province was established. Sand flies were also collected from some localities across the province. Prediction maps for main vectors were developed using MaxEnt model...
December 13, 2017: Journal of Medical Entomology
https://www.readbyqxmd.com/read/29227779/terry-s-parrot-died-adventures-in-voice-recognition
#13
Richard Travers
No abstract text is available yet for this article.
December 11, 2017: Medical Journal of Australia
https://www.readbyqxmd.com/read/29212853/emergence-of-high-avidity-melan-a-specific-clonotypes-as-a-reflection-of-anti-pd-1-clinical-efficacy
#14
Sylvain Simon, Virginie Vignard, Emilie Varey, Tiphaine Parrot, Anne-Chantal Knol, Amir Khammari, Nadine Gervois, Francois Lang, Brigitte Dreno, Nathalie Labarriere
Therapeutic strategies using anti-PD-1-blocking antibodies reported unparalleled effectiveness for melanoma immunotherapy, but deciphering immune responses modulated by anti-PD-1 treatment remains a crucial issue. Here, we analyzed the composition and functions of the large Melan-A-specific T-cell repertoire in the peripheral blood of 9 melanoma patients before and after 2 months of treatment with anti-PD-1. We observed amplification of Melan-A-specific Vß subfamilies undetectable before therapy (thereafter called emerging Vß subfamilies) in responding patients, with a predominant expansion in patients with a complete response...
December 6, 2017: Cancer Research
https://www.readbyqxmd.com/read/29146029/gut-brain-axis-and-its-microbiota-regulation-in-mammals-and-birds
#15
REVIEW
Jan S Suchodolski
This article provides a brief overview of the advances made in microbiota research in parrots and pet birds. It describes this complex ecosystem and the contribution of the intestinal microbiota to host health and disease, including the nervous system.
January 2018: Veterinary Clinics of North America. Exotic Animal Practice
https://www.readbyqxmd.com/read/29121071/from-nerves-to-brain-to-gastrointestinal-tract-a-time-based-study-of-parrot-bornavirus-2-pabv-2-pathogenesis-in-cockatiels-nymphicus-hollandicus
#16
Jeann Leal de Araujo, Raquel R Rech, J Jill Heatley, Jianhua Guo, Paula R Giaretta, Ian Tizard, Aline Rodrigues-Hoffmann
Parrot bornaviruses (PaBVs) are the causative agents of proventricular dilatation disease, however key aspects of its pathogenesis, such as route of infection, viral spread and distribution, and target cells remain unclear. Our study aimed to track the viral spread and lesion development at 5, 10, 20, 25, 35, 40, 60, 80, 95 and 114 dpi using histopathology, immunohistochemistry, and RT-PCR. After intramuscular inoculation of parrot bornavirus 2 (PaBV-2) in the pectoral muscle of cockatiels, this virus was first detected in macrophages and lymphocytes in the inoculation site and adjacent nerves, then reached the brachial plexus, centripetally spread to the thoracic segment of the spinal cord, and subsequently invaded the other spinal segments and brain...
2017: PloS One
https://www.readbyqxmd.com/read/29117242/the-keybox-shape-frame-fitting-during-tool-use-in-goffin-s-cockatoos-cacatua-goffiniana
#17
Cornelia Habl, Alice Marie Isabel Auersperg
The ability to move an object in alignment to a surface develops early in human ontogeny. However, aligning not just your own body but also the object itself in relation to a surface with a specific shape requires using landmarks rather than the own body as a frame of reference for orientation. The ability to do so is considered important in the development of tool use behaviour in human and non-human animals. Aside from humans, with the exception of a single study on habitually tool using primates, shape-frame matching abilities remain largely unstudied...
2017: PloS One
https://www.readbyqxmd.com/read/29104565/the-low-diversity-fecal-microbiota-of-the-critically-endangered-k%C3%A4-k%C3%A4-p%C3%A5-is-robust-to-anthropogenic-dietary-and-geographic-influences
#18
Elena K Perry, Andrew Digby, Michael W Taylor
The critically endangered kākāpō, an herbivorous parrot endemic to New Zealand, is subject to intensive management to increase its population size. Key aspects of the management program include supplementary feeding and translocation of kākāpō between different predator-free islands to optimize the genetic composition of the breeding populations. While these practices have helped boost the kākāpō population, their impact on the kākāpō fecal microbiota is uncertain. Previous studies have found that the kākāpō possesses a low-diversity fecal microbiota, typically dominated by Escherichia/Shigella spp...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29092573/allometric-trends-reveal-distinct-evolutionary-trajectories-for-avian-communication
#19
Ingrid M D Torres, Luiz C S Lopez, Carlos B de Araújo
Acoustic signal production is affected by allometric relationships, by which the larger the animal, the lower its call frequency. In this paper, three evolutionary acoustic hypotheses were tested: the Signal-to-Noise Ratio Hypothesis (SNRH), in which evolution maximizes call ranges by increasing the signal-to-noise ratio; the Stimulus Threshold Hypothesis (STH), in which evolution maximizes the range of a specific signal threshold; and the Body Size Hypothesis (BSH), in which the emission of long wavelengths is enabled by body size...
October 2017: Journal of the Acoustical Society of America
https://www.readbyqxmd.com/read/29091816/chemical-analysis-of-the-alphaproteobacterium-strain-mola1416-associated-with-the-marine-lichen-lichina-pygmaea
#20
Delphine Parrot, Laurent Intertaglia, Philippe Jehan, Martin Grube, Marcelino T Suzuki, Sophie Tomasi
Alphaproteobacterium strain MOLA1416, related to Mycoplana ramosa DSM 7292 and Chelativorans intermedius CC-MHSW-5 (93.6% 16S rRNA sequence identity) was isolated from the marine lichen, Lichina pygmaea and its chemical composition was characterized by a metabolomic network analysis using LC-MS/MS data. Twenty-five putative different compounds were revealed using a dereplication workflow based on MS/MS signatures available through GNPS (https://gnps.ucsd.edu/). In total, ten chemical families were highlighted including isocoumarins, macrolactones, erythrinan alkaloids, prodiginines, isoflavones, cyclohexane-diones, sterols, diketopiperazines, amino-acids and most likely glucocorticoids...
October 29, 2017: Phytochemistry
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